Commit upstream/latest - exonerate

+26

-1

ChangeLog less more

	0
	1	2.3.0 -> 2.4.0
	2	o Fixed many thread safety bugs
	3	o Fixed bugs with large files over 4GB
	4	o Modified client to work with multiple servers
	5	o Fixed server to handle SIGPIPE
	6	o Added support for FOSN input (can be files, directories or servers)
	7	o Fixed bug with --wordambiguity and --wordjump (with normal FSM)
	8	o Added %pS to --ryo (percent self score over equivalenced regions)
	9
	10	2.2.0 -> 2.3.0
	11	o Fixed several bugs with thread safety for exonerate-server
	12	o Fixed bug with custom genetic codes not working
	13	o Fixed bug with overflow of seedrepeat horizon in hspset
	14	o Added passing of wordlimit params to server
	15	o Implemented --cores option for multi-threaded alignment
	16	o Added identity and similarity score for GFF genes and exons
	17	o Increased default FSM memory limit to 256Mb
	18	o Added --revcomp option to disable searching of reverse complement
	19	o Fixed bug with compact-FSM (VFSM) based database searching
	20	o Added --wordambiguity option for searching ambiguous reference seqs
	21	o Fixed bug with esd2esi and .esd files >2Gb
	22
0	23	2.1.0 -> 2.2.0
1	24	o Fixed bug with esd2esi when softmasking is off
2		o Replaced GMemChunk due to caching problems with glib-2
	25	o Removed all GMemChunk usage due to caching problems with glib-2
3	26	o Fixed various minor memory leaks
4	27
5	28	2.0.0 -> 2.1.0

336	359	o Converted est2genome model to use PSSM splice site prediction
337	360	o Fixed C4_Model_select() to avoid copying redundant calcs
338	361
	362
	363
339	364	--

+1

-0

Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+19

-6

configure less more

678	678	host_cpu
679	679	host_vendor
680	680	host_os
	681	custom_guint64_format
681	682	source_root_dir
682	683	PKG_CONFIG
683	684	GLIB_CONFIG

1939	1940
1940	1941	PACKAGE=exonerate
1941	1942
1942		VERSION=2.2.0
	1943	VERSION=2.4.0
1943	1944
1944	1945	if test "`cd $srcdir && pwd`" != "`pwd`" && test -f $srcdir/config.status; then
1945	1946	{ { echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5

4120	4121	# AVOID autoconf WARNINGS ABOUT --datarootdir
4121	4122
4122	4123
	4124	custom_guint64_format="llu"
	4125
4123	4126	# TRY TO GET TO BUILD ON ALL PLATFORMS BY DEFAULT
4124	4127	echo ""$host
4125	4128	case $host in

4137	4140	CC="cc"
4138	4141	GCC= # No longer true (prevents GCC specific CFLAGS being set)
4139	4142	CFLAGS="-O3 -arch ev6 -fast"
4140		C4_CC="$CC"
4141		C4_CFLAGS="$CFLAGS"
4142	4143	;;
4143	4144	-irix)
4144	4145	echo "Customising build for IRIX"

4150	4151	C4_AR_INIT="cq"
4151	4152	C4_AR_APPEND="q"
4152	4153	;;
	4154	x86_64-*)
	4155	echo "Customising build for X86_64"
	4156	custom_guint64_format="lu"
	4157	;;
	4158	*)
	4159	echo "* Unknown build platform: $host *"
	4160	;;
4153	4161	esac
	4162
	4163
4154	4164
4155	4165	# SET SOURCE_ROOT_DIR (REQUIRED FOR viterbi.h)
4156	4166	source_root_dir=`pwd`

4520	4530	# model_extra_programs="bootstrapper"
4521	4531	codegen_extra_sources=""
4522	4532	codegen_extra_ldadd="`pwd`/src/c4/viterbi.o \
4523		`pwd`/src/c4/scheduler.o"
	4533	`pwd`/src/sdp/scheduler.o"
4524	4534	else
4525	4535	echo "error: must be yes or no:"
4526	4536	echo " --enable-compiledmodels:$enable_compiledmodels"

4568	4578	if test "$enable_pthreads" = yes; then
4569	4579	echo "Using PTHREADS"
4570	4580	CFLAGS="$CFLAGS -DUSE_PTHREADS"
4571		LDFLAGS="$LDFLAGS -lpthread"
	4581	# for g_thread_init()
	4582	g_thread_init_ldflags=`pkg-config --libs gthread-2.0`
	4583	LDFLAGS="$LDFLAGS $g_thread_init_ldflags -lpthread"
4572	4584	elif test "$enable_pthreads" = no; then
4573	4585	echo "Not using pthreads"
4574	4586	else

5300	5312	host_cpu!$host_cpu$ac_delim
5301	5313	host_vendor!$host_vendor$ac_delim
5302	5314	host_os!$host_os$ac_delim
	5315	custom_guint64_format!$custom_guint64_format$ac_delim
5303	5316	source_root_dir!$source_root_dir$ac_delim
5304	5317	PKG_CONFIG!$PKG_CONFIG$ac_delim
5305	5318	GLIB_CONFIG!$GLIB_CONFIG$ac_delim

5313	5326	LTLIBOBJS!$LTLIBOBJS$ac_delim
5314	5327	_ACEOF
5315	5328
5316		if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed \| grep -c X` = 77; then
	5329	if test `sed -n "s/.*$ac_delim\$/X/p" conf$$subs.sed \| grep -c X` = 78; then
5317	5330	break
5318	5331	elif $ac_last_try; then
5319	5332	{ { echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5

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-5

configure.in less more

4	4	# ( Borrowed some config tricks from gtk+, gnet, xscreensaver, mutt )
5	5
6	6	AC_INIT(src/sequence/sequence.c)
7		AM_INIT_AUTOMAKE(exonerate,2.2.0)
	7	AM_INIT_AUTOMAKE(exonerate,2.4.0)
8	8	AC_PROG_CC
9	9	AC_PROG_INSTALL
10	10	AC_PROG_MAKE_SET

25	25
26	26	# AVOID autoconf WARNINGS ABOUT --datarootdir
27	27	AC_SUBST(datarootdir)
	28
	29	custom_guint64_format="llu"
28	30
29	31	# TRY TO GET TO BUILD ON ALL PLATFORMS BY DEFAULT
30	32	echo ""$host

43	45	CC="cc"
44	46	GCC= # No longer true (prevents GCC specific CFLAGS being set)
45	47	CFLAGS="-O3 -arch ev6 -fast"
46		C4_CC="$CC"
47		C4_CFLAGS="$CFLAGS"
48	48	;;
49	49	-irix)
50	50	echo "Customising build for IRIX"

56	56	C4_AR_INIT="cq"
57	57	C4_AR_APPEND="q"
58	58	;;
	59	x86_64-*)
	60	echo "Customising build for X86_64"
	61	custom_guint64_format="lu"
	62	;;
	63	*)
	64	echo "* Unknown build platform: $host *"
	65	;;
59	66	esac
	67
	68	AC_SUBST(custom_guint64_format)
60	69
61	70	# SET SOURCE_ROOT_DIR (REQUIRED FOR viterbi.h)
62	71	source_root_dir=`pwd`

244	253	# model_extra_programs="bootstrapper"
245	254	codegen_extra_sources=""
246	255	codegen_extra_ldadd="`pwd`/src/c4/viterbi.o \
247		`pwd`/src/c4/scheduler.o"
	256	`pwd`/src/sdp/scheduler.o"
248	257	else
249	258	echo "error: must be yes or no:"
250	259	echo " --enable-compiledmodels:[$enable_compiledmodels]"

288	297	if test "$enable_pthreads" = yes; then
289	298	echo "Using PTHREADS"
290	299	CFLAGS="$CFLAGS -DUSE_PTHREADS"
291		LDFLAGS="$LDFLAGS -lpthread"
	300	# for g_thread_init()
	301	g_thread_init_ldflags=`pkg-config --libs gthread-2.0`
	302	LDFLAGS="$LDFLAGS $g_thread_init_ldflags -lpthread"
292	303	elif test "$enable_pthreads" = no; then
293	304	echo "Not using pthreads"
294	305	else

+1

-0

doc/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

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doc/man/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

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doc/man/man1/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+50

-15

doc/man/man1/exonerate.1 less more

135	135	Specify the target sequences required. Also, must be in a FASTA
136	136	format file. As with the query sequences, single or multiple target
137	137	sequences and files may be supplied.
138		.B NEW:
139		the target filename may by replace by a server name and port number
	138	The target filename may by replace by a server name and port number
140	139	in the form of
141	140	.B hostname:port
142	141	when using

144	143	See the man page for
145	144	.B exonerate-server
146	145	for more information on running exonerate in client:server mode.
147
	146	.B NEW(v2.4.0):
	147	multiple servers may now be used. These will be queried in parallel
	148	if you have set the
	149	.B --cores
	150	option.
	151	.B NEW(v2.4.0):
	152	If an input file is not a FASTA format file,
	153	it is assumed to contain a list of other fasta files,
	154	directories or servers (one per line).
148	155	.\"
149	156	.TP
150	157	.B "-Q \| \--querytype" <dna \| protein>

221	228	This is very memory efficient and fast when both sequences
222	229	are chromosome-sized, but currently does not currently permit the use
223	230	of a word neighbourhood (ie. exactly matching seeds only).
	231	.\"
	232	.TP
	233	.B "\--revcomp" <boolean>
	234	Include comparison of the reverse complement of the query and target
	235	where possible. By default, this option is enabled,
	236	but when you know the gene is definitely on the forward strand
	237	of the query and target,
	238	this option can halve the time taken to compute alignments.
224	239	.\"
225	240	.TP
226	241	.B "\--forcescan" <none \| query \| target>

245	260	.\"
246	261	.TP
247	262	.B "\--customserver" <command>
248		.B NEW:
249	263	When using exonerate in client:server mode with a non-standard
250	264	server, this command allows you to send a custom command to the
251	265	server. This command is sent by the client (exonerate)

254	268	.B exonerate-server
255	269	man page for more information on running exonerate in client:server mode.
256	270	.\"
257
258		.RE
	271	.TP
	272	.B "\--cores" <number>
	273	The number of cores/CPUs/threads that should be used.
	274	On a multi-core or multi-CPU machine, increasing this ammount
	275	allows alignment computations to run in parallel on separate CPUs/cores.
	276	NB. Generally, it is better to parallelise the analysis
	277	by splitting it up into separate jobs, but this option may prove
	278	useful for problems such as interactive single-gene queries.
	279	.\"
	280
259	281	.SH FASTA DATABASE OPTIONS
260	282	.TP
261	283	.B "\--fastasuffix" <extension>

347	369	.\"
348	370	.TP
349	371	.B protein2dna:bestfit
350		.B NEW:
351	372	This is a bestfit version of the protein2dna model,
352	373	with which the entire protein is included in the alignment.
353	374	It is currently only available when using exhaustive alignment.

361	382	.\"
362	383	.TP
363	384	.B protein2genome:bestfit
364		.B NEW:
365	385	This is a bestfit version of the protein2genome model,
366	386	with which the entire protein is included in the alignment.
367	387	It is currently only available when using exhaustive alignment.

599	619	Equivalenced {total,id,similarity,mismatches}
600	620	(ie. %em == (%et - %ei))
601	621	.TP
602		.B %p[is]
603		Percent {id,similarity}
	622	.B %p[isS]
	623	Percent {id,similarity,Self}
604	624	over the equivalenced portions of the alignment.
605		(ie. %pi == 100*(%ei / %et))
	625	(ie. %pi == 100*(%ei / %et)).
	626	Percent Self is the score over the equivalenced portions
	627	of the alignment as a percentage of the self comparison score
	628	of the query sequence.
606	629	.TP
607	630	.B %g
608	631	Gene orientation ('+' = forward, '-' = reverse, '.' = unknown)

916	939	query sequences, and makes the search run faster, but it also
917	940	damages search sensitivity when high values are set.
918	941	.\"
	942	.TP
	943	.B "\--wordambiguity" <limit>
	944	This option may be used to allow alignment seeds containing
	945	IUPAC ambiguity symbols.
	946	The limit is the maximum number of ambiguous words
	947	allowed at a single position. If this limit is reached
	948	then the position is not used for alignment seeding.
	949	Using this option may slow down a search.
	950	For large datasets,
	951	it is recommended to use
	952	.B esd2esi --wordambiguity
	953	instead, as then the speed overhead is only incurred
	954	during indexing, rather than during the database searching itself.
	955	NB. This option only works for IUPAC symbols in the target sequence.
	956	Query words containing IUPAC symbols are (currently) excluded from seeding.
	957	.\"
919	958	.SH AFFINE MODEL OPTIONS
920	959	.TP
921	960	.B "\-o \| \--gapopen" <penalty>

980	1019	.SH TRANSLATION OPTIONS
981	1020	.TP
982	1021	.B "\--geneticcode" <code>
983		.B NEW:
984	1022	Specify an alternative genetic code. The default code (1) is the standard
985	1023	genetic code. Other genetic codes may be specified by in shorthand or
986	1024	longhand form.

1080	1118	.\"
1081	1119	.TP
1082	1120	.B "\--seedrepeat" <count>
1083		.B NEW:
1084	1121	The seedrepeat parameter sets the number of seeds which must be found
1085	1122	on the same diagonal or reading frame before HSP extension will occur.
1086	1123	Increasing the value for

1150	1187	.\"
1151	1188	.TP
1152	1189	.B "\--geneseedrepeat" <count>
1153		.B NEW:
1154	1190	The geneseedrepeat parameter is like the seedrepeat parameter,
1155	1191	but is only applied when looking for the geneseed hsps.
1156	1192	Using a larger value for

1183	1219	.B "\--splice3" <path>
1184	1220	.TP
1185	1221	.B "\--splice5" <path>
1186		.B NEW:
1187	1222	Provide a file containing a custom PSSM (position specific score matrix)
1188	1223	for prediction of the intron splice sites.
1189	1224

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src/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

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src/bsdp/Makefile.am less more

21	21	$(top_srcdir)/src/sequence/translate.o \
22	22	$(top_srcdir)/src/general/argument.o \
23	23	$(top_srcdir)/src/general/lineparse.o \
	24	$(top_srcdir)/src/general/threadref.o \
24	25	-lm
25	26
26	27	C4_OBJ = $(top_srcdir)/src/c4/c4.o \

53	54	hpair_test_LDADD = $(top_srcdir)/src/struct/slist.o \
54	55	$(top_srcdir)/src/struct/pqueue.o \
55	56	$(top_srcdir)/src/struct/recyclebin.o \
	57	$(top_srcdir)/src/struct/rangetree.o \
56	58	$(top_srcdir)/src/comparison/hspset.o \
57	59	$(top_srcdir)/src/comparison/wordhood.o \
58		$(top_srcdir)/src/struct/rangetree.o \
59	60	$(ALIGNMENT_OBJ)
60	61
61	62	sar_test_SOURCES = sar.test.c sar.c heuristic.c

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src/bsdp/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

86	87
87	88	noinst_HEADERS = heuristic.h bsdp.h hpair.h sar.h
88	89
89		SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
	90	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/threadref.o -lm
90	91
91	92
92	93	C4_OBJ = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o

104	105
105	106
106	107	hpair_test_SOURCES = hpair.test.c hpair.c heuristic.c bsdp.c sar.c
107		hpair_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/struct/rangetree.o $(ALIGNMENT_OBJ)
	108	hpair_test_LDADD = $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(ALIGNMENT_OBJ)
108	109
109	110
110	111	sar_test_SOURCES = sar.test.c sar.c heuristic.c

140	141	$(top_srcdir)/src/sequence/splice.o \
141	142	$(top_srcdir)/src/sequence/translate.o \
142	143	$(top_srcdir)/src/general/argument.o \
143		$(top_srcdir)/src/general/lineparse.o
	144	$(top_srcdir)/src/general/lineparse.o \
	145	$(top_srcdir)/src/general/threadref.o
144	146	heuristic_test_LDFLAGS =
145	147	bsdp_test_OBJECTS = bsdp.test.o bsdp.o
146	148	bsdp_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \

149	151	hpair_test_OBJECTS = hpair.test.o hpair.o heuristic.o bsdp.o sar.o
150	152	hpair_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \
151	153	$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
	154	$(top_srcdir)/src/struct/rangetree.o \
152	155	$(top_srcdir)/src/comparison/hspset.o \
153	156	$(top_srcdir)/src/comparison/wordhood.o \
154		$(top_srcdir)/src/struct/rangetree.o \
155	157	$(top_srcdir)/src/comparison/match.o \
156	158	$(top_srcdir)/src/sequence/codonsubmat.o \
157	159	$(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/c4/c4.o \

165	167	$(top_srcdir)/src/sequence/splice.o \
166	168	$(top_srcdir)/src/sequence/translate.o \
167	169	$(top_srcdir)/src/general/argument.o \
168		$(top_srcdir)/src/general/lineparse.o
	170	$(top_srcdir)/src/general/lineparse.o \
	171	$(top_srcdir)/src/general/threadref.o
169	172	hpair_test_LDFLAGS =
170	173	sar_test_OBJECTS = sar.test.o sar.o heuristic.o
171	174	sar_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

184	187	$(top_srcdir)/src/sequence/splice.o \
185	188	$(top_srcdir)/src/sequence/translate.o \
186	189	$(top_srcdir)/src/general/argument.o \
187		$(top_srcdir)/src/general/lineparse.o
	190	$(top_srcdir)/src/general/lineparse.o \
	191	$(top_srcdir)/src/general/threadref.o
188	192	sar_test_LDFLAGS =
189	193	CFLAGS = @CFLAGS@
190	194	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)

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src/bsdp/bsdp.c less more

2	2	* BSDP : Bounded Sparse Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

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src/bsdp/bsdp.h less more

2	2	* BSDP: Bounded Sparse Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

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src/bsdp/bsdp.test.c less more

2	2	* BSDP : Bounded Sparse Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

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src/bsdp/heuristic.c less more

2	2	* C4 dynamic programming library - code for heuristics *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/heuristic.h less more

2	2	* C4 dynamic programming library - code for heuristics *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/heuristic.test.c less more

2	2	* C4 dynamic programming library - code for heuristics *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/hpair.c less more

2	2	* C4 dynamic programming library - code for heuristic pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/hpair.h less more

2	2	* C4 dynamic programming library - code for heuristic pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/hpair.test.c less more

2	2	* C4 dynamic programming library - code for heuristic pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/sar.c less more

2	2	* C4 dynamic programming library - sub-alignment regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/sar.h less more

2	2	* C4 dynamic programming library - sub-alignment regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/bsdp/sar.test.c less more

2	2	* C4 dynamic programming library - sub-alignment regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+6

-3

src/c4/Makefile.am less more

18	18	region_test_SOURCES = region.test.c region.c
19	19
20	20	c4_test_SOURCES = c4.test.c c4.c region.c
21		c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o
	21	c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o \
	22	$(top_srcdir)/src/general/threadref.o
22	23
23	24	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
24	25	$(top_srcdir)/src/struct/matrix.o \

33	34	ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \
34	35	$(top_srcdir)/src/sequence/codonsubmat.o \
35	36	$(top_srcdir)/src/sequence/submat.o \
	37	$(top_srcdir)/src/general/threadref.o \
36	38	$(SEQUENCE_OBJ)
37	39	alignment_test_SOURCES = alignment.test.c alignment.c c4.c region.c
38	40	alignment_test_LDADD = $(ALIGNMENT_OBJ)

41	43	codegen_test_LDADD = $(top_srcdir)/src/general/argument.o
42	44
43	45	cgutil_test_SOURCES = cgutil.test.c cgutil.c codegen.c c4.c region.c
44		cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o \
45		$(top_srcdir)/src/struct/matrix.o
	46	cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o \
	47	$(top_srcdir)/src/struct/matrix.o \
	48	$(top_srcdir)/src/general/threadref.o
46	49
47	50	viterbi_test_SOURCES = viterbi.test.c viterbi.c c4.c region.c \
48	51	alignment.c codegen.c layout.c subopt.c \

+12

-5

src/c4/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

91	92	region_test_SOURCES = region.test.c region.c
92	93
93	94	c4_test_SOURCES = c4.test.c c4.c region.c
94		c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o
	95	c4_test_LDADD = $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/general/threadref.o
	96
95	97
96	98	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
97	99
98	100
99		ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(SEQUENCE_OBJ)
	101	ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/general/threadref.o $(SEQUENCE_OBJ)
100	102
101	103	alignment_test_SOURCES = alignment.test.c alignment.c c4.c region.c
102	104	alignment_test_LDADD = $(ALIGNMENT_OBJ)

105	107	codegen_test_LDADD = $(top_srcdir)/src/general/argument.o
106	108
107	109	cgutil_test_SOURCES = cgutil.test.c cgutil.c codegen.c c4.c region.c
108		cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/struct/matrix.o
	110	cgutil_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/general/threadref.o
109	111
110	112
111	113	viterbi_test_SOURCES = viterbi.test.c viterbi.c c4.c region.c alignment.c codegen.c layout.c subopt.c cgutil.c

147	149	region_test_DEPENDENCIES =
148	150	region_test_LDFLAGS =
149	151	c4_test_OBJECTS = c4.test.o c4.o region.o
150		c4_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o
	152	c4_test_DEPENDENCIES = $(top_srcdir)/src/struct/matrix.o \
	153	$(top_srcdir)/src/general/threadref.o
151	154	c4_test_LDFLAGS =
152	155	alignment_test_OBJECTS = alignment.test.o alignment.o c4.o region.o
153	156	alignment_test_DEPENDENCIES = $(top_srcdir)/src/comparison/match.o \
154	157	$(top_srcdir)/src/sequence/codonsubmat.o \
155	158	$(top_srcdir)/src/sequence/submat.o \
	159	$(top_srcdir)/src/general/threadref.o \
156	160	$(top_srcdir)/src/struct/sparsecache.o \
157	161	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
158	162	$(top_srcdir)/src/sequence/alphabet.o \

172	176	$(top_srcdir)/src/comparison/match.o \
173	177	$(top_srcdir)/src/sequence/codonsubmat.o \
174	178	$(top_srcdir)/src/sequence/submat.o \
	179	$(top_srcdir)/src/general/threadref.o \
175	180	$(top_srcdir)/src/struct/sparsecache.o \
176	181	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
177	182	$(top_srcdir)/src/sequence/alphabet.o \

191	196	$(top_srcdir)/src/comparison/match.o \
192	197	$(top_srcdir)/src/sequence/codonsubmat.o \
193	198	$(top_srcdir)/src/sequence/submat.o \
	199	$(top_srcdir)/src/general/threadref.o \
194	200	$(top_srcdir)/src/struct/sparsecache.o \
195	201	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
196	202	$(top_srcdir)/src/sequence/alphabet.o \

207	213	$(top_srcdir)/src/comparison/match.o \
208	214	$(top_srcdir)/src/sequence/codonsubmat.o \
209	215	$(top_srcdir)/src/sequence/submat.o \
	216	$(top_srcdir)/src/general/threadref.o \
210	217	$(top_srcdir)/src/struct/sparsecache.o \
211	218	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
212	219	$(top_srcdir)/src/sequence/alphabet.o \

221	228	subopt_test_LDFLAGS =
222	229	cgutil_test_OBJECTS = cgutil.test.o cgutil.o codegen.o c4.o region.o
223	230	cgutil_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
224		$(top_srcdir)/src/struct/matrix.o
	231	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/general/threadref.o
225	232	cgutil_test_LDFLAGS =
226	233	CFLAGS = @CFLAGS@
227	234	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)

+204

-18

src/c4/alignment.c less more

2	2	* C4 dynamic programming library - alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

537	537	register gint i, j;
538	538	register gint curr_query_pos = query_pos,
539	539	curr_target_pos = target_pos;
540		static gchar seq_string[4], match_string[4], gap_string[4];
	540	register gchar *seq_string = g_new(gchar, 4),
	541	*match_string = g_new(gchar, 4),
	542	*gap_string = g_new(gchar, 4);
541	543	register Alphabet_Type emitted_alphabet_type;
542	544	register gchar tr_codon, *tr_codon_name;
543	545	register gboolean is_translating

597	599	curr_query_pos += advance_query;
598	600	curr_target_pos += advance_target;
599	601	}
	602	g_free(seq_string);
	603	g_free(match_string);
	604	g_free(gap_string);
600	605	return;
601	606	}
602	607	/* Display gap:[- N] codon[<-> NNN] frameshift [-*N]

1415	1420	/* Reports the %id over the equivalenced regions of the alignment
1416	1421	*/
1417	1422
	1423	static gint Alignment_get_equivalenced_matching_region(Alignment *alignment,
	1424	Sequence query, Sequence target,
	1425	Translate *translate, gboolean report_id,
	1426	gpointer user_data, gint exon_query_start, gint exon_query_end){
	1427	register gint i, j, match = 0;
	1428	register AlignmentOperation *ao;
	1429	register gint query_pos = alignment->region->query_start,
	1430	target_pos = alignment->region->target_start;
	1431	register gchar qy_symbol, tg_symbol;
	1432	for(i = 0; i < alignment->operation_list->len; i++){
	1433	ao = alignment->operation_list->pdata[i];
	1434	if(ao->transition->label == C4_Label_MATCH){
	1435	for(j = 0; j < ao->length; j++){
	1436	if(query_pos > exon_query_end)
	1437	return match;
	1438	if(query_pos >= exon_query_start){
	1439	qy_symbol = Alignment_match_get_symbol(query, query_pos,
	1440	ao->transition->advance_query,
	1441	translate);
	1442	tg_symbol = Alignment_match_get_symbol(target,
	1443	target_pos,
	1444	ao->transition->advance_target,
	1445	translate);
	1446	if(report_id){
	1447	if(toupper(qy_symbol) == toupper(tg_symbol))
	1448	match++;
	1449	} else { /* report similarity */
	1450	if(C4_Calc_score(ao->transition->calc, query_pos,
	1451	target_pos, user_data) > 0)
	1452	match++;
	1453	}
	1454	}
	1455	query_pos += ao->transition->advance_query;
	1456	target_pos += ao->transition->advance_target;
	1457	}
	1458	} else {
	1459	query_pos += (ao->transition->advance_query
	1460	* ao->length);
	1461	target_pos += (ao->transition->advance_target
	1462	* ao->length);
	1463	}
	1464	}
	1465	return match;
	1466	}
	1467	/* Reports the %id over the equivalenced regions of the alignment
	1468	*/
	1469
1418	1470	static gint Alignment_get_equivalenced_total(Alignment *alignment){
1419	1471	register gint i, total = 0;
1420	1472	register AlignmentOperation *ao;

1426	1478	return total;
1427	1479	}
1428	1480
	1481	static gint Alignment_get_equivalenced_total_region(Alignment *alignment,
	1482	gint exon_query_start, gint exon_query_end){
	1483	register gint i, j, total = 0;
	1484	register gint query_pos = alignment->region->query_start,
	1485	target_pos = alignment->region->target_start;
	1486	register AlignmentOperation *ao;
	1487	for(i = 0; i < alignment->operation_list->len; i++){
	1488	ao = alignment->operation_list->pdata[i];
	1489	if(ao->transition->label == C4_Label_MATCH){
	1490	for(j = 0; j < ao->length; j++){
	1491	if(query_pos > exon_query_end)
	1492	return total;
	1493	if(query_pos >= exon_query_start)
	1494	total++;
	1495	query_pos += ao->transition->advance_query;
	1496	target_pos += ao->transition->advance_target;
	1497	}
	1498	} else {
	1499	query_pos += (ao->transition->advance_query
	1500	* ao->length);
	1501	target_pos += (ao->transition->advance_target
	1502	* ao->length);
	1503	}
	1504	}
	1505	return total;
	1506	}
	1507	/* FIXME: optimisation: should use gene object to avoid full alignment pass
	1508	*/
	1509
	1510	static gfloat Alignment_get_percent_score_region(Alignment *alignment,
	1511	Sequence query, Sequence target,
	1512	Translate *translate, gboolean report_id, gpointer user_data,
	1513	gint exon_query_start, gint exon_query_end){
	1514	return (((gfloat)Alignment_get_equivalenced_matching_region(alignment,
	1515	query, target, translate, report_id, user_data,
	1516	exon_query_start, exon_query_end))
	1517	/ ((gfloat)Alignment_get_equivalenced_total_region(alignment,
	1518	exon_query_start, exon_query_end)))*100;
	1519	}
	1520	/* FIXME: should also count split codons */
	1521
1429	1522	static gfloat Alignment_get_percent_score(Alignment *alignment,
1430	1523	Sequence query, Sequence target,
1431	1524	Translate *translate, gboolean report_id,

1434	1527	query, target, translate, report_id, user_data))
1435	1528	/ ((gfloat)Alignment_get_equivalenced_total(alignment)))*100;
1436	1529	}
	1530	/* FIXME: should also count split codons */
	1531
	1532	static gint Alignment_get_match_score(Alignment *alignment,
	1533	Sequence query, Sequence target,
	1534	gpointer user_data){
	1535	register gint i, j;
	1536	register AlignmentOperation *ao;
	1537	register C4_Score score = 0;
	1538	register gint query_pos = alignment->region->query_start,
	1539	target_pos = alignment->region->target_start;
	1540	for(i = 0; i < alignment->operation_list->len; i++){
	1541	ao = alignment->operation_list->pdata[i];
	1542	for(j = 0; j < ao->length; j++){
	1543	if(ao->transition->label == C4_Label_MATCH){
	1544	score += C4_Calc_score(ao->transition->calc, query_pos,
	1545	target_pos, user_data);
	1546	}
	1547	query_pos += ao->transition->advance_query;
	1548	target_pos += ao->transition->advance_target;
	1549	}
	1550	}
	1551	g_message("MATCH SCORE [%d]", score);
	1552	return score;
	1553	}
	1554
	1555	static gint Alignment_get_self_match_score(Alignment *alignment,
	1556	Sequence query, Sequence target,
	1557	gpointer self_data){
	1558	register gint i, j;
	1559	register AlignmentOperation *ao;
	1560	register C4_Score score = 0;
	1561	register gint query_pos = alignment->region->query_start;
	1562	for(i = 0; i < alignment->operation_list->len; i++){
	1563	ao = alignment->operation_list->pdata[i];
	1564	for(j = 0; j < ao->length; j++){
	1565	if(ao->transition->label == C4_Label_MATCH){
	1566	/* Use self_data to find self-comparison scores */
	1567	score += C4_Calc_score(ao->transition->calc, query_pos,
	1568	query_pos, self_data);
	1569	}
	1570	query_pos += ao->transition->advance_query;
	1571	}
	1572	}
	1573	g_message("SELF MATCH SCORE [%d]", score);
	1574	return score;
	1575	}
	1576
	1577	static gfloat Alignment_get_percent_self(Alignment *alignment,
	1578	Sequence query, Sequence target,
	1579	Translate *translate, gpointer user_data, gpointer self_data){
	1580	return (((gfloat)Alignment_get_match_score(alignment,
	1581	query, target, user_data))
	1582	/ ((gfloat)Alignment_get_self_match_score(alignment, query, target,
	1583	self_data)))*100;
	1584	}
	1585	/* Returns score as a percentage of maximum possible
	1586	* over the equivalenced transitions
	1587	*/
1437	1588
1438	1589	/**/
1439	1590

1611	1762	Alignment_RYO_TOKEN_RANK,
1612	1763	Alignment_RYO_TOKEN_PERCENT_ID,
1613	1764	Alignment_RYO_TOKEN_PERCENT_SIMILARITY,
	1765	Alignment_RYO_TOKEN_PERCENT_SELF,
1614	1766	Alignment_RYO_TOKEN_GENE_ORIENTATION,
1615	1767	Alignment_RYO_TOKEN_EQUIVALENCED_TOTAL,
1616	1768	Alignment_RYO_TOKEN_EQUIVALENCED_IDENTCAL,

1902	2054	case 's':
1903	2055	Alignment_RYO_add_token(token_list,
1904	2056	Alignment_RYO_TOKEN_PERCENT_SIMILARITY,
	2057	FALSE);
	2058	break;
	2059	case 'S':
	2060	Alignment_RYO_add_token(token_list,
	2061	Alignment_RYO_TOKEN_PERCENT_SELF,
1905	2062	FALSE);
1906	2063	break;
1907	2064	default:

1990	2147	* %s score
1991	2148	* %m model_name
1992	2149	* %r rank
1993		* %p[is] percent {id,similarity}
	2150	* %p[isS] percent {id,similarity,self}
1994	2151	* %e[tid] equivalenced {total,identical,similar}
1995	2152	* %g gene_orientation
1996	2153	* %S sugar block

2203	2360
2204	2361	static void Alignment_RYO_token_list_print(GPtrArray *token_list,
2205	2362	Alignment alignment, Sequence query, Sequence *target,
2206		Translate translate, gint rank, gpointer user_data, FILE fp){
	2363	Translate *translate, gint rank,
	2364	gpointer user_data, gpointer self_data, FILE *fp){
2207	2365	register gint i, j, pto_start = -1;
2208	2366	register Alignment_RYO_ComplexToken *rct;
2209	2367	register Sequence seq, subseq;

2322	2480	fprintf(fp, "%2.2f", Alignment_get_percent_score(
2323	2481	alignment, query, target,
2324	2482	translate, FALSE, user_data));
	2483	break;
	2484	case Alignment_RYO_TOKEN_PERCENT_SELF:
	2485	fprintf(fp, "%2.2f", Alignment_get_percent_self(
	2486	alignment, query, target,
	2487	translate, user_data, self_data));
2325	2488	break;
2326	2489	case Alignment_RYO_TOKEN_GENE_ORIENTATION:
2327	2490	fprintf(fp, "%c",

2445	2608
2446	2609	void Alignment_display_ryo(Alignment *alignment,
2447	2610	Sequence query, Sequence target, gchar *format,
2448		Translate translate, gint rank, gpointer user_data, FILE fp){
	2611	Translate *translate, gint rank,
	2612	gpointer user_data, gpointer self_data, FILE *fp){
2449	2613	register GPtrArray *token_list = Alignment_RYO_tokenise(format);
2450	2614	Alignment_RYO_token_list_print(token_list, alignment,
2451	2615	query, target, translate, rank,
2452		user_data, fp);
	2616	user_data, self_data, fp);
2453	2617	Alignment_RYO_token_list_destroy(token_list);
2454	2618	return;
2455	2619	}

2590	2754	static void Alignment_display_gff_exon(Alignment *alignment,
2591	2755	Sequence *query,
2592	2756	Sequence *target,
	2757	Translate *translate,
2593	2758	gboolean report_on_query,
2594	2759	gint query_pos,
2595	2760	gint target_pos,

2598	2763	gint exon_query_gap,
2599	2764	gint exon_target_gap,
2600	2765	gint exon_query_frameshift,
2601		gint exon_target_frameshift, FILE *fp){
	2766	gint exon_target_frameshift,
	2767	gpointer user_data, FILE *fp){
2602	2768	register GPtrArray *attribute_list = g_ptr_array_new();
2603	2769	g_ptr_array_add(attribute_list,
2604	2770	g_strdup_printf("insertions %d",

2608	2774	g_strdup_printf("deletions %d",
2609	2775	report_on_query?exon_target_gap
2610	2776	:exon_query_gap));
	2777	g_ptr_array_add(attribute_list,
	2778	g_strdup_printf("identity %2.2f",
	2779	Alignment_get_percent_score_region(alignment,
	2780	query, target, translate, TRUE, user_data,
	2781	exon_query_start, query_pos)));
	2782	g_ptr_array_add(attribute_list,
	2783	g_strdup_printf("similarity %2.2f",
	2784	Alignment_get_percent_score_region(alignment,
	2785	query, target, translate, FALSE, user_data,
	2786	exon_query_start, query_pos)));
2611	2787	if(report_on_query){
2612	2788	if(exon_query_frameshift)
2613	2789	g_ptr_array_add(attribute_list,

2666	2842	}
2667	2843
2668	2844	static void Alignment_display_gff_gene(Alignment *alignment,
2669		Sequence query, Sequence target, gboolean report_on_query,
2670		gint result_id, FILE *fp){
	2845	Sequence query, Sequence target, Translate *translate,
	2846	gboolean report_on_query,
	2847	gint result_id, gpointer user_data, FILE *fp){
2671	2848	register gint i;
2672	2849	register gint query_pos = alignment->region->query_start,
2673	2850	target_pos = alignment->region->target_start;

2691	2868	report_on_query?target->id:query->id));
2692	2869	g_ptr_array_add(attribute_list,
2693	2870	g_strdup_printf("gene_orientation %c", gene_orientation));
	2871	g_ptr_array_add(attribute_list,
	2872	g_strdup_printf("identity %2.2f",
	2873	Alignment_get_percent_score(alignment,
	2874	query, target, translate, TRUE, user_data)));
	2875	g_ptr_array_add(attribute_list,
	2876	g_strdup_printf("similarity %2.2f",
	2877	Alignment_get_percent_score(alignment,
	2878	query, target, translate, FALSE, user_data)));
2694	2879	Alignment_display_gff_line(alignment, query, target, report_on_query,
2695	2880	"gene",
2696	2881	alignment->region->query_start,

2769	2954	exon_query_start, exon_target_start,
2770	2955	query_pos, target_pos, fp);
2771	2956	Alignment_display_gff_exon(alignment,
2772		query, target, report_on_query,
	2957	query, target, translate, report_on_query,
2773	2958	query_pos, target_pos,
2774	2959	exon_query_start, exon_target_start,
2775	2960	exon_query_gap, exon_target_gap,
2776	2961	exon_query_frameshift,
2777		exon_target_frameshift, fp);
	2962	exon_target_frameshift, user_data, fp);
2778	2963	in_exon = FALSE;
2779	2964	}
2780	2965	attribute_list = g_ptr_array_new();

2810	2995	exon_query_start, exon_target_start,
2811	2996	query_pos, target_pos, fp);
2812	2997	Alignment_display_gff_exon(alignment,
2813		query, target, report_on_query,
	2998	query, target, translate, report_on_query,
2814	2999	query_pos, target_pos,
2815	3000	exon_query_start, exon_target_start,
2816	3001	exon_query_gap, exon_target_gap,
2817	3002	exon_query_frameshift,
2818		exon_target_frameshift, fp);
	3003	exon_target_frameshift, user_data, fp);
2819	3004	in_exon = FALSE;
2820	3005	}
2821	3006	if(gene_orientation == '+'){

2894	3079	}
2895	3080	}
2896	3081	Alignment_display_gff_exon(alignment,
2897		query, target, report_on_query,
	3082	query, target, translate, report_on_query,
2898	3083	query_pos, target_pos,
2899	3084	exon_query_start, exon_target_start,
2900	3085	exon_query_gap, exon_target_gap,
2901		exon_query_frameshift, exon_target_frameshift, fp);
	3086	exon_query_frameshift, exon_target_frameshift, user_data, fp);
2902	3087	}
2903	3088	return;
2904	3089	}

2973	3158
2974	3159	void Alignment_display_gff(Alignment *alignment,
2975	3160	Sequence query, Sequence target,
	3161	Translate *translate,
2976	3162	gboolean report_on_query,
2977	3163	gboolean report_on_genomic,
2978		gint result_id, FILE *fp){
	3164	gint result_id, gpointer user_data, FILE *fp){
2979	3165	fprintf(fp, "# --- START OF GFF DUMP ---\n#\n");
2980	3166	Alignment_display_gff_header(alignment, query, target,
2981	3167	report_on_query, fp);
2982	3168	if(report_on_genomic){
2983		Alignment_display_gff_gene(alignment, query, target,
2984		report_on_query, result_id, fp);
	3169	Alignment_display_gff_gene(alignment, query, target, translate,
	3170	report_on_query, result_id, user_data, fp);
2985	3171	}
2986	3172	Alignment_display_gff_similarity(alignment, query, target,
2987	3173	report_on_query, result_id, fp);

+5

-3

src/c4/alignment.h less more

2	2	* C4 dynamic programming library - alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

75	75
76	76	void Alignment_display_gff(Alignment *alignment,
77	77	Sequence query, Sequence target,
	78	Translate *translate,
78	79	gboolean report_on_query,
79	80	gboolean report_on_genomic,
80		gint result_id, FILE *fp);
	81	gint result_id, gpointer user_data, FILE *fp);
81	82
82	83	void Alignment_display_ryo(Alignment *alignment,
83	84	Sequence query, Sequence target, gchar *format,
84		Translate translate, gint rank, gpointer user_data, FILE fp);
	85	Translate *translate, gint rank,
	86	gpointer user_data, gpointer self_data, FILE *fp);
85	87
86	88	/**/
87	89

+1

-1

src/c4/alignment.test.c less more

2	2	* C4 dynamic programming library - alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+4

-4

src/c4/c4.c less more

2	2	* C4 dynamic programming library - code for models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

519	519	model->exit_func = NULL;
520	520	model->exit_macro = NULL;
521	521	/**/
522		model->ref_count = 1;
	522	model->thread_ref = ThreadRef_create();
523	523	model->is_open = TRUE;
524	524	/**/
525	525	model->state_list = g_ptr_array_new();

559	559	void C4_Model_destroy(C4_Model *model){
560	560	register gint i;
561	561	g_assert(model);
562		if(--model->ref_count)
	562	if(ThreadRef_destroy(model->thread_ref))
563	563	return;
564	564	g_free(model->name);
565	565	C4_Model_destroy_string_list(model->global_code_list);

596	596	C4_Model C4_Model_share(C4_Model model){
597	597	g_assert(model);
598	598	g_assert(!model->is_open);
599		model->ref_count++;
	599	ThreadRef_share(model->thread_ref);
600	600	return model;
601	601	}
602	602

+3

-2

src/c4/c4.h less more

2	2	* C4 dynamic programming library - code for models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

22	22	#include <glib.h>
23	23
24	24	#include "region.h"
	25	#include "threadref.h"
25	26
26	27	typedef gint C4_Score;
27	28	#define C4_IMPOSSIBLY_LOW_SCORE -987654321

176	177	gchar init_macro; / If NULL, use init_func */
177	178	C4_PrepFunc exit_func; /* If NULL, no initialisation */
178	179	gchar exit_macro; / If NULL, use exit_func */
179		gint ref_count;
	180	ThreadRef *thread_ref;
180	181	gboolean is_open;
181	182	GPtrArray *state_list;
182	183	GPtrArray *transition_list;

+1

-1

src/c4/c4.test.c less more

2	2	* C4 dynamic programming library - code for models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/cgutil.c less more

2	2	* Utilities to facilitate code generation DP implementations *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/cgutil.h less more

2	2	* Utilities to facilitate code generation DP implementations *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/cgutil.test.c less more

2	2	* Utilities to facilitate code generation DP implementations *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/codegen.c less more

2	2	* Code generation module for C4 *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/codegen.h less more

2	2	* Code generation module for C4 *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/codegen.test.c less more

2	2	* Code generation module for C4 *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/layout.c less more

2	2	* C4 dynamic programming library - DP layout code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/layout.h less more

2	2	* C4 dynamic programming library - DP layout code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/layout.test.c less more

2	2	* C4 dynamic programming library - optimal alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/opair.c less more

2	2	* C4 dynamic programming library - code for optimal pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/opair.h less more

2	2	* C4 dynamic programming library - code for optimal pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/opair.test.c less more

2	2	* C4 dynamic programming library - code for optimal pairs *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/optimal.c less more

2	2	* C4 dynamic programming library - optimal alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/optimal.h less more

2	2	* C4 dynamic programming library - optimal alignment code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/optimal.test.c less more

2	2	* C4 dynamic programming library - DP layout code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/region.c less more

2	2	* C4 dynamic programming library - code for regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/region.h less more

2	2	* C4 dynamic programming library - code for regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/region.test.c less more

2	2	* C4 dynamic programming library - code for regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/subopt.c less more

2	2	* C4 dynamic programming library - suboptimal alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/subopt.h less more

2	2	* C4 dynamic programming library - suboptimal alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/subopt.test.c less more

2	2	* C4 dynamic programming library - suboptimal alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/viterbi.c less more

2	2	* C4 dynamic programming library - the Viterbi implementation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/viterbi.h less more

2	2	* C4 dynamic programming library - the Viterbi implementation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/c4/viterbi.test.c less more

2	2	* C4 dynamic programming library - the Viterbi implementation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-0

src/comparison/Makefile.am less more

28	28	$(top_srcdir)/src/sequence/codonsubmat.o \
29	29	$(top_srcdir)/src/struct/pqueue.o \
30	30	$(top_srcdir)/src/struct/recyclebin.o \
	31	$(top_srcdir)/src/general/threadref.o \
31	32	$(SEQUENCE_OBJ)
32	33
33	34	pcr_test_SOURCES = pcr.test.c pcr.c wordhood.c

44	45	$(top_srcdir)/src/sequence/codonsubmat.o \
45	46	$(top_srcdir)/src/struct/recyclebin.o \
46	47	$(top_srcdir)/src/struct/pqueue.o \
	48	$(top_srcdir)/src/general/threadref.o \
47	49	$(SEQUENCE_OBJ)
48	50
49	51	match_test_SOURCES = match.test.c match.c

59	61	$(top_srcdir)/src/struct/fsm.o \
60	62	$(top_srcdir)/src/struct/vfsm.o \
61	63	$(top_srcdir)/src/struct/pqueue.o \
	64	$(top_srcdir)/src/general/threadref.o \
62	65	$(SEQUENCE_OBJ)
63	66
64	67	# Files to clear away

+7

-3

src/comparison/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

94	95	wordhood_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
95	96
96	97	hspset_test_SOURCES = hspset.test.c hspset.c match.c wordhood.c
97		hspset_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(SEQUENCE_OBJ)
	98	hspset_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/general/threadref.o $(SEQUENCE_OBJ)
98	99
99	100
100	101	pcr_test_SOURCES = pcr.test.c pcr.c wordhood.c

103	104
104	105	comparison_test_SOURCES = comparison.test.c comparison.c hspset.c match.c wordhood.c
105	106
106		comparison_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/pqueue.o $(SEQUENCE_OBJ)
	107	comparison_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/general/threadref.o $(SEQUENCE_OBJ)
107	108
108	109
109	110	match_test_SOURCES = match.test.c match.c

112	113
113	114	seeder_test_SOURCES = seeder.test.c seeder.c wordhood.c hspset.c match.c comparison.c
114	115
115		seeder_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(SEQUENCE_OBJ)
	116	seeder_test_LDADD = $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/general/threadref.o $(SEQUENCE_OBJ)
116	117
117	118
118	119	# Files to clear away

142	143	hspset_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
143	144	$(top_srcdir)/src/sequence/codonsubmat.o \
144	145	$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
	146	$(top_srcdir)/src/general/threadref.o \
145	147	$(top_srcdir)/src/struct/sparsecache.o \
146	148	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
147	149	$(top_srcdir)/src/sequence/alphabet.o \

167	169	comparison_test_DEPENDENCIES = $(top_srcdir)/src/sequence/submat.o \
168	170	$(top_srcdir)/src/sequence/codonsubmat.o \
169	171	$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/pqueue.o \
	172	$(top_srcdir)/src/general/threadref.o \
170	173	$(top_srcdir)/src/struct/sparsecache.o \
171	174	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
172	175	$(top_srcdir)/src/sequence/alphabet.o \

192	195	$(top_srcdir)/src/sequence/codonsubmat.o \
193	196	$(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/fsm.o \
194	197	$(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o \
	198	$(top_srcdir)/src/general/threadref.o \
195	199	$(top_srcdir)/src/struct/sparsecache.o \
196	200	$(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o \
197	201	$(top_srcdir)/src/sequence/alphabet.o \

+13

-17

src/comparison/comparison.c less more

2	2	* Comparison : A module for pairwise sequence comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

35	35	HSP_Param *codon_hsp_param,
36	36	gboolean swap_param){
37	37	register Comparison_Param *param = g_new(Comparison_Param, 1);
38		param->ref_count = 1;
	38	param->thread_ref = NULL;
39	39	param->query_type = query_type;
40	40	param->target_type = target_type;
41	41	param->dna_hsp_param = Comparison_Param_get_hsp_param(dna_hsp_param,

63	63	dna_hsp_param, protein_hsp_param,
64	64	codon_hsp_param, TRUE);
65	65	param->mirror->mirror = param;
	66	param->mirror->thread_ref = param->thread_ref = ThreadRef_create();
66	67	return param;
67		}
68
69		static gint Comparison_Param_ref_count(Comparison_Param *param){
70		g_assert(param);
71		g_assert(param->mirror);
72		return param->ref_count + param->mirror->ref_count;
73	68	}
74	69
75	70	static void Comparison_Param_destroy_without_mirror(

88	83
89	84	void Comparison_Param_destroy(Comparison_Param *param){
90	85	g_assert(param);
91		param->ref_count--;
92		if(Comparison_Param_ref_count(param) > 1) /* Allow for mirror */
	86	if(ThreadRef_destroy(param->thread_ref))
93	87	return;
94	88	Comparison_Param_destroy_without_mirror(param->mirror);
95	89	Comparison_Param_destroy_without_mirror(param);

98	92
99	93	Comparison_Param Comparison_Param_share(Comparison_Param param){
100	94	g_assert(param);
101		param->ref_count++;
	95	ThreadRef_share(param->thread_ref);
102	96	return param;
103	97	}
104	98

131	125	g_assert(param);
132	126	g_assert(query);
133	127	g_assert(target);
134		comparison->ref_count = 1;
	128	comparison->thread_ref = ThreadRef_create();
135	129	comparison->param = Comparison_Param_share(param);
136	130	comparison->query = Sequence_share(query);
137	131	comparison->target = Sequence_share(target);
138		comparison->dna_hspset = param->dna_hsp_param
	132	ThreadRef_lock(comparison->param->thread_ref);
	133	comparison->dna_hspset = comparison->param->dna_hsp_param
139	134	? HSPset_create(query, target,
140	135	param->dna_hsp_param)
141	136	: NULL;

147	142	? HSPset_create(query, target,
148	143	param->codon_hsp_param)
149	144	: NULL;
	145	ThreadRef_unlock(comparison->param->thread_ref);
150	146	return comparison;
151	147	}
152	148
153	149	Comparison Comparison_share(Comparison comparison){
154		comparison->ref_count++;
	150	ThreadRef_share(comparison->thread_ref);
155	151	return comparison;
156	152	}
157	153
158	154	void Comparison_destroy(Comparison *comparison){
159	155	g_assert(comparison);
160		if(--comparison->ref_count)
	156	if(ThreadRef_destroy(comparison->thread_ref))
161	157	return;
162	158	Comparison_Param_destroy(comparison->param);
163	159	Sequence_destroy(comparison->query);

216	212
217	213	void Comparison_swap(Comparison *comparison){
218	214	register Sequence *query;
219		g_assert(comparison->ref_count == 1);
	215	g_assert(ThreadRef_get_count(comparison->thread_ref) == 1);
220	216	/* Mirror parameters */
221	217	comparison->param = Comparison_Param_share(comparison->param->mirror);
222	218	Comparison_Param_destroy(comparison->param->mirror);

241	237	void Comparison_revcomp(Comparison *comparison){
242	238	register Sequence *rc_query = Sequence_revcomp(comparison->query),
243	239	*rc_target = Sequence_revcomp(comparison->target);
244		g_assert(comparison->ref_count == 1);
	240	g_assert(ThreadRef_get_count(comparison->thread_ref) == 1);
245	241	g_assert(comparison->dna_hspset);
246	242	g_assert(!comparison->protein_hspset);
247	243	g_assert(!comparison->codon_hspset);

+6

-4

src/comparison/comparison.h less more

2	2	* Comparison : A module for pairwise sequence comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

26	26	#include "translate.h"
27	27	#include "submat.h"
28	28	#include "hspset.h"
	29	#include "threadref.h"
29	30
30	31	typedef struct Comparison_Param {
31		gint ref_count;
	32	ThreadRef *thread_ref;
32	33	Alphabet_Type query_type;
33	34	Alphabet_Type target_type;
34	35	HSP_Param *dna_hsp_param;

49	50	/**/
50	51
51	52	typedef struct {
52		gint ref_count;
	53	ThreadRef *thread_ref;
53	54	Comparison_Param *param;
54	55	Sequence *query;
55	56	Sequence *target;

63	64	Comparison Comparison_share(Comparison comparison);
64	65	void Comparison_destroy(Comparison *comparison);
65	66	void Comparison_print(Comparison *comparison);
66		HSPset_ArgumentSet Comparison_Param_get_HSPSet_Argument_Set(Comparison_Param param);
	67	HSPset_ArgumentSet *Comparison_Param_get_HSPSet_Argument_Set(
	68	Comparison_Param *param);
67	69
68	70	gboolean Comparison_has_hsps(Comparison *comparison);
69	71	void Comparison_finalise(Comparison *comparison);

+1

-1

src/comparison/comparison.test.c less more

2	2	* Comparison : A module for pairwise sequence comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+115

-44

src/comparison/hspset.c less more

2	2	* Library for HSP sets (high-scoring segment pairs) *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

65	65	/**/
66	66	ArgumentSet_add_option(as, 0, "dnawordlimit", "score",
67	67	"Score limit for dna word neighbourhood", "0",
68		Argument_parse_int, &has.dna_wordlimit);
	68	Argument_parse_int, &has.dna_word_limit);
69	69	ArgumentSet_add_option(as, 0, "proteinwordlimit", "score",
70	70	"Score limit for protein word neighbourhood", "4",
71		Argument_parse_int, &has.protein_wordlimit);
	71	Argument_parse_int, &has.protein_word_limit);
72	72	ArgumentSet_add_option(as, 0, "codonwordlimit", "score",
73	73	"Score limit for codon word neighbourhood", "4",
74		Argument_parse_int, &has.codon_wordlimit);
	74	Argument_parse_int, &has.codon_word_limit);
75	75	/**/
76	76	ArgumentSet_add_option(as, '\0', "geneseed", "threshold",
77	77	"Geneseed Threshold", "0",

141	141
142	142	/**/
143	143
	144	static void HSP_Param_refresh_wordhood(HSP_Param *hsp_param){
	145	register WordHood_Alphabet *wha = NULL;
	146	register Submat *submat;
	147	if(hsp_param->wordhood)
	148	WordHood_destroy(hsp_param->wordhood);
	149	if(hsp_param->has->use_wordhood_dropoff && (!hsp_param->wordlimit)){
	150	hsp_param->wordhood = NULL;
	151	} else {
	152	submat = (hsp_param->match->type == Match_Type_DNA2DNA)
	153	? hsp_param->match->mas->dna_submat
	154	: hsp_param->match->mas->protein_submat;
	155	wha = WordHood_Alphabet_create_from_Submat(
	156	(gchar*)hsp_param->match->comparison_alphabet->member,
	157	(gchar*)hsp_param->match->comparison_alphabet->member,
	158	submat, FALSE);
	159	g_assert(wha);
	160	hsp_param->wordhood = WordHood_create(wha, hsp_param->wordlimit,
	161	hsp_param->has->use_wordhood_dropoff);
	162	WordHood_Alphabet_destroy(wha);
	163	}
	164	return;
	165	}
	166	/* FIXME: optimisation: do not free/recreate wordhood when unnecessary */
	167
	168	void HSP_Param_set_dna_word_limit(HSP_Param *hsp_param,
	169	gint dna_word_limit){
	170	if(hsp_param->match->type == Match_Type_DNA2DNA){
	171	hsp_param->wordlimit = dna_word_limit;
	172	HSP_Param_refresh_wordhood(hsp_param);
	173	}
	174	return;
	175	}
	176
	177	void HSP_Param_set_protein_word_limit(HSP_Param *hsp_param,
	178	gint protein_word_limit){
	179	if((hsp_param->match->type == Match_Type_PROTEIN2PROTEIN)
	180	\|\| (hsp_param->match->type == Match_Type_PROTEIN2DNA)
	181	\|\| (hsp_param->match->type == Match_Type_DNA2PROTEIN)){
	182	hsp_param->wordlimit = protein_word_limit;
	183	HSP_Param_refresh_wordhood(hsp_param);
	184	}
	185	return;
	186	}
	187
	188	void HSP_Param_set_codon_word_limit(HSP_Param *hsp_param,
	189	gint codon_word_limit){
	190	if(hsp_param->match->type == Match_Type_CODON2CODON){
	191	hsp_param->threshold = codon_word_limit;
	192	HSP_Param_refresh_wordhood(hsp_param);
	193	}
	194	return;
	195	}
	196
	197	/**/
	198
144	199	void HSP_Param_set_dna_hsp_dropoff(HSP_Param *hsp_param,
145	200	gint dna_hsp_dropoff){
146	201	if(hsp_param->match->type == Match_Type_DNA2DNA)

180	235
181	236	HSP_Param HSP_Param_create(Match match, gboolean use_horizon){
182	237	register HSP_Param *hsp_param = g_new(HSP_Param, 1);
183		register WordHood_Alphabet *wha = NULL;
184		register Submat *submat;
185		hsp_param->ref_count = 1;
	238	hsp_param->thread_ref = ThreadRef_create();
186	239	hsp_param->has = HSPset_ArgumentSet_create(NULL);
187	240	hsp_param->match = match;
188	241	hsp_param->seed_repeat = hsp_param->has->seed_repeat;

191	244	hsp_param->dropoff = hsp_param->has->dna_hsp_dropoff;
192	245	hsp_param->threshold = hsp_param->has->dna_hsp_threshold;
193	246	HSP_Param_set_wordlen(hsp_param, hsp_param->has->dna_wordlen);
194		hsp_param->wordlimit = hsp_param->has->dna_wordlimit;
	247	hsp_param->wordlimit = hsp_param->has->dna_word_limit;
195	248	break;
196	249	case Match_Type_PROTEIN2PROTEIN: /fallthrough/
197	250	case Match_Type_PROTEIN2DNA: /fallthrough/

200	253	hsp_param->threshold
201	254	= hsp_param->has->protein_hsp_threshold;
202	255	HSP_Param_set_wordlen(hsp_param, hsp_param->has->protein_wordlen);
203		hsp_param->wordlimit = hsp_param->has->protein_wordlimit;
	256	hsp_param->wordlimit = hsp_param->has->protein_word_limit;
204	257	break;
205	258	case Match_Type_CODON2CODON:
206	259	hsp_param->dropoff = hsp_param->has->codon_hsp_dropoff;
207	260	hsp_param->threshold = hsp_param->has->codon_hsp_threshold;
208	261	HSP_Param_set_wordlen(hsp_param, hsp_param->has->codon_wordlen);
209		hsp_param->wordlimit = hsp_param->has->codon_wordlimit;
	262	hsp_param->wordlimit = hsp_param->has->codon_word_limit;
210	263	g_assert(!(hsp_param->wordlen % 3));
211	264	break;
212	265	default:

214	267	break;
215	268	}
216	269	hsp_param->use_horizon = use_horizon;
217		if(hsp_param->has->use_wordhood_dropoff && (!hsp_param->wordlimit)){
218		hsp_param->wordhood = NULL;
219		} else {
220		submat = (match->type == Match_Type_DNA2DNA)
221		? match->mas->dna_submat
222		: match->mas->protein_submat;
223		wha = WordHood_Alphabet_create_from_Submat(
224		(gchar*)match->comparison_alphabet->member,
225		(gchar*)match->comparison_alphabet->member, submat, FALSE);
226		g_assert(wha);
227		hsp_param->wordhood = WordHood_create(wha, hsp_param->wordlimit,
228		hsp_param->has->use_wordhood_dropoff);
229		WordHood_Alphabet_destroy(wha);
230		}
	270	#ifdef USE_PTHREADS
	271	pthread_mutex_init(&hsp_param->hsp_recycle_lock, NULL);
	272	#endif /* USE_PTHREADS */
	273	hsp_param->hsp_recycle = RecycleBin_create("HSP", sizeof(HSP), 64);
	274	hsp_param->wordhood = NULL;
	275	HSP_Param_refresh_wordhood(hsp_param);
231	276	return hsp_param;
232	277	}
233	278
234	279	void HSP_Param_destroy(HSP_Param *hsp_param){
235	280	g_assert(hsp_param);
236		if(--hsp_param->ref_count)
	281	if(ThreadRef_destroy(hsp_param->thread_ref))
237	282	return;
238	283	if(hsp_param->wordhood)
239	284	WordHood_destroy(hsp_param->wordhood);
	285	#ifdef USE_PTHREADS
	286	pthread_mutex_lock(&hsp_param->hsp_recycle_lock);
	287	#endif /* USE_PTHREADS */
	288	RecycleBin_destroy(hsp_param->hsp_recycle);
	289	#ifdef USE_PTHREADS
	290	pthread_mutex_unlock(&hsp_param->hsp_recycle_lock);
	291	pthread_mutex_destroy(&hsp_param->hsp_recycle_lock);
	292	#endif /* USE_PTHREADS */
240	293	g_free(hsp_param);
241	294	return;
242	295	}
243	296
244	297	HSP_Param HSP_Param_share(HSP_Param hsp_param){
245	298	g_assert(hsp_param);
246		hsp_param->ref_count++;
	299	ThreadRef_share(hsp_param->thread_ref);
247	300	return hsp_param;
248	301	}
249	302

252	305	return HSP_Param_create(Match_swap(hsp_param->match),
253	306	hsp_param->use_horizon);
254	307	}
255
256		static RecycleBin *global_hsp_recycle_bin = NULL;
257	308
258	309	HSPset HSPset_create(Sequence query, Sequence *target,
259	310	HSP_Param *hsp_param){

265	316	hsp_set->target = Sequence_share(target);
266	317	hsp_set->param = HSP_Param_share(hsp_param);
267	318	/**/
268		if(global_hsp_recycle_bin){
269		hsp_set->hsp_recycle = RecycleBin_share(global_hsp_recycle_bin);
270		} else {
271		global_hsp_recycle_bin = RecycleBin_create("HSP", sizeof(HSP), 64);
272		hsp_set->hsp_recycle = global_hsp_recycle_bin;
273		}
274	319	if(hsp_param->use_horizon){
275	320	hsp_set->horizon = (gint****)Matrix4d_create(
276		1 + ((hsp_param->seed_repeat > 1)?1:0),
	321	1 + ((hsp_param->seed_repeat > 1)?2:0),
277	322	query->len,
278	323	hsp_param->match->query->advance,
279	324	hsp_param->match->target->advance,

294	339	hsp_set->is_empty = TRUE;
295	340	return hsp_set;
296	341	}
	342	/* horizon[score(,repeat_count,diag)]
	343	* [query_len]
	344	* [query_advance]
	345	* [target_advance]
	346	*/
297	347
298	348	/**/
299	349

321	371	HSP_destroy(hsp);
322	372	}
323	373	g_ptr_array_free(hsp_set->hsp_list, TRUE);
324		if(hsp_set->hsp_recycle->ref_count == 1) /* last active hsp_set */
325		global_hsp_recycle_bin = NULL;
326		RecycleBin_destroy(hsp_set->hsp_recycle);
327	374	if(hsp_set->horizon)
328	375	g_free(hsp_set->horizon);
329	376	g_free(hsp_set);

519	566	}
520	567	HSP_Display_print_ruler(hd, hd->top->len-pos, pos, TRUE);
521	568	g_print(" query:[%.s]\n [%.s]\ntarget:[%.*s]\n",
522		hd->top->len-pos, hd->top->str+pos,
523		hd->mid->len-pos, hd->mid->str+pos,
524		hd->low->len-pos, hd->low->str+pos);
	569	(gint)(hd->top->len-pos), hd->top->str+pos,
	570	(gint)(hd->mid->len-pos), hd->mid->str+pos,
	571	(gint)(hd->low->len-pos), hd->low->str+pos);
525	572	HSP_Display_print_ruler(hd, hd->top->len-pos, pos, FALSE);
526	573	g_print("\n");
527	574	return;

765	812	return;
766	813	}
767	814	/* The score cannot be allowed to drop below zero in the HSP,
768		* as this can result in overlapping HSPs in some circurmstances.
	815	* as this can result in overlapping HSPs in some circumstances.
769	816	*/
770	817
771	818	static HSP HSP_create(HSP nh){
772		register HSP *hsp = RecycleBin_alloc(nh->hsp_set->hsp_recycle);
	819	register HSP *hsp;
	820	#ifdef USE_PTHREADS
	821	pthread_mutex_lock(&nh->hsp_set->param->hsp_recycle_lock);
	822	#endif /* USE_PTHREADS */
	823	hsp = RecycleBin_alloc(nh->hsp_set->param->hsp_recycle);
	824	#ifdef USE_PTHREADS
	825	pthread_mutex_unlock(&nh->hsp_set->param->hsp_recycle_lock);
	826	#endif /* USE_PTHREADS */
773	827	hsp->hsp_set = nh->hsp_set;
774	828	hsp->query_start = nh->query_start;
775	829	hsp->target_start = nh->target_start;

781	835
782	836	void HSP_destroy(HSP *hsp){
783	837	register HSPset *hsp_set = hsp->hsp_set;
784		RecycleBin_recycle(hsp_set->hsp_recycle, hsp);
	838	#ifdef USE_PTHREADS
	839	pthread_mutex_lock(&hsp_set->param->hsp_recycle_lock);
	840	#endif /* USE_PTHREADS */
	841	RecycleBin_recycle(hsp_set->param->hsp_recycle, hsp);
	842	#ifdef USE_PTHREADS
	843	pthread_mutex_unlock(&hsp_set->param->hsp_recycle_lock);
	844	#endif /* USE_PTHREADS */
785	845	return;
786	846	}
787	847

884	944	/**/
885	945	g_assert(section_pos >= 0);
886	946	g_assert(section_pos < hsp_set->query->len);
	947	/* Clear if diag has changed */
	948	if(hsp_set->param->seed_repeat > 1){
	949	if(hsp_set->horizon[2][section_pos][query_frame][target_frame]
	950	!= (diag_pos + hsp_set->query->len)){
	951	hsp_set->horizon[0][section_pos][query_frame][target_frame] = 0;
	952	hsp_set->horizon[1][section_pos][query_frame][target_frame] = 0;
	953	hsp_set->horizon[2][section_pos][query_frame][target_frame]
	954	= diag_pos + hsp_set->query->len;
	955	}
	956	}
887	957	/* Check whether we have seen this HSP already */
888	958	if(target_start < hsp_set->horizon[0]
889	959	[section_pos]

962	1032	horizon[0][query_frame][target_frame] = 0;
963	1033	horizon[2][query_frame][target_frame] = 0;
964	1034	}
	1035	/* FIXME: seedrepeat overflow here */
965	1036	if(++horizon[2][query_frame][target_frame] < hsp_set->param->seed_repeat)
966	1037	return;
967	1038	horizon[2][query_frame][target_frame] = 0;

+19

-8

src/comparison/hspset.h less more

2	2	* Library for HSP sets (high-scoring segment pairs) *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

31	31	#include "matrix.h"
32	32	#include "wordhood.h"
33	33	#include "recyclebin.h"
	34	#include "threadref.h"
34	35
35	36	typedef struct {
36	37	gint filter_threshold;

49	50	gint protein_hsp_threshold;
50	51	gint codon_hsp_threshold;
51	52	/**/
52		gint dna_wordlimit;
53		gint protein_wordlimit;
54		gint codon_wordlimit;
	53	gint dna_word_limit;
	54	gint protein_word_limit;
	55	gint codon_word_limit;
55	56	/**/
56	57	gint geneseed_threshold;
57	58	gint geneseed_repeat;

136	137	#define HSPset_is_empty(hspset) ((hspset)->is_empty)
137	138
138	139	typedef struct HSP_Param {
139		gint ref_count;
	140	ThreadRef *thread_ref;
140	141	HSPset_ArgumentSet *has;
141	142	Match *match;
142	143	gint wordlen;

147	148	WordHood *wordhood;
148	149	gboolean use_horizon;
149	150	gint seed_repeat;
	151	RecycleBin *hsp_recycle;
	152	#ifdef USE_PTHREADS
	153	pthread_mutex_t hsp_recycle_lock;
	154	#endif /* USE_PTHREADS */
150	155	} HSP_Param;
151	156
152	157	HSP_Param HSP_Param_create(Match match, gboolean use_horizon);

159	164	void HSP_Param_set_dna_hsp_threshold(HSP_Param *hsp_param,
160	165	gint dna_hsp_threshold);
161	166	void HSP_Param_set_protein_hsp_threshold(HSP_Param *hsp_param,
162		gint dna_hsp_threshold);
	167	gint protein_hsp_threshold);
163	168	void HSP_Param_set_codon_hsp_threshold(HSP_Param *hsp_param,
164		gint dna_hsp_threshold);
	169	gint protein_hsp_threshold);
	170	/**/
	171	void HSP_Param_set_dna_word_limit(HSP_Param *hsp_param,
	172	gint dna_word_limit);
	173	void HSP_Param_set_protein_word_limit(HSP_Param *hsp_param,
	174	gint protein_word_limit);
	175	void HSP_Param_set_codon_word_limit(HSP_Param *hsp_param,
	176	gint codon_word_limit);
165	177	/**/
166	178	void HSP_Param_set_dna_hsp_dropoff(HSP_Param *hsp_param,
167	179	gint dna_hsp_dropoff);

180	192	Sequence *query;
181	193	Sequence *target;
182	194	HSP_Param *param;
183		RecycleBin *hsp_recycle;
184	195	gint ****horizon;
185	196	GPtrArray *hsp_list;
186	197	/**/

+1

-1

src/comparison/hspset.test.c less more

2	2	* Library for HSP sets (high-scoring segment pairs) *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+6

-5

src/comparison/match.c less more

2	2	* Match : A module for pairwise symbol comparison *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

36	36	Match_ArgumentSet Match_ArgumentSet_create(Argument arg){
37	37	register ArgumentSet *as;
38	38	static Match_ArgumentSet mas = {0};
39		if(!mas.translate){
40		mas.translate = Translate_create(FALSE);
41		/* FIXME this should be freed somewhere */
42		}
43	39	if(arg){
44	40	as = ArgumentSet_create("Symbol Comparison Options");
45	41	ArgumentSet_add_option(as, 0, "softmaskquery", NULL,

59	55	Argument_absorb_ArgumentSet(arg, as);
60	56	Argument_add_cleanup(arg, Match_Argument_cleanup, NULL);
61	57	/**/
	58	} else {
	59	if(!mas.translate){
	60	mas.translate = Translate_create(FALSE);
	61	/* FIXME this should be freed somewhere */
	62	}
62	63	}
63	64	return &mas;
64	65	}

+1

-1

src/comparison/match.h less more

2	2	* Match : A module for pairwise symbol comparison *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/match.test.c less more

2	2	* Match : A module for pairwise symbol comparison *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/pcr.c less more

2	2	* Library for PCR simulation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/pcr.h less more

2	2	* Library for PCR simulation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/pcr.test.c less more

2	2	* Library for PCR simulation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+157

-17

src/comparison/seeder.c less more

2	2	* Seeder : A module for seeding pairwise alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

24	24	((type)((char*)(instance) + (offset)))
25	25	#endif /* OFFSET_ITEM */
26	26
	27	#ifndef Swap
	28	#define Swap(x,y,temp) ((temp)=(x),(x)=(y),(y)=(temp))
	29	#endif /* Swap */
	30
27	31	Seeder_ArgumentSet Seeder_ArgumentSet_create(Argument arg){
28	32	register ArgumentSet *as;
29	33	static Seeder_ArgumentSet sas;
30	34	if(arg){
31	35	as = ArgumentSet_create("Alignment Seeding Options");
32	36	ArgumentSet_add_option(as, 'M', "fsmmemory", "Mb",
33		"Memory limit for FSM scanning", "64",
	37	"Memory limit for FSM scanning", "256",
34	38	Argument_parse_int, &sas.fsm_memory_limit);
35	39	ArgumentSet_add_option(as, '\0', "forcefsm", "fsm type",
36	40	"Force FSM type ( normal \| compact )", "none",

38	42	ArgumentSet_add_option(as, 0, "wordjump", NULL,
39	43	"Jump between query words", "1",
40	44	Argument_parse_int, &sas.word_jump);
	45	ArgumentSet_add_option(as, 0, "wordambiguity", NULL,
	46	"Number of ambiguous words to expand", "1",
	47	Argument_parse_int, &sas.word_ambiguity);
41	48	Argument_absorb_ArgumentSet(arg, as);
42	49	}
43	50	return &sas;

301	308	gpointer user_data){
302	309	register Seeder *seeder = g_new0(Seeder, 1);
303	310	seeder->sas = Seeder_ArgumentSet_create(NULL);
	311	if(seeder->sas->word_ambiguity < 1)
	312	g_error("Word ambiguity cannot be less than one.");
	313	if(seeder->sas->word_ambiguity > 1){
	314	if(comparison_param->protein_hsp_param)
	315	g_error("Protein ambuiguity symbols not implemented");
	316	g_warning("setting --wordambiguity in exonerate will be SLOW.");
	317	g_warning("... use esd2esi --wordambiguity and exonerate-server instead");
	318	}
304	319	seeder->is_prepared = FALSE;
305	320	seeder->verbosity = verbosity;
306	321	seeder->report_func = report_func;

412	427	}
413	428
414	429	void Seeder_memory_info(Seeder *seeder){
415		g_message("Seeder Total = %dMb", Seeder_memory_usage(seeder)>>20);
	430	g_message("Seeder Total = %dMb", (gint)(Seeder_memory_usage(seeder)>>20));
416	431	g_assert(seeder);
417	432	if(seeder->seeder_fsm)
418	433	g_message(" -> FSM memory = %dMb",
419		Seeder_FSM_memory_usage(seeder->seeder_fsm)>>20);
	434	(gint)(Seeder_FSM_memory_usage(seeder->seeder_fsm)>>20));
420	435	else
421	436	g_message(" -> VFSM memory = %dMb",
422		Seeder_VFSM_memory_usage(seeder->seeder_vfsm)>>20);
	437	(gint)(Seeder_VFSM_memory_usage(seeder->seeder_vfsm)>>20));
423	438	g_message(" -> QueryInfo memory = %dMb",
424		(seeder->query_info_list->len
	439	(gint)(seeder->query_info_list->len
425	440	*(sizeof(gpointer)+sizeof(Seeder_QueryInfo)))>>20);
426	441	g_message(" -> Recycle_Wordinfo Memory = %dMb",
427		RecycleBin_memory_usage(seeder->recycle_wordinfo)>>20);
	442	(gint)(RecycleBin_memory_usage(seeder->recycle_wordinfo)>>20));
428	443	g_message(" -> Recycle_Seed Memory = %dMb",
429		RecycleBin_memory_usage(seeder->recycle_seed)>>20);
	444	(gint)(RecycleBin_memory_usage(seeder->recycle_seed)>>20));
430	445	g_message(" -> Recycle_Neighbour Memory = %dMb",
431		RecycleBin_memory_usage(seeder->recycle_neighbour)>>20);
	446	(gint)(RecycleBin_memory_usage(seeder->recycle_neighbour)>>20));
432	447	g_message(" -> Recycle_Context Memory = %dMb",
433		RecycleBin_memory_usage(seeder->recycle_context)>>20);
	448	(gint)(RecycleBin_memory_usage(seeder->recycle_context)>>20));
434	449	return;
435	450	}
436	451

514	529	} else {
515	530	leaf = VFSM_state2leaf(vfsm, state);
516	531	word_info = seeder->seeder_vfsm->leaf[leaf];
517		if(!word_info)
	532	if(!word_info){
518	533	word_info = Seeder_WordInfo_create(seeder);
	534	seeder->seeder_vfsm->leaf[leaf] = word_info;
	535	}
519	536	}
520	537	g_assert(word_info);
521	538	if(frame)

674	691	return;
675	692	}
676	693
677		static void Seeder_VFSM_traverse(Seeder seeder, gchar seq,
678		Seeder_TargetInfo *target_info){
	694	static void Seeder_VFSM_traverse_single(Seeder seeder, gchar seq,
	695	Seeder_TargetInfo *target_info){
679	696	register gint i, ch;
680	697	register VFSM_Int state = 0, leaf;
681	698	register VFSM *vfsm = seeder->seeder_vfsm->vfsm;

699	716	return;
700	717	}
701	718
	719	static void Seeder_VFSM_traverse_ambig(Seeder seeder, gchar seq,
	720	Seeder_TargetInfo *target_info){
	721	register gint i, j, k, ch;
	722	register VFSM_Int state, next_state, leaf;
	723	register VFSM *vfsm = seeder->seeder_vfsm->vfsm;
	724	register Seeder_WordInfo *word_info;
	725	register gchar *ambig;
	726	register VFSM_Int *temp_state_list,
	727	*curr_state_list = g_new0(VFSM_Int,
	728	seeder->sas->word_ambiguity),
	729	*next_state_list = g_new0(VFSM_Int,
	730	seeder->sas->word_ambiguity);
	731	register gint curr_state_list_len = 1, next_state_list_len = 0;
	732	g_assert(vfsm);
	733	for(i = 0; seq[i]; i++){
	734	ch = toupper(seq[i]); /* FIXME: filter properly */
	735	if((!(ambig = Alphabet_nt2ambig(ch)))
	736	\|\| ((strlen(ambig) * curr_state_list_len)
	737	> seeder->sas->word_ambiguity)){
	738	next_state_list_len = 0;
	739	curr_state_list_len = 1;
	740	curr_state_list[0] = 0;
	741	continue;
	742	}
	743	for(j = 0; j < curr_state_list_len; j++){
	744	state = curr_state_list[j];
	745	for(k = 0; ambig[k]; k++){
	746	g_assert(vfsm->index[(guchar)ambig[k]]);
	747	next_state = VFSM_change_state_M(vfsm,
	748	state, (guchar)ambig[k]);
	749	/* FIXME: use POW2 versions where applicable */
	750	if(next_state_list_len
	751	&& ((next_state == next_state_list[0])
	752	\|\| (next_state == next_state_list[next_state_list_len-1])))
	753	break;
	754	next_state_list[next_state_list_len++] = next_state;
	755	if(VFSM_state_is_leaf(vfsm, next_state)){
	756	leaf = VFSM_state2leaf(vfsm, next_state);
	757	word_info = seeder->seeder_vfsm->leaf[leaf];
	758	if(word_info)
	759	Seeder_FSM_traverse_func(i, word_info, target_info);
	760	}
	761	}
	762	}
	763	curr_state_list_len = next_state_list_len;
	764	next_state_list_len = 0;
	765	Swap(next_state_list, curr_state_list, temp_state_list);
	766	}
	767	g_free(curr_state_list);
	768	g_free(next_state_list);
	769	return;
	770	}
	771
	772	static void Seeder_VFSM_traverse(Seeder seeder, gchar seq,
	773	Seeder_TargetInfo *target_info){
	774	if(seeder->sas->word_ambiguity > 1)
	775	Seeder_VFSM_traverse_ambig(seeder, seq, target_info);
	776	else
	777	Seeder_VFSM_traverse_single(seeder, seq, target_info);
	778	return;
	779	}
	780
702	781	static void Seeder_prepare(Seeder *seeder){
703	782	g_assert(!seeder->is_prepared);
704	783	if(seeder->seeder_fsm)
705	784	FSM_compile(seeder->seeder_fsm->fsm);
706	785	seeder->is_prepared = TRUE;
	786	return;
	787	}
	788
	789	static void Seeder_FSM_traverse_ambig(Seeder seeder, gchar seq,
	790	FSM_Traverse_Func ftf, gpointer user_data){
	791	register FSM *f = seeder->seeder_fsm->fsm;
	792	register FSM_Node n, next_state;
	793	register gint c;
	794	register gchar *ambig;
	795	register gint i, j, k;
	796	register FSM_Node **temp_state_list,
	797	*curr_state_list = g_new0(FSM_Node,
	798	seeder->sas->word_ambiguity),
	799	*next_state_list = g_new0(FSM_Node,
	800	seeder->sas->word_ambiguity);
	801	register gint curr_state_list_len = 1, next_state_list_len = 0;
	802	g_assert(f->is_compiled);
	803	curr_state_list[0] = f->root;
	804	for(i = 0; seq[i]; i++){
	805	if((!(ambig = Alphabet_nt2ambig(seq[i])))
	806	\|\| ((strlen(ambig) * curr_state_list_len)
	807	> seeder->sas->word_ambiguity)){
	808	next_state_list_len = 0;
	809	curr_state_list_len = 1;
	810	curr_state_list[0] = f->root;
	811	continue;
	812	}
	813	for(j = 0; j < curr_state_list_len; j++){
	814	n = curr_state_list[j];
	815	for(k = 0; ambig[k]; k++){
	816	c = f->traversal_filter[(guchar)ambig[k]];
	817	if(n[c].data)
	818	ftf(i, n[c].data, user_data);
	819	next_state = n[c].next;
	820	if(next_state_list_len
	821	&& ((next_state == next_state_list[0])
	822	\|\| (next_state ==
	823	next_state_list[next_state_list_len-1]))){
	824	break;
	825	}
	826	next_state_list[next_state_list_len++] = next_state;
	827	}
	828	}
	829	curr_state_list_len = next_state_list_len;
	830	next_state_list_len = 0;
	831	/* g_message("set curr [%d]", curr_state_list_len); */
	832	Swap(next_state_list, curr_state_list, temp_state_list);
	833	}
	834	g_free(curr_state_list);
	835	g_free(next_state_list);
	836	return;
	837	}
	838	/* Slow (ambiguous) version of FSM_traverse */
	839	/* FIXME: optimisation: remove strlen() etc */
	840
	841	static void Seeder_FSM_traverse(Seeder seeder, gchar seq, FSM_Traverse_Func ftf,
	842	gpointer user_data){
	843	if(seeder->sas->word_ambiguity > 1)
	844	Seeder_FSM_traverse_ambig(seeder, seq, ftf, user_data);
	845	else
	846	FSM_traverse(seeder->seeder_fsm->fsm, seq, ftf, user_data);
707	847	return;
708	848	}
709	849

734	874	seq = Sequence_get_str(target_masked);
735	875	Sequence_destroy(target_masked);
736	876	if(seeder->seeder_fsm)
737		FSM_traverse(seeder->seeder_fsm->fsm, seq,
738		Seeder_FSM_traverse_func, &target_info);
	877	Seeder_FSM_traverse(seeder, seq,
	878	Seeder_FSM_traverse_func, &target_info);
739	879	else
740	880	Seeder_VFSM_traverse(seeder, seq, &target_info);
741	881	g_free(seq);

746	886	seq = Sequence_get_str(target_masked);
747	887	Sequence_destroy(target_masked);
748	888	if(seeder->seeder_fsm){
749		FSM_traverse(seeder->seeder_fsm->fsm, seq,
750		Seeder_FSM_traverse_func, &target_info);
	889	Seeder_FSM_traverse(seeder, seq,
	890	Seeder_FSM_traverse_func, &target_info);
751	891	} else {
752	892	Seeder_VFSM_traverse(seeder, seq, &target_info);
753	893	}

+2

-1

src/comparison/seeder.h less more

2	2	* Seeder : A module for seeding pairwise alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

31	31	gsize fsm_memory_limit;
32	32	gchar *force_fsm;
33	33	gint word_jump;
	34	gint word_ambiguity;
34	35	} Seeder_ArgumentSet;
35	36
36	37	Seeder_ArgumentSet Seeder_ArgumentSet_create(Argument arg);

+1

-1

src/comparison/seeder.test.c less more

2	2	* Seeder : A module for seeding pairwise alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/wordhood.c less more

2	2	* Library for word-neighbourhood generation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/wordhood.h less more

2	2	* Library for word-neighbourhood generation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/comparison/wordhood.test.c less more

2	2	* Library for word-neighbourhood generation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+15

-1

src/database/Makefile.am less more

0	0
1	1	TESTS = fastadb.test fastapipe.test dataset.test index.test
	2	# seqfmi.test
2	3	noinst_PROGRAMS = $(TESTS)
3	4
4	5	INCLUDES = -I$(top_srcdir)/src/sequence \
5	6	-I$(top_srcdir)/src/struct \
6	7	-I$(top_srcdir)/src/general \
7		-I$(top_srcdir)/src/comparison
	8	-I$(top_srcdir)/src/comparison \
	9	-DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
8	10
9	11	noinst_HEADERS = fastadb.h fastapipe.h dataset.h index.h
	12	# seqfmi.h
10	13
11	14	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o \
12	15	$(top_srcdir)/src/struct/matrix.o \

35	38	index_test_SOURCES = index.test.c index.c
36	39	index_test_LDADD = fastadb.o dataset.o \
37	40	$(top_srcdir)/src/general/compoundfile.o \
	41	$(top_srcdir)/src/general/threadref.o \
38	42	$(top_srcdir)/src/struct/bitarray.o \
39	43	$(top_srcdir)/src/struct/vfsm.o \
40	44	$(top_srcdir)/src/struct/pqueue.o \

49	53	$(top_srcdir)/src/sequence/codonsubmat.o \
50	54	$(SEQUENCE_OBJ)
51	55
	56	# seqfmi_test_SOURCES = seqfmi.test.c seqfmi.c
	57	# seqfmi_test_LDADD = fastadb.o \
	58	# $(top_srcdir)/src/general/compoundfile.o \
	59	# $(top_srcdir)/src/struct/fmindex.o \
	60	# $(top_srcdir)/src/struct/bitarray.o \
	61	# $(top_srcdir)/src/struct/pqueue.o \
	62	# $(top_srcdir)/src/struct/recyclebin.o \
	63	# $(top_srcdir)/src/struct/huffman.o \
	64	# $(SEQUENCE_OBJ)
	65
52	66	# Files to clear away
53	67
54	68	MAINTAINERCLEANFILES = Makefile.in

+17

-3

src/database/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

78	79	use_pthreads = @use_pthreads@
79	80
80	81	TESTS = fastadb.test fastapipe.test dataset.test index.test
	82	# seqfmi.test
81	83	noinst_PROGRAMS = $(TESTS)
82	84
83		INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/general -I$(top_srcdir)/src/comparison
	85	INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/general -I$(top_srcdir)/src/comparison -DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
84	86
85	87
86	88	noinst_HEADERS = fastadb.h fastapipe.h dataset.h index.h
	89	# seqfmi.h
87	90
88	91	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
89	92

100	103
101	104
102	105	index_test_SOURCES = index.test.c index.c
103		index_test_LDADD = fastadb.o dataset.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
104
	106	index_test_LDADD = fastadb.o dataset.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/threadref.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(SEQUENCE_OBJ)
	107
	108
	109	# seqfmi_test_SOURCES = seqfmi.test.c seqfmi.c
	110	# seqfmi_test_LDADD = fastadb.o \
	111	# $(top_srcdir)/src/general/compoundfile.o \
	112	# $(top_srcdir)/src/struct/fmindex.o \
	113	# $(top_srcdir)/src/struct/bitarray.o \
	114	# $(top_srcdir)/src/struct/pqueue.o \
	115	# $(top_srcdir)/src/struct/recyclebin.o \
	116	# $(top_srcdir)/src/struct/huffman.o \
	117	# $(SEQUENCE_OBJ)
105	118
106	119	# Files to clear away
107	120

151	164	index_test_OBJECTS = index.test.o index.o
152	165	index_test_DEPENDENCIES = fastadb.o dataset.o \
153	166	$(top_srcdir)/src/general/compoundfile.o \
	167	$(top_srcdir)/src/general/threadref.o \
154	168	$(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o \
155	169	$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
156	170	$(top_srcdir)/src/struct/rangetree.o \

+22

-5

src/database/dataset.c less more

2	2	* Library for manipulation of exonerate dataset files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

22	22	/**/
23	23
24	24	#define DATASET_HEADER_MAGIC (('e' << 16)\|('s' << 8)\|('d'))
25		#define DATASET_HEADER_VERSION 2
	25	#define DATASET_HEADER_VERSION 3
26	26
27	27	static Dataset_Header *Dataset_Header_create(Alphabet_Type alphabet_type,
28	28	gboolean softmask_input){

300	300	+ dataset_sequence_memory;
301	301	}
302	302
	303	void Dataset_info(Dataset *dataset){
	304	g_print("Sequence Dataset:\n"
	305	"----------------\n"
	306	" version: %d\n"
	307	" type: %s, %s\n"
	308	" total size: %d Mb\n"
	309	" number of sequences: %lld\n"
	310	" longest sequence: %lld\n\n",
	311	(gint)dataset->header->version,
	312	(dataset->header->type & 1)?"DNA":"PROTEIN",
	313	(dataset->header->type & 2)?"masked":"unmasked",
	314	(gint)(dataset->header->total_db_len >> 20),
	315	dataset->header->number_of_seqs,
	316	dataset->header->max_seq_len);
	317	return;
	318	}
	319
303	320	void Dataset_destroy(Dataset *dataset){
304	321	register gint i;
305	322	register Dataset_Sequence *seq;

377	394	}
378	395
379	396	static void Dataset_read_seq_data(Dataset dataset, FILE fp){
380		register gint i, j = 0, ipos, dpos;
	397	register gint64 i, j = 0, ipos, dpos;
381	398	register Dataset_Sequence *ds;
382		register gint len = dataset->header->seq_info_offset
383		- dataset->header->seq_data_offset;
	399	register guint64 len = dataset->header->seq_info_offset
	400	- dataset->header->seq_data_offset;
384	401	register gchar *buf = g_new(gchar, len+1);
385	402	if(!fread(buf, sizeof(gchar), len, fp))
386	403	g_error("Problem reading seq data");

+2

-1

src/database/dataset.h less more

2	2	* Library for manipulation of exonerate dataset files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

96	96	gboolean softmask_input);
97	97	Dataset Dataset_share(Dataset dataset);
98	98	void Dataset_destroy(Dataset *dataset);
	99	void Dataset_info(Dataset *dataset);
99	100	gsize Dataset_memory_usage(Dataset *dataset);
100	101	gboolean Dataset_check_filetype(gchar *path);
101	102	/* Returns TRUE when magic number is correct for this filetype */

+1

-1

src/database/dataset.test.c less more

2	2	* Library for manipulation of FASTA format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+38

-1

src/database/fastadb.c less more

2	2	* Library for manipulation of FASTA format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

201	201	return fdb;
202	202	}
203	203
	204	FastaDB FastaDB_dup(FastaDB fdb){
	205	register FastaDB *nfdb = g_new(FastaDB, 1);
	206	nfdb->ref_count = 1;
	207	nfdb->alphabet = Alphabet_create(fdb->alphabet->type,
	208	fdb->alphabet->is_soft_masked);
	209	nfdb->cf = CompoundFile_dup(fdb->cf);
	210	nfdb->out_buffer_alloc = FASTADB_OUT_BUFFER_CHUNK_SIZE;
	211	nfdb->out_buffer = g_malloc(sizeof(gchar)*nfdb->out_buffer_alloc);
	212	nfdb->line_length = -1;
	213	FastaDB_rewind(nfdb);
	214	return nfdb;
	215	}
	216
204	217	void FastaDB_close(FastaDB *fdb){
205	218	g_assert(fdb);
206	219	if(--fdb->ref_count)

236	249	}
237	250	return CompoundFile_ftell(fdb->cf)-1;
238	251	}
	252
	253	gboolean FastaDB_file_is_fasta(gchar *path){
	254	register FILE *fp = fopen(path, "r");
	255	register gint ch;
	256	register gboolean result = FALSE;
	257	if(!fp)
	258	g_error("Could not open file [%s]", path);
	259	while(((ch = getc(fp)) != EOF)){
	260	if(isspace(ch))
	261	continue;
	262	else
	263	if(ch == '>'){ /* Assume is fasta format */
	264	result = TRUE;
	265	break;
	266	}
	267	else
	268	break;
	269	}
	270	fclose(fp);
	271	return result;
	272	}
	273	/* Assumes a file is fasta format
	274	* if the first non-whitespace character is '>'
	275	*/
239	276
240	277	gboolean FastaDB_is_finished(FastaDB *fdb){
241	278	g_assert(fdb);

+5

-1

src/database/fastadb.h less more

2	2	* Library for manipulation of FASTA format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

72	72	Alphabet *alphabet, gint chunk_id, gint chunk_total);
73	73	FastaDB FastaDB_open(gchar path, Alphabet *alphabet);
74	74	FastaDB FastaDB_share(FastaDB fdb);
	75	FastaDB FastaDB_dup(FastaDB fdb); /* For use in a separate thread */
75	76	void FastaDB_close(FastaDB *fdb);
76	77	void FastaDB_rewind(FastaDB *fdb);
77	78	gboolean FastaDB_is_finished(FastaDB *fdb);

82	83	FastaDB_Seq FastaDB_next(FastaDB fdb, FastaDB_Mask mask);
83	84	CompoundFile_Pos FastaDB_find_next_start(FastaDB *fdb,
84	85	CompoundFile_Pos pos);
	86
	87	gboolean FastaDB_file_is_fasta(gchar *path);
	88	/* Returns true if first non-whitespace character in file is '>' */
85	89
86	90	typedef struct {
87	91	FastaDB *source;

+1

-1

src/database/fastadb.test.c less more

2	2	* Library for manipulation of FASTA format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+14

-8

src/database/fastapipe.c less more

2	2	* Library for All-vs-All Fasta Database Comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

20	20	FastaPipe_Boundary_Func term_func,
21	21	FastaPipe_NextSeq_Func query_func,
22	22	FastaPipe_NextSeq_Func target_func,
23		FastaDB_Mask mask, gboolean translate_both){
	23	FastaDB_Mask mask, gboolean translate_both,
	24	gboolean use_revcomp){
24	25	register FastaPipe *fasta_pipe = g_new(FastaPipe, 1);
25	26	g_assert(init_func);
26	27	g_assert(prep_func);

36	37	fasta_pipe->target_func = target_func;
37	38	fasta_pipe->mask = mask;
38	39	fasta_pipe->is_full = FALSE;
39		fasta_pipe->revcomp_query
40		= (query_fdb->alphabet->type == Alphabet_Type_DNA);
41		fasta_pipe->revcomp_target
42		= (((query_fdb->alphabet->type == Alphabet_Type_PROTEIN)
43		&& (target_fdb->alphabet->type == Alphabet_Type_DNA))
44		\|\| translate_both);
	40	if(use_revcomp){
	41	fasta_pipe->revcomp_query
	42	= (query_fdb->alphabet->type == Alphabet_Type_DNA);
	43	fasta_pipe->revcomp_target
	44	= (((query_fdb->alphabet->type == Alphabet_Type_PROTEIN)
	45	&& (target_fdb->alphabet->type == Alphabet_Type_DNA))
	46	\|\| translate_both);
	47	} else {
	48	fasta_pipe->revcomp_query = FALSE;
	49	fasta_pipe->revcomp_target = FALSE;
	50	}
45	51	fasta_pipe->prev_query = NULL;
46	52	fasta_pipe->prev_target = NULL;
47	53	return fasta_pipe;

+3

-2

src/database/fastapipe.h less more

2	2	* Library for All-vs-All Fasta Database Comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

49	49	FastaPipe_Boundary_Func term_func,
50	50	FastaPipe_NextSeq_Func query_func,
51	51	FastaPipe_NextSeq_Func target_func,
52		FastaDB_Mask mask, gboolean translate_both);
	52	FastaDB_Mask mask, gboolean translate_both,
	53	gboolean use_revcomp);
53	54	/* query_func can return TRUE to finish loading current pipeline
54	55	* target_func can return TRUE to finish processing of the pipeline
55	56	*/

+2

-2

src/database/fastapipe.test.c less more

2	2	* Library for All-vs-All Fasta Database Comparisons *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

67	67	fasta_pipe = FastaPipe_create(query_fdb, target_fdb,
68	68	test_init_func, test_prep_func, test_term_func,
69	69	test_query_func, test_target_func, FastaDB_Mask_ALL,
70		FALSE);
	70	FALSE, TRUE);
71	71	Alphabet_destroy(alphabet);
72	72	while(FastaPipe_process(fasta_pipe, &count)){
73	73	g_message("Processing pipeline");

+125

-23

src/database/index.c less more

2	2	* Library for manipulation of exonerate index files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

25	25	#include "noitree.h"
26	26
27	27	#define INDEX_HEADER_MAGIC (('e' << 16)\|('s' << 8)\|('i'))
28		#define INDEX_HEADER_VERSION 2
	28	#define INDEX_HEADER_VERSION 3
29	29
30	30	static off_t Index_ftell(FILE *fp){
31	31	return ftello(fp);

37	37	static off_t Index_fseek(FILE *fp, off_t offset, int whence){
38	38	return fseeko(fp, offset, whence);
39	39	}
40		/* FIXME: need alternatives in absence of ftello()
	40	/* FIXME: need alternatives in absence of fseeko()
41	41	* lseek(fileno(fp), offset, whence); ??
42	42	*/
43	43

77	77
78	78	static Index_Header *Index_Header_create(gint dataset_path_len,
79	79	gboolean is_translated,
80		gint word_length, gint word_jump,
	80	gint word_length,
	81	gint word_jump,
	82	gint word_ambiguity,
81	83	gint saturate_threshold){
82	84	register Index_Header *index_header = g_new0(Index_Header, 1);
83	85	index_header->magic = INDEX_HEADER_MAGIC;

87	89	/**/
88	90	index_header->word_length = word_length;
89	91	index_header->word_jump = word_jump;
	92	index_header->word_ambiguity = word_ambiguity;
90	93	index_header->saturate_threshold = saturate_threshold;
91	94	return index_header;
92	95	}

99	102	#if 0
100	103	static void Index_Header_info(Index_Header *index_header){
101	104	g_message("Index_Header:\n"
102		" magic [%d]\n"
103		" version [%d]\n"
104		" type [%d]\n"
105		" dataset_path_len [%d]\n"
	105	" magic [%lld]\n"
	106	" version [%lld]\n"
	107	" type [%lld]\n"
	108	" dataset_path_len [%lld]\n"
106	109	"\n"
107		" word_length [%d]\n"
108		" word_jump [%d]\n"
109		" saturate_threshold [%d]\n",
110		(gint)index_header->magic,
111		(gint)index_header->version,
112		(gint)index_header->type,
113		(gint)index_header->dataset_path_len,
114		(gint)index_header->word_length,
115		(gint)index_header->word_jump,
116		(gint)index_header->saturate_threshold);
	110	" word_length [%lld]\n"
	111	" word_jump [%lld]\n"
	112	" word_ambiguity [%lld]\n"
	113	" saturate_threshold [%lld]\n",
	114	index_header->magic,
	115	index_header->version,
	116	index_header->type,
	117	index_header->dataset_path_len,
	118	index_header->word_length,
	119	index_header->word_jump,
	120	index_header->word_ambiguity,
	121	index_header->saturate_threshold);
117	122	return;
118	123	}
119	124	#endif /* 0 */

127	132	/**/
128	133	BitArray_write_int(index_header->word_length, fp);
129	134	BitArray_write_int(index_header->word_jump, fp);
	135	BitArray_write_int(index_header->word_ambiguity, fp);
130	136	BitArray_write_int(index_header->saturate_threshold, fp);
131	137	/**/
132	138	return;

145	151	/**/
146	152	index_header->word_length = BitArray_read_int(fp);
147	153	index_header->word_jump = BitArray_read_int(fp);
	154	index_header->word_ambiguity = BitArray_read_int(fp);
148	155	index_header->saturate_threshold = BitArray_read_int(fp);
149	156	/* Index_Header_info(index_header); */
150	157	return index_header;

185	192	gint seq_pos, gint leaf_id,
186	193	gpointer user_data);
187	194
188		static void Index_visit_seq_words(Index index, Index_Strand index_strand,
	195	static void Index_visit_seq_words_single(Index index, Index_Strand index_strand,
189	196	gint seq_id, Sequence *seq,
190	197	Index_WordVisit_Func iwvf, gint frame,
191	198	gpointer user_data){

210	217	}
211	218	}
212	219	g_free(str);
	220	return;
	221	}
	222	/* FIXME: needs to work with softmasked sequences */
	223
	224	#ifndef Swap
	225	#define Swap(x,y,temp) ((temp)=(x),(x)=(y),(y)=(temp))
	226	#endif /* Swap */
	227
	228	static void Index_visit_seq_words_ambig(Index index, Index_Strand index_strand,
	229	gint seq_id, Sequence *seq,
	230	Index_WordVisit_Func iwvf, gint frame,
	231	gpointer user_data){
	232	register gint i, j, k, jump_ctr = 0, pos;
	233	register gchar ambig, str = Sequence_get_str(seq);
	234	register VFSM_Int state, next_state, leaf;
	235	register VFSM_Int *temp_state_list,
	236	*curr_state_list = g_new0(VFSM_Int,
	237	index->header->word_ambiguity),
	238	*next_state_list = g_new0(VFSM_Int,
	239	index->header->word_ambiguity);
	240	register gint curr_state_list_len = 1, next_state_list_len = 0;
	241	for(i = 0; str[i]; i++){
	242	if(jump_ctr--)
	243	continue;
	244	jump_ctr = index->header->word_jump - 1;
	245	if((!(ambig = Alphabet_nt2ambig(str[i])))
	246	\|\| ((strlen(ambig) * curr_state_list_len)
	247	> index->header->word_ambiguity)){
	248	next_state_list_len = 0; /* Clear next state list */
	249	curr_state_list_len = 1; /* Set single null state */
	250	curr_state_list[0] = 0;
	251	continue;
	252	}
	253	for(j = 0; j < curr_state_list_len; j++){
	254	state = curr_state_list[j];
	255	for(k = 0; ambig[k]; k++){
	256	g_assert(index->vfsm->index[(guchar)ambig[k]]);
	257	next_state = VFSM_change_state_M(index->vfsm,
	258	state, (guchar)ambig[k]);
	259	if(next_state_list_len
	260	&& ((next_state == next_state_list[0])
	261	\|\| (next_state == next_state_list[next_state_list_len-1])))
	262	break;
	263	next_state_list[next_state_list_len++] = next_state;
	264	if(VFSM_state_is_leaf(index->vfsm, next_state)){
	265	leaf = VFSM_state2leaf(index->vfsm, next_state);
	266	pos = i-(index->vfsm->depth-1);
	267	if(frame)
	268	pos = (pos * 3) + frame - 1;
	269	iwvf(index, index_strand, seq_id, pos, leaf, user_data);
	270	}
	271	}
	272	}
	273	curr_state_list_len = next_state_list_len;
	274	next_state_list_len = 0;
	275	Swap(next_state_list, curr_state_list, temp_state_list);
	276	}
	277	g_free(str);
	278	g_free(curr_state_list);
	279	g_free(next_state_list);
	280	return;
	281	}
	282	/* FIXME: needs to work with softmasked sequences */
	283	/* FIXME: optimisation: remove strlen() call */
	284
	285	static void Index_visit_seq_words(Index index, Index_Strand index_strand,
	286	gint seq_id, Sequence *seq,
	287	Index_WordVisit_Func iwvf, gint frame,
	288	gpointer user_data){
	289	if(index->header->word_ambiguity > 1)
	290	Index_visit_seq_words_ambig(index, index_strand, seq_id, seq,
	291	iwvf, frame, user_data);
	292	else
	293	Index_visit_seq_words_single(index, index_strand, seq_id, seq,
	294	iwvf, frame, user_data);
213	295	return;
214	296	}
215	297	/* FIXME: needs to work with softmasked sequences */

291	373	removed_instances += index_strand->word_table[i];
292	374	index_strand->word_table[i] = -1;
293	375	}
294		g_message("Removed [%lld] words, [%lld] instances",
	376	g_message("Removed [%" CUSTOM_GUINT64_FORMAT
	377	"] words, [%" CUSTOM_GUINT64_FORMAT "] instances",
295	378	removed_words, removed_instances);
296	379	return;
297	380	}

662	745	return;
663	746	}
664	747
665		Index Index_create(Dataset dataset, gboolean is_translated,
666		gint word_length, gint word_jump, gint saturate_threshold,
	748	Index Index_create(Dataset dataset, gboolean is_translated, gint word_length,
	749	gint word_jump, gint word_ambiguity, gint saturate_threshold,
667	750	gchar index_path, gchar dataset_path, gint memory_limit){
668	751	register Index *index = g_new0(Index, 1);
669	752	register gchar *member;

683	766	index->dataset = Dataset_share(dataset);
684	767	index->header = Index_Header_create(strlen(dataset_path),
685	768	is_translated, word_length,
686		word_jump, saturate_threshold);
	769	word_jump, word_ambiguity,
	770	saturate_threshold);
687	771	if(is_translated){
688	772	alphabet = Alphabet_create(Alphabet_Type_PROTEIN, FALSE);
689	773	member = (gchar*)alphabet->member;

777	861	pthread_mutex_destroy(&index->index_mutex);
778	862	#endif /* USE_PTHREADS */
779	863	g_free(index);
	864	return;
	865	}
	866
	867	void Index_info(Index *index){
	868	g_print("Sequence Index:\n"
	869	"--------------\n"
	870	" version: %d\n"
	871	" type: %s\n"
	872	" word length: %d\n"
	873	" word jump: %d\n"
	874	" word ambiguity: %d\n"
	875	" saturate threshold: %d\n\n",
	876	(gint)index->header->version,
	877	(index->header->type & 1) ? "translated" : "normal",
	878	(gint)index->header->word_length,
	879	(gint)index->header->word_jump,
	880	(gint)index->header->word_ambiguity,
	881	(gint)index->header->saturate_threshold);
780	882	return;
781	883	}
782	884

+6

-4

src/database/index.h less more

2	2	* Library for manipulation of exonerate index files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

59	59	/**/
60	60	guint64 word_length;
61	61	guint64 word_jump;
	62	guint64 word_ambiguity;
62	63	guint64 saturate_threshold;
63	64	} Index_Header;
64	65

116	117
117	118	/**/
118	119
119		Index Index_create(Dataset dataset, gboolean is_translated,
120		gint word_length, gint word_jump, gint saturate_threshold,
	120	Index Index_create(Dataset dataset, gboolean is_translated, gint word_length,
	121	gint word_jump, gint word_ambiguity, gint saturate_threshold,
121	122	gchar index_path, gchar dataset_path, gint memory_limit);
122	123	Index Index_share(Index index);
123	124	void Index_destroy(Index *index);
	125	void Index_info(Index *index);
124	126	Index Index_open(gchar path);
125	127	guint64 Index_memory_usage(Index *index);
126	128	void Index_preload_index(Index *index);

149	151	}
150	152	#endif /* __cplusplus */
151	153
152		#endif /* INCLUDED_DATASET_H */
	154	#endif /* INCLUDED_INDEX_H */
153	155

+1

-1

src/database/index.test.c less more

2	2	* Library for manipulation of FASTA format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+12

-3

src/general/Makefile.am less more

0	0
1		TESTS = argument.test lineparse.test compoundfile.test socket.test
	1	TESTS = argument.test lineparse.test compoundfile.test socket.test \
	2	jobqueue.test threadref.test
2	3	noinst_PROGRAMS = $(TESTS)
3	4
4		noinst_HEADERS = argument.h lineparse.h compoundfile.h socket.h
	5	noinst_HEADERS = argument.h lineparse.h compoundfile.h socket.h \
	6	jobqueue.h threadref.h
5	7
6		INCLUDES = -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
	8	INCLUDES = -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
	9	-DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\"" \
	10	-I$(top_srcdir)/src/struct
7	11
8	12	argument_test_SOURCES = argument.test.c argument.c
9	13	lineparse_test_SOURCES = lineparse.test.c lineparse.c
10	14	compoundfile_test_SOURCES = compoundfile.test.c compoundfile.c
11	15	socket_test_SOURCES = socket.test.c socket.c
	16	jobqueue_test_SOURCES = jobqueue.test.c jobqueue.c
	17	jobqueue_test_LDADD = $(top_srcdir)/src/struct/pqueue.o \
	18	$(top_srcdir)/src/struct/recyclebin.o
	19	threadref_test_SOURCES = threadref.test.c threadref.c
	20	threadref_test_LDADD = -lpthread
12	21
13	22	# Files to clear away
14	23

+30

-6

src/general/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

77	78	source_root_dir = @source_root_dir@
78	79	use_pthreads = @use_pthreads@
79	80
80		TESTS = argument.test lineparse.test compoundfile.test socket.test
	81	TESTS = argument.test lineparse.test compoundfile.test socket.test jobqueue.test threadref.test
	82
81	83	noinst_PROGRAMS = $(TESTS)
82	84
83		noinst_HEADERS = argument.h lineparse.h compoundfile.h socket.h
84
85		INCLUDES = -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
	85	noinst_HEADERS = argument.h lineparse.h compoundfile.h socket.h jobqueue.h threadref.h
	86
	87
	88	INCLUDES = -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\"" -I$(top_srcdir)/src/struct
	89
86	90
87	91	argument_test_SOURCES = argument.test.c argument.c
88	92	lineparse_test_SOURCES = lineparse.test.c lineparse.c
89	93	compoundfile_test_SOURCES = compoundfile.test.c compoundfile.c
90	94	socket_test_SOURCES = socket.test.c socket.c
	95	jobqueue_test_SOURCES = jobqueue.test.c jobqueue.c
	96	jobqueue_test_LDADD = $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o
	97
	98	threadref_test_SOURCES = threadref.test.c threadref.c
	99	threadref_test_LDADD = -lpthread
91	100
92	101	# Files to clear away
93	102

117	126	socket_test_LDADD = $(LDADD)
118	127	socket_test_DEPENDENCIES =
119	128	socket_test_LDFLAGS =
	129	jobqueue_test_OBJECTS = jobqueue.test.o jobqueue.o
	130	jobqueue_test_DEPENDENCIES = $(top_srcdir)/src/struct/pqueue.o \
	131	$(top_srcdir)/src/struct/recyclebin.o
	132	jobqueue_test_LDFLAGS =
	133	threadref_test_OBJECTS = threadref.test.o threadref.o
	134	threadref_test_DEPENDENCIES =
	135	threadref_test_LDFLAGS =
120	136	CFLAGS = @CFLAGS@
121	137	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
122	138	CCLD = $(CC)

130	146
131	147	TAR = tar
132	148	GZIP_ENV = --best
133		SOURCES = $(argument_test_SOURCES) $(lineparse_test_SOURCES) $(compoundfile_test_SOURCES) $(socket_test_SOURCES)
134		OBJECTS = $(argument_test_OBJECTS) $(lineparse_test_OBJECTS) $(compoundfile_test_OBJECTS) $(socket_test_OBJECTS)
	149	SOURCES = $(argument_test_SOURCES) $(lineparse_test_SOURCES) $(compoundfile_test_SOURCES) $(socket_test_SOURCES) $(jobqueue_test_SOURCES) $(threadref_test_SOURCES)
	150	OBJECTS = $(argument_test_OBJECTS) $(lineparse_test_OBJECTS) $(compoundfile_test_OBJECTS) $(socket_test_OBJECTS) $(jobqueue_test_OBJECTS) $(threadref_test_OBJECTS)
135	151
136	152	all: all-redirect
137	153	.SUFFIXES:

187	203	socket.test: $(socket_test_OBJECTS) $(socket_test_DEPENDENCIES)
188	204	@rm -f socket.test
189	205	$(LINK) $(socket_test_LDFLAGS) $(socket_test_OBJECTS) $(socket_test_LDADD) $(LIBS)
	206
	207	jobqueue.test: $(jobqueue_test_OBJECTS) $(jobqueue_test_DEPENDENCIES)
	208	@rm -f jobqueue.test
	209	$(LINK) $(jobqueue_test_LDFLAGS) $(jobqueue_test_OBJECTS) $(jobqueue_test_LDADD) $(LIBS)
	210
	211	threadref.test: $(threadref_test_OBJECTS) $(threadref_test_DEPENDENCIES)
	212	@rm -f threadref.test
	213	$(LINK) $(threadref_test_LDFLAGS) $(threadref_test_OBJECTS) $(threadref_test_LDADD) $(LIBS)
190	214
191	215	tags: TAGS
192	216

+7

-4

src/general/argument.c less more

2	2	* Library for command line argument processing *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

172	172	g_print("Built on %s\n", __DATE__);
173	173	if(strlen(branch) >= 10)
174	174	g_print("Branch: %.*s\n", (gint)(strlen(branch)-9), branch+7);
175		else
176		g_print("Branch: unnamed branch\n");
177	175	return;
178	176	}
179	177

301	299	*/
302	300
303	301	int main(int argc, char **argv){
304		register Argument *arg = Argument_create(argc, argv);
	302	register Argument *arg;
305	303	register gint retval;
	304	#ifdef USE_PTHREADS
	305	if(!g_thread_supported())
	306	g_thread_init(NULL);
	307	#endif /* USE_PTHREADS */
	308	arg = Argument_create(argc, argv);
306	309	g_log_set_handler(NULL, G_LOG_LEVEL_ERROR\|G_LOG_FLAG_FATAL,
307	310	Argument_error_handler, arg);
308	311	g_assert(Argument_assertion_warning());

+1

-1

src/general/argument.h less more

2	2	* Library for command line argument processing *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/general/argument.test.c less more

2	2	* Library for command line argument processing *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+47

-3

src/general/compoundfile.c less more

2	2	* Library for reading large and/or split files. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

157	157	CompoundFile CompoundFile_share(CompoundFile cf){
158	158	cf->ref_count++;
159	159	return cf;
	160	}
	161
	162	static GPtrArray CompoundFile_get_path_list(CompoundFile cf){
	163	register gint i;
	164	register gchar *path;
	165	register GPtrArray *path_list = g_ptr_array_new();
	166	register CompoundFile_Element *element;
	167	for(i = 0; i < cf->element_list->len; i++){
	168	element = cf->element_list->pdata[i];
	169	path = g_strdup(element->path);
	170	g_ptr_array_add(path_list, path);
	171	}
	172	return path_list;
	173	}
	174
	175	CompoundFile CompoundFile_dup(CompoundFile cf){
	176	register CompoundFile *ncf;
	177	register CompoundFile_Location nstart = NULL, nstop = NULL;
	178	register gint i;
	179	register gchar *path;
	180	register GPtrArray *path_list = CompoundFile_get_path_list(cf);
	181	g_assert(path_list);
	182	ncf = CompoundFile_create(path_list, FALSE);
	183	if(cf->start_limit)
	184	nstart = CompoundFile_Location_create(ncf,
	185	cf->start_limit->pos,
	186	cf->start_limit->element_id);
	187	if(cf->stop_limit)
	188	nstop = CompoundFile_Location_create(ncf,
	189	cf->stop_limit->pos,
	190	cf->stop_limit->element_id);
	191	CompoundFile_set_limits(ncf, nstart, nstop);
	192	if(nstart)
	193	CompoundFile_Location_destroy(nstart);
	194	if(nstop)
	195	CompoundFile_Location_destroy(nstop);
	196	for(i = 0; i < path_list->len; i++){
	197	path = path_list->pdata[i];
	198	g_free(path);
	199	}
	200	g_ptr_array_free(path_list, TRUE);
	201	return ncf;
160	202	}
161	203
162	204	gchar CompoundFile_current_path(CompoundFile cf){

343	385	CompoundFile_Location_destroy(cf->start_limit);
344	386	if(cf->stop_limit)
345	387	CompoundFile_Location_destroy(cf->stop_limit);
346		cf->start_limit = CompoundFile_Location_share(start);
347		cf->stop_limit = CompoundFile_Location_share(stop);
	388	if(start)
	389	cf->start_limit = CompoundFile_Location_share(start);
	390	if(stop)
	391	cf->stop_limit = CompoundFile_Location_share(stop);
348	392	CompoundFile_rewind(cf);
349	393	return;
350	394	}

+14

-9

src/general/compoundfile.h less more

2	2	* Library for reading large and/or split files. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

24	24
25	25	#include <sys/types.h> /* For lseek() and off_t */
26	26	#include <unistd.h> /* For lseek() and off_t */
	27	#include <inttypes.h> /* For PRIuPTR */
27	28
28	29	#ifdef USE_PTHREADS
29	30	#include <pthread.h>

44	45
45	46	typedef off_t CompoundFile_Pos;
46	47
47		#if _FILE_OFFSET_BITS==64
48		#define CompoundFile_Pos_format "%lld"
49		#else /* Assume _FILE_OFFSET_BITS==32 */
50		#define CompoundFile_Pos_format "%ld"
51		#endif /* _FILE_OFFSET_BITS */
52
	48	#if __STDC_VERSION__ >= 199901L
53	49	#define CompoundFile_Pos_print(fp, pos) \
54		CompoundFile_Pragma fprintf((fp), CompoundFile_Pos_format, (pos))
	50	CompoundFile_Pragma fprintf((fp), "%jd", (intmax_t)(pos))
	51	typedef intmax_t CompoundFile_Pos_scan_type;
55	52	#define CompoundFile_Pos_scan(src, dst) \
56		CompoundFile_Pragma sscanf((src), CompoundFile_Pos_format, (dst))
	53	CompoundFile_Pragma sscanf((src), "%jd", (intmax_t*)(dst))
	54	#else /* __STDC_VERSION__ */
	55	#define CompoundFile_Pos_print(fp, pos) \
	56	CompoundFile_Pragma fprintf((fp), "%lld", (long long int)(pos))
	57	typedef long long int CompoundFile_Pos_scan_type;
	58	#define CompoundFile_Pos_scan(src, dst) \
	59	CompoundFile_Pragma sscanf((src), "%lld", (dst))
	60	#endif /* __STDC_VERSION__ */
57	61
58	62	typedef struct {
59	63	gchar *path;

80	84	gboolean sort_on_file_size);
81	85	void CompoundFile_destroy(CompoundFile *cf);
82	86	CompoundFile CompoundFile_share(CompoundFile cf);
	87	CompoundFile CompoundFile_dup(CompoundFile cf);
83	88	gchar CompoundFile_current_path(CompoundFile cf);
84	89
85	90	#define CompoundFile_buffer_is_empty(cf) \

+1

-1

src/general/compoundfile.test.c less more

2	2	* Library for reading large and/or split files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+137

-0

src/general/jobqueue.c less more

	0	/****************************************************************\
	1	* *
	2	* Library for Queueing Multi-Threaded Jobs *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#include "jobqueue.h"
	16	#include <unistd.h> /* For usleep() */
	17
	18	#ifdef USE_PTHREADS
	19	static JobQueue_Task *JobQueue_Task_create(JobQueue_Func job_func,
	20	gpointer job_data, gint priority){
	21	register JobQueue_Task *task = g_new(JobQueue_Task, 1);
	22	task->job_func = job_func;
	23	task->job_data = job_data;
	24	task->priority = priority;
	25	return task;
	26	}
	27
	28	static void JobQueue_Task_destroy(JobQueue_Task *task){
	29	g_free(task);
	30	return;
	31	}
	32
	33	static void JobQueue_thread_func(void data){
	34	register JobQueue *jq = data;
	35	register JobQueue_Task *task;
	36	do {
	37	pthread_mutex_lock(&jq->queue_lock);
	38	task = PQueue_pop(jq->pq);
	39	if(task){
	40	jq->running_count++;
	41	pthread_mutex_unlock(&jq->queue_lock);
	42	task->job_func(task->job_data);
	43	JobQueue_Task_destroy(task);
	44	pthread_mutex_lock(&jq->queue_lock);
	45	jq->running_count--;
	46	pthread_mutex_unlock(&jq->queue_lock);
	47	} else {
	48	pthread_mutex_unlock(&jq->queue_lock);
	49	usleep(1000); /* wait before checking job queue again */
	50	}
	51	} while(!jq->is_complete);
	52	return NULL;
	53	}
	54
	55	static gboolean JobQueue_Task_compare(gpointer low, gpointer high,
	56	gpointer user_data){
	57	register JobQueue_Task low_task = (JobQueue_Task)low,
	58	high_task = (JobQueue_Task)high;
	59	return low_task->priority < high_task->priority;
	60	}
	61	#endif /* USE_PTHREADS */
	62
	63	JobQueue *JobQueue_create(gint thread_total){
	64	register JobQueue *jq = g_new(JobQueue, 1);
	65	#ifdef USE_PTHREADS
	66	register gint i;
	67	jq->is_complete = FALSE;
	68	jq->thread_total = thread_total;
	69	jq->running_count = 0;
	70	pthread_mutex_init(&jq->queue_lock, NULL);
	71	jq->thread = g_new0(pthread_t, thread_total);
	72	jq->pq_set = PQueueSet_create();
	73	jq->pq = PQueue_create(jq->pq_set, JobQueue_Task_compare, NULL);
	74	for(i = 0; i < thread_total; i++)
	75	pthread_create(&jq->thread[i], NULL, JobQueue_thread_func, jq);
	76	#endif /* USE_PTHREADS */
	77	return jq;
	78	}
	79
	80	static void JobQueue_Task_free_func(gpointer data, gpointer user_data){
	81	register JobQueue_Task *task = data;
	82	JobQueue_Task_destroy(task);
	83	return;
	84	}
	85
	86	void JobQueue_destroy(JobQueue *jq){
	87	#ifdef USE_PTHREADS
	88	g_assert(!PQueue_total(jq->pq));
	89	PQueue_destroy(jq->pq, JobQueue_Task_free_func, NULL);
	90	PQueueSet_destroy(jq->pq_set);
	91	pthread_mutex_destroy(&jq->queue_lock);
	92	g_free(jq->thread);
	93	#endif /* USE_PTHREADS */
	94	g_free(jq);
	95	return;
	96	}
	97
	98	void JobQueue_submit(JobQueue *jq, JobQueue_Func job_func,
	99	gpointer job_data, gint priority){
	100	#ifdef USE_PTHREADS
	101	register JobQueue_Task *task;
	102	g_assert(jq);
	103	pthread_mutex_lock(&jq->queue_lock);
	104	task = JobQueue_Task_create(job_func, job_data, priority);
	105	PQueue_push(jq->pq, task);
	106	pthread_mutex_unlock(&jq->queue_lock);
	107	#else /* USE_PTHREADS */
	108	jq->job_func(job_data); /* when no threads available, just run the job */
	109	#endif /* USE_PTHREADS */
	110	return;
	111	}
	112	/* waits until less than (thread_total * 2) jobs are queued
	113	*/
	114
	115	void JobQueue_complete(JobQueue *jq){
	116	#ifdef USE_PTHREADS
	117	register gint i, job_total;
	118	do { /* wait for job queue to empty */
	119	pthread_mutex_lock(&jq->queue_lock);
	120	job_total = PQueue_total(jq->pq) + jq->running_count;
	121	pthread_mutex_unlock(&jq->queue_lock);
	122	usleep(1000); /* wait before checking if queue is empty again */
	123	} while(job_total);
	124	jq->is_complete = TRUE;
	125	/* wait for threads to finish */
	126	for(i = 0; i < jq->thread_total; i++)
	127	pthread_join(jq->thread[i], NULL);
	128	#endif /* USE_PTHREADS */
	129	return;
	130	}
	131	/* waits until the queue is empty and no jobs are running,
	132	* to catch any jobs which are added to the queue by runnning jobs
	133	*/
	134
	135	/**/
	136

+67

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src/general/jobqueue.h less more

	0	/****************************************************************\
	1	* *
	2	* Library for Queueing Multi-Threaded Jobs *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#ifndef INCLUDED_JOBQUEUE_H
	16	#define INCLUDED_JOBQUEUE_H
	17
	18	#ifdef __cplusplus
	19	extern "C" {
	20	#endif /* __cplusplus */
	21
	22	#include <glib.h>
	23
	24	#ifdef USE_PTHREADS
	25	#include <pthread.h>
	26	#endif /* USE_PTHREADS */
	27
	28	#include "pqueue.h"
	29
	30	typedef void (*JobQueue_Func)(gpointer job_data);
	31
	32	typedef struct JobQueue_Task {
	33	JobQueue_Func job_func;
	34	gpointer job_data;
	35	gint priority;
	36	} JobQueue_Task;
	37
	38	typedef struct {
	39	#ifdef USE_PTHREADS
	40	gboolean is_complete;
	41	gint thread_total;
	42	gint running_count;
	43	pthread_mutex_t queue_lock;
	44	pthread_t *thread;
	45	PQueue *pq;
	46	PQueueSet *pq_set;
	47	#endif /* USE_PTHREADS */
	48	} JobQueue;
	49
	50	JobQueue *JobQueue_create(gint thread_total);
	51	void JobQueue_destroy(JobQueue *jq);
	52	void JobQueue_submit(JobQueue *jq, JobQueue_Func job_func,
	53	gpointer job_data, gint priority);
	54	void JobQueue_complete(JobQueue *jq);
	55
	56	/* Lower priority jobs are run first */
	57
	58	#ifdef __cplusplus
	59	}
	60	#endif /* __cplusplus */
	61
	62	#endif /* INCLUDED_JOBQUEUE_H */
	63
	64
	65	/**/
	66

+44

-0

src/general/jobqueue.test.c less more

	0	/****************************************************************\
	1	* *
	2	* Library for Queueing Multi-Threaded Jobs *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#include <unistd.h> /* For usleep() */
	16	#include "jobqueue.h"
	17
	18	static void test_run_func(gpointer job_data){
	19	register gchar *name = job_data;
	20	g_message("running job [%s]", name);
	21	usleep(1000000); /* test job length */
	22	return;
	23	}
	24
	25	int main(void){
	26	register gint i;
	27	register JobQueue *jq = JobQueue_create(2);
	28	gchar *test_str[10] = {"one", "two", "three", "four", "five",
	29	"six", "seven", "eight", "nine", "ten"};
	30
	31	/* Initialise threads as not using Argument library */
	32	#ifdef USE_PTHREADS
	33	if(!g_thread_supported())
	34	g_thread_init(NULL);
	35	#endif /* USE_PTHREADS */
	36
	37	for(i = 0; i < 10; i++)
	38	JobQueue_submit(jq, test_run_func, test_str[i], 0);
	39	JobQueue_complete(jq);
	40	JobQueue_destroy(jq);
	41	return 0;
	42	}
	43

+1

-1

src/general/lineparse.c less more

2	2	* Library for basic line-by-line parsing of text files. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/general/lineparse.h less more

2	2	* Library for basic line-by-line parsing of text files. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/general/lineparse.test.c less more

2	2	* Library for basic line-by-line parsing of text files. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+45

-7

src/general/socket.c less more

2	2	* Simple client-server code library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

55	55	struct sockaddr_in server;
56	56	struct hostent *hp = gethostbyname(host);
57	57	register gchar *reply;
	58	#ifdef USE_PTHREADS
	59	pthread_mutex_init(&client->connection_mutex, NULL);
	60	#endif /* USE_PTHREADS */
58	61	if(!hp){
59		perror("lookup up hostname");
	62	perror("looking up hostname");
60	63	exit(1);
61	64	}
62	65	client->connection = SocketConnection_create(host, port);

102	105	}
103	106
104	107	static gchar *SocketConnection_read(gint sock){
105		register gint i, len, line_complete = 0, line_expect = 1;
	108	register gint i, len = 0, line_complete = 0, line_expect = 1;
106	109	register gchar *reply;
107	110	register GString *string = g_string_sized_new(Socket_BUFSIZE);
108	111	register gboolean line_count_given = FALSE;

124	127	g_error("linecount: must be > 1");
125	128	}
126	129	if(line_complete > line_expect){
127		if(line_count_given)
	130	if(line_count_given){
128	131	g_error("Received [%d] socket message lines, but expected [%d]",
129	132	line_complete, line_count_given);
130		else
	133	} else {
131	134	g_error("Multiline socket messages must use linecount:");
	135	}
132	136	}
133	137	g_string_append(string, buffer);
134	138	} while(line_complete < line_expect);

170	174	}
171	175
172	176	gchar SocketClient_send(SocketClient client, gchar *msg){
	177	register gchar *reply;
	178	#ifdef USE_PTHREADS
	179	pthread_mutex_lock(&client->connection_mutex);
	180	#endif /* USE_PTHREADS */
173	181	Socket_send(client->connection->sock, msg, "writing client message");
174		return SocketConnection_read(client->connection->sock);
	182	reply = SocketConnection_read(client->connection->sock);
	183	g_assert(reply);
	184	#ifdef USE_PTHREADS
	185	pthread_mutex_unlock(&client->connection_mutex);
	186	#endif /* USE_PTHREADS */
	187	return reply;
175	188	}
176	189
177	190	void SocketClient_destroy(SocketClient *client){
178	191	SocketConnection_destroy(client->connection);
	192	#ifdef USE_PTHREADS
	193	pthread_mutex_destroy(&client->connection_mutex);
	194	#endif /* USE_PTHREADS */
179	195	g_free(client);
180	196	return;
181	197	}

195	211	static void SocketServer_shutdown(int signum){
196	212	g_message("Server shutting down");
197	213	exit(0);
	214	return;
	215	}
	216
	217	static void SocketServer_broken_pipe(int signum){
	218	g_message("Server detected broken pipe - closing thread");
	219	pthread_exit(NULL);
198	220	return;
199	221	}
200	222

244	266	register gboolean ok = TRUE;
245	267	gchar *reply;
246	268	do {
	269	#ifdef USE_PTHREADS
	270	pthread_mutex_lock(&server->connection_mutex);
	271	#endif /* USE_PTHREADS */
247	272	msg = SocketConnection_read(msgsock);
	273	#ifdef USE_PTHREADS
	274	pthread_mutex_unlock(&server->connection_mutex);
	275	#endif /* USE_PTHREADS */
248	276	reply = NULL;
249	277	if(!msg)
250	278	break;

252	280	server->user_data);
253	281	g_free(msg);
254	282	if(reply){
	283	#ifdef USE_PTHREADS
	284	pthread_mutex_lock(&server->connection_mutex);
	285	#endif /* USE_PTHREADS */
255	286	Socket_send(msgsock, reply, "writing reply");
	287	#ifdef USE_PTHREADS
	288	pthread_mutex_unlock(&server->connection_mutex);
	289	#endif /* USE_PTHREADS */
256	290	g_free(reply);
	291	} else {
	292	g_error("no reply from server");
257	293	}
258	294	} while(ok);
259	295	if(server->connection_close_func)

264	300	#ifdef USE_PTHREADS
265	301	static void SocketServer_pthread_func(void data){
266	302	register SocketServer_pthread_Data sspd = (SocketServer_pthread_Data)data;
	303	signal(SIGPIPE, SocketServer_broken_pipe);
267	304	SocketServer_process_connection(sspd->server, sspd->msgsock);
268	305	pthread_mutex_lock(&sspd->server->connection_mutex);
269	306	g_message("cleaning up connection [%d]", global_connection_count);

278	315
279	316	gboolean SocketServer_listen(SocketServer *server){
280	317	register int msgsock;
281		register gint i;
282	318	struct sockaddr_in client_addr;
283	319	socklen_t client_len = sizeof(struct sockaddr_in);
284	320	#ifdef USE_PTHREADS
	321	register gint i;
285	322	pthread_attr_t pt_attr;
286	323	pthread_attr_init(&pt_attr);
287	324	pthread_attr_setdetachstate(&pt_attr, PTHREAD_CREATE_DETACHED);

350	387	return;
351	388	}
352	389
	390

+4

-1

src/general/socket.h less more

2	2	* Simple client-server code library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

44	44
45	45	typedef struct {
46	46	SocketConnection *connection;
	47	#ifdef USE_PTHREADS
	48	pthread_mutex_t connection_mutex;
	49	#endif /* USE_PTHREADS */
47	50	} SocketClient;
48	51
49	52	#ifdef USE_PTHREADS

+1

-1

src/general/socket.test.c less more

2	2	* Simple client-server code library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+69

-0

src/general/threadref.c less more

	0	/****************************************************************\
	1	* *
	2	* Basic library for thread-safe reference counting. *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#include "threadref.h"
	16
	17	ThreadRef *ThreadRef_create(void){
	18	register ThreadRef *threadref = g_new(ThreadRef, 1);
	19	threadref->ref_count = 1;
	20	#ifdef USE_PTHREADS
	21	pthread_mutex_init(&threadref->ref_lock, NULL);
	22	#endif /* USE_PTHREADS */
	23	return threadref;
	24	}
	25
	26	ThreadRef ThreadRef_destroy(ThreadRef threadref){
	27	ThreadRef_lock(threadref);
	28	if(--threadref->ref_count){
	29	ThreadRef_unlock(threadref);
	30	return threadref;
	31	}
	32	ThreadRef_unlock(threadref);
	33	#ifdef USE_PTHREADS
	34	pthread_mutex_destroy(&threadref->ref_lock);
	35	#endif /* USE_PTHREADS */
	36	g_free(threadref);
	37	return NULL;
	38	}
	39
	40	ThreadRef ThreadRef_share(ThreadRef threadref){
	41	ThreadRef_lock(threadref);
	42	threadref->ref_count++;
	43	ThreadRef_unlock(threadref);
	44	return threadref;
	45	}
	46
	47	gint ThreadRef_get_count(ThreadRef *threadref){
	48	register gint ref_count;
	49	ThreadRef_lock(threadref);
	50	ref_count = threadref->ref_count;
	51	ThreadRef_unlock(threadref);
	52	return ref_count;
	53	}
	54
	55	void ThreadRef_lock(ThreadRef *threadref){
	56	#ifdef USE_PTHREADS
	57	pthread_mutex_lock(&threadref->ref_lock);
	58	#endif /* USE_PTHREADS */
	59	return;
	60	}
	61
	62	void ThreadRef_unlock(ThreadRef *threadref){
	63	#ifdef USE_PTHREADS
	64	pthread_mutex_unlock(&threadref->ref_lock);
	65	#endif /* USE_PTHREADS */
	66	return;
	67	}
	68

+49

-0

src/general/threadref.h less more

	0	/****************************************************************\
	1	* *
	2	* Basic library for thread-safe reference counting. *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#ifndef INCLUDED_THREADREF_H
	16	#define INCLUDED_THREADREF_H
	17
	18	#ifdef __cplusplus
	19	extern "C" {
	20	#endif /* __cplusplus */
	21
	22	#include <glib.h>
	23
	24	#ifdef USE_PTHREADS
	25	#include <pthread.h>
	26	#endif /* USE_PTHREADS */
	27
	28
	29	typedef struct {
	30	gint ref_count;
	31	#ifdef USE_PTHREADS
	32	pthread_mutex_t ref_lock;
	33	#endif /* USE_PTHREADS */
	34	} ThreadRef;
	35
	36	ThreadRef *ThreadRef_create(void);
	37	ThreadRef ThreadRef_destroy(ThreadRef threadref);
	38	ThreadRef ThreadRef_share(ThreadRef threadref);
	39	gint ThreadRef_get_count(ThreadRef *threadref);
	40	void ThreadRef_lock(ThreadRef *threadref);
	41	void ThreadRef_unlock(ThreadRef *threadref);
	42
	43	#ifdef __cplusplus
	44	}
	45	#endif /* __cplusplus */
	46
	47	#endif /* INCLUDED_THREADREF_H */
	48

+28

-0

src/general/threadref.test.c less more

	0	/****************************************************************\
	1	* *
	2	* Basic library for thread-safe reference counting. *
	3	* *
	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
	6	* *
	7	* This source code is distributed under the terms of the *
	8	* GNU General Public License, version 3. See the file COPYING *
	9	* or http://www.gnu.org/licenses/gpl.txt for details *
	10	* *
	11	* If you use this code, please keep this notice intact. *
	12	* *
	13	\****************************************************************/
	14
	15	#include <stdio.h>
	16	#include "threadref.h"
	17
	18	int main(void){
	19	register ThreadRef tr = ThreadRef_create(), tr2;
	20	tr2 = ThreadRef_share(tr);
	21	ThreadRef_destroy(tr2);
	22	ThreadRef_lock(tr);
	23	ThreadRef_unlock(tr);
	24	ThreadRef_destroy(tr);
	25	return 0;
	26	}
	27

+4

-0

src/hub/Makefile.am less more

59	59	$(top_srcdir)/src/model/modeltype.o \
60	60	$(top_srcdir)/src/general/argument.o \
61	61	$(top_srcdir)/src/general/lineparse.o \
	62	$(top_srcdir)/src/general/jobqueue.o \
62	63	$(top_srcdir)/src/comparison/match.o \
63	64	$(top_srcdir)/src/sequence/submat.o \
64	65	$(top_srcdir)/src/sequence/codonsubmat.o \

70	71	$(top_srcdir)/src/comparison/wordhood.o \
71	72	$(top_srcdir)/src/struct/sparsecache.o \
72	73	$(top_srcdir)/src/general/compoundfile.o \
	74	$(top_srcdir)/src/general/threadref.o \
73	75	$(C4_OBJECTS)
74	76
75	77	bsam_test_SOURCES = bsam.test.c bsam.c
76	78	bsam_test_LDADD = $(top_srcdir)/src/general/argument.o \
77	79	$(top_srcdir)/src/general/lineparse.o \
	80	$(top_srcdir)/src/general/threadref.o \
78	81	$(top_srcdir)/src/comparison/hspset.o \
79	82	$(top_srcdir)/src/comparison/comparison.o \
80	83	$(top_srcdir)/src/comparison/match.o \

104	107	$(top_srcdir)/src/struct/sparsecache.o \
105	108	$(top_srcdir)/src/general/compoundfile.o \
106	109	$(top_srcdir)/src/general/socket.o \
	110	$(top_srcdir)/src/general/threadref.o \
107	111	$(C4_OBJECTS)
108	112
109	113	# Files to clear away

+12

-6

src/hub/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

85	86
86	87	noinst_HEADERS = gam.h analysis.h bsam.h
87	88
88		C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o -lm
	89	C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/scheduler.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/jobqueue.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o -lm
89	90
90	91
91	92	gam_test_SOURCES = gam.test.c gam.c
92		gam_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(C4_OBJECTS)
	93	gam_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/threadref.o $(C4_OBJECTS)
93	94
94	95
95	96	bsam_test_SOURCES = bsam.test.c bsam.c
96		bsam_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/matrix.o -lm
	97	bsam_test_LDADD = $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/threadref.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/matrix.o -lm
97	98
98	99	analysis_test_SOURCES = analysis.test.c analysis.c gam.c bsam.c
99		analysis_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/socket.o $(C4_OBJECTS)
	100	analysis_test_LDADD = $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/general/threadref.o $(C4_OBJECTS)
100	101
101	102
102	103	# Files to clear away

116	117	$(top_srcdir)/src/comparison/comparison.o \
117	118	$(top_srcdir)/src/comparison/wordhood.o \
118	119	$(top_srcdir)/src/struct/sparsecache.o \
119		$(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/c4/c4.o \
	120	$(top_srcdir)/src/general/compoundfile.o \
	121	$(top_srcdir)/src/general/threadref.o $(top_srcdir)/src/c4/c4.o \
120	122	$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
121	123	$(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o \
122	124	$(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \

145	147	$(top_srcdir)/src/model/modeltype.o \
146	148	$(top_srcdir)/src/general/argument.o \
147	149	$(top_srcdir)/src/general/lineparse.o \
	150	$(top_srcdir)/src/general/jobqueue.o \
148	151	$(top_srcdir)/src/comparison/match.o \
149	152	$(top_srcdir)/src/sequence/submat.o \
150	153	$(top_srcdir)/src/sequence/codonsubmat.o

159	162	$(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o \
160	163	$(top_srcdir)/src/struct/sparsecache.o \
161	164	$(top_srcdir)/src/general/compoundfile.o \
162		$(top_srcdir)/src/general/socket.o $(top_srcdir)/src/c4/c4.o \
	165	$(top_srcdir)/src/general/socket.o \
	166	$(top_srcdir)/src/general/threadref.o $(top_srcdir)/src/c4/c4.o \
163	167	$(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o \
164	168	$(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o \
165	169	$(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/viterbi.o \

188	192	$(top_srcdir)/src/model/modeltype.o \
189	193	$(top_srcdir)/src/general/argument.o \
190	194	$(top_srcdir)/src/general/lineparse.o \
	195	$(top_srcdir)/src/general/jobqueue.o \
191	196	$(top_srcdir)/src/comparison/match.o \
192	197	$(top_srcdir)/src/sequence/submat.o \
193	198	$(top_srcdir)/src/sequence/codonsubmat.o

195	200	bsam_test_OBJECTS = bsam.test.o bsam.o
196	201	bsam_test_DEPENDENCIES = $(top_srcdir)/src/general/argument.o \
197	202	$(top_srcdir)/src/general/lineparse.o \
	203	$(top_srcdir)/src/general/threadref.o \
198	204	$(top_srcdir)/src/comparison/hspset.o \
199	205	$(top_srcdir)/src/comparison/comparison.o \
200	206	$(top_srcdir)/src/comparison/match.o \

+360

-58

src/hub/analysis.c less more

2	2	* Analysis module for exonerate *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

16	16	#include "ungapped.h"
17	17	#include "compoundfile.h"
18	18	#include "hspset.h"
	19	#include "lineparse.h"
19	20
20	21	#include <stdlib.h> /* For atoi() */
21	22	#include <unistd.h> /* For sleep() */
22	23	#include <string.h> /* For strcmp() */
23	24	#include <ctype.h> /* For isdigit() */
	25
	26	#include <sys/types.h> /* For stat() */
	27	#include <sys/stat.h> /* For stat() */
	28	#include <unistd.h> /* For stat() */
24	29
25	30	Analysis_ArgumentSet Analysis_ArgumentSet_create(Argument arg){
26	31	register ArgumentSet *as;

33	38	ArgumentSet_add_option(as, 'B', "bigseq", NULL,
34	39	"Allow rapid comparison between big sequences", "FALSE",
35	40	Argument_parse_boolean, &aas.use_bigseq);
	41	ArgumentSet_add_option(as, 'r', "revcomp", NULL,
	42	"Also search reverse complement of query and target", "TRUE",
	43	Argument_parse_boolean, &aas.use_revcomp);
36	44	ArgumentSet_add_option(as, '\0', "forcescan", "[q\|t]",
37	45	"Force FSM scan on query or target sequences", "none",
38	46	Argument_parse_string, &aas.force_scan);

44	52	ArgumentSet_add_option(as, 0, "customserver", "command",
45	53	"Custom command to send non-standard server", "NULL",
46	54	Argument_parse_string, &aas.custom_server_command);
	55	ArgumentSet_add_option(as, 'c', "cores", "number",
	56	"Number of cores/CPUs/threads for alignment computation", "1",
	57	Argument_parse_int, &aas.thread_count);
47	58	Argument_absorb_ArgumentSet(arg, as);
48	59	}
49	60	return &aas;
50	61	}
51	62
52	63	/**/
	64
	65	typedef struct {
	66	GAM *gam;
	67	Comparison *comparison;
	68	} Analysis_HeuristicJob;
	69
	70	static Analysis_HeuristicJob Analysis_HeuristicJob_create(GAM gam,
	71	Comparison *comparison){
	72	register Analysis_HeuristicJob *ahj = g_new(Analysis_HeuristicJob, 1);
	73	ahj->gam = GAM_share(gam);
	74	ahj->comparison = Comparison_share(comparison);
	75	return ahj;
	76	}
	77
	78	static void Analysis_HeuristicJob_destroy(Analysis_HeuristicJob *ahj){
	79	Comparison_destroy(ahj->comparison);
	80	GAM_destroy(ahj->gam);
	81	g_free(ahj);
	82	return;
	83	}
	84
	85	static void Analysis_HeuristicJob_run(gpointer data){
	86	register Analysis_HeuristicJob *ahj = data;
	87	register GAM_Result *gam_result
	88	= GAM_Result_heuristic_create(ahj->gam, ahj->comparison);
	89	if(gam_result){
	90	GAM_Result_submit(gam_result);
	91	GAM_Result_destroy(gam_result);
	92	}
	93	Analysis_HeuristicJob_destroy(ahj);
	94	return;
	95	}
53	96
54	97	static void Analysis_report_func(Comparison *comparison,
55	98	gpointer user_data){
56	99	register Analysis *analysis = user_data;
57	100	register GAM_Result *gam_result;
	101	register Analysis_HeuristicJob *ahj;
58	102	g_assert(Comparison_has_hsps(comparison));
59	103	if(analysis->scan_query){
60	104	/* Swap back query and target after a query scan */

69	113	Comparison_revcomp(comparison);
70	114	}
71	115	if(Model_Type_is_gapped(analysis->gam->gas->type)){
72		gam_result = GAM_Result_heuristic_create(analysis->gam,
73		comparison);
	116	ahj = Analysis_HeuristicJob_create(analysis->gam, comparison);
	117	#ifdef USE_PTHREADS
	118	g_assert(analysis->job_queue);
	119	/* FIXME: need to use priority here */
	120	JobQueue_submit(analysis->job_queue, Analysis_HeuristicJob_run, ahj, 2);
	121	#else /* USE_PTHREADS */
	122	Analysis_HeuristicJob_run(ahj);
	123	#endif /* USE_PTHREADS */
74	124	} else {
75	125	gam_result = GAM_Result_ungapped_create(analysis->gam,
76	126	comparison);
77		}
78		if(gam_result){
79		GAM_Result_submit(gam_result);
80		GAM_Result_destroy(gam_result);
	127	if(gam_result){
	128	GAM_Result_submit(gam_result);
	129	GAM_Result_destroy(gam_result);
	130	}
81	131	}
82	132	return;
83	133	}

107	157	/* Called after query pipeline analysis */
108	158
109	159	static gboolean Analysis_FastaPipe_Pair_query_func(FastaDB_Seq *fdbs,
110		gpointer user_data){
	160	gpointer user_data){
111	161	register Analysis *analysis = user_data;
112	162	g_assert(!analysis->curr_query);
113	163	/*

138	188
139	189	/**/
140	190
	191	typedef struct {
	192	GAM *gam;
	193	Sequence *query;
	194	Sequence *target;
	195	} Analysis_ExhaustiveJob;
	196
	197	static Analysis_ExhaustiveJob Analysis_ExhaustiveJob_create(GAM gam,
	198	Sequence query, Sequence target){
	199	register Analysis_ExhaustiveJob *aej = g_new(Analysis_ExhaustiveJob, 1);
	200	aej->gam = GAM_share(gam);
	201	aej->query = Sequence_share(query);
	202	aej->target = Sequence_share(target);
	203	return aej;
	204	}
	205
	206	static void Analysis_ExhaustiveJob_destroy(Analysis_ExhaustiveJob *aej){
	207	GAM_destroy(aej->gam);
	208	Sequence_destroy(aej->query);
	209	Sequence_destroy(aej->target);
	210	g_free(aej);
	211	return;
	212	}
	213
	214	static void Analysis_ExhaustiveJob_run(gpointer data){
	215	register Analysis_ExhaustiveJob *aej = data;
	216	register GAM_Result *gam_result;
	217	gam_result = GAM_Result_exhaustive_create(aej->gam,
	218	aej->query, aej->target);
	219	if(gam_result){
	220	GAM_Result_submit(gam_result);
	221	GAM_Result_destroy(gam_result);
	222	}
	223	Analysis_ExhaustiveJob_destroy(aej);
	224	return;
	225	}
	226
141	227	static void Analysis_Pair_compare(Analysis *analysis,
142	228	FastaDB_Seq *fdbs){
143		register GAM_Result *gam_result;
	229	register Analysis_ExhaustiveJob *aej;
144	230	if(analysis->aas->use_exhaustive){
145		gam_result = GAM_Result_exhaustive_create(analysis->gam,
146		analysis->curr_query->seq, fdbs->seq);
147		if(gam_result){
148		GAM_Result_submit(gam_result);
149		GAM_Result_destroy(gam_result);
150		}
	231	aej = Analysis_ExhaustiveJob_create(analysis->gam,
	232	analysis->curr_query->seq,
	233	fdbs->seq);
	234	#ifdef USE_PTHREADS
	235	g_assert(analysis->job_queue);
	236	JobQueue_submit(analysis->job_queue, Analysis_ExhaustiveJob_run, aej, 1);
	237	#else /* USE_PTHREADS */
	238	Analysis_ExhaustiveJob_run(aej);
	239	#endif /* USE_PTHREADS */
151	240	} else {
152	241	Analysis_BSAM_compare(analysis, analysis->curr_query, fdbs);
153	242	}
154	243	return;
155	244	}
	245
	246	/**/
156	247
157	248	static gboolean Analysis_FastaPipe_Pair_target_func(FastaDB_Seq *fdbs,
158	249	gpointer user_data){

419	510	g_free(msg);
420	511	g_free(reply);
421	512	/**/
	513	msg = g_strdup_printf("set param dnawordlimit %d",
	514	has->dna_word_limit);
	515	reply = Analysis_Client_send(aclient, msg, "ok:", FALSE);
	516	g_free(msg);
	517	g_free(reply);
	518	/**/
	519	msg = g_strdup_printf("set param proteinwordlimit %d",
	520	has->protein_word_limit);
	521	reply = Analysis_Client_send(aclient, msg, "ok:", FALSE);
	522	g_free(msg);
	523	g_free(reply);
	524	/**/
	525	msg = g_strdup_printf("set param codonwordlimit %d",
	526	has->codon_word_limit);
	527	reply = Analysis_Client_send(aclient, msg, "ok:", FALSE);
	528	g_free(msg);
	529	g_free(reply);
	530	/**/
422	531	msg = g_strdup_printf("set param dnahspdropoff %d",
423	532	has->dna_hsp_dropoff);
424	533	reply = Analysis_Client_send(aclient, msg, "ok:", FALSE);

461	570	g_free(msg);
462	571	g_free(reply);
463	572	/**/
	573	return;
	574	}
	575
	576	static void Analysis_Client_info(Analysis_Client *aclient){
464	577	return;
465	578	}
466	579

472	585	if(!sc)
473	586	return NULL;
474	587	aclient = g_new(Analysis_Client, 1);
	588	aclient->ref_count = 1;
475	589	aclient->sc = sc;
476	590	aclient->verbosity = verbosity;
477	591	aclient->probe_fdb = NULL;

507	621	g_free(dbinfo);
508	622	aclient->curr_query = NULL;
509	623	aclient->seq_cache = g_new0(Sequence*, aclient->num_seqs);
	624	Analysis_Client_info(aclient);
	625	return aclient;
	626	}
	627
	628	static Analysis_Client Analysis_Client_share(Analysis_Client aclient){
	629	aclient->ref_count++;
510	630	return aclient;
511	631	}
512	632
513	633	static void Analysis_Client_destroy(Analysis_Client *aclient){
514	634	register gint i;
515	635	register Sequence *seq;
	636	if(--aclient->ref_count)
	637	return;
516	638	if(aclient->curr_query)
517	639	Sequence_destroy(aclient->curr_query);
518	640	for(i = 0; i < aclient->num_seqs; i++){

532	654	static void Analysis_Client_set_probe_fdb(Analysis_Client *aclient,
533	655	FastaDB *probe_fdb){
534	656	g_assert(!aclient->probe_fdb);
535		aclient->probe_fdb = FastaDB_share(probe_fdb);
	657	aclient->probe_fdb = FastaDB_dup(probe_fdb);
536	658	return;
537	659	}
538	660

591	713	static Analysis_Client_Key Analysis_Client_Key_create(Analysis_Client aclient,
592	714	gint target_id, gint seq_len){
593	715	register Analysis_Client_Key *key = g_new(Analysis_Client_Key, 1);
594		key->aclient = aclient;
	716	key->aclient = Analysis_Client_share(aclient);
595	717	key->target_id = target_id;
596	718	key->seq_len = seq_len;
597	719	return key;
598	720	}
599	721
600	722	static void Analysis_Client_Key_destroy(Analysis_Client_Key *key){
	723	Analysis_Client_destroy(key->aclient);
601	724	g_free(key);
602	725	return;
603	726	}

847	970	Analysis *analysis,
848	971	Sequence *query,
849	972	gboolean swap_chains,
850		gboolean revcomp_target){
	973	gboolean revcomp_target,
	974	gint priority){
851	975	Analysis_Client_set_query(aclient, query);
852	976	Analysis_Client_get_hsp_sets(aclient, analysis, swap_chains, revcomp_target);
853	977	/* Revcomp query if DNA */

860	984	}
861	985
862	986	static void Analysis_Client_process(Analysis_Client aclient, Analysis analysis,
863		gboolean swap_chains){
	987	gboolean swap_chains, gint priority){
864	988	register FastaDB_Seq *fdbs;
865	989	/* FIXME: need to check for appropriate database type */
866	990	while((fdbs = FastaDB_next(aclient->probe_fdb, FastaDB_Mask_ALL))){
867	991	Analysis_Client_process_query(aclient, analysis, fdbs->seq,
868		swap_chains, FALSE);
	992	swap_chains, FALSE, priority);
869	993	/* Revcomp target if protein vs DNA or translate_both */
870	994	if(((aclient->curr_query->alphabet->type == Alphabet_Type_PROTEIN)
871	995	&& (aclient->server_alphabet->type == Alphabet_Type_DNA))
872	996	\|\| analysis->gam->translate_both){
873	997	Analysis_Client_revcomp_target(aclient);
874	998	Analysis_Client_process_query(aclient, analysis,
875		fdbs->seq, swap_chains, TRUE);
	999	fdbs->seq, swap_chains, TRUE,
	1000	priority);
876	1001	Analysis_Client_revcomp_target(aclient);
877	1002	}
878	1003	FastaDB_Seq_destroy(fdbs);

881	1006	}
882	1007
883	1008	/**/
	1009
	1010	static Analysis_Server Analysis_Server_create(Analysis_Builder ab,
	1011	gchar *name, gint priority){
	1012	register Analysis_Server *as = g_new(Analysis_Server, 1);
	1013	as->name = g_strdup(name);
	1014	as->ab = ab;
	1015	as->priority = priority;
	1016	return as;
	1017	}
	1018
	1019	static void Analysis_Server_destroy(Analysis_Server *as){
	1020	g_free(as->name);
	1021	g_free(as);
	1022	return;
	1023	}
	1024
	1025	/**/
	1026
	1027	static Analysis_Builder Analysis_Builder_create(GPtrArray path_list,
	1028	Analysis *analysis,
	1029	gint verbosity){
	1030	register Analysis_Builder *ab;
	1031	register gint i;
	1032	register Analysis_Client *ac;
	1033	register Analysis_Server *as;
	1034	g_assert(path_list->len);
	1035	ac = Analysis_Client_create(path_list->pdata[0], analysis->verbosity);
	1036	if(!ac)
	1037	return NULL;
	1038	/**/
	1039	ab = g_new(Analysis_Builder, 1);
	1040	ab->verbosity = verbosity;
	1041	ab->server_list = g_ptr_array_new();
	1042	ab->server_type = ac->server_alphabet->type;
	1043	ab->probe_fdb = NULL;
	1044	ab->analysis = analysis;
	1045	Analysis_Client_destroy(ac);
	1046	for(i = 0; i < path_list->len; i++){
	1047	as = Analysis_Server_create(ab, path_list->pdata[i], i);
	1048	g_ptr_array_add(ab->server_list, as);
	1049	}
	1050	return ab;
	1051	}
	1052
	1053	static void Analysis_Builder_destroy(Analysis_Builder *ab){
	1054	register gint i;
	1055	register Analysis_Server *as;
	1056	for(i = 0; i < ab->server_list->len; i++){
	1057	as = ab->server_list->pdata[i];
	1058	Analysis_Server_destroy(as);
	1059	}
	1060	g_ptr_array_free(ab->server_list, TRUE);
	1061	if(ab->probe_fdb)
	1062	FastaDB_close(ab->probe_fdb);
	1063	g_free(ab);
	1064	return;
	1065	}
	1066
	1067	static void Analysis_Server_run(gpointer data){
	1068	register Analysis_Server *server = data;
	1069	register Analysis_Client *client
	1070	= Analysis_Client_create(server->name,
	1071	server->ab->analysis->verbosity);
	1072	if(!client)
	1073	g_error("Could not connect to server [%s]", server->name);
	1074	Analysis_Client_set_param(client, server->ab->analysis->gam);
	1075	Analysis_Client_set_probe_fdb(client, server->ab->probe_fdb);
	1076	Analysis_Client_process(client, server->ab->analysis,
	1077	server->ab->swap_chains, server->priority);
	1078	/**/
	1079	Analysis_Client_destroy(client);
	1080	return;
	1081	}
	1082
	1083	static void Analysis_Builder_process(Analysis_Builder *ab,
	1084	Analysis *analysis, gboolean swap_chains){
	1085	register gint i;
	1086	register Analysis_Server *as;
	1087	ab->swap_chains = swap_chains;
	1088	for(i = 0; i < ab->server_list->len; i++){
	1089	as = ab->server_list->pdata[i];
	1090	#ifdef USE_PTHREADS
	1091	g_assert(analysis->job_queue);
	1092	JobQueue_submit(analysis->job_queue, Analysis_Server_run, as, i);
	1093	#else /* USE_PTHREADS */
	1094	Analysis_Server_run(as);
	1095	#endif /* USE_PTHREADS */
	1096	}
	1097	return;
	1098	}
	1099
	1100	static void Analysis_Builder_set_probe_fdb(Analysis_Builder *ab,
	1101	FastaDB *probe_fdb){
	1102	g_assert(!ab->probe_fdb);
	1103	ab->probe_fdb = FastaDB_share(probe_fdb);
	1104	return;
	1105	}
	1106
	1107	/**/
	1108
	1109	static void Analysis_path_list_destroy(GPtrArray *path_list){
	1110	register gint i;
	1111	register gchar *path;
	1112	for(i = 0; i < path_list->len; i++){
	1113	path = path_list->pdata[i];
	1114	g_free(path);
	1115	}
	1116	g_ptr_array_free(path_list, TRUE);
	1117	return;
	1118	}
	1119
	1120	static GPtrArray Analysis_FOSN_expand_path_list(GPtrArray path_list){
	1121	register gint i;
	1122	register gchar path, npath;
	1123	struct stat buf;
	1124	register gboolean expanded_list = FALSE;
	1125	register GPtrArray *npath_list = g_ptr_array_new();
	1126	register FILE *fp;
	1127	register LineParse *lp;
	1128	for(i = 0; i < path_list->len; i++){
	1129	path = path_list->pdata[i];
	1130	if((stat(path, &buf)) /* Cannot read file (ie. servername) */
	1131	\|\| (S_ISDIR(buf.st_mode)) /* Is directory */
	1132	\|\| (FastaDB_file_is_fasta(path))){ /* 1st non-whitespace char is '>' */
	1133	npath = g_strdup(path);
	1134	g_ptr_array_add(npath_list, npath);
	1135	} else { /* Assume to be fosn */
	1136	fp = fopen(path, "r");
	1137	if(!fp)
	1138	g_error("Could not open FOSN file [%s]", path);
	1139	lp = LineParse_create(fp);
	1140	while(LineParse_line(lp) != EOF){
	1141	g_strstrip(lp->line->str); /* strip whitespace */
	1142	if(lp->line->str[0]){
	1143	npath = g_strdup(lp->line->str);
	1144	g_ptr_array_add(npath_list, npath);
	1145	expanded_list = TRUE;
	1146	}
	1147	}
	1148	LineParse_destroy(lp);
	1149	fclose(fp);
	1150	}
	1151	}
	1152	if(!expanded_list){
	1153	for(i = 0; i < npath_list->len; i++){
	1154	npath = npath_list->pdata[i];
	1155	g_free(npath);
	1156	}
	1157	g_ptr_array_free(npath_list, TRUE);
	1158	return NULL;
	1159	}
	1160	return npath_list;
	1161	}
	1162	/* If members of the path list are files
	1163	* where the first non-whitespace character is not '>',
	1164	* it is assumed to be a FOSN, and parsed to expand the path_list.
	1165	*/
884	1166
885	1167	Analysis *Analysis_create(
886	1168	GPtrArray *query_path_list, Alphabet_Type query_type,

898	1180	*codon_hsp_param;
899	1181	register Match_ArgumentSet *mas = Match_ArgumentSet_create(NULL);
900	1182	register gboolean use_horizon;
	1183	register GPtrArray *expanded_query_path_list = NULL,
	1184	*expanded_target_path_list = NULL;
901	1185	g_assert(query_path_list);
902	1186	g_assert(target_path_list);
903	1187	g_assert(query_path_list->len);
904	1188	g_assert(target_path_list->len);
905	1189	analysis->aas = Analysis_ArgumentSet_create(NULL);
906
907	1190	analysis->verbosity = verbosity;
908		/**/
909		if(query_path_list->len == 1)
910		analysis->query_ac
911		= Analysis_Client_create((gchar*)query_path_list->pdata[0],
912		verbosity);
913		if(target_path_list->len == 1)
914		analysis->target_ac
915		= Analysis_Client_create((gchar*)target_path_list->pdata[0],
916		verbosity);
	1191	analysis->job_queue = JobQueue_create(analysis->aas->thread_count);
	1192	/* Expand FOSN paths */
	1193	expanded_query_path_list = Analysis_FOSN_expand_path_list(
	1194	query_path_list);
	1195	expanded_target_path_list = Analysis_FOSN_expand_path_list(
	1196	target_path_list);
	1197	if(expanded_query_path_list)
	1198	query_path_list = expanded_query_path_list;
	1199	if(expanded_target_path_list)
	1200	target_path_list = expanded_target_path_list;
	1201	/**/
	1202	analysis->query_builder = Analysis_Builder_create(query_path_list,
	1203	analysis, verbosity);
	1204	analysis->target_builder = Analysis_Builder_create(target_path_list,
	1205	analysis, verbosity);
917	1206	/**/
918	1207	if(query_type == Alphabet_Type_UNKNOWN){
919		if(analysis->query_ac){
920		query_type = analysis->query_ac->server_alphabet->type;
	1208	if(analysis->query_builder){
	1209	query_type = analysis->query_builder->server_type;
921	1210	} else {
922	1211	query_type = FastaDB_guess_type(
923	1212	(gchar*)query_path_list->pdata[0]);

927	1216	}
928	1217	}
929	1218	if(target_type == Alphabet_Type_UNKNOWN){
930		if(analysis->target_ac){
931		target_type = analysis->target_ac->server_alphabet->type;
	1219	if(analysis->target_builder){
	1220	target_type = analysis->target_builder->server_type;
932	1221	} else {
933	1222	target_type = FastaDB_guess_type(
934	1223	(gchar*)target_path_list->pdata[0]);

952	1241	analysis->aas->use_exhaustive,
953	1242	verbosity);
954	1243	/**/
955		if(analysis->query_ac)
956		Analysis_Client_set_param(analysis->query_ac, analysis->gam);
957		if(analysis->target_ac)
958		Analysis_Client_set_param(analysis->target_ac, analysis->gam);
959		/**/
960	1244	Analysis_find_matches(analysis, &dna_match, &protein_match,
961	1245	&codon_match);
962	1246	match = dna_match;

965	1249	if(!match)
966	1250	match = codon_match;
967	1251	g_assert(match);
968		if(!analysis->query_ac)
	1252	if(!analysis->query_builder)
969	1253	query_fdb = FastaDB_open_list_with_limit(query_path_list,
970	1254	match->query->alphabet, query_chunk_id, query_chunk_total);
971		if(!analysis->target_ac)
	1255	if(!analysis->target_builder)
972	1256	target_fdb = FastaDB_open_list_with_limit(target_path_list,
973	1257	match->target->alphabet, target_chunk_id, target_chunk_total);
974	1258	if(analysis->aas->use_exhaustive){
975		if(analysis->query_ac \|\| analysis->target_ac) /* FIXME: ni */
	1259	if(analysis->query_builder \|\| analysis->target_builder) /* FIXME: ni */
976	1260	g_error("Exhaustive alignment against server not implemented");
977	1261	analysis->fasta_pipe = FastaPipe_create(
978	1262	query_fdb, target_fdb,

982	1266	Analysis_FastaPipe_Pair_query_func,
983	1267	Analysis_FastaPipe_Pair_target_func,
984	1268	FastaDB_Mask_ALL,
985		analysis->gam->translate_both);
	1269	analysis->gam->translate_both,
	1270	analysis->aas->use_revcomp);
986	1271	analysis->curr_query = NULL;
987	1272	} else { /* Not exhaustive */
988	1273	use_horizon = (analysis->aas->use_bigseq
989		\|\| analysis->query_ac
990		\|\| analysis->target_ac)?FALSE:TRUE;
	1274	\|\| analysis->query_builder
	1275	\|\| analysis->target_builder)?FALSE:TRUE;
991	1276	dna_hsp_param = dna_match
992	1277	? HSP_Param_create(dna_match, use_horizon)
993	1278	: NULL;

1025	1310	= analysis->gam->gas->threshold;
1026	1311	}
1027	1312	/* Don't need HSP horizon for bigseq comparison */
1028		if(analysis->query_ac \|\| analysis->target_ac){
1029		if(analysis->query_ac && analysis->target_ac)
	1313	if(analysis->query_builder \|\| analysis->target_builder){
	1314	if(analysis->query_builder && analysis->target_builder)
1030	1315	g_error("Server vs server comparison not impelemented");
1031	1316	analysis->fasta_pipe = NULL;
1032		if(analysis->query_ac){
1033		Analysis_Client_set_probe_fdb(analysis->query_ac, target_fdb);
	1317	if(analysis->query_builder){
	1318	Analysis_Builder_set_probe_fdb(analysis->query_builder,
	1319	target_fdb);
1034	1320	} else {
1035		g_assert(analysis->target_ac);
1036		Analysis_Client_set_probe_fdb(analysis->target_ac, query_fdb);
	1321	g_assert(analysis->target_builder);
	1322	Analysis_Builder_set_probe_fdb(analysis->target_builder,
	1323	query_fdb);
1037	1324	}
1038	1325	} else {
1039	1326	if(analysis->aas->use_bigseq){

1048	1335	Analysis_FastaPipe_Pair_query_func,
1049	1336	Analysis_FastaPipe_Pair_target_func,
1050	1337	FastaDB_Mask_ALL,
1051		analysis->gam->translate_both);
	1338	analysis->gam->translate_both,
	1339	analysis->aas->use_revcomp);
1052	1340	analysis->curr_query = NULL;
1053	1341	} else { /* Use Seeder */
1054	1342	analysis->scan_query = Analysis_decide_scan_query(query_fdb,

1075	1363	Analysis_FastaPipe_Seeder_term_func,
1076	1364	Analysis_FastaPipe_Seeder_query_func,
1077	1365	Analysis_FastaPipe_Seeder_target_func,
1078		FastaDB_Mask_ALL, analysis->gam->translate_both);
	1366	FastaDB_Mask_ALL, analysis->gam->translate_both,
	1367	analysis->aas->use_revcomp);
1079	1368	}
1080	1369	}
1081	1370	}

1084	1373	if(target_fdb)
1085	1374	FastaDB_close(target_fdb);
1086	1375	/**/
	1376	if(expanded_query_path_list)
	1377	Analysis_path_list_destroy(expanded_query_path_list);
	1378	if(expanded_target_path_list)
	1379	Analysis_path_list_destroy(expanded_target_path_list);
1087	1380	return analysis;
1088	1381	}
1089	1382
1090	1383	void Analysis_destroy(Analysis *analysis){
	1384	JobQueue_destroy(analysis->job_queue);
1091	1385	if(analysis->fasta_pipe)
1092	1386	FastaPipe_destroy(analysis->fasta_pipe);
1093	1387	if(analysis->curr_query)

1098	1392	BSAM_destroy(analysis->bsam);
1099	1393	if(analysis->comparison_param)
1100	1394	Comparison_Param_destroy(analysis->comparison_param);
	1395	/*
1101	1396	if(analysis->query_ac)
1102	1397	Analysis_Client_destroy(analysis->query_ac);
1103	1398	if(analysis->target_ac)
1104	1399	Analysis_Client_destroy(analysis->target_ac);
	1400	*/
	1401	if(analysis->query_builder)
	1402	Analysis_Builder_destroy(analysis->query_builder);
	1403	if(analysis->target_builder)
	1404	Analysis_Builder_destroy(analysis->target_builder);
1105	1405	GAM_destroy(analysis->gam);
1106	1406	g_free(analysis);
1107	1407	return;
1108	1408	}
1109	1409
1110	1410	void Analysis_process(Analysis *analysis){
1111		if(analysis->query_ac){
1112		Analysis_Client_process(analysis->query_ac, analysis, TRUE);
1113		} else if(analysis->target_ac){
1114		Analysis_Client_process(analysis->target_ac, analysis, FALSE);
	1411	if(analysis->query_builder){
	1412	Analysis_Builder_process(analysis->query_builder, analysis, TRUE);
	1413	} else if(analysis->target_builder){
	1414	Analysis_Builder_process(analysis->target_builder, analysis, FALSE);
1115	1415	} else {
1116	1416	while(FastaPipe_process(analysis->fasta_pipe, analysis));
1117	1417	}
	1418	if(analysis->job_queue)
	1419	JobQueue_complete(analysis->job_queue);
1118	1420	GAM_report(analysis->gam);
1119	1421	return;
1120	1422	}

+26

-2

src/hub/analysis.h less more

2	2	* Analysis module for exonerate *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

29	29	#include "seeder.h"
30	30	#include "comparison.h"
31	31	#include "socket.h"
	32	#include "jobqueue.h"
32	33
33	34	typedef struct {
34	35	gboolean use_exhaustive;
35	36	gboolean use_bigseq;
	37	gboolean use_revcomp;
36	38	gchar *force_scan;
37	39	gint saturate_threshold;
38	40	gchar *custom_server_command;
	41	gint thread_count;
39	42	} Analysis_ArgumentSet;
40	43
41	44	Analysis_ArgumentSet Analysis_ArgumentSet_create(Argument arg);

43	46	/**/
44	47
45	48	typedef struct {
46		SocketClient *sc;
47	49	gint verbosity;
	50	gint ref_count;
48	51	Alphabet *server_alphabet;
49	52	gboolean is_masked;
50	53	guint64 num_seqs;
51	54	guint64 max_seq_len;
52	55	guint64 total_seq_len;
53	56	/**/
	57	SocketClient *sc;
54	58	FastaDB *probe_fdb;
55	59	Sequence *curr_query;
56	60	Sequence **seq_cache;
57	61	} Analysis_Client;
58	62
59	63	typedef struct {
	64	gchar *name;
	65	gint priority; /* used for job queues */
	66	struct Analysis_Builder *ab;
	67	} Analysis_Server;
	68
	69	typedef struct Analysis_Builder {
	70	gint verbosity;
	71	FastaDB *probe_fdb;
	72	GPtrArray server_list; / Contains Analysis_Server objects */
	73	Alphabet_Type server_type;
	74	struct Analysis *analysis;
	75	gboolean swap_chains;
	76	} Analysis_Builder;
	77
	78	typedef struct Analysis {
60	79	FastaPipe *fasta_pipe;
61	80	GAM *gam;
62	81	BSAM *bsam;

66	85	gboolean scan_query;
67	86	Comparison_Param *comparison_param;
68	87	gint verbosity;
	88	/*
69	89	Analysis_Client *query_ac;
70	90	Analysis_Client *target_ac;
	91	*/
	92	Analysis_Builder *query_builder;
	93	Analysis_Builder *target_builder;
	94	JobQueue *job_queue;
71	95	} Analysis;
72	96
73	97	Analysis *Analysis_create(

+1

-1

src/hub/analysis.test.c less more

2	2	* Analysis module for exonerate *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/hub/bsam.c less more

2	2	* BSAM: Big Sequence Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/hub/bsam.h less more

2	2	* BSAM: Big Sequence Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/hub/bsam.test.c less more

2	2	* BSAM: Big Sequence Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+66

-38

src/hub/gam.c less more

2	2	* GAM: Gapped Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

161	161
162	162	static void GAM_display_alignment(GAM *gam,
163	163	Alignment alignment, Sequence query, Sequence *target,
164		gint result_id, gint rank, gpointer user_data, FILE *fp);
165
166		#if 0
167		static FILE *GAM_bestn_tmp_file = NULL;
168
169		static void GAM_StoredResult_print(const gchar *string){
170		g_assert(GAM_bestn_tmp_file);
171		fprintf(GAM_bestn_tmp_file, "%s", string);
172		return;
173		}
174		#endif /* 0 */
	164	gint result_id, gint rank,
	165	gpointer user_data, gpointer self_data, FILE *fp);
175	166
176	167	static GAM_StoredResult GAM_StoredResult_create(GAM gam,
177	168	Sequence query, Sequence target,
178		Alignment *alignment, gpointer user_data){
	169	Alignment *alignment,
	170	gpointer user_data, gpointer self_data){
179	171	register GAM_StoredResult *gsr = g_new(GAM_StoredResult, 1);
180		/* register GPrintFunc prev_print_func; */
181	172	gsr->score = alignment->score;
182	173	gsr->pos = ftell(gam->bestn_tmp_file);
183		/*
184		GAM_bestn_tmp_file = gam->bestn_tmp_file;
185		prev_print_func = g_set_print_handler(GAM_StoredResult_print);
186		*/
187	174	GAM_display_alignment(gam, alignment, query, target,
188		0, -1, user_data, gam->bestn_tmp_file);
189		/* g_set_print_handler(prev_print_func); */
	175	0, -1, user_data, self_data, gam->bestn_tmp_file);
190	176	gsr->len = ftell(gam->bestn_tmp_file)
191	177	- gsr->pos;
192	178	return gsr;

267	253	gam_result->query,
268	254	gam_result->target,
269	255	alignment,
270		gam_result->user_data);
	256	gam_result->user_data,
	257	gam_result->self_data);
271	258	PQueue_push(gqr->pq, gsr);
272	259	return;
273	260	}

336	323	/**/
337	324
338	325	static gboolean GAM_QueryResult_report_traverse_func(gpointer data,
339		gpointer user_data){
	326	gpointer user_data){
340	327	register GAM_StoredResult *gsr = data;
341	328	register GPtrArray *result_list = user_data;
342	329	g_ptr_array_add(result_list, gsr);

423	410	register GAM *gam = g_new0(GAM, 1);
424	411	register gint i;
425	412	register C4_Span *span;
426		gam->ref_count = 1;
	413	gam->thread_ref = ThreadRef_create();
427	414	gam->dna_submat = Submat_share(dna_submat);
428	415	gam->protein_submat = Submat_share(protein_submat);
429	416	gam->translate = Translate_share(translate);
430	417	gam->gas = GAM_ArgumentSet_create(NULL);
431	418	if(use_exhaustive && gam->gas->use_subopt)
432	419	g_warning("Exhaustively generating suboptimal alignments"
433		" will be VERY SLOW");
	420	" will be VERY SLOW: use -S no");
434	421	gam->query_type = query_type;
435	422	gam->target_type = target_type;
436	423	if(gam->gas->best_n){

445	432	gam->model = Model_Type_get_model(gam->gas->type,
446	433	query_type, target_type);
447	434	if((!use_exhaustive) && (!C4_Model_is_local(gam->model)))
448		g_error("Cannot perform heuristic alignment using non-local model");
	435	g_error("Cannot perform heuristic alignments using non-local models: use -E");
449	436	gam->match_list = GAM_build_match_list(gam->model);
450	437	if(use_exhaustive){
451	438	gam->optimal = Optimal_create(gam->model, NULL,

479	466	if(gam->max_target_span < span->max_target)
480	467	gam->max_target_span = span->max_target;
481	468	}
	469	#ifdef USE_PTHREADS
	470	pthread_mutex_init(&gam->gam_lock, NULL);
	471	#endif /* USE_PTHREADS */
482	472	return gam;
483	473	}
484	474
485	475	GAM GAM_share(GAM gam){
486	476	g_assert(gam);
487		gam->ref_count++;
	477	ThreadRef_share(gam->thread_ref);
488	478	return gam;
489	479	}
490	480

556	546
557	547	void GAM_destroy(GAM *gam){
558	548	g_assert(gam);
559		if(--gam->ref_count)
	549	if(ThreadRef_destroy(gam->thread_ref))
560	550	return;
	551	#ifdef USE_PTHREADS
	552	pthread_mutex_destroy(&gam->gam_lock);
	553	#endif /* USE_PTHREADS */
561	554	g_assert(gam->model);
562	555	g_ptr_array_free(gam->match_list, TRUE);
563	556	C4_Model_destroy(gam->model);

638	631	gam_result->target = Sequence_share(target);
639	632	gam_result->user_data = Model_Type_create_data(gam->gas->type,
640	633	query, target);
	634	gam_result->self_data = Model_Type_create_data(gam->gas->type,
	635	query, query);
641	636	gam_result->subopt = SubOpt_create(query->len, target->len);
642	637	return gam_result;
643	638	}

1107	1102	/* Keep HSPs marked as keep */
1108	1103	hsp_id = GAM_Result_geneseed_select(comparison->dna_hspset,
1109	1104	gsd.fwd_keep, gsd.rev_keep, hsp_id);
1110		hsp_id = GAM_Result_geneseed_select(comparison->protein_hspset, gsd.fwd_keep, gsd.rev_keep, hsp_id);
	1105	hsp_id = GAM_Result_geneseed_select(comparison->protein_hspset,
	1106	gsd.fwd_keep, gsd.rev_keep, hsp_id);
1111	1107	hsp_id = GAM_Result_geneseed_select(comparison->codon_hspset,
1112	1108	gsd.fwd_keep, gsd.rev_keep, hsp_id);
1113	1109	/**/

1151	1147	/* Raise score threshold to geneseed
1152	1148	* to prevent low-scoring subopt alignments.
1153	1149	*/
	1150	GAM_lock(gam);
1154	1151	if(gam->gas->threshold < has->geneseed_threshold)
1155	1152	gam->gas->threshold = has->geneseed_threshold;
	1153	GAM_unlock(gam);
1156	1154	GAM_Result_geneseed_filter(gam, comparison);
1157	1155	}
1158	1156	if(!Comparison_has_hsps(comparison))

1178	1176	Sequence *target){
1179	1177	register Alignment *alignment;
1180	1178	register C4_Score threshold;
1181		register GAM_Result *gam_result = GAM_Result_create(gam,
1182		query, target);
	1179	register GAM_Result *gam_result;
1183	1180	register OPair *opair;
1184	1181	g_assert(gam->optimal);
	1182	GAM_lock(gam);
	1183	Sequence_lock(query);
	1184	Sequence_lock(target);
	1185	gam_result = GAM_Result_create(gam, query, target);
	1186	Sequence_unlock(query);
	1187	Sequence_unlock(target);
1185	1188	opair = OPair_create(gam->optimal, gam_result->subopt,
1186	1189	query->len, target->len, gam_result->user_data);
	1190	GAM_unlock(gam);
1187	1191	if(gam->verbosity > 1)
1188	1192	g_message("Exhaustive alignment of [%s] [%s]",
1189		query->id, target->id);
	1193	query->id, target->id);
1190	1194	/**/
1191	1195	do {
	1196	GAM_lock(gam);
1192	1197	threshold = GAM_get_query_threshold(gam, query);
	1198	GAM_unlock(gam);
1193	1199	alignment = OPair_next_path(opair, threshold);
1194	1200	if(!alignment)
1195	1201	break;

1223	1229	}
1224	1230	Model_Type_destroy_data(gam_result->gam->gas->type,
1225	1231	gam_result->user_data);
	1232	Model_Type_destroy_data(gam_result->gam->gas->type,
	1233	gam_result->self_data);
1226	1234	Sequence_destroy(gam_result->query);
1227	1235	Sequence_destroy(gam_result->target);
	1236	GAM_lock(gam_result->gam);
1228	1237	GAM_destroy(gam_result->gam);
1229	1238	SubOpt_destroy(gam_result->subopt);
	1239	GAM_unlock(gam_result->gam);
1230	1240	g_free(gam_result);
1231	1241	return;
1232	1242	}
1233	1243
1234	1244	static void GAM_display_alignment(GAM gam, Alignment alignment,
1235	1245	Sequence query, Sequence target,
1236		gint result_id, gint rank, gpointer user_data, FILE *fp){
	1246	gint result_id, gint rank,
	1247	gpointer user_data, gpointer self_data, FILE *fp){
1237	1248	if(gam->gas->show_alignment)
1238	1249	Alignment_display(alignment, query, target,
1239	1250	gam->dna_submat, gam->protein_submat,

1245	1256	if(gam->gas->show_vulgar)
1246	1257	Alignment_display_vulgar(alignment, query, target, fp);
1247	1258	if(gam->gas->show_query_gff)
1248		Alignment_display_gff(alignment, query, target,
1249		TRUE, FALSE, result_id, fp);
	1259	Alignment_display_gff(alignment, query, target, gam->translate,
	1260	TRUE, FALSE, result_id, user_data, fp);
1250	1261	if(gam->gas->show_target_gff)
1251		Alignment_display_gff(alignment, query, target, FALSE,
1252		Model_Type_has_genomic_target(gam->gas->type), result_id, fp);
	1262	Alignment_display_gff(alignment, query, target, gam->translate,
	1263	FALSE, Model_Type_has_genomic_target(gam->gas->type),
	1264	result_id, user_data, fp);
1253	1265	if(gam->gas->ryo)
1254	1266	Alignment_display_ryo(alignment, query, target,
1255	1267	gam->gas->ryo, gam->translate, rank,
1256		user_data, fp);
	1268	user_data, self_data, fp);
1257	1269	fflush(fp);
1258	1270	return;
1259	1271	}

1266	1278	alignment = gam_result->alignment_list->pdata[i];
1267	1279	GAM_display_alignment(gam_result->gam, alignment,
1268	1280	gam_result->query, gam_result->target,
1269		i+1, 0, gam_result->user_data, stdout);
	1281	i+1, 0, gam_result->user_data, gam_result->self_data, stdout);
1270	1282	}
1271	1283	return;
1272	1284	}

1274	1286	void GAM_Result_submit(GAM_Result *gam_result){
1275	1287	register GAM_QueryResult *gqr;
1276	1288	g_assert(gam_result);
	1289	GAM_lock(gam_result->gam);
1277	1290	if(gam_result->gam->gas->best_n){
1278	1291	gqr = g_tree_lookup(gam_result->gam->bestn_tree,
1279	1292	gam_result->query->id);

1289	1302	} else {
1290	1303	GAM_Result_display(gam_result);
1291	1304	}
	1305	GAM_unlock(gam_result->gam);
	1306	return;
	1307	}
	1308
	1309	void GAM_lock(GAM *gam){
	1310	#ifdef USE_PTHREADS
	1311	pthread_mutex_lock(&gam->gam_lock);
	1312	#endif /* USE_PTHREADS */
	1313	return;
	1314	}
	1315
	1316	void GAM_unlock(GAM *gam){
	1317	#ifdef USE_PTHREADS
	1318	pthread_mutex_unlock(&gam->gam_lock);
	1319	#endif /* USE_PTHREADS */
1292	1320	return;
1293	1321	}
1294	1322

+14

-2

src/hub/gam.h less more

2	2	* GAM: Gapped Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

21	21
22	22	#include <glib.h>
23	23
	24	#ifdef USE_PTHREADS
	25	#include <pthread.h>
	26	#endif /* USE_PTHREADS */
	27
24	28	#include "sequence.h"
25	29	#include "c4.h"
26	30	#include "heuristic.h"

35	39	#include "comparison.h"
36	40	#include "sdp.h"
37	41	#include "subopt.h"
	42	#include "threadref.h"
38	43
39	44	typedef enum {
40	45	GAM_Refinement_NONE,

83	88	} GAM_QueryInfo;
84	89
85	90	typedef struct {
86		gint ref_count;
	91	ThreadRef *thread_ref;
87	92	Alphabet_Type query_type;
88	93	Alphabet_Type target_type;
89	94	C4_Model *model;

105	110	PQueueSet *pqueue_set;
106	111	gint max_query_span;
107	112	gint max_target_span;
	113	#ifdef USE_PTHREADS
	114	pthread_mutex_t gam_lock;
	115	#endif /* USE_PTHREADS */
108	116	} GAM;
109	117
110	118	GAM *GAM_create(Alphabet_Type query_type, Alphabet_Type target_type,

122	130	Sequence *target;
123	131	GPtrArray *alignment_list;
124	132	gpointer user_data;
	133	gpointer self_data;
125	134	SubOpt *subopt;
126	135	} GAM_Result;
127	136

141	150	void GAM_Result_destroy(GAM_Result *gam_result);
142	151	void GAM_Result_submit(GAM_Result *gam_result);
143	152
	153	void GAM_lock(GAM *gam);
	154	void GAM_unlock(GAM *gam);
	155
144	156	#ifdef __cplusplus
145	157	}
146	158	#endif /* __cplusplus */

+1

-1

src/hub/gam.test.c less more

2	2	* GAM: Gapped Alignment Manager *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-0

src/model/Makefile.am less more

25	25	$(top_srcdir)/src/sequence/translate.o \
26	26	$(top_srcdir)/src/general/argument.o \
27	27	$(top_srcdir)/src/general/lineparse.o \
	28	$(top_srcdir)/src/general/threadref.o \
28	29	-lm
29	30
30	31	ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o \

+34

-17

src/model/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

85	86	INCLUDES = -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/general -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DGLIB_CFLAGS="\"@glib_cflags@\""
86	87
87	88
88		SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
	89	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/threadref.o -lm
89	90
90	91
91	92	ALIGNMENT_OBJ = $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/sequence/submat.o $(SEQUENCE_OBJ)

186	187	$(top_srcdir)/src/sequence/splice.o \
187	188	$(top_srcdir)/src/sequence/translate.o \
188	189	$(top_srcdir)/src/general/argument.o \
189		$(top_srcdir)/src/general/lineparse.o
	190	$(top_srcdir)/src/general/lineparse.o \
	191	$(top_srcdir)/src/general/threadref.o
190	192	edit_distance_test_LDFLAGS =
191	193	affine_test_OBJECTS = affine.test.o affine.o ungapped.o
192	194	affine_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

205	207	$(top_srcdir)/src/sequence/splice.o \
206	208	$(top_srcdir)/src/sequence/translate.o \
207	209	$(top_srcdir)/src/general/argument.o \
208		$(top_srcdir)/src/general/lineparse.o
	210	$(top_srcdir)/src/general/lineparse.o \
	211	$(top_srcdir)/src/general/threadref.o
209	212	affine_test_LDFLAGS =
210	213	protein2dna_test_OBJECTS = protein2dna.test.o protein2dna.o affine.o \
211	214	ungapped.o frameshift.o

225	228	$(top_srcdir)/src/sequence/splice.o \
226	229	$(top_srcdir)/src/sequence/translate.o \
227	230	$(top_srcdir)/src/general/argument.o \
228		$(top_srcdir)/src/general/lineparse.o
	231	$(top_srcdir)/src/general/lineparse.o \
	232	$(top_srcdir)/src/general/threadref.o
229	233	protein2dna_test_LDFLAGS =
230	234	ner_test_OBJECTS = ner.test.o ner.o affine.o ungapped.o
231	235	ner_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

244	248	$(top_srcdir)/src/sequence/splice.o \
245	249	$(top_srcdir)/src/sequence/translate.o \
246	250	$(top_srcdir)/src/general/argument.o \
247		$(top_srcdir)/src/general/lineparse.o
	251	$(top_srcdir)/src/general/lineparse.o \
	252	$(top_srcdir)/src/general/threadref.o
248	253	ner_test_LDFLAGS =
249	254	est2genome_test_OBJECTS = est2genome.test.o est2genome.o affine.o \
250	255	ungapped.o intron.o

264	269	$(top_srcdir)/src/sequence/splice.o \
265	270	$(top_srcdir)/src/sequence/translate.o \
266	271	$(top_srcdir)/src/general/argument.o \
267		$(top_srcdir)/src/general/lineparse.o
	272	$(top_srcdir)/src/general/lineparse.o \
	273	$(top_srcdir)/src/general/threadref.o
268	274	est2genome_test_LDFLAGS =
269	275	ungapped_test_OBJECTS = ungapped.test.o ungapped.o
270	276	ungapped_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

283	289	$(top_srcdir)/src/sequence/splice.o \
284	290	$(top_srcdir)/src/sequence/translate.o \
285	291	$(top_srcdir)/src/general/argument.o \
286		$(top_srcdir)/src/general/lineparse.o
	292	$(top_srcdir)/src/general/lineparse.o \
	293	$(top_srcdir)/src/general/threadref.o
287	294	ungapped_test_LDFLAGS =
288	295	intron_test_OBJECTS = intron.test.o intron.o
289	296	intron_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

302	309	$(top_srcdir)/src/sequence/splice.o \
303	310	$(top_srcdir)/src/sequence/translate.o \
304	311	$(top_srcdir)/src/general/argument.o \
305		$(top_srcdir)/src/general/lineparse.o
	312	$(top_srcdir)/src/general/lineparse.o \
	313	$(top_srcdir)/src/general/threadref.o
306	314	intron_test_LDFLAGS =
307	315	protein2genome_test_OBJECTS = protein2genome.test.o protein2genome.o \
308	316	protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o

322	330	$(top_srcdir)/src/sequence/splice.o \
323	331	$(top_srcdir)/src/sequence/translate.o \
324	332	$(top_srcdir)/src/general/argument.o \
325		$(top_srcdir)/src/general/lineparse.o
	333	$(top_srcdir)/src/general/lineparse.o \
	334	$(top_srcdir)/src/general/threadref.o
326	335	protein2genome_test_LDFLAGS =
327	336	coding2coding_test_OBJECTS = coding2coding.test.o coding2coding.o \
328	337	affine.o ungapped.o frameshift.o

342	351	$(top_srcdir)/src/sequence/splice.o \
343	352	$(top_srcdir)/src/sequence/translate.o \
344	353	$(top_srcdir)/src/general/argument.o \
345		$(top_srcdir)/src/general/lineparse.o
	354	$(top_srcdir)/src/general/lineparse.o \
	355	$(top_srcdir)/src/general/threadref.o
346	356	coding2coding_test_LDFLAGS =
347	357	frameshift_test_OBJECTS = frameshift.test.o frameshift.o
348	358	frameshift_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

361	371	$(top_srcdir)/src/sequence/splice.o \
362	372	$(top_srcdir)/src/sequence/translate.o \
363	373	$(top_srcdir)/src/general/argument.o \
364		$(top_srcdir)/src/general/lineparse.o
	374	$(top_srcdir)/src/general/lineparse.o \
	375	$(top_srcdir)/src/general/threadref.o
365	376	frameshift_test_LDFLAGS =
366	377	coding2genome_test_OBJECTS = coding2genome.test.o coding2genome.o \
367	378	coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o

381	392	$(top_srcdir)/src/sequence/splice.o \
382	393	$(top_srcdir)/src/sequence/translate.o \
383	394	$(top_srcdir)/src/general/argument.o \
384		$(top_srcdir)/src/general/lineparse.o
	395	$(top_srcdir)/src/general/lineparse.o \
	396	$(top_srcdir)/src/general/threadref.o
385	397	coding2genome_test_LDFLAGS =
386	398	cdna2genome_test_OBJECTS = cdna2genome.test.o cdna2genome.o affine.o \
387	399	ungapped.o frameshift.o intron.o phase.o coding2coding.o \

402	414	$(top_srcdir)/src/sequence/splice.o \
403	415	$(top_srcdir)/src/sequence/translate.o \
404	416	$(top_srcdir)/src/general/argument.o \
405		$(top_srcdir)/src/general/lineparse.o
	417	$(top_srcdir)/src/general/lineparse.o \
	418	$(top_srcdir)/src/general/threadref.o
406	419	cdna2genome_test_LDFLAGS =
407	420	genome2genome_test_OBJECTS = genome2genome.test.o genome2genome.o \
408	421	coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o \

423	436	$(top_srcdir)/src/sequence/splice.o \
424	437	$(top_srcdir)/src/sequence/translate.o \
425	438	$(top_srcdir)/src/general/argument.o \
426		$(top_srcdir)/src/general/lineparse.o
	439	$(top_srcdir)/src/general/lineparse.o \
	440	$(top_srcdir)/src/general/threadref.o
427	441	genome2genome_test_LDFLAGS =
428	442	phase_test_OBJECTS = phase.test.o phase.o intron.o
429	443	phase_test_DEPENDENCIES = $(top_srcdir)/src/struct/slist.o \

442	456	$(top_srcdir)/src/sequence/splice.o \
443	457	$(top_srcdir)/src/sequence/translate.o \
444	458	$(top_srcdir)/src/general/argument.o \
445		$(top_srcdir)/src/general/lineparse.o
	459	$(top_srcdir)/src/general/lineparse.o \
	460	$(top_srcdir)/src/general/threadref.o
446	461	phase_test_LDFLAGS =
447	462	modeltype_test_OBJECTS = modeltype.test.o modeltype.o ungapped.o \
448	463	affine.o est2genome.o ner.o protein2dna.o protein2genome.o \

464	479	$(top_srcdir)/src/sequence/splice.o \
465	480	$(top_srcdir)/src/sequence/translate.o \
466	481	$(top_srcdir)/src/general/argument.o \
467		$(top_srcdir)/src/general/lineparse.o
	482	$(top_srcdir)/src/general/lineparse.o \
	483	$(top_srcdir)/src/general/threadref.o
468	484	modeltype_test_LDFLAGS =
469	485	bootstrapper_OBJECTS = bootstrapper.o modeltype.o ungapped.o affine.o \
470	486	est2genome.o ner.o protein2dna.o protein2genome.o coding2coding.o \

492	508	$(top_srcdir)/src/sequence/splice.o \
493	509	$(top_srcdir)/src/sequence/translate.o \
494	510	$(top_srcdir)/src/general/argument.o \
495		$(top_srcdir)/src/general/lineparse.o
	511	$(top_srcdir)/src/general/lineparse.o \
	512	$(top_srcdir)/src/general/threadref.o
496	513	bootstrapper_LDFLAGS =
497	514	CFLAGS = @CFLAGS@
498	515	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)

+1

-1

src/model/affine.c less more

2	2	* Module for various affine gapped models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/affine.h less more

2	2	* Module for various affine gapped models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/affine.test.c less more

2	2	* Module for various affine gapped models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/bootstrapper.c less more

2	2	* bootstrapper: required prior to static model linking *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/cdna2genome.c less more

2	2	* cDNA <-> genomic alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/cdna2genome.h less more

2	2	* cDNA <-> genomic alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+2

-2

src/model/cdna2genome.test.c less more

2	2	* cDNA <-> genomic alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

31	31	query->len, target->len);
32	32	score = Optimal_find_score(optimal, region, cd2gd, NULL);
33	33	g_message("Score is [%d]", score);
34		g_assert(score == 1290);
	34	g_assert(score == 1281);
35	35	alignment = Optimal_find_path(optimal, region, cd2gd,
36	36	C4_IMPOSSIBLY_LOW_SCORE, NULL);
37	37	g_message("Alignment score is [%d]", alignment->score);

+1

-1

src/model/coding2coding.c less more

2	2	* Coding DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/coding2coding.h less more

2	2	* Coding DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/coding2coding.test.c less more

2	2	* Coding DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/coding2genome.c less more

2	2	* Coding <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/coding2genome.h less more

2	2	* Coding <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/coding2genome.test.c less more

2	2	* Coding <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/edit_distance.c less more

2	2	* edit distance model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/edit_distance.h less more

2	2	* edit distance model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/edit_distance.test.c less more

2	2	* edit distance model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/est2genome.c less more

2	2	* Module for EST <-> genome alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/est2genome.h less more

2	2	* Module for EST <-> genome alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+2

-2

src/model/est2genome.test.c less more

2	2	* Module for EST <-> genome alignments *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

59	59	e2gd = EST2Genome_Data_create(query, target);
60	60	score = Optimal_find_score(optimal, region, e2gd, NULL);
61	61	g_message("Score is [%d]", score);
62		g_assert(score == 159);
	62	g_assert(score == 157);
63	63	/**/
64	64	alignment = Optimal_find_path(optimal, region, e2gd,
65	65	C4_IMPOSSIBLY_LOW_SCORE, NULL);

+1

-1

src/model/frameshift.c less more

2	2	* Module for frameshift modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/frameshift.h less more

2	2	* Module for frameshift modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/frameshift.test.c less more

2	2	* Module for frameshift modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/genome2genome.c less more

2	2	* Genome <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/genome2genome.h less more

2	2	* Genome <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/genome2genome.test.c less more

2	2	* Genome <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/intron.c less more

2	2	* Module of splice site and intron modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/intron.h less more

2	2	* Module of splice site and intron modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/intron.test.c less more

2	2	* Module for splice site and intron modelling *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/modeltype.c less more

2	2	* Interface for different types of alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/modeltype.h less more

2	2	* Interface for different types of alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/modeltype.test.c less more

2	2	* Interface for different types of alignment model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/ner.c less more

2	2	* Model for alignments with non-equivalenced regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/ner.h less more

2	2	* Model for alignments with non-equivalenced regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/ner.test.c less more

2	2	* Model for alignments with non-equivalenced regions *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/phase.c less more

2	2	* Model for phased introns. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/phase.h less more

2	2	* Model for phased introns. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/phase.test.c less more

2	2	* Model for phased introns. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/protein2dna.c less more

2	2	* Protein <-> DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/protein2dna.h less more

2	2	* Protein <-> DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/protein2dna.test.c less more

2	2	* Protein <-> DNA comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/protein2genome.c less more

2	2	* Protein <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/protein2genome.h less more

2	2	* Protein <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-3

src/model/protein2genome.test.c less more

2	2	* Protein <-> Genome comparison model *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

29	29	register Region *region = Region_create(0, 0,
30	30	query->len, target->len);
31	31	score = Optimal_find_score(optimal, region, p2gd, NULL);
32		g_message("Score is [%d] (expect 131)", score);
33		g_assert(score == 129);
	32	g_message("Score is [%d] (expect 125)", score);
	33	g_assert(score == 125);
34	34	alignment = Optimal_find_path(optimal, region, p2gd,
35	35	C4_IMPOSSIBLY_LOW_SCORE, NULL);
36	36	g_message("Alignment score is [%d]", alignment->score);

+1

-1

src/model/ungapped.c less more

2	2	* Module for various ungapped alignment models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/ungapped.h less more

2	2	* Module for various ungapped alignment models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/model/ungapped.test.c less more

2	2	* Module for various ungapped alignment models *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+5

-1

src/program/Makefile.am less more

11	11	-I$(top_srcdir)/src/hub \
12	12	-I$(top_srcdir)/src/general \
13	13	-DHOSTTYPE="\"@host@\"" \
14		-DSOURCE_ROOT_DIR="\"@source_root_dir@\""
	14	-DSOURCE_ROOT_DIR="\"@source_root_dir@\"" \
	15	-DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
15	16
16	17	# Missing viterb.o and scheduler.o so codegen versions may be substituted
17	18	C4_OBJECTS = $(top_srcdir)/src/c4/c4.o \

57	58	$(top_srcdir)/src/general/argument.o \
58	59	$(top_srcdir)/src/general/lineparse.o \
59	60	$(top_srcdir)/src/general/socket.o \
	61	$(top_srcdir)/src/general/jobqueue.o \
60	62	$(top_srcdir)/src/comparison/match.o \
61	63	$(top_srcdir)/src/sequence/submat.o \
62	64	$(top_srcdir)/src/sequence/codonsubmat.o

95	97	$(top_srcdir)/src/hub/bsam.o \
96	98	$(top_srcdir)/src/hub/analysis.o \
97	99	$(top_srcdir)/src/general/compoundfile.o \
	100	$(top_srcdir)/src/general/threadref.o \
98	101	$(C4_OBJECTS)
99	102
100	103	exonerate_SOURCES = exonerate.c

156	159	$(top_srcdir)/src/sequence/codonsubmat.o \
157	160	$(top_srcdir)/src/general/compoundfile.o \
158	161	$(top_srcdir)/src/general/lineparse.o \
	162	$(top_srcdir)/src/general/threadref.o \
159	163	-lm
160	164
161	165	CLEANFILES = $(EXTRA_exonerate_SOURCES) @codegen_extra_sources@ \

+7

-5

src/program/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

79	80
80	81	bin_PROGRAMS = exonerate ipcress exonerate-server
81	82
82		INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/database -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/model -I$(top_srcdir)/src/hub -I$(top_srcdir)/src/general -DHOSTTYPE="\"@host@\"" -DSOURCE_ROOT_DIR="\"@source_root_dir@\""
	83	INCLUDES = -I$(top_srcdir)/src/sequence -I$(top_srcdir)/src/database -I$(top_srcdir)/src/comparison -I$(top_srcdir)/src/struct -I$(top_srcdir)/src/c4 -I$(top_srcdir)/src/bsdp -I$(top_srcdir)/src/sdp -I$(top_srcdir)/src/model -I$(top_srcdir)/src/hub -I$(top_srcdir)/src/general -DHOSTTYPE="\"@host@\"" -DSOURCE_ROOT_DIR="\"@source_root_dir@\"" -DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
83	84
84	85
85	86	# Missing viterb.o and scheduler.o so codegen versions may be substituted
86		C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o
	87	C4_OBJECTS = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/cgutil.o $(top_srcdir)/src/c4/opair.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/bsdp/bsdp.o $(top_srcdir)/src/bsdp/sar.o $(top_srcdir)/src/bsdp/heuristic.o $(top_srcdir)/src/bsdp/hpair.o $(top_srcdir)/src/sdp/boundary.o $(top_srcdir)/src/sdp/sdp.o $(top_srcdir)/src/sdp/lookahead.o $(top_srcdir)/src/sdp/straceback.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/slist.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/model/affine.o $(top_srcdir)/src/model/est2genome.o $(top_srcdir)/src/model/ner.o $(top_srcdir)/src/model/protein2dna.o $(top_srcdir)/src/model/protein2genome.o $(top_srcdir)/src/model/coding2coding.o $(top_srcdir)/src/model/coding2genome.o $(top_srcdir)/src/model/cdna2genome.o $(top_srcdir)/src/model/genome2genome.o $(top_srcdir)/src/model/ungapped.o $(top_srcdir)/src/model/intron.o $(top_srcdir)/src/model/frameshift.o $(top_srcdir)/src/model/phase.o $(top_srcdir)/src/model/modeltype.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/general/jobqueue.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o
87	88
88	89
89	90	EXTRA_exonerate_SOURCES = c4_model_archive.a c4_model_archive.h

91	92	BUILT_SOURCES = c4_model_archive.a
92	93	BOOTSTRAPPER = $(top_srcdir)/src/model/bootstrapper
93	94
94		exonerate_COMPONENTS = @codegen_extra_ldadd@ $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/hub/gam.o $(top_srcdir)/src/hub/bsam.o $(top_srcdir)/src/hub/analysis.o $(top_srcdir)/src/general/compoundfile.o $(C4_OBJECTS)
	95	exonerate_COMPONENTS = @codegen_extra_ldadd@ $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/seeder.o $(top_srcdir)/src/comparison/comparison.o $(top_srcdir)/src/database/fastapipe.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/dejavu.o $(top_srcdir)/src/struct/fsm.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/hub/gam.o $(top_srcdir)/src/hub/bsam.o $(top_srcdir)/src/hub/analysis.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/threadref.o $(C4_OBJECTS)
95	96
96	97
97	98	exonerate_SOURCES = exonerate.c

105	106	# Files to clear away
106	107
107	108	exonerate_server_SOURCES = exonerate-server.c
108		exonerate_server_LDADD = $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/lineparse.o -lm
	109	exonerate_server_LDADD = $(top_srcdir)/src/general/socket.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/database/fastadb.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/general/compoundfile.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/threadref.o -lm
109	110
110	111
111	112	CLEANFILES = $(EXTRA_exonerate_SOURCES) @codegen_extra_sources@ @codegen_extra_ld_add@

159	160	$(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/submat.o \
160	161	$(top_srcdir)/src/sequence/codonsubmat.o \
161	162	$(top_srcdir)/src/general/compoundfile.o \
162		$(top_srcdir)/src/general/lineparse.o
	163	$(top_srcdir)/src/general/lineparse.o \
	164	$(top_srcdir)/src/general/threadref.o
163	165	exonerate_server_LDFLAGS =
164	166	CFLAGS = @CFLAGS@
165	167	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)

+73

-4

src/program/exonerate-server.c less more

2	2	* The exonerate server *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

65	65	if(preload)
66	66	Dataset_preload_seqs(exonerate_server->dataset);
67	67	exonerate_server->verbosity = verbosity;
	68	if(verbosity >= 1){
	69	Dataset_info(exonerate_server->dataset);
	70	Index_info(exonerate_server->index);
	71	}
68	72	return exonerate_server;
69	73	}
70	74

92	96	gint dna_hsp_threshold;
93	97	gint protein_hsp_threshold;
94	98	gint codon_hsp_threshold;
	99	gint dna_word_limit;
	100	gint protein_word_limit;
	101	gint codon_word_limit;
95	102	gint dna_hsp_dropoff;
96	103	gint protein_hsp_dropoff;
97	104	gint codon_hsp_dropoff;

117	124	connection->dna_hsp_threshold = has->dna_hsp_threshold;
118	125	connection->protein_hsp_threshold = has->protein_hsp_threshold;
119	126	connection->codon_hsp_threshold = has->codon_hsp_threshold;
	127	connection->dna_word_limit = has->dna_word_limit;
	128	connection->protein_word_limit = has->protein_word_limit;
	129	connection->codon_word_limit = has->codon_word_limit;
120	130	connection->dna_hsp_dropoff = has->dna_hsp_dropoff;
121	131	connection->protein_hsp_dropoff = has->protein_hsp_dropoff;
122	132	connection->codon_hsp_dropoff = has->codon_hsp_dropoff;

142	152	/**/
143	153
144	154	static gpointer Exonerate_Server_Connection_open(gpointer user_data){
145		g_message("[%s]", __FUNCTION__);
146	155	return Exonerate_Server_Connection_create();
147	156	}
148	157

150	159	gpointer user_data){
151	160	register Exonerate_Server_Connection *server_connection
152	161	= connection_data;
153		g_message("[%s]", __FUNCTION__);
154	162	Exonerate_Server_Connection_destroy(server_connection);
155	163	return;
156	164	}

220	228	"\n"
221	229	" valid parameters:\n"
222	230	" seedrepeat\n"
	231	"\n"
223	232	" dnahspthreshold\n"
224	233	" proteinhspthreshold\n"
225	234	" codonhspthreshold\n"
	235	"\n"
	236	" dnawordlimit\n"
	237	" proteinwordlimit\n"
	238	" codonwordlimit\n"
226	239	"\n"
227	240	" geneseedthreshold\n"
228	241	" geneseedrepeat\n"

391	404	HSP_Param_set_codon_hsp_threshold(connection->hsp_param,
392	405	connection->codon_hsp_threshold);
393	406	/**/
	407	HSP_Param_set_dna_word_limit(connection->hsp_param,
	408	connection->dna_word_limit);
	409	HSP_Param_set_protein_word_limit(connection->hsp_param,
	410	connection->protein_word_limit);
	411	HSP_Param_set_codon_word_limit(connection->hsp_param,
	412	connection->codon_word_limit);
	413	/**/
394	414	HSP_Param_set_dna_hsp_dropoff(connection->hsp_param,
395	415	connection->dna_hsp_dropoff);
396	416	HSP_Param_set_protein_hsp_dropoff(connection->hsp_param,

452	472	if(connection->hsp_param)
453	473	HSP_Param_set_codon_hsp_threshold(connection->hsp_param,
454	474	codonhspthreshold);
	475	return g_strdup_printf("ok: set\n");
	476	}
	477
	478	/**/
	479
	480	static gchar *Exonerate_Server_set_param_dnawordlimit(
	481	Exonerate_Server_Connection connection, GPtrArray word_list){
	482	register gint dnawordlimit = atoi(word_list->pdata[3]);
	483	if(dnawordlimit < 0)
	484	return g_strdup_printf("error: dnawordlimit must be >= 0\n");
	485	connection->dna_word_limit = dnawordlimit;
	486	if(connection->hsp_param)
	487	HSP_Param_set_dna_word_limit(connection->hsp_param, dnawordlimit);
	488	return g_strdup_printf("ok: set\n");
	489	}
	490
	491	static gchar *Exonerate_Server_set_param_proteinwordlimit(
	492	Exonerate_Server_Connection connection, GPtrArray word_list){
	493	register gint proteinwordlimit = atoi(word_list->pdata[3]);
	494	if(proteinwordlimit < 0)
	495	return g_strdup_printf("error: proteinwordlimit must be >= 0\n");
	496	connection->protein_word_limit = proteinwordlimit;
	497	if(connection->hsp_param)
	498	HSP_Param_set_protein_word_limit(connection->hsp_param,
	499	proteinwordlimit);
	500	return g_strdup_printf("ok: set\n");
	501	}
	502
	503	static gchar *Exonerate_Server_set_param_codonwordlimit(
	504	Exonerate_Server_Connection connection, GPtrArray word_list){
	505	register gint codonwordlimit = atoi(word_list->pdata[3]);
	506	if(codonwordlimit < 0)
	507	return g_strdup_printf("error: codonwordlimit must be >= 0\n");
	508	connection->codon_word_limit = codonwordlimit;
	509	if(connection->hsp_param)
	510	HSP_Param_set_codon_word_limit(connection->hsp_param,
	511	codonwordlimit);
455	512	return g_strdup_printf("ok: set\n");
456	513	}
457	514

544	601	} else if(!strcmp(name, "codonhspthreshold")){
545	602	reply = Exonerate_Server_set_param_codonhspthreshold(connection,
546	603	word_list);
	604	} else if(!strcmp(name, "dnawordlimit")){
	605	reply = Exonerate_Server_set_param_dnawordlimit(connection,
	606	word_list);
	607	} else if(!strcmp(name, "proteinwordlimit")){
	608	reply = Exonerate_Server_set_param_proteinwordlimit(connection,
	609	word_list);
	610	} else if(!strcmp(name, "codonwordlimit")){
	611	reply = Exonerate_Server_set_param_codonwordlimit(connection,
	612	word_list);
547	613	} else if(!strcmp(name, "dnahspdropoff")){
548	614	reply = Exonerate_Server_set_param_dnahspdropoff(connection, word_list);
549	615	} else if(!strcmp(name, "proteinhspdropoff")){

599	665	(*reply) = NULL;
600	666	keep_connection = FALSE;
601	667	} else if(!strcmp(word, "dbinfo")){
602		(*reply) = g_strdup_printf("dbinfo: %s %s %lld %lld %lld\n",
	668	(*reply) = g_strdup_printf("dbinfo: %s %s"
	669	" %" CUSTOM_GUINT64_FORMAT
	670	" %" CUSTOM_GUINT64_FORMAT
	671	" %" CUSTOM_GUINT64_FORMAT "\n",
603	672	(server->dataset->header->type & 1)?"dna":"protein",
604	673	(server->dataset->header->type & (1<<1))
605	674	?"softmasked":"unmasked",

+5

-3

src/program/exonerate.c less more

2	2	* exonerate : a generic sequence comparison tool *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

76	76	Argument_parse_int, &verbosity);
77	77	/**/
78	78	Argument_absorb_ArgumentSet(arg, as_input);
	79	Translate_ArgumentSet_create(arg);
79	80	Analysis_ArgumentSet_create(arg);
80	81	FastaDB_ArgumentSet_create(arg);
81	82	GAM_ArgumentSet_create(arg);

93	94	Intron_ArgumentSet_create(arg);
94	95	Frameshift_ArgumentSet_create(arg);
95	96	Alphabet_ArgumentSet_create(arg);
96		Translate_ArgumentSet_create(arg);
97	97	HSPset_ArgumentSet_create(arg);
98	98	Alignment_ArgumentSet_create(arg);
99	99	SAR_ArgumentSet_create(arg);

101	101	/**/
102	102	Argument_process(arg, "exonerate",
103	103	"A generic sequence comparison tool\n"
104		"Guy St.C. Slater. guy@ebi.ac.uk. 2000-2008.\n",
	104	"Guy St.C. Slater. guy@ebi.ac.uk. 2000-2009.\n",
105	105	"\n"
106	106	"Examples of use:\n"
107	107	"\n"

135	135	return 0;
136	136	}
137	137
	138	/**/
	139

+1

-1

src/program/ipcress.c less more

2	2	* ipcress : in-silico PCR experiment simulation system *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-0

src/sdp/Makefile.am less more

22	22	$(top_srcdir)/src/sequence/translate.o \
23	23	$(top_srcdir)/src/general/argument.o \
24	24	$(top_srcdir)/src/general/lineparse.o \
	25	$(top_srcdir)/src/general/threadref.o \
25	26	-lm
26	27
27	28	C4_OBJ = $(top_srcdir)/src/c4/c4.o \

+8

-4

src/sdp/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

87	88
88	89	noinst_HEADERS = scheduler.h sdp.h lookahead.h boundary.h straceback.h
89	90
90		SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o -lm
	91	SEQUENCE_OBJ = $(top_srcdir)/src/struct/sparsecache.o $(top_srcdir)/src/struct/matrix.o $(top_srcdir)/src/sequence/sequence.o $(top_srcdir)/src/sequence/alphabet.o $(top_srcdir)/src/sequence/splice.o $(top_srcdir)/src/sequence/translate.o $(top_srcdir)/src/general/argument.o $(top_srcdir)/src/general/lineparse.o $(top_srcdir)/src/general/threadref.o -lm
91	92
92	93
93	94	C4_OBJ = $(top_srcdir)/src/c4/c4.o $(top_srcdir)/src/c4/alignment.o $(top_srcdir)/src/c4/optimal.o $(top_srcdir)/src/c4/codegen.o $(top_srcdir)/src/c4/region.o $(top_srcdir)/src/c4/layout.o $(top_srcdir)/src/c4/viterbi.o $(top_srcdir)/src/c4/subopt.o $(top_srcdir)/src/c4/cgutil.o

149	150	$(top_srcdir)/src/sequence/splice.o \
150	151	$(top_srcdir)/src/sequence/translate.o \
151	152	$(top_srcdir)/src/general/argument.o \
152		$(top_srcdir)/src/general/lineparse.o
	153	$(top_srcdir)/src/general/lineparse.o \
	154	$(top_srcdir)/src/general/threadref.o
153	155	sdp_test_LDFLAGS =
154	156	lookahead_test_OBJECTS = lookahead.test.o lookahead.o
155	157	lookahead_test_LDADD = $(LDADD)

176	178	$(top_srcdir)/src/sequence/splice.o \
177	179	$(top_srcdir)/src/sequence/translate.o \
178	180	$(top_srcdir)/src/general/argument.o \
179		$(top_srcdir)/src/general/lineparse.o
	181	$(top_srcdir)/src/general/lineparse.o \
	182	$(top_srcdir)/src/general/threadref.o
180	183	scheduler_test_LDFLAGS =
181	184	straceback_test_OBJECTS = straceback.test.o straceback.o
182	185	straceback_test_DEPENDENCIES = $(top_srcdir)/src/struct/recyclebin.o \

191	194	$(top_srcdir)/src/sequence/splice.o \
192	195	$(top_srcdir)/src/sequence/translate.o \
193	196	$(top_srcdir)/src/general/argument.o \
194		$(top_srcdir)/src/general/lineparse.o
	197	$(top_srcdir)/src/general/lineparse.o \
	198	$(top_srcdir)/src/general/threadref.o
195	199	straceback_test_LDFLAGS =
196	200	CFLAGS = @CFLAGS@
197	201	COMPILE = $(CC) $(DEFS) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)

+1

-1

src/sdp/boundary.c less more

2	2	* C4 dynamic programming library - Boundary Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/boundary.h less more

2	2	* C4 dynamic programming library - Boundary Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/boundary.test.c less more

2	2	* C4 dynamic programming library - Boundary Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/lookahead.c less more

2	2	* C4 dynamic programming library - SDP Lookahead Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/lookahead.h less more

2	2	* C4 dynamic programming library - SDP Lookahead Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/lookahead.test.c less more

2	2	* C4 dynamic programming library - SDP Lookahead Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/scheduler.c less more

2	2	* C4 dynamic programming library - DP Scheduler *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/scheduler.h less more

2	2	* C4 dynamic programming library - DP Scheduler *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/scheduler.test.c less more

2	2	* C4 dynamic programming library - DP Scheduler *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+4

-4

src/sdp/sdp.c less more

2	2	* C4 dynamic programming library - Seeded Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

299	299	register SDP *sdp = g_new0(SDP, 1);
300	300	register C4_Portal *portal;
301	301	/**/
302		sdp->ref_count = 1;
	302	sdp->thread_ref = ThreadRef_create();
303	303	sdp->sas = SDP_ArgumentSet_create(NULL);
304	304	g_assert(model);
305	305	g_assert(!model->is_open);

355	355
356	356	SDP SDP_share(SDP sdp){
357	357	g_assert(sdp);
358		sdp->ref_count++;
	358	ThreadRef_share(sdp->thread_ref);
359	359	return sdp;
360	360	}
361	361
362	362	void SDP_destroy(SDP *sdp){
363	363	g_assert(sdp);
364		if(--sdp->ref_count)
	364	if(ThreadRef_destroy(sdp->thread_ref))
365	365	return;
366	366	if(sdp->find_starts_scheduler)
367	367	Scheduler_destroy(sdp->find_starts_scheduler);

+3

-2

src/sdp/sdp.h less more

2	2	* C4 dynamic programming library - Seeded Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

32	32	#include "sparsecache.h"
33	33	#include "boundary.h"
34	34	#include "scheduler.h"
	35	#include "threadref.h"
35	36
36	37	/**/
37	38

65	66	/**/
66	67
67	68	typedef struct {
68		gint ref_count;
	69	ThreadRef *thread_ref;
69	70	SDP_ArgumentSet *sas;
70	71	C4_Model *model;
71	72	gboolean use_boundary;

+1

-1

src/sdp/sdp.test.c less more

2	2	* C4 dynamic programming library - Seeded Dynamic Programming *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/straceback.c less more

2	2	* C4 dynamic programming library - Scheduler Traceback *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/straceback.h less more

2	2	* C4 dynamic programming library - Scheduler Traceback *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sdp/straceback.test.c less more

2	2	* C4 dynamic programming library - Scheduler Traceback *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-0

src/sequence/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+43

-1

src/sequence/alphabet.c less more

2	2	* Simple Alphabet Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

150	150	register Alphabet *a = g_new0(Alphabet, 1);
151	151	a->ref_count = 1;
152	152	a->type = type;
	153	a->is_soft_masked = is_soft_masked;
153	154	/* Set look-up tables */
154	155	a->unmasked = Alphabet_Filter_get(Alphabet_Filter_TO_UPPER);
155	156	if(is_soft_masked){

371	372	return short_names[index[(guchar)aa]];
372	373	}
373	374
	375	gchar *Alphabet_nt2ambig(gchar nt){
	376	static gchar *ambig[16] = {
	377	/* - */ NULL,
	378	/* G */ "G",
	379	/* A */ "A",
	380	/* R */ "AG",
	381	/* T */ "T",
	382	/* K */ "GT",
	383	/* W */ "AT",
	384	/* D */ "AGT",
	385	/* C */ "C",
	386	/* S */ "CG",
	387	/* M */ "AC",
	388	/* V */ "ACG",
	389	/* Y */ "CT",
	390	/* B */ "CGT",
	391	/* H */ "ACT",
	392	/* N */ "ACGT"
	393	};
	394	static guchar index[(1<<8)] = { /* GARTKWDCSMVYBHN */
	395	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	396	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	397	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	398	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	399	0, 2, 13, 8, 7, 0, 0, 1, 14, 0, 0, 5, 0, 10, 15, 0,
	400	0, 0, 3, 9, 4, 0, 11, 6, 0, 12, 0, 0, 0, 0, 0, 0,
	401	0, 2, 13, 8, 7, 0, 0, 1, 14, 0, 0, 5, 0, 10, 15, 0,
	402	0, 0, 3, 9, 4, 0, 11, 6, 0, 12, 0, 0, 0, 0, 0, 0,
	403	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	404	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	405	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	406	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	407	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	408	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	409	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	410	0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
	411	};
	412	g_assert(index[(guchar)nt]);
	413	return ambig[index[(guchar)nt]];
	414	}
	415

+8

-1

src/sequence/alphabet.h less more

2	2	* Simple Alphabet Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

48	48
49	49	typedef struct {
50	50	gint ref_count;
	51	gboolean is_soft_masked;
51	52	guchar *member;
52	53	Alphabet_Type type;
53	54	guchar *is_member;

112	113	/* Give three-letter-abbreviation for amino acid.
113	114	* eg 'M' -> "Met" etc */
114	115
	116	gchar *Alphabet_nt2ambig(gchar nt);
	117	/* Returns the ambiguity bases for the given nucleotide
	118	* The returned string does not need to be freed.
	119	*/
	120
	121
115	122	/**/
116	123
117	124	#ifdef __cplusplus

+1

-1

src/sequence/alphabet.test.c less more

2	2	* Simple Alphabet Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sequence/codonsubmat.c less more

2	2	* Codon Substutition Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sequence/codonsubmat.h less more

2	2	* Codon Substitution Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sequence/codonsubmat.test.c less more

2	2	* Codon Substitution Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+103

-2

src/sequence/sequence.c less more

2	2	* Simple Sequence Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

180	180	? g_tree_lookup(sas->annotation_tree, s->id)
181	181	: NULL;
182	182	s->len = len;
	183	#ifdef USE_PTHREADS
	184	pthread_mutex_init(&s->seq_lock, NULL);
	185	#endif /* USE_PTHREADS */
183	186	return s;
184	187	}
185	188

235	238
236	239	Sequence Sequence_share(Sequence s){
237	240	g_assert(s);
	241	Sequence_lock(s);
238	242	g_assert(s->ref_count);
239	243	s->ref_count++;
	244	Sequence_unlock(s);
240	245	return s;
241	246	}
242	247

539	544
540	545	/**/
541	546
	547	#if 0
542	548	static void Sequence_print_type(Sequence *s){
543	549	register Sequence_Subseq *subseq;
544	550	register Sequence *revcomp;

579	585	}
580	586	return;
581	587	}
	588	#endif /* 0 */
	589
582	590
583	591	void Sequence_strncpy(Sequence s, gint start, gint length, gchar dst){
584	592	register gint i;

646	654
647	655	void Sequence_destroy(Sequence *s){
648	656	g_assert(s);
649		if(--s->ref_count)
	657	#ifdef USE_PTHREADS
	658	pthread_mutex_lock(&s->seq_lock);
	659	#endif /* USE_PTHREADS */
	660	if(--s->ref_count){
	661	#ifdef USE_PTHREADS
	662	pthread_mutex_unlock(&s->seq_lock);
	663	#endif /* USE_PTHREADS */
650	664	return;
	665	}
	666	#ifdef USE_PTHREADS
	667	pthread_mutex_unlock(&s->seq_lock);
	668	#endif /* USE_PTHREADS */
651	669	if(s->id)
652	670	g_free(s->id);
653	671	if(s->def)

678	696	}
679	697	}
680	698	Alphabet_destroy(s->alphabet);
	699	#ifdef USE_PTHREADS
	700	pthread_mutex_destroy(&s->seq_lock);
	701	#endif /* USE_PTHREADS */
681	702	g_free(s);
682	703	return;
683	704	}

784	805	}
785	806
786	807
	808	void Sequence_lock(Sequence *s){
	809	register Sequence_Subseq *subseq;
	810	register Sequence_Filter *filter;
	811	register Sequence_Translation *translation;
	812	register Sequence *revcomp;
	813	g_assert(s);
	814	#ifdef USE_PTHREADS
	815	pthread_mutex_lock(&s->seq_lock);
	816	if(s->data){
	817	switch(s->type){
	818	case Sequence_Type_INTMEM:
	819	break;
	820	case Sequence_Type_EXTMEM:
	821	break;
	822	case Sequence_Type_SUBSEQ:
	823	subseq = s->data;
	824	Sequence_lock(subseq->sequence);
	825	break;
	826	case Sequence_Type_REVCOMP:
	827	revcomp = s->data;
	828	Sequence_lock(revcomp);
	829	break;
	830	case Sequence_Type_FILTER:
	831	filter = s->data;
	832	Sequence_lock(filter->sequence);
	833	break;
	834	case Sequence_Type_TRANSLATE:
	835	translation = s->data;
	836	Sequence_lock(translation->sequence);
	837	break;
	838	default:
	839	g_error("Unknown Sequence type [%d]", s->type);
	840	break;
	841	}
	842	}
	843	#endif /* USE_PTHREADS */
	844	return;
	845	}
	846
	847	void Sequence_unlock(Sequence *s){
	848	register Sequence_Subseq *subseq;
	849	register Sequence_Filter *filter;
	850	register Sequence_Translation *translation;
	851	register Sequence *revcomp;
	852	g_assert(s);
	853	#ifdef USE_PTHREADS
	854	pthread_mutex_unlock(&s->seq_lock);
	855	if(s->data){
	856	switch(s->type){
	857	case Sequence_Type_INTMEM:
	858	break;
	859	case Sequence_Type_EXTMEM:
	860	break;
	861	case Sequence_Type_SUBSEQ:
	862	subseq = s->data;
	863	Sequence_unlock(subseq->sequence);
	864	break;
	865	case Sequence_Type_REVCOMP:
	866	revcomp = s->data;
	867	Sequence_unlock(revcomp);
	868	break;
	869	case Sequence_Type_FILTER:
	870	filter = s->data;
	871	Sequence_unlock(filter->sequence);
	872	break;
	873	case Sequence_Type_TRANSLATE:
	874	translation = s->data;
	875	Sequence_unlock(translation->sequence);
	876	break;
	877	default:
	878	g_error("Unknown Sequence type [%d]", s->type);
	879	break;
	880	}
	881	}
	882	#endif /* USE_PTHREADS */
	883	return;
	884	}
	885
	886
	887

+10

-1

src/sequence/sequence.h less more

2	2	* Simple Sequence Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

21	21
22	22	#include <stdio.h>
23	23	#include <glib.h>
	24
	25	#ifdef USE_PTHREADS
	26	#include <pthread.h>
	27	#endif /* USE_PTHREADS */
24	28
25	29	#include "alphabet.h"
26	30	#include "translate.h"

82	86	gpointer data;
83	87	Sequence_Type type;
84	88	gint (*get_symbol)(gpointer data, gint pos);
	89	#ifdef USE_PTHREADS
	90	pthread_mutex_t seq_lock;
	91	#endif /* USE_PTHREADS */
85	92	} Sequence;
86	93
87	94	#define Sequence_get_symbol(sequence, pos) \

133	140	Sequence Sequence_translate(Sequence s, Translate *translate, gint frame);
134	141
135	142	Sequence Sequence_mask(Sequence s);
	143	void Sequence_lock(Sequence *s);
	144	void Sequence_unlock(Sequence *s);
136	145
137	146	/**/
138	147

+1

-1

src/sequence/sequence.test.c less more

2	2	* Simple Sequence Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+2

-2

src/sequence/splice.c less more

2	2	* Library for Splice site prediction. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

281	281	for(j = 0; j < 4; j++){
282	282	sp->model_data[i][j] = (((gfloat)(1+sp->model_data[i][j]))
283	283	/((25.0+1.0)));
284		sp->model_data[i][j] = log(sp->model_data[i][j]) * 2.0;
	284	sp->model_data[i][j] = log(sp->model_data[i][j]) * 1.5;
285	285	}
286	286	sp->model_data[i][4] = 0.0;
287	287	}

+1

-1

src/sequence/splice.h less more

2	2	* Library for Splice site prediction. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sequence/splice.test.c less more

2	2	* Library for Splice site prediction. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+2

-2

src/sequence/submat.c less more

2	2	* Substutition Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

265	265	}
266	266	break;
267	267	case '0': case '1': case '2': case '3': case '4':
268		case '5': case '6': case '7': case '8': case '9':
	268	case '5': case '6': case '7': case '8': case '9':
269	269	num *= 10;
270	270	num += (ch-'0');
271	271	seen = TRUE;

+1

-1

src/sequence/submat.h less more

2	2	* Substitution Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/sequence/submat.test.c less more

2	2	* Substitution Matrix Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-3

src/sequence/translate.c less more

2	2	* Nucleotide Translation Code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

19	19	#include "translate.h"
20	20
21	21	/* ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
	22	CTAG
22	23	0 - 0000 - blank Representation of Nucleotides
23	24	1 G 0001 C -----------------------------
24	25	2 A 0010 T

71	72	"pon", "jihP", "fCcd", "rHmpi", "xfrj", "Xx*" };
72	73	for(i = 0; i < Translate_AA_SET_SIZE; i++)
73	74	t->aa2d[t->aa[i]] = i;
74		for(i = 1; i < 22; i++)
	75	for(i = 1; i < 23; i++)
75	76	t->aamask[i] = (1L<<(i-1)); /* First is zero */
76	77	for(i = 0; i < Translate_PIMA_SET_SIZE; i++){
77	78	t->aamask[t->aa2d[pimagrp[i][0]]]

137	138	result[n++] = code[(table[a] << 4)
138	139	\| (table[b] << 2)
139	140	\| table[c]];
140		/* g_print("generated genetic code [%s]\n", result); */
141	141	return result;
142	142	}
143	143	/* Converts genetic code from NCBI format (TCAG order)

+1

-1

src/sequence/translate.h less more

2	2	* Nucleotide Translation Code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+7

-3

src/sequence/translate.test.c less more

2	2	* Nucleotide Translation Code *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

23	23
24	24	static void check_translate(Translate t, gchar codon, gchar crib){
25	25	register gchar aa = Translate_codon(t, codon);
	26	g_message("Translate [%s] -> [%c] (crib:[%c]", codon, aa, crib);
26	27	g_assert(aa == crib);
27		g_message("Translate [%s] -> [%c] (crib:[%c]", codon, aa, crib);
28	28	return;
29	29	}
30	30

38	38	}
39	39
40	40	gint Argument_main(Argument *arg){
41		register Translate *t = Translate_create(FALSE);
	41	register Translate *t;
	42	Translate_ArgumentSet_create(arg);
	43	Argument_process(arg, "translate.test", NULL, NULL);
	44	t = Translate_create(FALSE);
42	45	check_translate(t, "ATG", 'M');
43	46	check_translate(t, "GGX", 'G');
44	47	check_translate(t, "NGT", 'X');
	48	check_translate(t, "TGA", '*');
45	49	/**/
46	50	check_reverse_translate(t, "S*MXG", 72);
47	51	check_reverse_translate(t, "SSSSS", 7776);

+12

-1

src/struct/Makefile.am less more

0	0
1	1	TESTS = fsm.test matrix.test pqueue.test slist.test rangetree.test \
2	2	vfsm.test recyclebin.test sparsecache.test dejavu.test \
3		bitarray.test splaytree.test noitree.test
	3	bitarray.test splaytree.test noitree.test
	4	# huffman.test fmindex.test
	5
4	6	noinst_PROGRAMS = $(TESTS)
5	7
6	8	noinst_HEADERS = fsm.h matrix.h pqueue.h slist.h rangetree.h vfsm.h \
7	9	recyclebin.h sparsecache.h dejavu.h bitarray.h \
8	10	splaytree.h noitree.h
	11	# huffman.h fmindex.h
	12
	13	INCLUDES = -DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
9	14
10	15	fsm_test_SOURCES = fsm.test.c fsm.c
11	16	fsm_test_LDADD = recyclebin.o

30	35	noitree_test_SOURCES = noitree.test.c noitree.c
31	36	noitree_test_LDADD = recyclebin.o splaytree.o
32	37
	38	# huffman_test_SOURCES = huffman.test.c huffman.c
	39	# huffman_test_LDADD = bitarray.o pqueue.o recyclebin.o
	40
	41	# fmindex_test_SOURCES = fmindex.test.c fmindex.c
	42	# fmindex_test_LDADD = bitarray.o pqueue.o recyclebin.o huffman.o
	43
33	44	# Files to clear away
34	45
35	46	MAINTAINERCLEANFILES = Makefile.in

+13

-1

src/struct/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

77	78	source_root_dir = @source_root_dir@
78	79	use_pthreads = @use_pthreads@
79	80
80		TESTS = fsm.test matrix.test pqueue.test slist.test rangetree.test vfsm.test recyclebin.test sparsecache.test dejavu.test bitarray.test splaytree.test noitree.test
	81	TESTS = fsm.test matrix.test pqueue.test slist.test rangetree.test vfsm.test recyclebin.test sparsecache.test dejavu.test bitarray.test splaytree.test noitree.test
	82
	83	# huffman.test fmindex.test
81	84
82	85	noinst_PROGRAMS = $(TESTS)
83	86
84	87	noinst_HEADERS = fsm.h matrix.h pqueue.h slist.h rangetree.h vfsm.h recyclebin.h sparsecache.h dejavu.h bitarray.h splaytree.h noitree.h
85	88
	89	# huffman.h fmindex.h
	90
	91	INCLUDES = -DCUSTOM_GUINT64_FORMAT="\"@custom_guint64_format@\""
86	92
87	93	fsm_test_SOURCES = fsm.test.c fsm.c
88	94	fsm_test_LDADD = recyclebin.o

106	112
107	113	noitree_test_SOURCES = noitree.test.c noitree.c
108	114	noitree_test_LDADD = recyclebin.o splaytree.o
	115
	116	# huffman_test_SOURCES = huffman.test.c huffman.c
	117	# huffman_test_LDADD = bitarray.o pqueue.o recyclebin.o
	118
	119	# fmindex_test_SOURCES = fmindex.test.c fmindex.c
	120	# fmindex_test_LDADD = bitarray.o pqueue.o recyclebin.o huffman.o
109	121
110	122	# Files to clear away
111	123

+1

-1

src/struct/bitarray.c less more

2	2	* A simple bitarray data structure *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-1

src/struct/bitarray.h less more

2	2	* A simple bitarray data structure *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

51	51
52	52	void BitArray_write_int(guint64 num, FILE *fp);
53	53	guint64 BitArray_read_int(FILE *fp);
	54	void BitArray_int_print(guint64 num);
	55	gchar *BitArray_int_sprintf(guint64 num);
54	56
55	57	#ifdef __cplusplus
56	58	}

+1

-1

src/struct/bitarray.test.c less more

2	2	* A simple bitarray data structure *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+2

-3

src/struct/dejavu.c less more

2	2	* Deja-vu library for fast linear space repeat finding *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

68	68	continue;
69	69	if(first[ch] == -1)
70	70	first[ch] = i;
71		if(last[ch] != -1){
	71	if(last[ch] != -1)
72	72	dv->next[last[ch]] = i;
73		}
74	73	last[ch] = i;
75	74	}
76	75	for(i = 0; i < ALPHABET_SIZE; i++){

+1

-1

src/struct/dejavu.h less more

2	2	* Deja-vu library for fast linear space repeat finding *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/dejavu.test.c less more

2	2	* Deja-vu library for fast linear space repeat finding *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-1

src/struct/fsm.c less more

2	2	* Library for FSM-based word matching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

217	217	return;
218	218	}
219	219
	220	/**/
	221

+1

-1

src/struct/fsm.h less more

2	2	* Library for FSM-based word matching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/fsm.test.c less more

2	2	* Library for FSM-based word matching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/matrix.c less more

2	2	* Simple matrix creation routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/matrix.h less more

2	2	* Simple matrix creation routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/matrix.test.c less more

2	2	* Simple matrix creation routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/noitree.c less more

2	2	* NOI_Tree : non-overlapping interval tree *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/noitree.h less more

2	2	* NOI_Tree : non-overlapping interval tree *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/noitree.test.c less more

2	2	* NOI_Tree : non-overlapping interval tree *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/pqueue.c less more

2	2	* Priority queue library using pairing heaps. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/pqueue.h less more

2	2	* Priority queue library using pairing heaps. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/pqueue.test.c less more

2	2	* Priority queue library using pairing heaps. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/rangetree.c less more

2	2	* Trees for 2D range searching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/rangetree.h less more

2	2	* Trees for 2D range searching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/rangetree.test.c less more

2	2	* Trees for 2D range searching. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+15

-1

src/struct/recyclebin.c less more

2	2	* Efficient Memory Allocation Routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

15	15	#include <string.h>
16	16	#include "recyclebin.h"
17	17
	18	#ifndef USE_PTHREADS
18	19	static GTree *global_recycle_bin_tree = NULL;
	20	#endif /* USE_PTHREADS */
19	21
	22	#ifndef USE_PTHREADS
20	23	static gint RecycleBin_compare(gconstpointer a,
21	24	gconstpointer b){
22	25	return a - b;
23	26	}
	27	#endif /* USE_PTHREADS */
24	28
25	29	RecycleBin RecycleBin_create(gchar name, gsize node_size,
26	30	gint nodes_per_chunk){

35	39	recycle_bin->node_size = node_size;
36	40	recycle_bin->count = 0;
37	41	recycle_bin->recycle = NULL;
	42	#ifndef USE_PTHREADS
38	43	if(!global_recycle_bin_tree)
39	44	global_recycle_bin_tree = g_tree_new(RecycleBin_compare);
40	45	g_tree_insert(global_recycle_bin_tree, recycle_bin, recycle_bin);
	46	#endif /* USE_PTHREADS */
41	47	return recycle_bin;
42	48	}
43	49

45	51	register gint i;
46	52	if(--recycle_bin->ref_count)
47	53	return;
	54	#ifndef USE_PTHREADS
48	55	g_assert(global_recycle_bin_tree);
49	56	g_assert(g_tree_lookup(global_recycle_bin_tree, recycle_bin));
50	57	g_tree_remove(global_recycle_bin_tree, recycle_bin);

52	59	g_tree_destroy(global_recycle_bin_tree);
53	60	global_recycle_bin_tree = NULL;
54	61	}
	62	#endif /* USE_PTHREADS */
55	63	for(i = 0; i < recycle_bin->chunk_list->len; i++)
56	64	g_free(recycle_bin->chunk_list->pdata[i]);
57	65	g_ptr_array_free(recycle_bin->chunk_list, TRUE);

114	122	return;
115	123	}
116	124
	125	#ifndef USE_PTHREADS
117	126	static gint RecycleBin_profile_traverse(gpointer key,
118	127	gpointer value,
119	128	gpointer data){

125	134	recycle_bin->count);
126	135	return FALSE;
127	136	}
	137	#endif /* USE_PTHREADS */
128	138
129	139	void RecycleBin_profile(void){
130	140	g_message("BEGIN RecycleBin profile");
	141	#ifdef USE_PTHREADS
	142	g_message("multi-threaded RecycleBin_profile() not implemented");
	143	#else /* USE_PTHREADS */
131	144	if(global_recycle_bin_tree)
132	145	g_tree_traverse(global_recycle_bin_tree,
133	146	RecycleBin_profile_traverse, G_IN_ORDER, NULL);
134	147	else
135	148	g_message("no active RecycleBins");
	149	#endif /* USE_PTHREADS */
136	150	g_message("END RecycleBin profile");
137	151	return;
138	152	}

+1

-1

src/struct/recyclebin.h less more

2	2	* Efficient Memory Allocation Routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/recyclebin.test.c less more

2	2	* Efficient Memory Allocation Routines *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/slist.c less more

2	2	* Efficient single-linked list routines. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/slist.h less more

2	2	* Efficient single-linked list routines. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/slist.test.c less more

2	2	* Efficient single-linked list routines. *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/sparsecache.c less more

2	2	* Sparse Cache Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/sparsecache.h less more

2	2	* Sparse Cache Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/sparsecache.test.c less more

2	2	* Sparse Cache Object *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/splaytree.c less more

2	2	* Splay Tree Library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/splaytree.h less more

2	2	* Splay Tree Library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/splaytree.test.c less more

2	2	* Splay Tree Library *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/struct/vfsm.c less more

2	2	* VFSM Library : complete trie navigation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+5

-1

src/struct/vfsm.h less more

2	2	* VFSM Library : complete trie navigation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

21	21	#ifdef G_HAVE_GINT64
22	22	typedef guint64 VFSM_Int;
23	23	#define VFSM_MAX G_GINT64_CONSTANT(18446744073709551615U)
	24	#ifdef CUSTOM_GUINT64_FORMAT
	25	#define VFSM_PRINT_FORMAT CUSTOM_GUINT64_FORMAT
	26	#else /* CUSTOM_GUINT64_FORMAT */
24	27	#define VFSM_PRINT_FORMAT "llu"
	28	#endif /* CUSTOM_GUINT64_FORMAT */
25	29	#else /* G_HAVE_GINT64 */
26	30	typedef guint32 VFSM_Int;
27	31	#define VFSM_MAX 4294967295U

+1

-1

src/struct/vfsm.test.c less more

2	2	* VFSM Library : complete trie navigation *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-0

src/util/Makefile.am less more

56	56
57	57	esd2esi_LDADD = $(top_srcdir)/src/database/dataset.o \
58	58	$(top_srcdir)/src/database/index.o \
	59	$(top_srcdir)/src/general/threadref.o \
59	60	$(top_srcdir)/src/struct/bitarray.o \
60	61	$(top_srcdir)/src/struct/vfsm.o \
61	62	$(top_srcdir)/src/struct/pqueue.o \

+6

-4

src/util/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

115	116	fasta2esd_LDADD = $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/struct/bitarray.o $(LDADD)
116	117
117	118
118		esd2esi_LDADD = $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(LDADD)
	119	esd2esi_LDADD = $(top_srcdir)/src/database/dataset.o $(top_srcdir)/src/database/index.o $(top_srcdir)/src/general/threadref.o $(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o $(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/noitree.o $(top_srcdir)/src/struct/splaytree.o $(top_srcdir)/src/sequence/submat.o $(top_srcdir)/src/sequence/codonsubmat.o $(top_srcdir)/src/comparison/wordhood.o $(top_srcdir)/src/comparison/hspset.o $(top_srcdir)/src/comparison/match.o $(LDADD)
119	120
120	121
121	122	EXTRA_fastavalidcds_SOURCES = fastavalidcds.c

435	436	fastaannotatecdna_LDFLAGS =
436	437	esd2esi_OBJECTS = esd2esi.o
437	438	esd2esi_DEPENDENCIES = $(top_srcdir)/src/database/dataset.o \
438		$(top_srcdir)/src/database/index.o $(top_srcdir)/src/struct/bitarray.o \
439		$(top_srcdir)/src/struct/vfsm.o $(top_srcdir)/src/struct/pqueue.o \
440		$(top_srcdir)/src/struct/recyclebin.o \
	439	$(top_srcdir)/src/database/index.o \
	440	$(top_srcdir)/src/general/threadref.o \
	441	$(top_srcdir)/src/struct/bitarray.o $(top_srcdir)/src/struct/vfsm.o \
	442	$(top_srcdir)/src/struct/pqueue.o $(top_srcdir)/src/struct/recyclebin.o \
441	443	$(top_srcdir)/src/struct/rangetree.o $(top_srcdir)/src/struct/noitree.o \
442	444	$(top_srcdir)/src/struct/splaytree.o \
443	445	$(top_srcdir)/src/sequence/submat.o \

+13

-3

src/util/esd2esi.c less more

2	2	* esd2esi - generate an exonerate index file from a dataset *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

25	25	gboolean is_translated = FALSE;
26	26	register gint word_length;
27	27	gint dna_word_length, protein_word_length,
28		word_jump, saturate_threshold, memory_limit;
	28	word_jump, word_ambiguity,
	29	saturate_threshold, memory_limit;
29	30	/**/
30	31	ArgumentSet_add_option(as, 'd', "dataset", "path",
31	32	"Exonerate dataset file", NULL,

47	48	ArgumentSet_add_option(as, 0, "wordjump", NULL,
48	49	"Jump between database words", "1",
49	50	Argument_parse_int, &word_jump);
	51	ArgumentSet_add_option(as, 0, "wordambiguity", NULL,
	52	"Number of ambiguous words to index", "1",
	53	Argument_parse_int, &word_ambiguity);
50	54	ArgumentSet_add_option(as, 0, "saturatethreshold", NULL,
51	55	"Word saturation threshold", "10",
52	56	Argument_parse_int, &saturate_threshold);

64	68	\|\| (dataset->alphabet->type == Alphabet_Type_PROTEIN))
65	69	? protein_word_length
66	70	: dna_word_length;
	71	if(word_ambiguity < 1)
	72	g_error("Word ambiguity cannot be less than one.");
	73	if((word_ambiguity > 1)
	74	&& (dataset->alphabet->type == Alphabet_Type_PROTEIN))
	75	g_error("Protein ambuigity symbols not implemented");
67	76	g_message("Building index");
68		index = Index_create(dataset, is_translated, word_length, word_jump,
	77	index = Index_create(dataset, is_translated, word_length,
	78	word_jump, word_ambiguity,
69	79	saturate_threshold, index_path, dataset_path,
70	80	memory_limit);
71	81	Index_destroy(index);

+1

-1

src/util/fasta2esd.c less more

2	2	* fasta2esd - generate an exonerate sequence database file *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaannotatecdna.c less more

2	2	* fastaannotatecdna : a utility to annotate cDNA with a protein *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastachecksum.c less more

2	2	* fastachecksum : a utility to print GCG checksums *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaclean.c less more

2	2	* fastaclean : a utility to clean fasta format files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaclip.c less more

2	2	* fastaclip : clip terminal Ns from fasta format sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastacomposition.c less more

2	2	* fastacomposition : a utility to dump sequence composition *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastadiff.c less more

2	2	* fastadiff : a utility to compare fasta sequence files *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaexplode.c less more

2	2	* fastaexplode : break a fasta file into individual sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+3

-3

src/util/fastafetch.c less more

2	2	* fastafetch : fetch a sequence from a fasta format file *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

43	43	static CompoundFile_Pos fasta_index_lookup(FastaDB fdb, FILE index_fp,
44	44	gchar *id){
45	45	register long left, right, pos;
46		CompoundFile_Pos result = -1;
	46	CompoundFile_Pos_scan_type result = -1;
47	47	register GString *curr = g_string_sized_new(100);
48	48	register gint cond;
49	49	left = 0;

79	79	}
80	80	}
81	81	g_string_free(curr, TRUE);
82		return result;
	82	return (CompoundFile_Pos)result;
83	83	}
84	84
85	85	static FastaDB_Seq fasta_index_fetch(FastaDB fdb, FILE *index_fp,

+1

-1

src/util/fastahardmask.c less more

2	2	* fastahardmask : convert lower case chars to 'N's *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaindex.c less more

2	2	* fastaindex : index a fasta format file *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastalength.c less more

2	2	* fastalength : a utility to print fasta sequence length *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastanrdb.c less more

2	2	* fastanrdb : create non-redundant versions of fasta database *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaoverlap.c less more

2	2	* fastaoverlap: generate overlapping sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastareformat.c less more

2	2	* fastalength : a utility to reformat fasta format sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastaremove.c less more

2	2	* fastaremove : remove sequences from a fasta format file *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastarevcomp.c less more

2	2	* fastarevcomp : a utility to revcomp fasta format sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastasoftmask.c less more

2	2	* fastasoftmask: merge masked and unmasked files to softmask *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastasort.c less more

2	2	* fastasort : a utility for sorting fasta format databases *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastasplit.c less more

2	2	* fastasplit: split a fasta format file into chunks *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-1

src/util/fastasubseq.c less more

2	2	* fastasubseq: extract subsequences from fasta format sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+5

-3

src/util/fastatranslate.c less more

2	2	* fastatranslate: a utility to translate fasta format sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

36	36	} else {
37	37	aa_seq = Sequence_translate(fdbs->seq, translate, frame);
38	38	}
39		Sequence_print_fasta(aa_seq, stdout, FALSE);
	39	if(aa_seq->len)
	40	Sequence_print_fasta(aa_seq, stdout, FALSE);
40	41	Sequence_destroy(aa_seq);
41	42	return;
42	43	}

46	47	register FastaDB_Seq *fdbs;
47	48	register ArgumentSet *as
48	49	= ArgumentSet_create("Sequence Input Options");
49		register Translate *translate = Translate_create(FALSE);
	50	register Translate *translate;
50	51	register Alphabet *dna_alphabet
51	52	= Alphabet_create(Alphabet_Type_DNA, FALSE);
52	53	register Alphabet *protein_alphabet

65	66	"A utility to translate fasta format sequences\n"
66	67	"Guy St.C. Slater. guy@ebi.ac.uk. 2000-2003.\n", NULL);
67	68	fdb = FastaDB_open(query_path, dna_alphabet);
	69	translate = Translate_create(FALSE);
68	70	while((fdbs = FastaDB_next(fdb, FastaDB_Mask_ALL))){
69	71	fasta_translate_seq(fdbs, translate, frame, protein_alphabet);
70	72	FastaDB_Seq_destroy(fdbs);

+1

-1

src/util/fastavalidcds.c less more

2	2	* fastavalidcds: a utility to check for valid CDS sequences *
3	3	* *
4	4	* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
5		* Copyright (C) 2000-2008. All Rights Reserved. *
	5	* Copyright (C) 2000-2009. All Rights Reserved. *
6	6	* *
7	7	* This source code is distributed under the terms of the *
8	8	* GNU General Public License, version 3. See the file COPYING *

+1

-0

test/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/data/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/data/cdna/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/data/protein/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/exonerate/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/ipcress/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@

+1

-0

test/util/Makefile.in less more

69	69	VERSION = @VERSION@
70	70	codegen_extra_ldadd = @codegen_extra_ldadd@
71	71	codegen_extra_sources = @codegen_extra_sources@
	72	custom_guint64_format = @custom_guint64_format@
72	73	datarootdir = @datarootdir@
73	74	glib_cflags = @glib_cflags@
74	75	glib_libs = @glib_libs@