New Upstream Snapshot - prottest
Ready changes
Summary
Merged new upstream version: 3.4.2+git20180122.1.b6120b9+dfsg (was: 3.4.2+dfsg).
Resulting package
Built on 2023-01-18T19:56 (took 24m51s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots prottest
Lintian Result
Diff
diff --git a/README.md b/README.md
index 98cad56..82a4da3 100644
--- a/README.md
+++ b/README.md
@@ -24,8 +24,8 @@ For technical doubts, bug reports or comments, please use the ProtTest forum: ht
Download
--------
-New distributions of ProtTest will be hosted in google drive: ProtTest3 Downloads
-https://drive.google.com/folderview?id=0ByrkKOPtF_n_dVBBbDVBOEM5b1U
+New releases of ProtTest 3 can be downloaded from the releases section:
+https://github.com/ddarriba/prottest3/releases
--------
News!
diff --git a/debian/changelog b/debian/changelog
index 041e35d..189b90e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+prottest (3.4.2+git20180122.1.b6120b9+dfsg-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+ * Drop patch read-stats-file.patch, present upstream.
+
+ -- Debian Janitor <janitor@jelmer.uk> Wed, 18 Jan 2023 19:34:10 -0000
+
prottest (3.4.2+dfsg-8) unstable; urgency=medium
* Fix watch file
diff --git a/debian/patches/alter-import.patch b/debian/patches/alter-import.patch
index a5a8f71..1e9f05f 100644
--- a/debian/patches/alter-import.patch
+++ b/debian/patches/alter-import.patch
@@ -6,8 +6,10 @@ Subject: alter import
.../es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
---- a/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
-+++ b/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
+Index: prottest.git/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
+===================================================================
+--- prottest.git.orig/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
++++ prottest.git/src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java
@@ -17,9 +17,9 @@ Foundation, Inc., 59 Temple Place, Suite
*/
package es.uvigo.darwin.prottest.util.fileio;
diff --git a/debian/patches/build.patch b/debian/patches/build.patch
index b27859e..b470835 100644
--- a/debian/patches/build.patch
+++ b/debian/patches/build.patch
@@ -3,8 +3,10 @@ From: Markus Koschany <apo@gambaru.de>,
Last_Update: Mon, 09 May 2016 21:03:00 +0200
Subject: build using Debian packaged jars
---- a/build.xml
-+++ b/build.xml
+Index: prottest.git/build.xml
+===================================================================
+--- prottest.git.orig/build.xml
++++ prottest.git/build.xml
@@ -4,7 +4,7 @@
<property name="src.dir" location="src/main/java" />
<property name="build.base.dir" location="build" />
diff --git a/debian/patches/read-stats-file.patch b/debian/patches/read-stats-file.patch
deleted file mode 100644
index 5906c46..0000000
--- a/debian/patches/read-stats-file.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Description: properly resolve stats and tree files, add missing dot
-Author: Nilesh Patra <nilesh@debian.org>
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997886
-Last-Update: 2021-10-29
---- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
-+++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
-@@ -378,7 +378,7 @@
- if (!(statsFile.exists() && statsFile.canRead()))
- {
- /* try with txt suffix */
-- statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt");
-+ statsFile = new File(workAlignment + STATS_FILE_SUFFIX + ".txt");
- if (!(statsFile.exists() && statsFile.canRead()))
- throw new StatsFileFormatException("PhyML",
- "Stats file does not exist. Please check if PhyML is working.");
-@@ -389,7 +389,7 @@
- if (!(treeFile.exists() && treeFile.canRead()))
- {
- /* try with txt suffix */
-- treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt");
-+ treeFile = new File(workAlignment + TREE_FILE_SUFFIX + ".txt");
- if (!(treeFile.exists() && treeFile.canRead()))
- throw new TreeFormatException(
- "Tree file does not exist. Please check if PhyML is working correctly.");
diff --git a/debian/patches/series b/debian/patches/series
index 3e6109e..dca9da1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
use_debian_packaged_phyml.patch
build.patch
alter-import.patch
-read-stats-file.patch
diff --git a/debian/patches/use_debian_packaged_phyml.patch b/debian/patches/use_debian_packaged_phyml.patch
index c08a791..02299c9 100644
--- a/debian/patches/use_debian_packaged_phyml.patch
+++ b/debian/patches/use_debian_packaged_phyml.patch
@@ -2,8 +2,10 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 09 May 2016 21:03:00 +0200
Description: Follow a hint from upstream how to uses system wide installed phyml
---- a/src/main/resources/prottest.properties
-+++ b/src/main/resources/prottest.properties
+Index: prottest.git/src/main/resources/prottest.properties
+===================================================================
+--- prottest.git.orig/src/main/resources/prottest.properties
++++ prottest.git/src/main/resources/prottest.properties
@@ -20,7 +20,7 @@ analyzer=phyml
# and ProtTest will use the global binary instead of
# local ones.
diff --git a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
index a3b42d7..a856fd4 100644
--- a/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
+++ b/src/main/java/es/uvigo/darwin/prottest/ProtTest.java
@@ -24,6 +24,8 @@ import java.util.Set;
import java.util.logging.Handler;
import java.util.logging.Level;
+import static es.uvigo.darwin.prottest.global.ApplicationGlobals.APPLICATION_PROPERTIES;
+
import mpi.MPI;
import pal.misc.Identifier;
import pal.tree.Tree;
@@ -54,6 +56,7 @@ import es.uvigo.darwin.prottest.util.exception.ProtTestInternalException;
import es.uvigo.darwin.prottest.util.factory.ProtTestFactory;
import es.uvigo.darwin.prottest.util.logging.ProtTestLogger;
import es.uvigo.darwin.prottest.util.printer.ProtTestPrinter;
+import es.uvigo.darwin.xprottest.XProtTestApp;
/**
* This is the main class of ProtTest. It calls the methods in the
@@ -89,6 +92,31 @@ public class ProtTest {
*/
public static void main(String[] args) {
+ if (args.length < 1) {
+ XProtTestApp.launch(XProtTestApp.class, args);
+ return;
+ }
+
+ // initializing MPJ environment (if available)
+ try {
+ String[] argsApp = MPI.Init(args);
+ MPJ_ME = MPI.COMM_WORLD.Rank();
+ MPJ_SIZE = MPI.COMM_WORLD.Size();
+ MPJ_RUN = true;
+ args = argsApp;
+ } catch (Exception e) {
+ MPJ_ME = 0;
+ MPJ_SIZE = 1;
+ MPJ_RUN = false;
+ }
+
+ // force static initialization
+ if (APPLICATION_PROPERTIES == null)
+ {
+ System.err.println("Error initialization ProtTest properties");
+ finalize(1);
+ }
+
try {
args = ProtTestFactory.initialize(args);
} catch (IllegalArgumentException e) {
@@ -102,19 +130,6 @@ public class ProtTest {
{
finalize(1);
}
-
- // initializing MPJ environment (if available)
- try {
- String[] argsApp = MPI.Init(args);
- MPJ_ME = MPI.COMM_WORLD.Rank();
- MPJ_SIZE = MPI.COMM_WORLD.Size();
- MPJ_RUN = true;
- args = argsApp;
- } catch (Exception e) {
- MPJ_ME = 0;
- MPJ_SIZE = 1;
- MPJ_RUN = false;
- }
ProtTestLogger logger = ProtTestLogger.getDefaultLogger();
logger.setStdHandlerLevel(Level.INFO);
diff --git a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
index 870e99e..6ba93e6 100644
--- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
+++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
@@ -378,7 +378,7 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
if (!(statsFile.exists() && statsFile.canRead()))
{
/* try with txt suffix */
- statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt");
+ statsFile = new File(workAlignment + STATS_FILE_SUFFIX + ".txt");
if (!(statsFile.exists() && statsFile.canRead()))
throw new StatsFileFormatException("PhyML",
"Stats file does not exist. Please check if PhyML is working.");
@@ -389,7 +389,7 @@ public class PhyMLv3AminoAcidRunEstimator extends AminoAcidRunEstimator {
if (!(treeFile.exists() && treeFile.canRead()))
{
/* try with txt suffix */
- treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt");
+ treeFile = new File(workAlignment + TREE_FILE_SUFFIX + ".txt");
if (!(treeFile.exists() && treeFile.canRead()))
throw new TreeFormatException(
"Tree file does not exist. Please check if PhyML is working correctly.");
diff --git a/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java b/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java
index 7e0d5ec..3159ebe 100644
--- a/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java
+++ b/src/main/java/es/uvigo/darwin/prottest/global/ApplicationGlobals.java
@@ -32,22 +32,36 @@ public abstract class ApplicationGlobals implements ProtTestConstants {
/** The application APPLICATION_PROPERTIES. */
public static final Properties APPLICATION_PROPERTIES;
- public static final String JAR_PATH = ProtTest.class.getProtectionDomain().getCodeSource().getLocation().getFile()
- .replace("%20", " ");
- public static final String PATH = JAR_PATH.replaceFirst(new File(JAR_PATH).getName(),"");
+ public static final String ENV_PATH;
+ public static final String JAR_PATH = ProtTest.class.getProtectionDomain()
+ .getCodeSource()
+ .getLocation()
+ .getFile()
+ .replace("%20", " ");
+ public static final String PATH;
+ public static final String DEFAULT_SNAPSHOT_DIR = "snapshot/";
static {
- APPLICATION_PROPERTIES = new Properties();
- try {
- FileInputStream prop = new FileInputStream(PATH + "prottest.properties");
- APPLICATION_PROPERTIES.load(prop);
- } catch (IOException e) {
- System.err.println("Properties file (prottest.properties) cannot be resolved");
- System.exit(EXIT_NO_PROPERTIES);
- }
-
+ ENV_PATH = System.getenv("PROTTEST_PATH");
+ if (ENV_PATH != null)
+ PATH = ENV_PATH;
+ else {
+ if (ProtTest.MPJ_RUN)
+ PATH = System.getProperty("user.dir");
+ else
+ PATH = JAR_PATH.replaceFirst(new File(JAR_PATH).getName(), "");
+ }
+ APPLICATION_PROPERTIES = new Properties();
+ try {
+ FileInputStream prop = new FileInputStream(
+ PATH + File.separator + "prottest.properties");
+ APPLICATION_PROPERTIES.load(prop);
+ } catch (IOException e) {
+ System.err.println("Properties file (" + PATH + File.separator
+ + "prottest.properties) cannot be resolved");
+ System.exit(EXIT_NO_PROPERTIES);
+ }
}
- public static final String DEFAULT_SNAPSHOT_DIR = "snapshot/";
/**
* Gets the supported matrices.
Debdiff
File lists identical (after any substitutions)
No differences were encountered in the control files