| 56 | 56 |
* reported by the underlying operating system. Callers can check for these
|
| 57 | 57 |
* situations using a program fragment such as the following:
|
| 58 | 58 |
* @if cpp
|
| 59 | |
@@ -4917,7 +4917,7 @@ void example (SBase sb)
|
|
59 |
@@ -5681,7 +5681,7 @@ void example (SBase sb)
|
| 60 | 60 |
* Hierarchical %Model Composition (“comp”) package, and
|
| 61 | 61 |
* extracted parts of that model in order to construct a new model in
|
| 62 | 62 |
* memory. The new, in-memory model will not accept a component drawn from
|
|
| 65 | 65 |
* You could reconstruct the same namespaces in the in-memory model first,
|
| 66 | 66 |
* but as a shortcut, you could also disable the package namespace on the
|
| 67 | 67 |
* object being added. Here is a code example to help clarify this:
|
| 68 | |
@@ -56612,7 +56612,7 @@ on yyyy-MM-dd HH:mm with libSBML version
|
|
68 |
@@ -63406,7 +63406,7 @@ on yyyy-MM-dd HH:mm with libSBML version
|
| 69 | 69 |
<td class=\'s-error\'></td>
|
| 70 | 70 |
</tr>
|
| 71 | 71 |
<tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences@endlink</td>
|
|
| 74 | 74 |
<td class=\'s-na\'></td>
|
| 75 | 75 |
<td class=\'s-na\'></td>
|
| 76 | 76 |
<td class=\'s-na\'></td>
|
| 77 | |
@@ -56972,7 +56972,7 @@ on yyyy-MM-dd HH:mm with libSBML version
|
|
77 |
@@ -63802,7 +63802,7 @@ on yyyy-MM-dd HH:mm with libSBML version
|
| 78 | 78 |
<td class=\'s-error\'></td>
|
| 79 | 79 |
</tr>
|
| 80 | 80 |
<tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction@endlink</td>
|
|
| 83 | 83 |
<td class=\'s-na\'></td>
|
| 84 | 84 |
<td class=\'s-na\'></td>
|
| 85 | 85 |
<td class=\'s-na\'></td>
|
| 86 | |
@@ -66948,7 +66948,7 @@ if (doc->getLevel() == 2)
|
|
86 |
@@ -75118,7 +75118,7 @@ if (doc->getLevel() == 2)
|
| 87 | 87 |
* <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
|
| 88 | 88 |
*
|
| 89 | 89 |
* Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 94 | 94 |
* and MathML, coupled with the desire to maintain stability and backward
|
| 95 | 95 |
--- a/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
|
| 96 | 96 |
+++ b/src/bindings/java/java-files/org/sbml/libsbml/ASTNode.java
|
| 97 | |
@@ -211,7 +211,7 @@ defined in SBML.
|
|
97 |
@@ -244,7 +244,7 @@ defined in SBML.
|
| 98 | 98 |
* <h3><a class='anchor' name='math-history'>Historical notes</a></h3>
|
| 99 | 99 |
<p>
|
| 100 | 100 |
* Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 105 | 105 |
* and MathML, coupled with the desire to maintain stability and backward
|
| 106 | 106 |
--- a/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
|
| 107 | 107 |
+++ b/src/bindings/java/java-files/org/sbml/libsbml/SBMLError.java
|
| 108 | |
@@ -5350,7 +5350,7 @@ defined in SBML.
|
|
108 |
@@ -6166,7 +6166,7 @@ defined in SBML.
|
| 109 | 109 |
<td class='s-error'></td>
|
| 110 | 110 |
</tr>
|
| 111 | 111 |
<tr><td class='code'>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences}</td>
|
|
| 114 | 114 |
<td class='s-na'></td>
|
| 115 | 115 |
<td class='s-na'></td>
|
| 116 | 116 |
<td class='s-na'></td>
|
| 117 | |
@@ -5710,7 +5710,7 @@ defined in SBML.
|
|
117 |
@@ -6562,7 +6562,7 @@ defined in SBML.
|
| 118 | 118 |
<td class='s-error'></td>
|
| 119 | 119 |
</tr>
|
| 120 | 120 |
<tr><td class='code'>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction}</td>
|
|
| 145 | 145 |
<p>
|
| 146 | 146 |
--- a/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
|
| 147 | 147 |
+++ b/src/bindings/java/java-files/org/sbml/libsbml/SBase.java
|
| 148 | |
@@ -3015,7 +3015,7 @@ void example (SBase sb)
|
|
148 |
@@ -3726,7 +3726,7 @@ void example (SBase sb)
|
| 149 | 149 |
* Hierarchical Model Composition (“comp”) package, and
|
| 150 | 150 |
* extracted parts of that model in order to construct a new model in
|
| 151 | 151 |
* memory. The new, in-memory model will not accept a component drawn from
|
|
| 156 | 156 |
* object being added. Here is a code example to help clarify this:
|
| 157 | 157 |
--- a/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
|
| 158 | 158 |
+++ b/src/bindings/java/java-files/org/sbml/libsbml/libsbml.java
|
| 159 | |
@@ -593,7 +593,7 @@ public class libsbml implements libsbmlC
|
|
159 |
@@ -606,7 +606,7 @@ public class libsbml implements libsbmlC
|
| 160 | 160 |
* appear first. The error code can provide a clue about what
|
| 161 | 161 |
* happened. For example, a file might be unreadable (either because it does
|
| 162 | 162 |
* not actually exist or because the user does not have the necessary access
|
|
| 165 | 165 |
* reported by the underlying operating system. Callers can check for these
|
| 166 | 166 |
* situations using a program fragment such as the following:
|
| 167 | 167 |
<p>
|
| 168 | |
@@ -669,7 +669,7 @@ if (doc.getNumErrors() > 0)
|
|
168 |
@@ -682,7 +682,7 @@ if (doc.getNumErrors() > 0)
|
| 169 | 169 |
* appear first. The error code can provide a clue about what
|
| 170 | 170 |
* happened. For example, a file might be unreadable (either because it does
|
| 171 | 171 |
* not actually exist or because the user does not have the necessary access
|
|
| 212 | 212 |
* reported by the underlying operating system. Callers can check for these
|
| 213 | 213 |
* situations using a program fragment such as the following:
|
| 214 | 214 |
<p>
|
| 215 | |
@@ -4268,7 +4268,7 @@ void example (SBase sb)
|
|
215 |
@@ -4984,7 +4984,7 @@ void example (SBase sb)
|
| 216 | 216 |
* Hierarchical Model Composition (“comp”) package, and
|
| 217 | 217 |
* extracted parts of that model in order to construct a new model in
|
| 218 | 218 |
* memory. The new, in-memory model will not accept a component drawn from
|
|
| 221 | 221 |
* You could reconstruct the same namespaces in the in-memory model first,
|
| 222 | 222 |
* but as a shortcut, you could also disable the package namespace on the
|
| 223 | 223 |
* object being added. Here is a code example to help clarify this:
|
| 224 | |
@@ -53291,7 +53291,7 @@ defined in SBML.
|
|
224 |
@@ -59490,7 +59490,7 @@ defined in SBML.
|
| 225 | 225 |
<td class=\'s-error\'></td>
|
| 226 | 226 |
</tr>
|
| 227 | 227 |
<tr><td class=\'code\'>{@link libsbmlConstants#CompNoMultipleReferences CompNoMultipleReferences}</td>
|
|
| 230 | 230 |
<td class=\'s-na\'></td>
|
| 231 | 231 |
<td class=\'s-na\'></td>
|
| 232 | 232 |
<td class=\'s-na\'></td>
|
| 233 | |
@@ -53651,7 +53651,7 @@ defined in SBML.
|
|
233 |
@@ -59886,7 +59886,7 @@ defined in SBML.
|
| 234 | 234 |
<td class=\'s-error\'></td>
|
| 235 | 235 |
</tr>
|
| 236 | 236 |
<tr><td class=\'code\'>{@link libsbmlConstants#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction}</td>
|
|
| 239 | 239 |
<td class=\'s-na\'></td>
|
| 240 | 240 |
<td class=\'s-na\'></td>
|
| 241 | 241 |
<td class=\'s-na\'></td>
|
| 242 | |
@@ -62461,7 +62461,7 @@ defined in SBML.
|
|
242 |
@@ -70026,7 +70026,7 @@ defined in SBML.
|
| 243 | 243 |
* <h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
|
| 244 | 244 |
<p>
|
| 245 | 245 |
* Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 250 | 250 |
* and MathML, coupled with the desire to maintain stability and backward
|
| 251 | 251 |
--- a/src/bindings/perl/LibSBML.pm
|
| 252 | 252 |
+++ b/src/bindings/perl/LibSBML.pm
|
| 253 | |
@@ -2591,7 +2591,7 @@ application read an SBML document contai
|
|
253 |
@@ -2645,7 +2645,7 @@ application read an SBML document contai
|
| 254 | 254 |
Hierarchical Model Composition (“comp”) package, and
|
| 255 | 255 |
extracted parts of that model in order to construct a new model in
|
| 256 | 256 |
memory. The new, in-memory model will not accept a component drawn from
|
|
| 259 | 259 |
You could reconstruct the same namespaces in the in-memory model first,
|
| 260 | 260 |
but as a shortcut, you could also disable the package namespace on the
|
| 261 | 261 |
object being added. Here is a code example to help clarify this:
|
| 262 | |
@@ -33633,7 +33633,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
|
| 263 | |
explanations of the infix syntax they accept.
|
|
262 |
@@ -34380,7 +34380,7 @@ as if an invalid variable name was used.
|
|
263 |
attribute for the package in question must be set to "true".
|
| 264 | 264 |
<h3><a class="anchor" name="math-history">Historical notes</a></h3>
|
| 265 | 265 |
Readers may wonder why this part of libSBML uses a seemingly less
|
| 266 | 266 |
-object-oriented design than other parts. Originally, much of libSBML was
|
|
| 270 | 270 |
and MathML, coupled with the desire to maintain stability and backward
|
| 271 | 271 |
--- a/src/bindings/perl/LibSBML.pod
|
| 272 | 272 |
+++ b/src/bindings/perl/LibSBML.pod
|
| 273 | |
@@ -2578,7 +2578,7 @@ application read an SBML document contai
|
|
273 |
@@ -2632,7 +2632,7 @@ application read an SBML document contai
|
| 274 | 274 |
Hierarchical Model Composition (“comp”) package, and
|
| 275 | 275 |
extracted parts of that model in order to construct a new model in
|
| 276 | 276 |
memory. The new, in-memory model will not accept a component drawn from
|
|
| 279 | 279 |
You could reconstruct the same namespaces in the in-memory model first,
|
| 280 | 280 |
but as a shortcut, you could also disable the package namespace on the
|
| 281 | 281 |
object being added. Here is a code example to help clarify this:
|
| 282 | |
@@ -33620,7 +33620,7 @@ ASTNode} and @sbmlfunction{parseL3Formul
|
| 283 | |
explanations of the infix syntax they accept.
|
|
282 |
@@ -34367,7 +34367,7 @@ as if an invalid variable name was used.
|
|
283 |
attribute for the package in question must be set to "true".
|
| 284 | 284 |
<h3><a class="anchor" name="math-history">Historical notes</a></h3>
|
| 285 | 285 |
Readers may wonder why this part of libSBML uses a seemingly less
|
| 286 | 286 |
-object-oriented design than other parts. Originally, much of libSBML was
|
|
| 290 | 290 |
and MathML, coupled with the desire to maintain stability and backward
|
| 291 | 291 |
--- a/src/bindings/python/libsbml-doxygen.py
|
| 292 | 292 |
+++ b/src/bindings/python/libsbml-doxygen.py
|
| 293 | |
@@ -1188,7 +1188,7 @@ class SBMLReader(_object):
|
|
293 |
@@ -1202,7 +1202,7 @@ class SBMLReader(_object):
|
| 294 | 294 |
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
|
| 295 | 295 |
happened. For example, a file might be unreadable (either because it does
|
| 296 | 296 |
not actually exist or because the user does not have the necessary access
|
|
| 299 | 299 |
reported by the underlying operating system. Callers can check for these
|
| 300 | 300 |
situations using a program fragment such as the following:
|
| 301 | 301 |
@if cpp
|
| 302 | |
@@ -1379,7 +1379,7 @@ class SBMLReader(_object):
|
|
302 |
@@ -1393,7 +1393,7 @@ class SBMLReader(_object):
|
| 303 | 303 |
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
|
| 304 | 304 |
happened. For example, a file might be unreadable (either because it does
|
| 305 | 305 |
not actually exist or because the user does not have the necessary access
|
|
| 308 | 308 |
reported by the underlying operating system. Callers can check for these
|
| 309 | 309 |
situations using a program fragment such as the following:
|
| 310 | 310 |
@if cpp
|
| 311 | |
@@ -1722,7 +1722,7 @@ def readSBML(*args):
|
|
311 |
@@ -1736,7 +1736,7 @@ def readSBML(*args):
|
| 312 | 312 |
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
|
| 313 | 313 |
happened. For example, a file might be unreadable (either because it does
|
| 314 | 314 |
not actually exist or because the user does not have the necessary access
|
|
| 317 | 317 |
reported by the underlying operating system. Callers can check for these
|
| 318 | 318 |
situations using a program fragment such as the following:
|
| 319 | 319 |
@if cpp
|
| 320 | |
@@ -1889,7 +1889,7 @@ def readSBMLFromFile(*args):
|
|
320 |
@@ -1903,7 +1903,7 @@ def readSBMLFromFile(*args):
|
| 321 | 321 |
enumeration #XMLErrorCode_t)@endif@~ can provide a clue about what
|
| 322 | 322 |
happened. For example, a file might be unreadable (either because it does
|
| 323 | 323 |
not actually exist or because the user does not have the necessary access
|
|
| 326 | 326 |
reported by the underlying operating system. Callers can check for these
|
| 327 | 327 |
situations using a program fragment such as the following:
|
| 328 | 328 |
@if cpp
|
| 329 | |
@@ -5566,7 +5566,7 @@ class SBase(_object):
|
|
329 |
@@ -6260,7 +6260,7 @@ class SBase(_object):
|
| 330 | 330 |
Hierarchical %Model Composition (“comp”) package, and
|
| 331 | 331 |
extracted parts of that model in order to construct a new model in
|
| 332 | 332 |
memory. The new, in-memory model will not accept a component drawn from
|
|
| 335 | 335 |
You could reconstruct the same namespaces in the in-memory model first,
|
| 336 | 336 |
but as a shortcut, you could also disable the package namespace on the
|
| 337 | 337 |
object being added. Here is a code example to help clarify this:
|
| 338 | |
@@ -58581,7 +58581,7 @@ class SBMLError(XMLError):
|
|
338 |
@@ -64936,7 +64936,7 @@ class SBMLError(XMLError):
|
| 339 | 339 |
<td class='s-error'></td>
|
| 340 | 340 |
</tr>
|
| 341 | 341 |
<tr><td class='code'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences@endlink</td>
|
|
| 344 | 344 |
<td class='s-na'></td>
|
| 345 | 345 |
<td class='s-na'></td>
|
| 346 | 346 |
<td class='s-na'></td>
|
| 347 | |
@@ -58941,7 +58941,7 @@ class SBMLError(XMLError):
|
|
347 |
@@ -65332,7 +65332,7 @@ class SBMLError(XMLError):
|
| 348 | 348 |
<td class='s-error'></td>
|
| 349 | 349 |
</tr>
|
| 350 | 350 |
<tr><td class='code'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction@endlink</td>
|
|
| 353 | 353 |
<td class='s-na'></td>
|
| 354 | 354 |
<td class='s-na'></td>
|
| 355 | 355 |
<td class='s-na'></td>
|
| 356 | |
@@ -69613,7 +69613,7 @@ class ASTNode(ASTBase):
|
|
356 |
@@ -77359,7 +77359,7 @@ class ASTNode(ASTBase):
|
| 357 | 357 |
<h3><a class='anchor' name='math-history'>Historical notes</a></h3>
|
| 358 | 358 |
|
| 359 | 359 |
Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 364 | 364 |
and MathML, coupled with the desire to maintain stability and backward
|
| 365 | 365 |
--- a/src/bindings/python/libsbml.py
|
| 366 | 366 |
+++ b/src/bindings/python/libsbml.py
|
| 367 | |
@@ -812,7 +812,7 @@ def readSBML(*args):
|
|
367 |
@@ -824,7 +824,7 @@ def readSBML(*args):
|
| 368 | 368 |
appear first. The error code can provide a clue about what happened.
|
| 369 | 369 |
For example, a file might be unreadable (either because it does not
|
| 370 | 370 |
actually exist or because the user does not have the necessary access
|
|
| 373 | 373 |
been reported by the underlying operating system. Callers can check
|
| 374 | 374 |
for these situations using a program fragment such as the following:
|
| 375 | 375 |
|
| 376 | |
@@ -1601,7 +1601,7 @@ class SBMLReader(_object):
|
|
376 |
@@ -1699,7 +1699,7 @@ class SBMLReader(_object):
|
| 377 | 377 |
appear first. The error code can provide a clue about what happened.
|
| 378 | 378 |
For example, a file might be unreadable (either because it does not
|
| 379 | 379 |
actually exist or because the user does not have the necessary access
|
|
| 382 | 382 |
been reported by the underlying operating system. Callers can check
|
| 383 | 383 |
for these situations using a program fragment such as the following:
|
| 384 | 384 |
|
| 385 | |
@@ -1681,7 +1681,7 @@ class SBMLReader(_object):
|
|
385 |
@@ -1779,7 +1779,7 @@ class SBMLReader(_object):
|
| 386 | 386 |
appear first. The error code can provide a clue about what happened.
|
| 387 | 387 |
For example, a file might be unreadable (either because it does not
|
| 388 | 388 |
actually exist or because the user does not have the necessary access
|
|
| 391 | 391 |
been reported by the underlying operating system. Callers can check
|
| 392 | 392 |
for these situations using a program fragment such as the following:
|
| 393 | 393 |
|
| 394 | |
@@ -1906,7 +1906,7 @@ def readSBMLFromFile(*args):
|
|
394 |
@@ -2004,7 +2004,7 @@ def readSBMLFromFile(*args):
|
| 395 | 395 |
appear first. The error code can provide a clue about what happened.
|
| 396 | 396 |
For example, a file might be unreadable (either because it does not
|
| 397 | 397 |
actually exist or because the user does not have the necessary access
|
|
| 400 | 400 |
been reported by the underlying operating system. Callers can check
|
| 401 | 401 |
for these situations using a program fragment such as the following:
|
| 402 | 402 |
|
| 403 | |
@@ -50754,7 +50754,7 @@ class SBMLError(XMLError):
|
| 404 | |
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
|
| 405 | |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
|
| 406 | |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
|
| 407 | |
- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | |
|
| 408 | |
+ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | |
|
| 409 | |
|CompPortMustReferenceObject |Port must reference an object | | | | | | | |
|
| 410 | |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
|
| 411 | |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
|
| 412 | |
@@ -50790,7 +50790,7 @@ class SBMLError(XMLError):
|
| 413 | |
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
|
| 414 | |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
|
| 415 | |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
|
| 416 | |
- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | |
|
| 417 | |
+ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. | | | | | | | |
|
| 418 | |
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
|
| 419 | |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
|
| 420 | |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
|
| 421 | |
@@ -57539,7 +57539,7 @@ class ASTNode(ASTBase):
|
|
403 |
@@ -56002,7 +56002,7 @@ class SBMLError(XMLError):
|
|
404 |
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | | |
|
|
405 |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | | |
|
|
406 |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | | |
|
|
407 |
- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | | |
|
|
408 |
+ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | | |
|
|
409 |
|CompPortMustReferenceObject |Port must reference an object | | | | | | | | |
|
|
410 |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | | |
|
|
411 |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | | |
|
|
412 |
@@ -56038,7 +56038,7 @@ class SBMLError(XMLError):
|
|
413 |
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | | |
|
|
414 |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | | |
|
|
415 |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | | |
|
|
416 |
- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | | |
|
|
417 |
+ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fucntions is deprecated. | | | | | | | | |
|
|
418 |
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | | |
|
|
419 |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | | |
|
|
420 |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | | |
|
|
421 |
@@ -63070,7 +63070,7 @@ class ASTNode(ASTBase):
|
| 422 | 422 |
......................................................................
|
| 423 | 423 |
|
| 424 | 424 |
Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 429 | 429 |
AST and MathML, coupled with the desire to maintain stability and
|
| 430 | 430 |
--- a/src/bindings/python/libsbml_wrap.cpp
|
| 431 | 431 |
+++ b/src/bindings/python/libsbml_wrap.cpp
|
| 432 | |
@@ -119949,7 +119949,7 @@ static PyMethodDef SwigMethods[] = {
|
|
432 |
@@ -123366,7 +123366,7 @@ static PyMethodDef SwigMethods[] = {
|
| 433 | 433 |
"appear first. The error code can provide a clue about what happened.\n"
|
| 434 | 434 |
"For example, a file might be unreadable (either because it does not\n"
|
| 435 | 435 |
"actually exist or because the user does not have the necessary access\n"
|
|
| 438 | 438 |
"been reported by the underlying operating system. Callers can check\n"
|
| 439 | 439 |
"for these situations using a program fragment such as the following:\n"
|
| 440 | 440 |
"\n"
|
| 441 | |
@@ -120030,7 +120030,7 @@ static PyMethodDef SwigMethods[] = {
|
|
441 |
@@ -123447,7 +123447,7 @@ static PyMethodDef SwigMethods[] = {
|
| 442 | 442 |
"appear first. The error code can provide a clue about what happened.\n"
|
| 443 | 443 |
"For example, a file might be unreadable (either because it does not\n"
|
| 444 | 444 |
"actually exist or because the user does not have the necessary access\n"
|
|
| 447 | 447 |
"been reported by the underlying operating system. Callers can check\n"
|
| 448 | 448 |
"for these situations using a program fragment such as the following:\n"
|
| 449 | 449 |
"\n"
|
| 450 | |
@@ -120191,7 +120191,7 @@ static PyMethodDef SwigMethods[] = {
|
|
450 |
@@ -123608,7 +123608,7 @@ static PyMethodDef SwigMethods[] = {
|
| 451 | 451 |
"appear first. The error code can provide a clue about what happened.\n"
|
| 452 | 452 |
"For example, a file might be unreadable (either because it does not\n"
|
| 453 | 453 |
"actually exist or because the user does not have the necessary access\n"
|
|
| 458 | 458 |
"\n"
|
| 459 | 459 |
--- a/src/bindings/python/local.i
|
| 460 | 460 |
+++ b/src/bindings/python/local.i
|
| 461 | |
@@ -560,7 +560,7 @@ SBMLReader::readSBML(const std::string&)
|
|
461 |
@@ -567,7 +567,7 @@ SBMLReader::readSBML(const std::string&)
|
| 462 | 462 |
appear first. The error code can provide a clue about what happened.
|
| 463 | 463 |
For example, a file might be unreadable (either because it does not
|
| 464 | 464 |
actually exist or because the user does not have the necessary access
|
|
| 467 | 467 |
been reported by the underlying operating system. Callers can check
|
| 468 | 468 |
for these situations using a program fragment such as the following:
|
| 469 | 469 |
|
| 470 | |
@@ -643,7 +643,7 @@ SBMLReader::readSBMLFromFile(const std::
|
|
470 |
@@ -650,7 +650,7 @@ SBMLReader::readSBMLFromFile(const std::
|
| 471 | 471 |
appear first. The error code can provide a clue about what happened.
|
| 472 | 472 |
For example, a file might be unreadable (either because it does not
|
| 473 | 473 |
actually exist or because the user does not have the necessary access
|
|
| 476 | 476 |
been reported by the underlying operating system. Callers can check
|
| 477 | 477 |
for these situations using a program fragment such as the following:
|
| 478 | 478 |
|
| 479 | |
@@ -724,7 +724,7 @@ def readSBML(*args):
|
|
479 |
@@ -731,7 +731,7 @@ def readSBML(*args):
|
| 480 | 480 |
appear first. The error code can provide a clue about what happened.
|
| 481 | 481 |
For example, a file might be unreadable (either because it does not
|
| 482 | 482 |
actually exist or because the user does not have the necessary access
|
|
| 523 | 523 |
reported by the underlying operating system. Callers can check for these
|
| 524 | 524 |
situations using a program fragment such as the following:
|
| 525 | 525 |
@if cpp
|
| 526 | |
@@ -4067,7 +4067,7 @@ application read an SBML document contai
|
|
526 |
@@ -4735,7 +4735,7 @@ application read an SBML document contai
|
| 527 | 527 |
Hierarchical %Model Composition (“comp”) package, and
|
| 528 | 528 |
extracted parts of that model in order to construct a new model in
|
| 529 | 529 |
memory. The new, in-memory model will not accept a component drawn from
|
|
| 532 | 532 |
You could reconstruct the same namespaces in the in-memory model first,
|
| 533 | 533 |
but as a shortcut, you could also disable the package namespace on the
|
| 534 | 534 |
object being added. Here is a code example to help clarify this:
|
| 535 | |
@@ -51075,7 +51075,7 @@ from libSBML core.@endif
|
|
535 |
@@ -57184,7 +57184,7 @@ from libSBML core.@endif
|
| 536 | 536 |
<td class=\'s-error\'></td>
|
| 537 | 537 |
</tr>
|
| 538 | 538 |
<tr><td class=\'code\'>@link libsbml#CompNoMultipleReferences CompNoMultipleReferences@endlink</td>
|
|
| 541 | 541 |
<td class=\'s-na\'></td>
|
| 542 | 542 |
<td class=\'s-na\'></td>
|
| 543 | 543 |
<td class=\'s-na\'></td>
|
| 544 | |
@@ -51435,7 +51435,7 @@ from libSBML core.@endif
|
|
544 |
@@ -57580,7 +57580,7 @@ from libSBML core.@endif
|
| 545 | 545 |
<td class=\'s-error\'></td>
|
| 546 | 546 |
</tr>
|
| 547 | 547 |
<tr><td class=\'code\'>@link libsbml#CompDeprecatedReplaceFunction CompDeprecatedReplaceFunction@endlink</td>
|
|
| 550 | 550 |
<td class=\'s-na\'></td>
|
| 551 | 551 |
<td class=\'s-na\'></td>
|
| 552 | 552 |
<td class=\'s-na\'></td>
|
| 553 | |
@@ -60481,7 +60481,7 @@ explanations of the infix syntax they ac
|
|
553 |
@@ -67956,7 +67956,7 @@ attribute for the package in question mu
|
| 554 | 554 |
<h3><a class=\'anchor\' name=\'math-history\'>Historical notes</a></h3>
|
| 555 | 555 |
|
| 556 | 556 |
Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 597 | 597 |
been reported by the underlying operating system. Callers can check
|
| 598 | 598 |
for these situations using a program fragment such as the following:
|
| 599 | 599 |
|
| 600 | |
@@ -41952,7 +41952,7 @@ If the name of a code does not begin wit
|
| 601 | |
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | |
|
| 602 | |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | |
|
| 603 | |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | |
|
| 604 | |
- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | |
|
| 605 | |
+ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | |
|
| 606 | |
|CompPortMustReferenceObject |Port must reference an object | | | | | | | |
|
| 607 | |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | |
|
| 608 | |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | |
|
| 609 | |
@@ -41988,7 +41988,7 @@ If the name of a code does not begin wit
|
| 610 | |
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | |
|
| 611 | |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | |
|
| 612 | |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | |
|
| 613 | |
- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | |
|
| 614 | |
+ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. | | | | | | | |
|
| 615 | |
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | |
|
| 616 | |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | |
|
| 617 | |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | |
|
| 618 | |
@@ -46983,7 +46983,7 @@ Historical notes
|
|
600 |
@@ -46872,7 +46872,7 @@ If the name of a code does not begin wit
|
|
601 |
|CompDeprecatedSBaseRefSpelling |The spelling 'sbaseRef' is deprecated | | | | | | | | |
|
|
602 |
|CompSBaseRefMustReferenceObject |An SBaseRef must reference an object. | | | | | | | | |
|
|
603 |
|CompSBaseRefMustReferenceOnlyOneObject |An SBaseRef must reference only one other object. | | | | | | | | |
|
|
604 |
- |CompNoMultipleReferences |Objects may not be referenced by mutiple SBaseRef constructs. | | | | | | | | |
|
|
605 |
+ |CompNoMultipleReferences |Objects may not be referenced by multiple SBaseRef constructs. | | | | | | | | |
|
|
606 |
|CompPortMustReferenceObject |Port must reference an object | | | | | | | | |
|
|
607 |
|CompPortMustReferenceOnlyOneObject |Port must reference only one other object. | | | | | | | | |
|
|
608 |
|CompPortAllowedAttributes |Allowed attributes on a Port | | | | | | | | |
|
|
609 |
@@ -46908,7 +46908,7 @@ If the name of a code does not begin wit
|
|
610 |
|CompFlatteningNotImplementedReqd |Flattening not implemented for required package. | | | | | | | | |
|
|
611 |
|CompFlatteningWarning |Flattening reference may come from package. | | | | | | | | |
|
|
612 |
|CompDeprecatedDeleteFunction |The performDeletions functions is deprecated. | | | | | | | | |
|
|
613 |
- |CompDeprecatedReplaceFunction |The performReplacementsAndConversions fuctions is deprecated. | | | | | | | | |
|
|
614 |
+ |CompDeprecatedReplaceFunction |The performReplacementsAndConversions functions is deprecated. | | | | | | | | |
|
|
615 |
|CompDeletedReplacement |Element deleted before a subelement could be replaced. | | | | | | | | |
|
|
616 |
|CompIdRefMayReferenceUnknownPackage |The 'comp:idRef' attribute must be the 'id' of a model element | | | | | | | | |
|
|
617 |
|CompMetaIdRefMayReferenceUnknownPkg |The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | | | | | | | | |
|
|
618 |
@@ -52160,7 +52160,7 @@ Historical notes
|
| 619 | 619 |
......................................................................
|
| 620 | 620 |
|
| 621 | 621 |
Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 637 | 637 |
* @if cpp
|
| 638 | 638 |
--- a/src/sbml/SBase.h
|
| 639 | 639 |
+++ b/src/sbml/SBase.h
|
| 640 | |
@@ -2785,7 +2785,7 @@ s.setNotes("<body xmlns='http://www.w3.o
|
|
640 |
@@ -2753,7 +2753,7 @@ s.setNotes("<body xmlns='http://www.w3.o
|
| 641 | 641 |
* Hierarchical %Model Composition (“comp”) package, and
|
| 642 | 642 |
* extracted parts of that model in order to construct a new model in
|
| 643 | 643 |
* memory. The new, in-memory model will not accept a component drawn from
|
|
| 648 | 648 |
* object being added. Here is a code example to help clarify this:
|
| 649 | 649 |
--- a/src/sbml/common/common-sbmlerror-codes.h
|
| 650 | 650 |
+++ b/src/sbml/common/common-sbmlerror-codes.h
|
| 651 | |
@@ -5197,7 +5197,7 @@
|
|
651 |
@@ -6013,7 +6013,7 @@
|
| 652 | 652 |
<td class="s-error"></td>
|
| 653 | 653 |
</tr>
|
| 654 | 654 |
<tr><td class="code">@sbmlconstant{CompNoMultipleReferences, SBMLErrorCode_t}</td>
|
|
| 657 | 657 |
<td class="s-na"></td>
|
| 658 | 658 |
<td class="s-na"></td>
|
| 659 | 659 |
<td class="s-na"></td>
|
| 660 | |
@@ -5557,7 +5557,7 @@
|
|
660 |
@@ -6409,7 +6409,7 @@
|
| 661 | 661 |
<td class="s-error"></td>
|
| 662 | 662 |
</tr>
|
| 663 | 663 |
<tr><td class="code">@sbmlconstant{CompDeprecatedReplaceFunction, SBMLErrorCode_t}</td>
|
|
| 668 | 668 |
<td class="s-na"></td>
|
| 669 | 669 |
--- a/src/sbml/math/ASTNode.h
|
| 670 | 670 |
+++ b/src/sbml/math/ASTNode.h
|
| 671 | |
@@ -71,7 +71,7 @@
|
|
671 |
@@ -89,7 +89,7 @@
|
| 672 | 672 |
* <h3><a class="anchor" name="math-history">Historical notes</a></h3>
|
| 673 | 673 |
*
|
| 674 | 674 |
* Readers may wonder why this part of libSBML uses a seemingly less
|
|
| 728 | 728 |
*
|
| 729 | 729 |
* @param node the XMLNode object reference that describes the ColorDefinition
|
| 730 | 730 |
* object to be instantiated.
|
| 731 | |
@@ -634,7 +634,7 @@ bool ColorDefinition::accept (SBMLVisito
|
|
731 |
@@ -636,7 +636,7 @@ bool ColorDefinition::accept (SBMLVisito
|
| 732 | 732 |
* The XMLNode object has to contain a valid XML representation of a
|
| 733 | 733 |
* ListOfColorDefinitions object as defined in the render extension specification.
|
| 734 | 734 |
* This method is normally called when render information is read from a file and
|
|
| 830 | 830 |
*
|
| 831 | 831 |
* @param node the XMLNode object reference that describes the GradientBase
|
| 832 | 832 |
* object to be instantiated.
|
| 833 | |
@@ -733,7 +733,7 @@ bool GradientBase::accept (SBMLVisitor&
|
|
833 |
@@ -736,7 +736,7 @@ bool GradientBase::accept (SBMLVisitor&
|
| 834 | 834 |
* The XMLNode object has to contain a valid XML representation of a
|
| 835 | 835 |
* ListOfGradientDefinitions object as defined in the render extension specification.
|
| 836 | 836 |
* This method is normally called when render information is read from a file and
|
|
| 901 | 901 |
* object to be instantiated.
|
| 902 | 902 |
--- a/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
|
| 903 | 903 |
+++ b/src/sbml/packages/render/sbml/GraphicalPrimitive1D.cpp
|
| 904 | |
@@ -113,7 +113,7 @@ GraphicalPrimitive1D::~GraphicalPrimitiv
|
|
904 |
@@ -114,7 +114,7 @@ GraphicalPrimitive1D::~GraphicalPrimitiv
|
| 905 | 905 |
* The XMLNode object has to contain a valid XML representation of a
|
| 906 | 906 |
* GraphicalPrimitive1D object as defined in the render extension specification.
|
| 907 | 907 |
* This method is normally called when render information is read from a file and
|
|
| 972 | 972 |
*
|
| 973 | 973 |
* @param node the XMLNode object reference that describes the Image
|
| 974 | 974 |
* object to be instantiated.
|
| 975 | |
@@ -347,7 +347,7 @@ const std::string& Image::getImageRefere
|
|
975 |
@@ -349,7 +349,7 @@ const std::string& Image::getImageRefere
|
| 976 | 976 |
/** @cond doxygenLibsbmlInternal */
|
| 977 | 977 |
/*
|
| 978 | 978 |
* Sets the position of the image relative to its viewport.
|
|
| 981 | 981 |
* or a combination of both.
|
| 982 | 982 |
* The z coordinatee can be omitted. In that case it is set to 0.
|
| 983 | 983 |
*
|
| 984 | |
@@ -366,7 +366,7 @@ void Image::setCoordinates(const RelAbsV
|
|
984 |
@@ -368,7 +368,7 @@ void Image::setCoordinates(const RelAbsV
|
| 985 | 985 |
/** @cond doxygenLibsbmlInternal */
|
| 986 | 986 |
/*
|
| 987 | 987 |
* Sets the x coordinate of the image position.
|
|
| 990 | 990 |
* or a combination of both.
|
| 991 | 991 |
*
|
| 992 | 992 |
* @param x x coordinate of the image position
|
| 993 | |
@@ -380,7 +380,7 @@ void Image::setX(const RelAbsVector& coo
|
|
993 |
@@ -382,7 +382,7 @@ void Image::setX(const RelAbsVector& coo
|
| 994 | 994 |
/** @cond doxygenLibsbmlInternal */
|
| 995 | 995 |
/*
|
| 996 | 996 |
* Sets the y coordinate of the image position.
|
|
| 999 | 999 |
* or a combination of both.
|
| 1000 | 1000 |
*
|
| 1001 | 1001 |
* @param y y coordinate of the image position
|
| 1002 | |
@@ -394,7 +394,7 @@ void Image::setY(const RelAbsVector& coo
|
|
1002 |
@@ -396,7 +396,7 @@ void Image::setY(const RelAbsVector& coo
|
| 1003 | 1003 |
/** @cond doxygenLibsbmlInternal */
|
| 1004 | 1004 |
/*
|
| 1005 | 1005 |
* Sets the z coordinate of the image position.
|
|
| 1324 | 1324 |
* object to be instantiated.
|
| 1325 | 1325 |
--- a/src/sbml/packages/render/sbml/RenderInformationBase.cpp
|
| 1326 | 1326 |
+++ b/src/sbml/packages/render/sbml/RenderInformationBase.cpp
|
| 1327 | |
@@ -307,9 +307,9 @@ void RenderInformationBase::setProgramVe
|
|
1327 |
@@ -308,9 +308,9 @@ void RenderInformationBase::setProgramVe
|
| 1328 | 1328 |
* Global render information objects can only reference other global
|
| 1329 | 1329 |
* render information objects, local render information objects can reference other local
|
| 1330 | 1330 |
* render information objects from the same list of local render information or other
|
|
| 1336 | 1336 |
*/
|
| 1337 | 1337 |
const std::string& RenderInformationBase::getReferenceRenderInformationId() const
|
| 1338 | 1338 |
{
|
| 1339 | |
@@ -320,10 +320,10 @@ const std::string& RenderInformationBase
|
|
1339 |
@@ -321,10 +321,10 @@ const std::string& RenderInformationBase
|
| 1340 | 1340 |
/** @cond doxygenLibsbmlInternal */
|
| 1341 | 1341 |
/*
|
| 1342 | 1342 |
* Sets the id of the referenced render information object.
|
|
| 1398 | 1398 |
* object to be instantiated.
|
| 1399 | 1399 |
--- a/src/sbml/packages/render/sbml/Style.cpp
|
| 1400 | 1400 |
+++ b/src/sbml/packages/render/sbml/Style.cpp
|
| 1401 | |
@@ -553,7 +553,7 @@ const std::string& Style::getElementName
|
|
1401 |
@@ -555,7 +555,7 @@ const std::string& Style::getElementName
|
| 1402 | 1402 |
* The XMLNode object has to contain a valid XML representation of a
|
| 1403 | 1403 |
* Style object as defined in the render extension specification.
|
| 1404 | 1404 |
* This method is normally called when render information is read from a file and
|