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[sbml-svn] SF.net SVN: sbml:[13063] trunk/libsbml/src
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From: <mh...@us...> - 2011-02-27 05:16:36
|
Revision: 13063
http://sbml.svn.sourceforge.net/sbml/?rev=13063&view=rev
Author: mhucka
Date: 2011-02-27 05:16:27 +0000 (Sun, 27 Feb 2011)
Log Message:
-----------
Improved handling of conditional documentation sections
for different languages. Now using @else inside @if...@endif, after having
modified swigdoc.py to make it work.
Modified Paths:
--------------
trunk/libsbml/src/annotation/CVTerm.h
trunk/libsbml/src/annotation/RDFAnnotation.h
trunk/libsbml/src/math/ASTNode.h
trunk/libsbml/src/math/FormulaFormatter.h
trunk/libsbml/src/math/FormulaParser.h
trunk/libsbml/src/sbml/Compartment.h
trunk/libsbml/src/sbml/CompartmentType.h
trunk/libsbml/src/sbml/InitialAssignment.h
trunk/libsbml/src/sbml/KineticLaw.h
trunk/libsbml/src/sbml/LocalParameter.h
trunk/libsbml/src/sbml/Model.h
trunk/libsbml/src/sbml/Parameter.h
trunk/libsbml/src/sbml/Rule.h
trunk/libsbml/src/sbml/SBMLDocument.h
trunk/libsbml/src/sbml/SBMLError.h
trunk/libsbml/src/sbml/SBMLErrorLog.h
trunk/libsbml/src/sbml/SBMLNamespaces.h
trunk/libsbml/src/sbml/SBMLReader.h
trunk/libsbml/src/sbml/SBMLWriter.h
trunk/libsbml/src/sbml/SBase.h
trunk/libsbml/src/sbml/Species.h
trunk/libsbml/src/sbml/SpeciesReference.h
trunk/libsbml/src/sbml/SpeciesType.h
trunk/libsbml/src/sbml/Unit.h
trunk/libsbml/src/sbml/UnitDefinition.h
trunk/libsbml/src/xml/XMLError.h
trunk/libsbml/src/xml/XMLErrorLog.h
trunk/libsbml/src/xml/XMLNamespaces.h
trunk/libsbml/src/xml/XMLNode.h
trunk/libsbml/src/xml/XMLToken.h
Modified: trunk/libsbml/src/annotation/CVTerm.h
===================================================================
--- trunk/libsbml/src/annotation/CVTerm.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/annotation/CVTerm.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -55,34 +55,34 @@
* such as Species, Compartment, etc. The following template illustrates
* the different parts of SBML annotations in XML form:
*
-<div class="fragment">
-<<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid="<span style="border-bottom: 1px solid black">meta id</span>" <span style="background-color: #d0eed0">+++</span>><br>
- <span style="background-color: #d0eed0">+++</span><br>
- <annotation><br>
- <span style="background-color: #d0eed0">+++</span><br>
- <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
- xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
- xmlns:dcterm="http://purl.org/dc/terms/"<br>
- xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
- xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
- xmlns:bqmodel="http://biomodels.net/model-qualifiers/" ><br>
- <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
- <span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
- <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <rdf:Bag><br>
- <rdf:li rdf:resource="<span style="background-color: #d0d0ee">URI</span>" /><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Bag><br>
- </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Description><br>
- <span style="background-color: #d0eed0">+++</span><br>
- </rdf:RDF><br>
- <span style="background-color: #d0eed0">+++</span><br>
- </annotation><br>
- <span style="background-color: #d0eed0">+++</span><br>
-</<span style="background-color: #bbb">SBML_ELEMENT</span>><br>
-</div>
+ <div class="fragment">
+ <<span style="background-color: #bbb">SBML_ELEMENT</span> <span style="background-color: #d0eed0">+++</span> metaid="<span style="border-bottom: 1px solid black">meta id</span>" <span style="background-color: #d0eed0">+++</span>><br>
+ <span style="background-color: #d0eed0">+++</span><br>
+ <annotation><br>
+ <span style="background-color: #d0eed0">+++</span><br>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<br>
+ xmlns:dc="http://purl.org/dc/elements/1.1/"<br>
+ xmlns:dcterm="http://purl.org/dc/terms/"<br>
+ xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#"<br>
+ xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"<br>
+ xmlns:bqmodel="http://biomodels.net/model-qualifiers/" ><br>
+ <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
+ <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
+ <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
+ <rdf:Bag><br>
+ <rdf:li rdf:resource="<span style="background-color: #d0d0ee">URI</span>" /><br>
+ <span style="background-color: #edd">...</span><br>
+ </rdf:Bag><br>
+ </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
+ <span style="background-color: #edd">...</span><br>
+ </rdf:Description><br>
+ <span style="background-color: #d0eed0">+++</span><br>
+ </rdf:RDF><br>
+ <span style="background-color: #d0eed0">+++</span><br>
+ </annotation><br>
+ <span style="background-color: #d0eed0">+++</span><br>
+ </<span style="background-color: #bbb">SBML_ELEMENT</span>><br>
+ </div>
*
* In the template above, the placeholder
* <span class="code" style="background-color: #bbb">SBML_ELEMENT</span> stands for
@@ -99,7 +99,7 @@
* <span class="code" style="background-color: #edd">...</span>
* are placeholders for zero or more elements of the same form as the
* immediately preceding element. The optional content
- * <span class="code" style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span>
+ * <span class="code" style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span>
* is a creation and modification history; in libSBML, this is stored
* using ModelHistory objects.
*
@@ -226,8 +226,7 @@
/**
* Creates an empty CVTerm, optionally with the given
- * @if clike #QualifierType_t@endif@if java qualifier type code@endif value
- * @p type.
+ * @if clike #QualifierType_t value@else qualifier@endif @p type.
*
* The SBML Level 2 and Level 3 specifications define a simple
* format for annotating models when (a) referring to controlled
@@ -253,8 +252,8 @@
* an explicit value for @p type is not given, this method defaults to
* using @link QualifierType_t#UNKNOWN_QUALIFIER
* UNKNOWN_QUALIFIER@endlink. The
- * @if clike #QualifierType_t@endif@if java qualifier type code@endif
- * type value can be set later using the
+ * @if clike #QualifierType_t value@else qualifier type@endif
+ * can be set later using the
* CVTerm::setQualifierType(@if java int type@endif) method.
*
* Different BioModels.net qualifier elements encode different types of
@@ -263,7 +262,7 @@
* qualifiers web page</a> for an explanation of the meaning of these
* different qualifiers.
*
- * @param type a @if clike #QualifierType_t@endif@if java qualifier type code@endif value
+ * @param type a @if clike #QualifierType_t value@else qualifier type@endif
*
* @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
*/
@@ -337,7 +336,7 @@
/**
- * Returns the qualifier type code for this CVTerm object.
+ * Returns the qualifier type of this CVTerm object.
*
* @htmlinclude cvterm-common-description-text.html
*
@@ -363,8 +362,8 @@
* the @em other two methods to call to find out the specific
* relationship.
*
- * @return the @if clike #QualifierType_t@endif@if java qualifier type code@endif value of this object or
- * @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
+ * @return the @if clike #QualifierType_t value@else qualifier type@endif
+ * of this object or @link QualifierType_t#UNKNOWN_QUALIFIER UNKNOWN_QUALIFIER@endlink
* (the default).
*
* @see getResources()
@@ -375,7 +374,7 @@
/**
- * Returns the model qualifier type code for this CVTerm object.
+ * Returns the model qualifier type of this CVTerm object.
*
* @htmlinclude cvterm-common-description-text.html
*
@@ -399,15 +398,15 @@
* unknown by libSBML and reported as
* @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink.
*
- * @return the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif value of this object or
- * @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink
+ * @return the @if clike #ModelQualifierType_t value@else model qualifier type@endif
+ * of this object or @link ModelQualifierType_t#BQM_UNKNOWN BQM_UNKNOWN@endlink
* (the default).
*/
ModelQualifierType_t getModelQualifierType();
/**
- * Returns the biological qualifier type code for this CVTerm object.
+ * Returns the biological qualifier type of this CVTerm object.
*
* @htmlinclude cvterm-common-description-text.html
*
@@ -440,8 +439,8 @@
* unknown by libSBML and reported as
* @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
*
- * @return the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif value of this object or
- * @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink
+ * @return the @if clike #BiolQualifierType_t value@else biology qualifier type@endif
+ * of this object or @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink
* (the default).
*/
BiolQualifierType_t getBiologicalQualifierType();
@@ -545,11 +544,11 @@
/**
- * Sets the @if clike #QualifierType_t@endif@if java qualifier type code@endif value of this CVTerm object.
+ * Sets the @if clike #QualifierType_t@else qualifier code@endif of this
+ * CVTerm object.
*
- * @param type the @if clike #QualifierType_t@endif@if java qualifier type code@endif type value
- * function. The possible values
- * returned by this function are:
+ * @param type the @if clike #QualifierType_t value@else qualifier type@endif.
+ * The possible values returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
*
* @see getQualifierType()
@@ -558,13 +557,13 @@
/**
- * Sets the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif value of this CVTerm object.
+ * Sets the @if clike #ModelQualifierType_t value@else model qualifier type@endif
+ * of this CVTerm object.
*
- * @param type the @if clike #ModelQualifierType_t@endif@if java model qualifier type code@endif value
+ * @param type the @if clike #ModelQualifierType_t value@else model qualifier type@endif
*
* @return integer value indicating success/failure of the
- * function. The possible values
- * returned by this function are:
+ * function. The possible values returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
*
@@ -580,19 +579,19 @@
/**
- * Sets the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif of this CVTerm object.
+ * Sets the @if clike #BiolQualifierType_t value@else biology qualifier type@endif
+ * of this CVTerm object.
*
- * @param type the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif value
+ * @param type the @if clike #BiolQualifierType_t value@else biology qualifier type@endif.
*
* @return integer value indicating success/failure of the
- * function. The possible values
- * returned by this function are:
+ * function. The possible values returned by this function are:
* @li @link OperationReturnValues_t#LIBSBML_OPERATION_SUCCESS LIBSBML_OPERATION_SUCCESS@endlink
* @li @link OperationReturnValues_t#LIBSBML_INVALID_ATTRIBUTE_VALUE LIBSBML_INVALID_ATTRIBUTE_VALUE@endlink
*
* @note If the Qualifier Type of this object is not
* @link QualifierType_t#BIOLOGICAL_QUALIFIER BIOLOGICAL_QUALIFIER@endlink,
- * then the @if clike #BiolQualifierType_t@endif@if java biology qualifier type code@endif value will default
+ * then the @if clike #BiolQualifierType_t value@else biology qualifier type@endif will default
* to @link BiolQualifierType_t#BQB_UNKNOWN BQB_UNKNOWN@endlink.
*
* @see getQualifierType()
@@ -620,18 +619,18 @@
* together identified uniquely using a URI. The following template
* illustrates the structure:
*
-<DIV class="fragment">
-<rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
- <span style="background-color: #ddd; border-bottom: 2px dotted #888">HISTORY</span><br>
- <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <rdf:Bag><br>
- <rdf:li rdf:resource="<span style="background-color: #d0d0ee">resource URI</span>" /><br>
- <span style="background-color: #edd">...</span><br>
- </rdf:Bag><br>
- </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
- <span style="background-color: #edd">...</span><br>
-</rdf:Description><br>
-</div>
+ <DIV class="fragment">
+ <rdf:Description rdf:about="#<span style="border-bottom: 1px solid black">meta id</span>"><br>
+ <span style="background-color: #e0e0e0; border-bottom: 2px dotted #888">HISTORY</span><br>
+ <<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
+ <rdf:Bag><br>
+ <rdf:li rdf:resource="<span style="background-color: #d0d0ee">resource URI</span>" /><br>
+ <span style="background-color: #edd">...</span><br>
+ </rdf:Bag><br>
+ </<span style="background-color: #bbb">RELATION_ELEMENT</span>><br>
+ <span style="background-color: #edd">...</span><br>
+ </rdf:Description><br>
+ </div>
*
* In the template above, the placeholder <span class="code"
* style="border-bottom: 1px solid black">meta id</span> stands for the
Modified: trunk/libsbml/src/annotation/RDFAnnotation.h
===================================================================
--- trunk/libsbml/src/annotation/RDFAnnotation.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/annotation/RDFAnnotation.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -44,7 +44,7 @@
* RDF-based annotations attached to a given SBML
* <code><annotation></code> element are read by RDFAnnotationParser
* and converted into a list of CVTerm objects. There
- * are different versions of the main method, @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List *CVTerms) @endif@if java RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, CVTermList *CVTerms) @endif
+ * are different versions of the main method, @if clike RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, %List *CVTerms) @else RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation, CVTermList *CVTerms) @endif
* and RDFAnnotationParser::parseRDFAnnotation(const XMLNode *annotation),
* used depending on whether the annotation in question concerns the MIRIAM
* model history or other MIRIAM resource annotations. A special object
@@ -128,7 +128,7 @@
int success; // Status code variable, used below.
XMLNode *RDF = createRDFAnnotation(); // Create RDF annotation XML structure.
-success = RDF->addChild(content); // Put some content into it.
+success = RDF->addChild(...content...); // Put some content into it.
... // Check "success" return code value.
XMLNode *ann = createAnnotation(); // Create <annotation> container.
@@ -138,12 +138,12 @@
success = sbmlObject->setAnnotation(ann); // Set object's annotation to what we built.
... // Check "success" return code value.
@endverbatim
-@endif@if java
+ * @endif@if java
@verbatim
int success; // Status code variable, used below.
XMLNode RDF = createRDFAnnotation(); // Create RDF annotation XML structure.
-success = RDF.addChild(content); // Put some content into it.
+success = RDF.addChild(...content...); // Put some content into it.
... // Check "success" return code value.
XMLNode ann = createAnnotation(); // Create <annotation> container.
@@ -153,7 +153,20 @@
success = sbmlObject.setAnnotation(ann); // Set object's annotation to what we built.
... // Check "success" return code value.
@endverbatim
-@endif
+ * @endif@if python
+@verbatim
+RDF = RDFAnnotationParser.createRDFAnnotation() # Create RDF annotation XML structure.
+success = RDF.addChild(...content...) # Put some content into it.
+... # Check "success" return code value.
+
+annot = RDFAnnotationParser.createAnnotation() # Create <annotation> container.
+success = annot.addChild(RDF) # Put the RDF annotation into it.
+... # Check "success" return code value.
+
+success = sbmlObject.setAnnotation(annot) # Set object's annotation to what we built.
+... # Check "success" return code value.
+@endverbatim
+ * @endif
* The SBML specification contains more information about the format of
* annotations. We urge readers to consult Section 6 of the SBML
* Level 2 (Versions 2–4) and SBML Level 3 specification
@@ -185,7 +198,7 @@
*
* Note that this does not create the containing SBML
* <code><annotation></code> element; the method
- * @if clike createAnnotation()@endif@if java RDFAnnotationParser::createAnnotation()@endif
+ * @if clike createAnnotation()@else RDFAnnotationParser::createAnnotation()@endif
* is available for creating the container.
*
* @return a pointer to an XMLNode
@@ -233,7 +246,7 @@
* Note that this method does @em not create a complete annotation or
* even an RDF element; it only creates the "Description" portion. Callers
* will need to use other methods such as
- * @if clike createRDFAnnotation()@endif@if java RDFAnnotationParser::createRDFAnnotation()@endif
+ * @if clike createRDFAnnotation()@else RDFAnnotationParser::createRDFAnnotation()@endif
* to create the rest of the structure for an annotation.
*
* @param object the object to which the "Description" refers
@@ -252,7 +265,7 @@
*
* This essentially takes the given SBML object, reads out the CVTerm objects
* attached to it, calls
- * @if clike createRDFDescription()@endif@if java RDFAnnotationParser::createRDFDescription(SBase object)@endif
+ * @if clike createRDFDescription()@else RDFAnnotationParser::createRDFDescription(SBase object)@endif
* to create an RDF "Description" element to hold the terms and adds
* each term with appropriate qualifiers.
*
@@ -269,13 +282,13 @@
* around it.
*
* This essentially takes the given SBML object, calls
- * @if clike RDFAnnotationParser::createCVTerms()@endif@if java RDFAnnotationParser::createCVTerms(SBase object)@endif
+ * @if clike RDFAnnotationParser::createCVTerms()@else RDFAnnotationParser::createCVTerms(SBase object)@endif
* to read out the CVTerm objects
* attached to it, calls
- * @if clike createRDFAnnotation()@endif@if java RDFAnnotationParser::createRDFAnnotation()@endif
+ * @if clike createRDFAnnotation()@else RDFAnnotationParser::createRDFAnnotation()@endif
* to create an RDF
* annotation to hold the terms, and finally calls
- * @if clike createAnnotation()@endif@if java RDFAnnotationParser::createAnnotation()@endif
+ * @if clike createAnnotation()@else RDFAnnotationParser::createAnnotation()@endif
* to wrap the result as an SBML <code><annotation></code> element.
*
* @param object the SBML object to start from
Modified: trunk/libsbml/src/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/math/ASTNode.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/ASTNode.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -80,7 +80,7 @@
*
*
* @if clike <h3><a class="anchor" name="ASTNodeType_t">
- * ASTNodeType_t</a></h3> @endif@if java <h3><a class="anchor"
+ * ASTNodeType_t</a></h3> @else <h3><a class="anchor"
* name="ASTNodeType_t">The set of possible %ASTNode types</a></h3> @endif
*
* @if clike Every ASTNode has an associated type code to indicate,
@@ -89,7 +89,7 @@
* @link ASTNode.h::ASTNodeType_t ASTNodeType_t@endlink. The list of
* possible types is quite long, because it covers all the mathematical
* functions that are permitted in SBML. The values are shown in the
- * following table: @endif@if java Every ASTNode has an associated
+ * following table: @else Every ASTNode has an associated
* type code to indicate, for example, whether it holds a number or stands for
* an arithmetic operator. The type is recorded as a value drawn from a
* set of static integer constants defined in the class {@link
@@ -142,8 +142,8 @@
*
* <h3><a class="anchor" name="math-convert">Converting between ASTs and text strings</a></h3>
*
- * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
- * read by @if clike SBML_parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
+ * read by @if clike SBML_parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
* are simple C-inspired infix notation taken from SBML Level 1. A
* formula in this text-string form can be handed to a program that
* understands SBML Level 1 mathematical expressions, or used as part
@@ -386,10 +386,10 @@
* AST_UNKNOWN@endlink. If the type isn't supplied when caling this
* constructor, the caller should set the node type to something else as
* soon as possible using
- * @if clike setType()@endif@if java ASTNode::setType(int)@endif.
+ * @if clike setType()@else ASTNode::setType(int)@endif.
*
* @param type an optional
- * @if clike @link #ASTNodeType_t ASTNodeType_t@endlink@endif@if java type@endif
+ * @if clike @link #ASTNodeType_t ASTNodeType_t@endlink@else type@endif
* code indicating the type of node to create.
*
* @if notcpp @docnote @htmlinclude warn-default-args-in-docs.html @endif
@@ -503,7 +503,7 @@
* render the representation invalid. Callers need to be careful to use
* this method in the context of other operations to create complete and
* correct formulas. The method
- * @if clike isWellFormedASTNode()@endif@if java ASTNode::isWellFormedASTNode()@endif
+ * @if clike isWellFormedASTNode()@else ASTNode::isWellFormedASTNode()@endif
* may also be useful for checking the results of node modifications.
*
* @see prependChild(ASTNode* child)
@@ -631,7 +631,7 @@
*
* @return the nth child of this ASTNode or @c NULL if this node has no nth
* child (<code>n > </code>
- * @if clike getNumChildren()@endif@if java ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
* <code>- 1</code>).
*/
LIBSBML_EXTERN
@@ -642,7 +642,7 @@
* Get the left child of this node.
*
* @return the left child of this ASTNode. This is equivalent to calling
- * @if clike getChild()@endif@if java ASTNode::getChild(unsigned int)@endif
+ * @if clike getChild()@else ASTNode::getChild(unsigned int)@endif
* with an argument of @c 0.
*/
LIBSBML_EXTERN
@@ -654,7 +654,7 @@
*
* @return the right child of this ASTNode, or @c NULL if this node has no
* right child. If
- * @if clike getNumChildren()@endif@if java ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
* <code>> 1</code>, then this is equivalent to:
* @code
* getChild( getNumChildren() - 1 );
@@ -721,7 +721,7 @@
*
* @return the nth annotation of this ASTNode, or @c NULL if this node has
* no nth annotation (<code>n ></code>
- * @if clike getNumChildren()@endif@if java ASTNode::getNumChildren()@endif
+ * @if clike getNumChildren()@else ASTNode::getNumChildren()@endif
* <code>- 1</code>).
*
* @see ASTNode::addSemanticsAnnotation(XMLNode* sAnnotation)
@@ -789,7 +789,7 @@
/**
* Get the value of this node as a single character. This function
* should be called only when
- * @if clike getType()@endif@if java ASTNode::getType()@endif returns
+ * @if clike getType()@else ASTNode::getType()@endif returns
* @link ASTNodeType_t#AST_PLUS AST_PLUS@endlink,
* @link ASTNodeType_t#AST_MINUS AST_MINUS@endlink,
* @link ASTNodeType_t#AST_TIMES AST_TIMES@endlink,
@@ -805,7 +805,7 @@
/**
* Get the value of this node as an integer. This function should be
* called only when
- * @if clike getType()@endif@if java ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif
* <code>== @link ASTNodeType_t#AST_INTEGER AST_INTEGER@endlink</code>.
*
* @return the value of this ASTNode as a (<code>long</code>) integer.
@@ -817,9 +817,9 @@
/**
* Get the value of this node as a string. This function may be called
* on nodes that (1) are not operators, i.e., nodes for which
- * @if clike isOperator()@endif@if java ASTNode::isOperator()@endif
+ * @if clike isOperator()@else ASTNode::isOperator()@endif
* returns @c false, and (2) are not numbers, i.e.,
- * @if clike isNumber()@endif@if java ASTNode::isNumber()@endif returns @c false.
+ * @if clike isNumber()@else ASTNode::isNumber()@endif returns @c false.
*
* @return the value of this ASTNode as a string.
*/
@@ -830,7 +830,7 @@
/**
* Get the value of the numerator of this node. This function should be
* called only when
- * @if clike getType()@endif@if java ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif
* <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink</code>.
*
* @return the value of the numerator of this ASTNode.
@@ -842,7 +842,7 @@
/**
* Get the value of the denominator of this node. This function should
* be called only when
- * @if clike getType()@endif@if java ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif
* <code>== @link ASTNodeType_t#AST_RATIONAL AST_RATIONAL@endlink</code>.
*
* @return the value of the denominator of this ASTNode.
@@ -854,7 +854,7 @@
/**
* Get the real-numbered value of this node. This function
* should be called only when
- * @if clike isReal()@endif@if java ASTNode::isReal()@endif
+ * @if clike isReal()@else ASTNode::isReal()@endif
* <code>== true</code>.
*
* This function performs the necessary arithmetic if the node type is
@@ -870,13 +870,13 @@
/**
* Get the mantissa value of this node. This function should be called
- * only when @if clike getType()@endif@if java ASTNode::getType()@endif
+ * only when @if clike getType()@else ASTNode::getType()@endif
* returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink
* or @link ASTNodeType_t#AST_REAL AST_REAL@endlink.
- * If @if clike getType()@endif@if java ASTNode::getType()@endif
+ * If @if clike getType()@else ASTNode::getType()@endif
* returns @link ASTNodeType_t#AST_REAL AST_REAL@endlink,
* this method is identical to
- * @if clike getReal()@endif@if java ASTNode::getReal()@endif.
+ * @if clike getReal()@else ASTNode::getReal()@endif.
*
* @return the value of the mantissa of this ASTNode.
*/
@@ -887,7 +887,7 @@
/**
* Get the exponent value of this ASTNode. This function should be
* called only when
- * @if clike getType()@endif@if java ASTNode::getType()@endif
+ * @if clike getType()@else ASTNode::getType()@endif
* returns @link ASTNodeType_t#AST_REAL_E AST_REAL_E@endlink
* or @link ASTNodeType_t#AST_REAL AST_REAL@endlink.
*
@@ -1158,7 +1158,7 @@
*
* For numbers, unary minus nodes can be "collapsed" by negating the
* number. In fact,
- * @if clike SBML_parseFormula()@endif@if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
+ * @if clike SBML_parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
* However, unary minus nodes for symbols
* (@link ASTNodeType_t#AST_NAME AST_NAME@endlink) cannot
* be "collapsed", so this predicate function is necessary.
@@ -1242,9 +1242,9 @@
* As a side-effect, this ASTNode object's type will be reset to
* @link ASTNodeType_t#AST_NAME AST_NAME@endlink if (and <em>only
* if</em>) the ASTNode was previously an operator (
- * @if clike isOperator()@endif@if java ASTNode::isOperator()@endif
+ * @if clike isOperator()@else ASTNode::isOperator()@endif
* <code>== true</code>), number (
- * @if clike isNumber()@endif@if java ASTNode::isNumber()@endif
+ * @if clike isNumber()@else ASTNode::isNumber()@endif
* <code>== true</code>), or unknown.
* This allows names to be set for @link ASTNodeType_t#AST_FUNCTION
* AST_FUNCTION@endlink nodes and the like.
@@ -1363,7 +1363,7 @@
* The units will be set @em only if this ASTNode object represents a
* MathML <code><cn></code> element, i.e., represents a number.
* Callers may use
- * @if clike isNumber()@endif@if java ASTNode::isNumber()@endif
+ * @if clike isNumber()@else ASTNode::isNumber()@endif
* to inquire whether the node is of that type.
*
* @htmlinclude about-sbml-units-attrib.html
Modified: trunk/libsbml/src/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/math/FormulaFormatter.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/FormulaFormatter.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -51,7 +51,7 @@
* this text-string form therefore can be handed to a program that
* understands SBML Level 1 mathematical expressions, or used as part
* of a formula translation system. The syntax is described in detail in
- * the documentation for ASTNode. @endif@if java The text-string form of
+ * the documentation for ASTNode. @else The text-string form of
* mathematical formulas produced by <code><a
* href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">
* libsbml.formulaToString()</a></code> and read by
Modified: trunk/libsbml/src/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/math/FormulaParser.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/math/FormulaParser.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -52,7 +52,7 @@
* this text-string form therefore can be handed to a program that
* understands SBML Level 1 mathematical expressions, or used as part
* of a formula translation system. The syntax is described in detail in
- * the documentation for ASTNode. @endif@if java The text-string form of
+ * the documentation for ASTNode. @else The text-string form of
* mathematical formulas produced by <code><a
* href="libsbml.html">libsbml.formulaToString()</a></code> and read by
* <code><a href="libsbml.html">libsbml.parseFormula()</a></code> are
Modified: trunk/libsbml/src/sbml/Compartment.h
===================================================================
--- trunk/libsbml/src/sbml/Compartment.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Compartment.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -376,8 +376,7 @@
* (identifier) attribute of a Compartment is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
- * method
- * @if clike setId()@endif@if python setId()@endif@if java Compartment::setId(String id)@endif.
+ * method @if java Compartment::setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
@@ -522,14 +521,14 @@
* Get the size of this Compartment.
*
* This method is identical to
- * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif.
+ * @if java Compartment::getVolume()@else getVolume()@endif.
* In SBML Level 1, compartments are always three-dimensional
* constructs and only have volumes, whereas in SBML Level 2,
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif and
- * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif for
+ * @if java Compartment::getSize()@else getSize()@endif and
+ * @if java Compartment::getVolume()@else getVolume()@endif for
* easier compatibility between SBML Levels.
*
* @return the value of the "size" attribute ("volume" in Level 1) of
@@ -545,14 +544,14 @@
* Get the volume of this Compartment.
*
* This method is identical to
- * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif. In
+ * @if java Compartment::getSize()@else getSize()@endif. In
* SBML Level 1, compartments are always three-dimensional
* constructs and only have volumes, whereas in SBML Level 2,
* compartments may be other than three-dimensional and therefore the
* "volume" attribute is named "size" in Level 2. LibSBML provides
* both
- * @if clike getSize()@endif@if python getSize()@endif@if java Compartment::getSize()@endif and
- * @if clike getVolume()@endif@if python getVolume()@endif@if java Compartment::getVolume()@endif
+ * @if java Compartment::getSize()@else getSize()@endif and
+ * @if java Compartment::getVolume()@else getVolume()@endif
* for easier compatibility between SBML Levels.
*
* @return the value of the "volume" attribute ("size" in Level 2) of
@@ -581,7 +580,7 @@
* @note @htmlinclude unassigned-units-are-not-a-default.html
*
* @see isSetUnits()
- * @see @if clike setUnits()@endif@if python setUnits()@endif@if java Compartment::setUnits(String sid)@endif
+ * @see @if java Compartment::setUnits(String sid)@else setUnits()@endif
* @see getSize()
*/
const std::string& getUnits () const;
@@ -647,14 +646,12 @@
* Compartment's "size" attribute is set.
*
* This method is similar but not identical to
- * @if clike isSetVolume()@endif@if python isSetVolume()@endif@if java Compartment::isSetVolume()@endif. The latter
+ * @if java Compartment::isSetVolume()@else isSetVolume()@endif. The latter
* should be used in the context of SBML Level 1 models instead of
- * @if clike isSetSize()@endif@if python isSetSize()@endif@if java Compartment::isSetSize()@endif
- * because
- * @if clike isSetVolume()@endif@if python isSetVolume()@endif@if java Compartment::isSetVolume()@endif
- * performs extra processing to take
- * into account the difference in default values between SBML Levels 1
- * and 2.
+ * @if java Compartment::isSetSize()@else isSetSize()@endif
+ * because @if java Compartment::isSetVolume()@else isSetVolume()@endif
+ * performs extra processing to take into account the difference in
+ * default values between SBML Levels 1 and 2.
*
* @return @c true if the "size" attribute ("volume" in Level 2) of
* this Compartment is set, @c false otherwise.
@@ -670,7 +667,7 @@
* "volume" attribute is set.
*
* This method is similar but not identical to
- * @if clike isSetSize()@endif@if python isSetSize()@endif@if java Compartment::isSetSize()@endif. The latter
+ * @if java Compartment::isSetSize()@else isSetSize()@endif. The latter
* should not be used in the context of SBML Level 1 models because this
* method performs extra processing to take into account
* the difference in default values between SBML Levels 1 and 2.
@@ -687,7 +684,7 @@
* therefore may or may not be set.
*
* @see isSetSize()
- * @see @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @see @if java Compartment::setVolume(double value)@else setVolume()@endif
*/
bool isSetVolume () const;
@@ -831,7 +828,7 @@
* Compartment.
*
* This method is identical to
- * @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @if java Compartment::setVolume(double value)@else setVolume()@endif
* and is provided for compatibility between
* SBML Level 1 and Level 2.
*
@@ -855,7 +852,7 @@
* Compartment.
*
* This method is identical to
- * @if clike setVolume()@endif@if python setVolume()@endif@if java Compartment::setVolume(double value)@endif
+ * @if java Compartment::setVolume(double value)@else setVolume()@endif
* and is provided for compatibility between SBML Level 1 and
* Level 2.
*
@@ -1050,7 +1047,7 @@
*
* Note that unit declarations for Compartment objects are specified in
* terms of the @em identifier of a unit (e.g., using
- * @if clike setUnits()@endif@if python setUnits()@endif@if java Compartment::setUnits(String sid)@endif), but
+ * @if java Compartment::setUnits(String sid)@else setUnits()@endif), but
* @em this method returns a UnitDefinition object, not a unit
* identifier. It does this by constructing an appropriate
* UnitDefinition. For SBML Level 2 models, it will do this even
Modified: trunk/libsbml/src/sbml/CompartmentType.h
===================================================================
--- trunk/libsbml/src/sbml/CompartmentType.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/CompartmentType.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -172,7 +172,7 @@
* (identifier) attribute of a CompartmentType is required to have a value.
* Thus, callers are cautioned to assign a value after calling this
* constructor. Setting the identifier can be accomplished using the
- * method @if clike setId() @endif@if python setId() @endif@if java setId(String id) @endif.
+ * method setId(@if java String id@endif).
*
* @param sbmlns an SBMLNamespaces object.
*
Modified: trunk/libsbml/src/sbml/InitialAssignment.h
===================================================================
--- trunk/libsbml/src/sbml/InitialAssignment.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/InitialAssignment.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -400,7 +400,7 @@
* The units are calculated based on the mathematical expression in the
* InitialAssignment and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -413,13 +413,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if python containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
+ * @if java InitialAssignment::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers
* may wish to take suitable actions in those scenarios.
*
@@ -439,7 +439,7 @@
* The units are calculated based on the mathematical expression in the
* InitialAssignment and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -452,13 +452,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if python containsUndeclaredUnits()@endif@if java InitialAssignment::containsUndeclaredUnits()@endif
+ * @if java InitialAssignment::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers
* may wish to take suitable actions in those scenarios.
*
@@ -481,7 +481,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -500,7 +500,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java InitialAssignment::getDerivedUnitDefinition()@endif
+ * @if java InitialAssignment::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
Modified: trunk/libsbml/src/sbml/KineticLaw.h
===================================================================
--- trunk/libsbml/src/sbml/KineticLaw.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/KineticLaw.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -226,7 +226,7 @@
* it as as a text string.
*
* This is fundamentally equivalent to
- * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if java KineticLaw::getMath()@else getMath()@endif.
* This variant is provided principally for compatibility compatibility
* with SBML Level 1.
*
@@ -244,7 +244,7 @@
* it as as an AST.
*
* This is fundamentally equivalent to
- * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif.
+ * @if java KineticLaw::getFormula()@else getFormula()@endif.
* The latter is provided principally for compatibility compatibility
* with SBML Level 1, which represented mathematical formulas in
* text-string form.
@@ -291,10 +291,10 @@
* KineticLaw's "formula" attribute is set.
*
* This is functionally identical to the method
- * @if clike isSetMath()@endif@if python isSetMath()@endif@if java KineticLaw::isSetMath()@endif. It is
+ * @if java KineticLaw::isSetMath()@else isSetMath()@endif. It is
* provided in order to mirror the parallel between
- * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif and
- * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if java KineticLaw::getFormula()@else getFormula()@endif and
+ * @if java KineticLaw::getMath()@else getMath()@endif.
*
* @return @c true if the formula (meaning the @c math subelement) of
* this KineticLaw is set, @c false otherwise.
@@ -311,10 +311,10 @@
* Kinetic's "math" subelement is set.
*
* This is identical to the method
- * @if clike isSetFormula()@endif@if python isSetFormula()@endif@if java KineticLaw::isSetFormula()@endif.
+ * @if java KineticLaw::isSetFormula()@else isSetFormula()@endif.
* It is provided in order to mirror the parallel between
- * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::getFormula()@endif and
- * @if clike getMath()@endif@if python getMath()@endif@if java KineticLaw::getMath()@endif.
+ * @if java KineticLaw::getFormula()@else getFormula()@endif and
+ * @if java KineticLaw::getMath()@else getMath()@endif.
*
* @return @c true if the formula (meaning the @c math subelement) of
* this KineticLaw is set, @c false otherwise.
@@ -384,7 +384,7 @@
* of the given ASTNode.
*
* This is fundamentally identical to
- * @if clike getFormula()@endif@if python getFormula()@endif@if java KineticLaw::setFormula(String formula)@endif.
+ * @if java KineticLaw::setFormula(String formula)@else getFormula()@endif.
* The latter is provided principally for compatibility compatibility with
* SBML Level 1, which represented mathematical formulas in text-string
* form.
@@ -511,7 +511,7 @@
* instance in the KineticLaw</em>. In addition, the caller should make
* sure to free the original object if it is no longer being used, or
* else a memory leak will result. Please see
- * @if clike createParameter()@endif@if python createParameter()@endif@if java KineticLaw::createParameter()@endif
+ * @if java KineticLaw::createParameter()@else createParameter()@endif
* for a method that does not lead to these issues.
*
* @see createParameter()
@@ -543,7 +543,7 @@
* instance in the KineticLaw</em>. In addition, the caller should make
* sure to free the original object if it is no longer being used, or
* else a memory leak will result. Please see
- * @if clike createParameter()@endif@if python createParameter()@endif@if java KineticLaw::createParameter()@endif
+ * @if java KineticLaw::createParameter()@else createParameter()@endif
* for a method that does not lead to these issues.
*
* @see createLocalParameter()
@@ -717,7 +717,7 @@
* The units are calculated based on the mathematical expression in the
* KineticLaw and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -730,13 +730,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if java KineticLaw::containsUndeclaredUnits()@endif
+ * @if java KineticLaw::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers may
* wish to take suitable actions in those scenarios.
*
@@ -756,7 +756,7 @@
* The units are calculated based on the mathematical expression in the
* KineticLaw and the model quantities referenced by
* <code><ci></code> elements used within that expression. The
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* method returns the calculated units.
*
* Note that the functionality that facilitates unit analysis depends
@@ -769,13 +769,13 @@
* units. In those cases, it is not possible to calculate the units of
* the overall expression without making assumptions. LibSBML does not
* make assumptions about the units, and
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* only returns the units as far as it is able to determine them. For
* example, in an expression <em>X + Y</em>, if <em>X</em> has
* unambiguously-defined units and <em>Y</em> does not, it will return
* the units of <em>X</em>. <strong>It is important that callers also
* invoke the method</strong>
- * @if clike containsUndeclaredUnits()@endif@if java KineticLaw::containsUndeclaredUnits()@endif
+ * @if java KineticLaw::containsUndeclaredUnits()@else containsUndeclaredUnits()@endif
* <strong>to determine whether this situation holds</strong>. Callers
* may wish to take suitable actions in those scenarios.
*
@@ -798,7 +798,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
@@ -817,7 +817,7 @@
*
* @note A return value of @c true indicates that the UnitDefinition
* returned by
- * @if clike getDerivedUnitDefinition()@endif@if python getDerivedUnitDefinition()@endif@if java KineticLaw::getDerivedUnitDefinition()@endif
+ * @if java KineticLaw::getDerivedUnitDefinition()@else getDerivedUnitDefinition()@endif
* may not accurately represent the units of the expression.
*
* @see getDerivedUnitDefinition()
Modified: trunk/libsbml/src/sbml/LocalParameter.h
===================================================================
--- trunk/libsbml/src/sbml/LocalParameter.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/LocalParameter.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -201,7 +201,7 @@
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
- * @if clike setId()@endif@if python setId()@endif@if java setId(String id)@endif.
+ * @if java setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
Modified: trunk/libsbml/src/sbml/Model.h
===================================================================
--- trunk/libsbml/src/sbml/Model.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Model.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -94,7 +94,8 @@
* @section approaches Approaches to creating objects using the libSBML API
*
* LibSBML provides two main mechanisms for creating objects: class
- * constructors (e.g., @if clike @link Species::Species() Species() @endlink @endif@if python @link Species::Species() Species() @endlink @endif@if java <a href="org/sbml/libsbml/Species.html">Species()</a> @endif),
+ * constructors
+ * (e.g., @if java <a href="org/sbml/libsbml/Species.html">Species()</a> @else Species::Species() @endif),
* and <code>create<span class="placeholder"><em>Object</em></span>()</code>
* methods (such as Model::createSpecies()) provided by certain <span
* class="placeholder"><em>Object</em></span> classes such as Model. These
@@ -127,7 +128,7 @@
Species *sp = model->createSpecies();
sp->setId("MySpecies");
@endverbatim
-@endif@if java
+ * @endif@if java
@verbatim
// Create an SBMLDocument object in Level 3 Version 1 format:
@@ -149,7 +150,7 @@
Species sp = model.createSpecies();
sp.setId("BestSpeciesEver");
@endverbatim
-@endif
+ * @endif
*
* The <code>create<span
* class="placeholder"><em>Object</em></span>()</code> methods return a
@@ -183,7 +184,7 @@
delete newsp;
@endverbatim
-@endif@if java
+ * @endif@if java
@verbatim
// Create a Species object and add it to the model.
// This uses the Species class constructor:
@@ -197,14 +198,14 @@
newsp.setId("NewId"); // Warning -- doesn't change the species in 'model'!
@endverbatim
-@endif
+ * @endif
*
- * The key point of the example above is that, because the @if clike Model::addSpecies() @endif@if python Model::addSpecies() @endif@if java Model::addSpecies(Species s) @endif
+ * The key point of the example above is that, because the
+ * @if java Model::addSpecies(Species s)@else Model::addSpecies()@endif
* call makes a copy of the object handed to it, care is needed
- * @if clike both when
- * attempting to make changes to the object, and when the original object
- * is no longer needed.@endif@if java when
- * attempting to make changes to the object.@endif
+ * @if clike both when attempting to make changes to the object, and when
+ * the original object is no longer needed.@else when attempting to make
+ * changes to the object.@endif
*
* @section checking Consistency and adherence to SBML specifications
*
Modified: trunk/libsbml/src/sbml/Parameter.h
===================================================================
--- trunk/libsbml/src/sbml/Parameter.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Parameter.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -229,7 +229,7 @@
* Thus, callers are cautioned to assign a value after calling this
* constructor if no identifier is provided as an argument. Setting the
* identifier can be accomplished using the method
- * @if clike setId()@endif@if python setId()@endif@if java setId(String id)@endif.
+ * @if java setId(String id)@else setId()@endif.
*
* @param sbmlns an SBMLNamespaces object.
*
Modified: trunk/libsbml/src/sbml/Rule.h
===================================================================
--- trunk/libsbml/src/sbml/Rule.h 2011-02-27 05:14:17 UTC (rev 13062)
+++ trunk/libsbml/src/sbml/Rule.h 2011-02-27 05:16:27 UTC (rev 13063)
@@ -174,7 +174,7 @@
* Level 3 for distinguishing rules; specifically, it uses an
* attribute whose value is drawn from an enumeration of 3 values. LibSBML
* supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@if notcpp with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
* values @endif listed in the following table.
*
* <p>
@@ -367,7 +367,7 @@
* Level 3 for distinguishing rules; specifically, it uses an
* attribute whose value is drawn from an enumeration of 3 values. LibSBML
* supports this using methods that work @if clike a libSBML enumeration
- * type, #RuleType_t, whose values are @endif@if notcpp with the enumeration
+ * type, #RuleType_t, whose values are @else with the enumeration
* values @endif listed in the following table.
*
* <p>
@@ -604,7 +604,7 @@
* Level 3 for distinguishing rules; specifically, it uses an
* attribute whose value is drawn from an enumeration of 3 values. LibSBML
* supports thi...
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