Systems Biology Markup Language (SBML)

Revision: 14592
          http://sbml.svn.sourceforge.net/sbml/?rev=14592&view=rev
Author:   fbergmann
Date:     2011-10-28 22:33:37 +0000 (Fri, 28 Oct 2011)
Log Message:
-----------
- remove warnings

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.cpp
    trunk/libsbml/src/sbml/math/ASTNode.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-10-28 22:33:23 UTC (rev 14591)
+++ trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-10-28 22:33:37 UTC (rev 14592)
@@ -185,8 +185,8 @@
   mId			 = "";
   mClass		 = "";
   mStyle		 = "";
+  mIsBvar = false;
   mUserData      = NULL;
-  mIsBvar = false;
 
   setType(type);
 
@@ -217,8 +217,8 @@
   mId			 = "";
   mClass		 = "";
   mStyle		 = "";
+  mIsBvar = false;
   mUserData      = NULL;
-  mIsBvar = false;
 
   mChildren             = new List;
   mSemanticsAnnotations = new List;
@@ -271,8 +271,8 @@
  ,mId                   ( orig.mId)
  ,mClass                ( orig.mClass)
  ,mStyle                ( orig.mStyle)
+ ,mIsBvar               ( orig.mIsBvar)
  ,mUserData             ( orig.mUserData )
- ,mIsBvar               ( orig.mIsBvar)
 {
   if (orig.mName)
   {
@@ -312,8 +312,8 @@
     mId                   = rhs.mId;
     mClass                = rhs.mClass;
     mStyle                = rhs.mStyle;
+    mIsBvar               = rhs.mIsBvar;
     mUserData             = rhs.mUserData;
-    mIsBvar               = rhs.mIsBvar;
     if (rhs.mName)
     {
       mName = safe_strdup(rhs.mName);

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2011-10-28 22:33:23 UTC (rev 14591)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2011-10-28 22:33:37 UTC (rev 14592)
@@ -1781,14 +1781,15 @@
   SBase *mParentSBMLObject;
 
   std::string mUnits;
-  void *mUserData;
-  bool mIsBvar;
 
   // additional MathML attributes
   std::string mId;
   std::string mClass;
   std::string mStyle;
 
+  bool mIsBvar;
+  void *mUserData;
+  
   friend class MathMLFormatter;
   friend class MathMLHandler;
 

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 14979
          http://sbml.svn.sourceforge.net/sbml/?rev=14979&view=rev
Author:   mhucka
Date:     2011-12-12 01:06:45 +0000 (Mon, 12 Dec 2011)
Log Message:
-----------
Documented Token_t and FormulaTokenizer.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/FormulaTokenizer.c
    trunk/libsbml/src/sbml/math/FormulaTokenizer.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-12 00:39:48 UTC (rev 14978)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-12 01:06:45 UTC (rev 14979)
@@ -396,9 +396,12 @@
 
 
   /**
-   * Creates a new ASTNode from the given Token.  The resulting ASTNode
-   * will contain the same data as the Token.
+   * Creates a new ASTNode from the given Token_t structure.
    *
+   * The resulting ASTNode will contain the same data as the Token_t
+   * object.  Please refer to the documentation for Token_t to learn
+   * about the possible contents.
+   *
    * @param token the Token to add.
    */
   LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaTokenizer.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaTokenizer.c	2011-12-12 00:39:48 UTC (rev 14978)
+++ trunk/libsbml/src/sbml/math/FormulaTokenizer.c	2011-12-12 01:06:45 UTC (rev 14979)
@@ -1,6 +1,4 @@
 /**
- * @cond doxygen-libsbml-internal
- *
  * @file    FormulaTokenizer.c
  * @brief   Tokenizes an SBML formula string
  * @author  Ben Bornstein
@@ -25,7 +23,16 @@
  * the Free Software Foundation.  A copy of the license agreement is provided
  * in the file named "LICENSE.txt" included with this software distribution and
  * also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
+ * ---------------------------------------------------------------------- -->
+ * 
+ * @class FormulaTokenizer
+ * @brief Tokenizes a mathematical formula string in SBML Level 1 syntax.
+ *
+ * @htmlinclude not-sbml-warning.html
+ *
+ * This file contains functions to tokenize a text string containing a
+ * mathematical formula in SBML Level 1 syntax.  
+ */
 
 #include <ctype.h>
 #include <sbml/common/common.h>
@@ -35,10 +42,14 @@
 
 /* Forward references */
 
+/** @cond doxygen-libsbml-internal */
+
 void Token_convertNaNInf (Token_t *t);
 
+/** @endcond */
 
-/**
+
+/*
  * Creates a new FormulaTokenizer for the given formula string and returns
  * a pointer to it.
  */
@@ -59,7 +70,7 @@
 }
 
 
-/**
+/*
  * Frees the given FormulaTokenizer.
  */
 LIBSBML_EXTERN
@@ -74,7 +85,9 @@
 }
 
 
-/**
+/** @cond doxygen-internal-libsbml */
+
+/*
  * Reads a TT_NAME from the FormulaTokenizer into the given Token.  This is
  * a supporting function for FormulaTokenizer_nextToken().
  *
@@ -114,7 +127,7 @@
 }
 
 
-/**
+/*
  * Reads either a TT_INTEGER or a TT_REAL from the FormulaTokenizer into
  * the given Token.  This is a supporting function for
  * FormulaTokenizer_nextToken().
@@ -242,8 +255,10 @@
   ft->formula[ endpos ] = endchar;
 }
 
+/** @endcond */
 
-/**
+
+/*
  * @return the next token in the formula string.  If no more tokens are
  * available, the token type will be TT_END.
  */
@@ -305,7 +320,9 @@
 }
 
 
-/**
+/** @cond doxygen-libsbml-internal */
+
+/*
  * Creates a new Token and returns a point to it.
  */
 LIBSBML_EXTERN
@@ -321,7 +338,7 @@
 }
 
 
-/**
+/*
  * Frees the given Token
  */
 LIBSBML_EXTERN
@@ -362,7 +379,7 @@
 }
 
 
-/**
+/*
  * @return the value of this Token as a (long) integer.  This function
  * should be called only when the Token's type is TT_INTEGER.  If the type
  * is TT_REAL or TT_REAL_E, the function will cope by truncating the
@@ -388,7 +405,7 @@
 }
 
 
-/**
+/*
  * @return the value of this Token as a real (double).  This function
  * should be called only when the Token's is a number (TT_REAL, TT_REAL_E
  * or TT_INTEGER).
@@ -418,7 +435,7 @@
 }
 
 
-/**
+/*
  * Negates the value of this Token.  This operation is only valid if the
  * Token's type is TT_INTEGER, TT_REAL, or TT_REAL_E.
  */
@@ -438,6 +455,4 @@
   }
 }
 
-
 /** @endcond */
-

Modified: trunk/libsbml/src/sbml/math/FormulaTokenizer.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2011-12-12 00:39:48 UTC (rev 14978)
+++ trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2011-12-12 01:06:45 UTC (rev 14979)
@@ -1,6 +1,4 @@
 /**
- * @cond doxygen-libsbml-internal
- *
  * @file    FormulaTokenizer.h
  * @brief   Tokenizes an SBML formula string
  * @author  Ben Bornstein
@@ -25,7 +23,37 @@
  * the Free Software Foundation.  A copy of the license agreement is provided
  * in the file named "LICENSE.txt" included with this software distribution and
  * also available online as http://sbml.org/software/libsbml/license.html
- * ---------------------------------------------------------------------- -->*/
+ * ---------------------------------------------------------------------- -->
+ * 
+ * @class FormulaTokenizer
+ * @brief Tokenizes a mathematical formula string in SBML Level 1 syntax.
+ *
+ * @htmlinclude not-sbml-warning.html
+ *
+ * This file contains functions to tokenize a text string containing a
+ * mathematical formula in SBML Level&nbsp;1 syntax.  The first entry
+ * point is the function FormulaTokenizer_createFromFormula(), which
+ * returns a FormulaTokenizer_t structure.  The structure tracks the
+ * current position in the string to be tokenized, and can be handed
+ * to other functions such as FormulaTokenizer_nextToken().  Tokens
+ * are returned as Token_t structures.
+ *
+ * @section Token_t The Token_t structure
+ *
+ * The Token_t structure is used to store a token returned by
+ * FormulaTokenizer_nextToken().  It contains a union whose members
+ * can store different types of tokens, such as numbers and symbols.
+ *
+ * @section FormulaTokenizer_t The FormulaTokenizer_t structure
+ *
+ * An instance of a FormulaTokenizer_t maintains its own internal copy of
+ * the formula being tokenized and the current position within the formula
+ * string.  Callers do not need to manipulate the fields of a
+ * FormulaTokenizer_t structure themselves; instances of FormulaTokenizer_t
+ * are only meant to be passed around between the functions of the formula
+ * tokenizer system, such as FormulaTokenizer_createFromFormula() and
+ * FormulaTokenizer_getName().
+ */
 
 #ifndef FormulaTokenizer_h
 #define FormulaTokenizer_h
@@ -38,8 +66,14 @@
 
 
 /**
- * A FormulaTokenizer maintains its own internal copy of the formula being
- * tokenized and the current position within the formula string.
+ * Structure used to track the state of tokenizing a string.
+ * 
+ * An instance of a FormulaTokenizer_t maintains its own internal copy of
+ * the formula being tokenized and the current position within the formula
+ * string.  The field @c formula holds the former, and the field @c pos
+ * holds the latter.  Callers do not need to manipulate these fields
+ * themselves; instances of FormulaTokenizer_t are only meant to be
+ * passed around between the functions of the formula tokenizer system.
  */
 typedef struct
 {
@@ -49,7 +83,11 @@
 
 
 /**
- * TT is short for TokenType.
+ * Enumeration of possible token types.
+ * 
+ * "TT" is short for "TokenType".
+ *
+ * @see Token_t
  */
 typedef enum
 {
@@ -71,104 +109,153 @@
 
 
 /**
- * A token has a type and a value.  The value field is a union of different
- * types and the type to reference depends on the value of TokenType_t.
+ * A token has a @c type and a @c value.  The @c value field is a union of
+ * different possible members; the member that holds the value for a given
+ * token (and thus the name of the member that is to be accessed
+ * programmatically) depends on the value of the @c TokenType_t field @c
+ * type.  The following table lists the possible scenarios:
  *
- *   TokenType_t      Use value.XXX
- *   -----------      --------------
- *   TT_NAME          name
- *   TT_INTEGER       integer
- *   TT_REAL          real
- *   TT_REAL_E        real, exponent
- *   Anything else    ch
- *
- * If a real number was encoded using e-notation, TokenType will be
- * TT_REAL_E instead of TT_REAL. The field value.real will contain the
- * mantissa and a separate Token field will contain the exponent.  For
- * example, the token (t) for '1.2e3':
- *
- *   t.type     = TT_REAL_E
- *   t.value    = 1.2
- *   t.exponent = 3
- *
- * In the case of TT_UNKNOWN, value.ch will contain the unrecognized
- * character.  For TT_END, value.ch will contain '\\0'.  For all others, the
- * value.ch will contain the corresponding character.
+ * <center>
+ * <table border="0" class="text-table width80 normal-font alt-row-colors">
+ * <tr><th>Value of the field <code>type</code></th><th>Member within <code>value</code> to use</th></tr>
+ * <tr><td><code>TT_NAME</code></td><td><code>name</code></td></tr>
+ * <tr><td><code>TT_INTEGER</code></td><td><code>integer</code></td></tr>
+ * <tr><td><code>TT_REAL</code></td><td><code>real</code></td></tr>
+ * <tr><td><code>TT_REAL</code>_E</td><td><code>real</code> and <code>exponent</code></td></tr>
+ * <tr><td><i>Anything else</i></td><td><code>ch</code></td></tr>
+ * </table>
+ * </center>
+ * 
+ * If this token encodes a real number in e-notation, @c type will be
+ * @c TT_REAL_E instead of @c TT_REAL. The field @c value.real will then contain
+ * the mantissa, and the separate field named @c exponent will contain (can you
+ * guess?) the exponent.  For example, if we have a pointer to a structure
+ * named @c t, then the representation for &quot;<code>1.2e3</code>&quot; will
+ * be:
+ * @verbatim
+t->type       = TT_REAL_E;
+t->value.real = 1.2;
+t->exponent   = 3;
+@endverbatim
+ * 
+ * When the @c type has a value of @c TT_UNKNOWN, the field @c ch will
+ * contain the unrecognized character.  When the type is @c TT_END, the
+ * field @c ch will contain @c '\\0'.  For all others, the @c value.ch will
+ * contain the corresponding character.
  */
 typedef struct
 {
-  TokenType_t type;
+  TokenType_t type; /*!< This token's type. */
 
   union
   {
-    char   ch;
-    char   *name;
-    long   integer;
-    double real;
-  } value;
+    char   ch;      /*!< Member used when the token is a character. */
+    char   *name;   /*!< Member used when the token is a symbol. */
+    long   integer; /*!< Member used when the token is an integer. */
+    double real;    /*!< Member used when the token is a real. */
+  } value;          /*!< Value of the token. */
 
-  long exponent;
+  long exponent;    /*!< Secondary field used when the token is a real in e-notation. */
 
 } Token_t;
 
 
 /**
- * Creates a new FormulaTokenizer for the given formula string and returns
- * a pointer to it.
+ * Creates a new FormulaTokenizer_t object for the given @p formula string
+ * and returns a pointer to it the object.
+ *
+ * @param formula the text string that contains the mathematical formula to
+ * be tokenized.
+ * 
+ * @return a FormulaTokenizer_t object that tracks the state of tokenizing
+ * the string.
  */
 LIBSBML_EXTERN
 FormulaTokenizer_t *
 FormulaTokenizer_createFromFormula (const char *formula);
 
+
 /**
- * Frees the given FormulaTokenizer.
+ * Frees the given FormulaTokenizer_t object @p ft.
  */
 LIBSBML_EXTERN
 void
 FormulaTokenizer_free (FormulaTokenizer_t *ft);
 
+
 /**
- * @return the next token in the formula string.  If no more tokens are
- * available, the token type will be TT_END.
+ * Returns the next token in the formula string.
+ *
+ * If no more tokens are available, the token type will be @c TT_END.
+ * Please consult the documentation for the structure Token_t for
+ * more information about the possible data values it can hold.
+ *
+ * @param ft the object tracking the current tokenization state.
+ *
+ * @return a pointer to a token.
  */
 LIBSBML_EXTERN
 Token_t *
 FormulaTokenizer_nextToken (FormulaTokenizer_t *ft);
 
+
+/** @cond doxygen-libsbml-internal */
+
 /**
  * Creates a new Token and returns a point to it.
+ *
+ * @return a pointer to a token.
  */
 LIBSBML_EXTERN
 Token_t *
 Token_create (void);
 
+
 /**
- * Frees the given Token
+ * Frees the given Token @p t.
  */
 LIBSBML_EXTERN
 void
 Token_free (Token_t *t);
 
+
 /**
- * @return the value of this Token as a (long) integer.  This function
- * should be called only when the Token's type is TT_INTEGER.  If the type
- * is TT_REAL or TT_REAL_E, the function will cope by truncating the
- * number's fractional part.
+ * Returns the value of this token as a (long) integer.
+ *
+ * This function should be called only when the token's type is @c
+ * TT_INTEGER.  If the type is @c TT_REAL or @c TT_REAL_E, the function
+ * will cope by truncating the number's fractional part.
+ *
+ * @param t the token to be parsed into an integer.
+ *
+ * @return the value of the token after it is interpreted as an integer.
  */
 long
 Token_getInteger (const Token_t *t);
 
+
 /**
- * @return the value of this Token as a real (double).  This function
- * should be called only when the Token's is a number (TT_REAL, TT_REAL_E
- * or TT_INTEGER).
+ * Returns the value of this token as a real (double).
+ *
+ * This function should be called only when the token is a number
+ * (@c TT_REAL, @c TT_REAL_E or @c TT_INTEGER).
+ *
+ * @param t the token to be parsed into a real number.
+ *
+ * @return the value of the token after it is interpreted as a
+ * real number.
  */
 double
 Token_getReal (const Token_t *t);
 
+
 /**
- * Negates the value of this Token.  This operation is only valid if the
- * Token's type is TT_INTEGER, TT_REAL, or TT_REAL_E.
+ * Negates the numerical value of the given token @p t.
+ *
+ * The token stored in @p t is modified in place.  This operation is only
+ * valid if the token's type is @c TT_INTEGER, @c TT_REAL, or @c TT_REAL_E.
+ *
+ * @param t the token whose value is to be negated.
  */
 void
 Token_negateValue (Token_t *t);
@@ -177,7 +264,6 @@
 END_C_DECLS
 LIBSBML_CPP_NAMESPACE_END
 
-#endif  /** FormulaTokenizer_h **/
-
 /** @endcond */
 
+#endif  /** FormulaTokenizer_h **/

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 14995
          http://sbml.svn.sourceforge.net/sbml/?rev=14995&view=rev
Author:   luciansmith
Date:     2011-12-13 22:53:12 +0000 (Tue, 13 Dec 2011)
Log Message:
-----------
Exposed the full isBoolean for Chris by creating a new 'ASTNode::isBooleanFor(Model*)' function.

Also, something needs to be done about the fact that ASTNode.h is included ALL OVER THE PLACE so you can't touch it without a near-total recompile.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.cpp
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/test/TestASTNode.c

Modified: trunk/libsbml/src/sbml/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-13 19:57:55 UTC (rev 14994)
+++ trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-13 22:53:12 UTC (rev 14995)
@@ -36,6 +36,7 @@
 #include <sbml/math/ASTNode.h>
 #include <sbml/xml/XMLAttributes.h>
 #include <sbml/xml/XMLNode.h>
+#include <sbml/Model.h>
 
 /** @cond doxygen-ignored */
 
@@ -1228,6 +1229,15 @@
 }
 
 
+LIBSBML_EXTERN
+bool
+ASTNode::isBooleanFor (const Model* model) const
+{
+  if (model==NULL) return false;
+  return model->isBoolean(this);
+}
+
+
 /*
  * @return true if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false otherwise.
@@ -2786,6 +2796,15 @@
 }
 
 
+LIBSBML_EXTERN
+int
+ASTNode_isBooleanFor (const ASTNode_t *node, const Model_t* model)
+{
+  if (node == NULL) return (int) false;
+  return (int) static_cast<const ASTNode*>(node)->isBooleanFor(model);
+}
+
+
 /**
  * @return true (non-zero) if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false (0) otherwise.

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-13 19:57:55 UTC (rev 14994)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-13 22:53:12 UTC (rev 14995)
@@ -396,12 +396,9 @@
 
 
   /**
-   * Creates a new ASTNode from the given Token_t structure.
+   * Creates a new ASTNode from the given Token.  The resulting ASTNode
+   * will contain the same data as the Token.
    *
-   * The resulting ASTNode will contain the same data as the Token_t
-   * object.  Please refer to the documentation for Token_t to learn
-   * about the possible contents.
-   *
    * @param token the Token to add.
    */
   LIBSBML_EXTERN
@@ -971,6 +968,18 @@
 
 
   /**
+   * Predicate returning @c true (non-zero) if this node has a boolean type
+   * (a logical operator, a relational operator, or the constants @c true
+   * or @c false), or if it is a piecewise function that always returns a
+   * boolean, or if it is a function definition that returns a boolean.
+   *
+   * @return true if this ASTNode returns a boolean, false otherwise.
+   */
+  LIBSBML_EXTERN
+  bool isBooleanFor (const Model* model) const;
+
+
+  /**
    * Predicate returning @c true (non-zero) if this node represents a MathML
    * constant (e.g., @c true, @c Pi).
    * 
@@ -2095,15 +2104,23 @@
  */
 LIBSBML_EXTERN
 int
-ASTNode_isBoolean (const ASTNode_t *node);
+ASTNode_isBoolean (const ASTNode_t * node);
 
 /**
+ * @return true (non-zero) if this ASTNode returns a boolean, false (0) otherwise.
+ */
+LIBSBML_EXTERN
+int
+ASTNode_isBooleanFor (const ASTNode_t *node, const Model_t* model);
+
+
+/**
  * @return true (non-zero) if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false (0) otherwise.
  */
 LIBSBML_EXTERN
 int
-ASTNode_isConstant (const ASTNode_t *node);
+ASTNode_isConstant (const ASTNode_t * node);
 
 /**
  * @return true (non-zero) if this ASTNode is a function in SBML L1, L2
@@ -2112,7 +2129,7 @@
  */
 LIBSBML_EXTERN
 int
-ASTNode_isFunction (const ASTNode_t *node);
+ASTNode_isFunction (const ASTNode_t * node);
 
 /**
  * @return true if this ASTNode is the special IEEE 754 value infinity,

Modified: trunk/libsbml/src/sbml/math/test/TestASTNode.c
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestASTNode.c	2011-12-13 19:57:55 UTC (rev 14994)
+++ trunk/libsbml/src/sbml/math/test/TestASTNode.c	2011-12-13 22:53:12 UTC (rev 14995)
@@ -31,6 +31,7 @@
 #include <sbml/math/ASTNode.h>
 #include <sbml/math/FormulaParser.h>
 #include <sbml/EventAssignment.h>
+#include <sbml/Model.h>
 #include <sbml/xml/XMLNode.h>
 
 #include <limits.h>
@@ -2258,6 +2259,7 @@
   fail_unless( ASTNode_hasUnits (NULL) == 0);
   fail_unless( ASTNode_insertChild (NULL, 0, NULL) == LIBSBML_INVALID_OBJECT);
   fail_unless( ASTNode_isBoolean (NULL) == 0);
+  fail_unless( ASTNode_isBooleanFor (NULL, NULL) == 0);
   fail_unless( ASTNode_isConstant (NULL) == 0);
   fail_unless( ASTNode_isFunction (NULL) == 0);
   fail_unless( ASTNode_isInfinity (NULL) == 0);
@@ -2508,6 +2510,38 @@
 }
 END_TEST
 
+START_TEST (test_ASTNode_isBooleanFor)
+{
+  ASTNode_t *n = ASTNode_create();
+  ASTNode_setName(n, "func1");
+  ASTNode_setType(n, AST_FUNCTION);
+
+  fail_unless(ASTNode_isBooleanFor(n, NULL) == 0);
+
+  Model_t* model = Model_create(3,1);
+  FunctionDefinition_t* fd = Model_createFunctionDefinition(model);
+  FunctionDefinition_setId(fd, "func1");
+  FunctionDefinition_setMath(fd, SBML_parseFormula("lambda(x, true)"));
+  fail_unless(ASTNode_isBooleanFor(n, model));
+
+  ASTNode_setName(n, "func2");
+  fd = Model_createFunctionDefinition(model);
+  FunctionDefinition_setId(fd, "func2");
+  FunctionDefinition_setMath(fd, SBML_parseFormula("lambda(x, 6)"));
+  fail_unless(!ASTNode_isBooleanFor(n, model));
+  ASTNode_free(n);
+
+  n = SBML_parseFormula("piecewise(true, geq(X, T), false)");
+  fail_unless(ASTNode_isBooleanFor(n, model));
+  ASTNode_free(n);
+
+  n = SBML_parseFormula("piecewise(true, geq(X, T), 5)");
+  fail_unless(!ASTNode_isBooleanFor(n, model));
+  ASTNode_free(n);
+
+}
+END_TEST
+
 Suite *
 create_suite_ASTNode (void) 
 { 
@@ -2561,6 +2595,7 @@
   tcase_add_test( tcase, test_ASTNode_avogadro_bug            );
   tcase_add_test( tcase, test_ASTNode_accessWithNULL          );
   tcase_add_test( tcase, test_ASTNode_isBoolean               );
+  tcase_add_test( tcase, test_ASTNode_isBooleanFor            );
 
   suite_add_tcase(suite, tcase);
 

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Revision: 15052
          http://sbml.svn.sourceforge.net/sbml/?rev=15052&view=rev
Author:   sarahkeating
Date:     2011-12-16 13:17:27 +0000 (Fri, 16 Dec 2011)
Log Message:
-----------
changed the isBooleanFor function to be 'returnsBoolean'. This function no longer takes a model as an argument; if the AST uses a function then it looks for the parent model.

Note this means that if the AST has not yet been added to a document it will not find a model and returnsBoolean will return false (if it uses a function).

I can see a scenario where you might want to know if an AST returns a boolean in the context of a model that it does not yet belong to. I would see this as a different function though.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.cpp
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/test/TestASTNode.c

Modified: trunk/libsbml/src/sbml/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-16 11:32:47 UTC (rev 15051)
+++ trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-16 13:17:27 UTC (rev 15052)
@@ -1233,13 +1233,53 @@
 
 LIBSBML_EXTERN
 bool
-ASTNode::isBooleanFor (const Model* model) const
+ASTNode::returnsBoolean () const
 {
-  if (model==NULL) return false;
-  return model->isBoolean(this);
+
+  if (isBoolean() == true)
+  {
+    return true;
+  }
+
+  else if (getType() == AST_FUNCTION)
+  {
+    const Model * model = (this->getParentSBMLObject() != NULL ? 
+      this->getParentSBMLObject()->getModel() : NULL);
+
+    if (model == NULL)
+    {
+      return false;
+    }
+    else
+    {
+      const FunctionDefinition* fd = model->getFunctionDefinition( getName() );
+
+      if (fd != NULL && fd->isSetMath())
+      {
+        return fd->getMath()->getRightChild()->returnsBoolean();
+      }
+      else
+      {
+        return false;
+      }
+    }
+  }
+
+  else if (getType() == AST_FUNCTION_PIECEWISE)
+  {
+    for (unsigned int c = 0; c < getNumChildren(); c += 2)
+    {
+      if ( getChild(c)->returnsBoolean() == false ) 
+        return false;
+    }
+
+    return true;
+  }
 }
 
 
+
+
 /*
  * @return true if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false otherwise.
@@ -2800,10 +2840,10 @@
 
 LIBSBML_EXTERN
 int
-ASTNode_isBooleanFor (const ASTNode_t *node, const Model_t* model)
+ASTNode_returnsBoolean (const ASTNode_t *node)
 {
   if (node == NULL) return (int) false;
-  return (int) static_cast<const ASTNode*>(node)->isBooleanFor(model);
+  return (int) static_cast<const ASTNode*>(node)->returnsBoolean();
 }
 
 

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-16 11:32:47 UTC (rev 15051)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-16 13:17:27 UTC (rev 15052)
@@ -968,15 +968,23 @@
 
 
   /**
-   * Predicate returning @c true (non-zero) if this node has a boolean type
-   * (a logical operator, a relational operator, or the constants @c true
-   * or @c false), or if it is a piecewise function that always returns a
-   * boolean, or if it is a function definition that returns a boolean.
+   * Predicate returning @c true (non-zero) if this node returns a boolean type
+   * or @c false (zero) otherwise.
    *
+   * This function looks at the whole ASTNode rather than just the top 
+   * level of the ASTNode. Thus it will consider return values from
+   * piecewise statements.  In addition, if this ASTNode uses a function
+   * call, the return value of the functionDefinition will be determined.
+   * Note that this is only possible where the ASTNode can trace its parent
+   * Model, that is, the ASTNode must represent the math element of some
+   * SBML object that has already been added to an instance of an SBMLDocument.
+   *
+   * @see isBoolean()
+   *
    * @return true if this ASTNode returns a boolean, false otherwise.
    */
   LIBSBML_EXTERN
-  bool isBooleanFor (const Model* model) const;
+  bool returnsBoolean () const;
 
 
   /**
@@ -2111,7 +2119,7 @@
  */
 LIBSBML_EXTERN
 int
-ASTNode_isBooleanFor (const ASTNode_t *node, const Model_t* model);
+ASTNode_returnsBoolean (const ASTNode_t *node);
 
 
 /**

Modified: trunk/libsbml/src/sbml/math/test/TestASTNode.c
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestASTNode.c	2011-12-16 11:32:47 UTC (rev 15051)
+++ trunk/libsbml/src/sbml/math/test/TestASTNode.c	2011-12-16 13:17:27 UTC (rev 15052)
@@ -32,6 +32,7 @@
 #include <sbml/math/FormulaParser.h>
 #include <sbml/EventAssignment.h>
 #include <sbml/Model.h>
+#include <sbml/SBMLDocument.h>
 #include <sbml/xml/XMLNode.h>
 
 #include <limits.h>
@@ -2259,7 +2260,7 @@
   fail_unless( ASTNode_hasUnits (NULL) == 0);
   fail_unless( ASTNode_insertChild (NULL, 0, NULL) == LIBSBML_INVALID_OBJECT);
   fail_unless( ASTNode_isBoolean (NULL) == 0);
-  fail_unless( ASTNode_isBooleanFor (NULL, NULL) == 0);
+  fail_unless( ASTNode_returnsBoolean (NULL) == 0);
   fail_unless( ASTNode_isConstant (NULL) == 0);
   fail_unless( ASTNode_isFunction (NULL) == 0);
   fail_unless( ASTNode_isInfinity (NULL) == 0);
@@ -2510,35 +2511,55 @@
 }
 END_TEST
 
-START_TEST (test_ASTNode_isBooleanFor)
+START_TEST (test_ASTNode_returnsBoolean)
 {
+
   ASTNode_t *n = ASTNode_create();
-  ASTNode_setName(n, "func1");
-  ASTNode_setType(n, AST_FUNCTION);
+  const ASTNode_t *math;
 
-  fail_unless(ASTNode_isBooleanFor(n, NULL) == 0);
+  // boolean function
+  n = SBML_parseFormula("geq(a,b)");
+  fail_unless(ASTNode_returnsBoolean(n) == 1);
 
-  Model_t* model = Model_create(3,1);
+  // not boolean function
+  n = SBML_parseFormula("times(a,b)");
+  fail_unless(ASTNode_returnsBoolean(n) == 0);
+
+  // piecewise with bool
+  n = SBML_parseFormula("piecewise(true, geq(X, T), false)");
+  fail_unless(ASTNode_returnsBoolean(n) == 1);
+
+  // piecewise no boolean
+  n = SBML_parseFormula("piecewise(true, geq(X, T), 5)");
+  fail_unless(ASTNode_returnsBoolean(n) == 0);
+
+  // func with no model
+  n = SBML_parseFormula("func1(X)");
+  fail_unless(ASTNode_returnsBoolean(n) == 0);
+
+  // func with model that does not contain that func
+  SBMLDocument_t *doc = SBMLDocument_createWithLevelAndVersion(3,1);
+  Model_t* model = SBMLDocument_createModel(doc);
+  Constraint *c = Model_createConstraint(model);
+  Constraint_setMath(c, n);
+
+  math = Constraint_getMath(c);
+  fail_unless(ASTNode_returnsBoolean(math) == 0);
+
+  // func with model but func has no math
   FunctionDefinition_t* fd = Model_createFunctionDefinition(model);
   FunctionDefinition_setId(fd, "func1");
+  fail_unless(ASTNode_returnsBoolean(math) == 0);
+
+  // func with model func returns boolean
   FunctionDefinition_setMath(fd, SBML_parseFormula("lambda(x, true)"));
-  fail_unless(ASTNode_isBooleanFor(n, model));
+  fail_unless(ASTNode_returnsBoolean(math) == 1);
 
-  ASTNode_setName(n, "func2");
-  fd = Model_createFunctionDefinition(model);
-  FunctionDefinition_setId(fd, "func2");
+  // func with model func returns number
   FunctionDefinition_setMath(fd, SBML_parseFormula("lambda(x, 6)"));
-  fail_unless(!ASTNode_isBooleanFor(n, model));
+  fail_unless(ASTNode_returnsBoolean(math) == 0);
   ASTNode_free(n);
-
-  n = SBML_parseFormula("piecewise(true, geq(X, T), false)");
-  fail_unless(ASTNode_isBooleanFor(n, model));
-  ASTNode_free(n);
-
-  n = SBML_parseFormula("piecewise(true, geq(X, T), 5)");
-  fail_unless(!ASTNode_isBooleanFor(n, model));
-  ASTNode_free(n);
-
+  SBMLDocument_free(doc);
 }
 END_TEST
 
@@ -2595,7 +2616,7 @@
   tcase_add_test( tcase, test_ASTNode_avogadro_bug            );
   tcase_add_test( tcase, test_ASTNode_accessWithNULL          );
   tcase_add_test( tcase, test_ASTNode_isBoolean               );
-  tcase_add_test( tcase, test_ASTNode_isBooleanFor            );
+  tcase_add_test( tcase, test_ASTNode_returnsBoolean            );
 
   suite_add_tcase(suite, tcase);
 

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Revision: 15054
          http://sbml.svn.sourceforge.net/sbml/?rev=15054&view=rev
Author:   fbergmann
Date:     2011-12-16 21:21:13 +0000 (Fri, 16 Dec 2011)
Log Message:
-----------
- we decided in the end on a default model argument, that can be passed to returnsBoolean
- of course for the C-API we don't have defaults, so there we have two methods: 

 ASTNode_returnsBoolean and
 ASTNode_returnsBooleanForModel

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.cpp
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp

Modified: trunk/libsbml/src/sbml/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-16 20:45:19 UTC (rev 15053)
+++ trunk/libsbml/src/sbml/math/ASTNode.cpp	2011-12-16 21:21:13 UTC (rev 15054)
@@ -1233,19 +1233,22 @@
 
 LIBSBML_EXTERN
 bool
-ASTNode::returnsBoolean () const
-{
+ASTNode::returnsBoolean (const Model* givenModel /*=NULL*/) const
+{   
 
   if (isBoolean() == true)
   {
     return true;
   }
 
-  else if (getType() == AST_FUNCTION)
+  const Model* model = givenModel;
+  if (givenModel == NULL && getParentSBMLObject() != NULL)
   {
-    const Model * model = (this->getParentSBMLObject() != NULL ? 
-      this->getParentSBMLObject()->getModel() : NULL);
+    model = getParentSBMLObject()->getModel();
+  }
 
+  if (getType() == AST_FUNCTION)
+  {
     if (model == NULL)
     {
       return false;
@@ -1275,6 +1278,9 @@
 
     return true;
   }
+
+  // add explicit return value in case we overlooked something
+  return false;
 }
 
 
@@ -2846,7 +2852,19 @@
   return (int) static_cast<const ASTNode*>(node)->returnsBoolean();
 }
 
+/**
+ * @return true (non-zero) if this ASTNode returns a boolean, false (0) otherwise.
+ */
+LIBSBML_EXTERN
+int
+ASTNode_returnsBooleanForModel (const ASTNode_t *node, const Model_t* model)
+{
+  if (node == NULL) return (int) false;
+  return (int) static_cast<const ASTNode*>(node)->returnsBoolean(model);
+}
 
+
+
 /**
  * @return true (non-zero) if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false (0) otherwise.

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-16 20:45:19 UTC (rev 15053)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2011-12-16 21:21:13 UTC (rev 15054)
@@ -984,7 +984,7 @@
    * @return true if this ASTNode returns a boolean, false otherwise.
    */
   LIBSBML_EXTERN
-  bool returnsBoolean () const;
+  bool returnsBoolean (const Model* model=NULL) const;
 
 
   /**
@@ -2123,6 +2123,14 @@
 
 
 /**
+ * @return true (non-zero) if this ASTNode returns a boolean, false (0) otherwise.
+ */
+LIBSBML_EXTERN
+int
+ASTNode_returnsBooleanForModel (const ASTNode_t *node, const Model_t* model);
+
+
+/**
  * @return true (non-zero) if this ASTNode is a MathML constant (true,
  * false, pi, exponentiale), false (0) otherwise.
  */

Modified: trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2011-12-16 20:45:19 UTC (rev 15053)
+++ trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2011-12-16 21:21:13 UTC (rev 15054)
@@ -229,7 +229,50 @@
 }
 END_TEST
 
+START_TEST (test_ValidASTNode_returnsBoolean)
+{ 
+  ASTNode node(AST_LOGICAL_AND);
+  fail_unless(node.returnsBoolean());
 
+  node.setType(AST_LOGICAL_NOT);
+  fail_unless(node.returnsBoolean());
+
+  node.setType(AST_LOGICAL_OR);  
+  fail_unless(node.returnsBoolean());
+
+  node.setType(AST_LOGICAL_XOR);
+  fail_unless(node.returnsBoolean());
+
+  node.setType(AST_FUNCTION_PIECEWISE);
+  fail_unless(node.returnsBoolean());
+
+  node.setType(AST_RELATIONAL_EQ);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_RELATIONAL_GEQ);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_RELATIONAL_GT);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_RELATIONAL_LEQ);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_RELATIONAL_LT);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_RELATIONAL_NEQ);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_CONSTANT_TRUE);
+  fail_unless(node.returnsBoolean());
+  
+  node.setType(AST_CONSTANT_FALSE);
+  fail_unless(node.returnsBoolean());
+  
+}
+END_TEST
+
 Suite *
 create_suite_TestValidASTNode ()
 {
@@ -237,6 +280,7 @@
   TCase *tcase = tcase_create("TestValidASTNode");
 
   tcase_add_test( tcase, test_ValidASTNode_Number       );
+  tcase_add_test( tcase, test_ValidASTNode_returnsBoolean );
   tcase_add_test( tcase, test_ValidASTNode_Name         );
   tcase_add_test( tcase, test_ValidASTNode_unary         );
   tcase_add_test( tcase, test_ValidASTNode_binary         );

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Revision: 15279
          http://sbml.svn.sourceforge.net/sbml/?rev=15279&view=rev
Author:   fbergmann
Date:     2012-01-19 19:31:06 +0000 (Thu, 19 Jan 2012)
Log Message:
-----------
- fix the mathml -> infix conversion in case of n-ary plus / times with n = 0
- added test 

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/FormulaFormatter.c
    trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-01-19 10:15:58 UTC (rev 15278)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-01-19 19:31:06 UTC (rev 15279)
@@ -371,7 +371,16 @@
   }
 }
 
+int ASTNode_isPlus0(const ASTNode_t *node)
+{
+  return ASTNode_getType(node) == AST_PLUS && ASTNode_getNumChildren(node) == 0;
+}
 
+int ASTNode_isTimes0(const ASTNode_t *node)
+{
+  return ASTNode_getType(node) == AST_TIMES && ASTNode_getNumChildren(node) == 0;
+}
+
 /**
  * Visits the given ASTNode node.  This function is really just a
  * dispatcher to either SBML_formulaToString_visitFunction() or
@@ -403,6 +412,14 @@
   {
     FormulaFormatter_visit(node, ASTNode_getChild(node, 0), sb);
   }
+  else if (ASTNode_isPlus0(node))
+  {
+    StringBuffer_appendInt(sb, 0);
+  }
+  else if (ASTNode_isTimes0(node))
+  {
+    StringBuffer_appendInt(sb, 1);
+  }
   else
   {
     FormulaFormatter_visitOther(parent, node, sb);

Modified: trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2012-01-19 10:15:58 UTC (rev 15278)
+++ trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2012-01-19 19:31:06 UTC (rev 15279)
@@ -49,6 +49,53 @@
 CK_CPPSTART
 
 
+START_TEST (test_ValidASTNode_infix_nary_plus)
+{
+  ASTNode *n = readMathMLFromString(
+     "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
+     "  <apply>"
+     "    <plus/>"
+     "  </apply>"
+     "</math>"
+    );
+
+  fail_unless( n != NULL );
+
+  string formula = SBML_formulaToString(n);
+
+  ASTNode *node = SBML_parseFormula(formula.c_str());
+
+  fail_unless( node != NULL );
+
+  delete n;
+  delete node;
+}
+END_TEST
+
+START_TEST (test_ValidASTNode_infix_nary_times)
+{
+   ASTNode *n = readMathMLFromString(
+     "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
+     "  <apply>"
+     "    <times/>"
+     "  </apply>"
+     "</math>"
+    );
+
+  fail_unless( n != NULL );
+
+  string formula = SBML_formulaToString(n);
+
+  ASTNode *node = SBML_parseFormula(formula.c_str());
+
+  fail_unless( node != NULL );
+
+  delete n;
+  delete node;
+}
+END_TEST
+
+
 START_TEST (test_ValidASTNode_Number)
 {
   ASTNode *n = SBML_parseFormula("1.2");
@@ -279,15 +326,17 @@
   Suite *suite = suite_create("TestValidASTNode");
   TCase *tcase = tcase_create("TestValidASTNode");
 
-  tcase_add_test( tcase, test_ValidASTNode_Number       );
-  tcase_add_test( tcase, test_ValidASTNode_returnsBoolean );
-  tcase_add_test( tcase, test_ValidASTNode_Name         );
-  tcase_add_test( tcase, test_ValidASTNode_unary         );
-  tcase_add_test( tcase, test_ValidASTNode_binary         );
-  tcase_add_test( tcase, test_ValidASTNode_nary         );
-  tcase_add_test( tcase, test_ValidASTNode_root        );
-  tcase_add_test( tcase, test_ValidASTNode_lambda        );
-  tcase_add_test( tcase, test_ValidASTNode_setType        );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_plus  );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_times );
+  tcase_add_test( tcase, test_ValidASTNode_Number           );
+  tcase_add_test( tcase, test_ValidASTNode_returnsBoolean   );
+  tcase_add_test( tcase, test_ValidASTNode_Name             );
+  tcase_add_test( tcase, test_ValidASTNode_unary            );
+  tcase_add_test( tcase, test_ValidASTNode_binary           );
+  tcase_add_test( tcase, test_ValidASTNode_nary             );
+  tcase_add_test( tcase, test_ValidASTNode_root             );
+  tcase_add_test( tcase, test_ValidASTNode_lambda           );
+  tcase_add_test( tcase, test_ValidASTNode_setType          );
 
   suite_add_tcase(suite, tcase);
 

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Revision: 15280
          http://sbml.svn.sourceforge.net/sbml/?rev=15280&view=rev
Author:   fbergmann
Date:     2012-01-19 20:02:00 +0000 (Thu, 19 Jan 2012)
Log Message:
-----------
- fix the mathml -> infix conversion in case of n-ary plus / times with n = 1
- added test 

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/FormulaFormatter.c
    trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-01-19 19:31:06 UTC (rev 15279)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-01-19 20:02:00 UTC (rev 15280)
@@ -381,6 +381,11 @@
   return ASTNode_getType(node) == AST_TIMES && ASTNode_getNumChildren(node) == 0;
 }
 
+int ASTNode_isTimes1(const ASTNode_t *node)
+{
+  return ASTNode_getType(node) == AST_TIMES && ASTNode_getNumChildren(node) == 1;
+}
+
 /**
  * Visits the given ASTNode node.  This function is really just a
  * dispatcher to either SBML_formulaToString_visitFunction() or
@@ -408,7 +413,7 @@
   {
     FormulaFormatter_visitUMinus(parent, node, sb);
   }
-  else if (ASTNode_isUPlus(node))
+  else if (ASTNode_isUPlus(node) || ASTNode_isTimes1(node))
   {
     FormulaFormatter_visit(node, ASTNode_getChild(node, 0), sb);
   }

Modified: trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2012-01-19 19:31:06 UTC (rev 15279)
+++ trunk/libsbml/src/sbml/math/test/TestValidASTNode.cpp	2012-01-19 20:02:00 UTC (rev 15280)
@@ -49,7 +49,7 @@
 CK_CPPSTART
 
 
-START_TEST (test_ValidASTNode_infix_nary_plus)
+START_TEST (test_ValidASTNode_infix_nary_plus0)
 {
   ASTNode *n = readMathMLFromString(
      "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
@@ -72,8 +72,32 @@
 }
 END_TEST
 
-START_TEST (test_ValidASTNode_infix_nary_times)
+START_TEST (test_ValidASTNode_infix_nary_plus1)
 {
+  ASTNode *n = readMathMLFromString(
+     "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
+     "  <apply>"
+     "    <plus/>"
+     "    <cn> 0 </cn>"
+     "  </apply>"
+     "</math>"
+    );
+
+  fail_unless( n != NULL );
+
+  string formula = SBML_formulaToString(n);
+
+  ASTNode *node = SBML_parseFormula(formula.c_str());
+
+  fail_unless( node != NULL );
+
+  delete n;
+  delete node;
+}
+END_TEST
+
+START_TEST (test_ValidASTNode_infix_nary_times0)
+{
    ASTNode *n = readMathMLFromString(
      "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
      "  <apply>"
@@ -96,6 +120,31 @@
 END_TEST
 
 
+START_TEST (test_ValidASTNode_infix_nary_times1)
+{
+   ASTNode *n = readMathMLFromString(
+     "<math xmlns='http://www.w3.org/1998/Math/MathML'>"
+     "  <apply>"
+     "    <times/>"
+     "    <cn> 0 </cn>"
+     "  </apply>"
+     "</math>"
+    );
+
+  fail_unless( n != NULL );
+
+  string formula = SBML_formulaToString(n);
+
+  ASTNode *node = SBML_parseFormula(formula.c_str());
+
+  fail_unless( node != NULL );
+
+  delete n;
+  delete node;
+}
+END_TEST
+
+
 START_TEST (test_ValidASTNode_Number)
 {
   ASTNode *n = SBML_parseFormula("1.2");
@@ -326,17 +375,19 @@
   Suite *suite = suite_create("TestValidASTNode");
   TCase *tcase = tcase_create("TestValidASTNode");
 
-  tcase_add_test( tcase, test_ValidASTNode_infix_nary_plus  );
-  tcase_add_test( tcase, test_ValidASTNode_infix_nary_times );
-  tcase_add_test( tcase, test_ValidASTNode_Number           );
-  tcase_add_test( tcase, test_ValidASTNode_returnsBoolean   );
-  tcase_add_test( tcase, test_ValidASTNode_Name             );
-  tcase_add_test( tcase, test_ValidASTNode_unary            );
-  tcase_add_test( tcase, test_ValidASTNode_binary           );
-  tcase_add_test( tcase, test_ValidASTNode_nary             );
-  tcase_add_test( tcase, test_ValidASTNode_root             );
-  tcase_add_test( tcase, test_ValidASTNode_lambda           );
-  tcase_add_test( tcase, test_ValidASTNode_setType          );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_plus0  );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_plus1  );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_times0 );
+  tcase_add_test( tcase, test_ValidASTNode_infix_nary_times1 );
+  tcase_add_test( tcase, test_ValidASTNode_Number            );
+  tcase_add_test( tcase, test_ValidASTNode_returnsBoolean    );
+  tcase_add_test( tcase, test_ValidASTNode_Name              );
+  tcase_add_test( tcase, test_ValidASTNode_unary             );
+  tcase_add_test( tcase, test_ValidASTNode_binary            );
+  tcase_add_test( tcase, test_ValidASTNode_nary              );
+  tcase_add_test( tcase, test_ValidASTNode_root              );
+  tcase_add_test( tcase, test_ValidASTNode_lambda            );
+  tcase_add_test( tcase, test_ValidASTNode_setType           );
 
   suite_add_tcase(suite, tcase);
 

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15550
          http://sbml.svn.sourceforge.net/sbml/?rev=15550&view=rev
Author:   sarahkeating
Date:     2012-03-22 11:55:45 +0000 (Thu, 22 Mar 2012)
Log Message:
-----------
fixed the issue with AST plus/times with more than 2 children; writing out the MathML was losing children - considered a very bad thing in most societies

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/MathML.cpp
    trunk/libsbml/src/sbml/math/test/Makefile.in
    trunk/libsbml/src/sbml/math/test/TestRunner.c

Added Paths:
-----------
    trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp

Modified: trunk/libsbml/src/sbml/math/MathML.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/MathML.cpp	2012-03-21 16:37:19 UTC (rev 15549)
+++ trunk/libsbml/src/sbml/math/MathML.cpp	2012-03-22 11:55:45 UTC (rev 15550)
@@ -1356,6 +1356,7 @@
   ASTNodeType_t type  = node.getType();
   ASTNode*      left  = node.getLeftChild();
   ASTNode*      right = node.getRightChild();
+  unsigned int num = node.getNumChildren();
 
 
   //
@@ -1366,24 +1367,44 @@
   // multiple levels of binary AST_PLUS or AST_TIMES nodes into an n-ary
   // expression.
   //
+
+  // BUT whilst it is true that the MathML reader will always create
+  // binary nodes; it is possible to create a PLUS or TIMES ASTNode with
+  // more than 2 children - need to deal with this as the function
+  // loses a child when written out
+
   if (type == AST_PLUS || type == AST_TIMES)
   {
-    if (left)
+    if (num <= 2)
     {
-      if (left->getType() == type) writeOperatorArgs(*left, stream, sbmlns);
-      else writeNode(*left, stream, sbmlns);
+      // two or less children - do what we always did
+      if (left != NULL)
+      {
+        if (left->getType() == type) writeOperatorArgs(*left, stream, sbmlns);
+        else writeNode(*left, stream, sbmlns);
+      }
+
+      if (right != NULL)
+      {
+        if (right->getType() == type) writeOperatorArgs(*right, stream, sbmlns);
+        else writeNode(*right, stream, sbmlns);
+      }
     }
+    else
+    {
+      // more than two children that might or might not be functions
+      for (unsigned int n = 0; n < num; n++)
+      {
+        writeNode(*(node.getChild(n)), stream, sbmlns);
+      }
 
-    if (right)
-    {
-      if (right->getType() == type) writeOperatorArgs(*right, stream, sbmlns);
-      else writeNode(*right, stream, sbmlns);
     }
+
   }
   else
   {
-    if (left)  writeNode(*left , stream, sbmlns);
-    if (right) writeNode(*right, stream, sbmlns);
+    if (left != NULL)  writeNode(*left , stream, sbmlns);
+    if (right != NULL) writeNode(*right, stream, sbmlns);
   }
 }
 

Modified: trunk/libsbml/src/sbml/math/test/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/math/test/Makefile.in	2012-03-21 16:37:19 UTC (rev 15549)
+++ trunk/libsbml/src/sbml/math/test/Makefile.in	2012-03-22 11:55:45 UTC (rev 15550)
@@ -57,6 +57,7 @@
   TestFormulaTokenizer.c \
   TestReadMathML.cpp     \
   TestWriteMathML.cpp    \
+  TestWriteMathMLFromAST.cpp    \
   TestReadFromFile1.cpp  \
   TestReadFromFile2.cpp  \
   TestValidASTNode.cpp   \

Modified: trunk/libsbml/src/sbml/math/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestRunner.c	2012-03-21 16:37:19 UTC (rev 15549)
+++ trunk/libsbml/src/sbml/math/test/TestRunner.c	2012-03-22 11:55:45 UTC (rev 15550)
@@ -57,6 +57,7 @@
 Suite *create_suite_FormulaTokenizer (void);
 Suite *create_suite_ReadMathML       (void);
 Suite *create_suite_WriteMathML      (void);
+Suite *create_suite_WriteMathMLFromAST      (void);
 
 Suite *create_suite_TestReadFromFile1      (void);
 Suite *create_suite_TestReadFromFile2      (void);
@@ -114,6 +115,7 @@
   srunner_add_suite( runner, create_suite_FormulaTokenizer () );
   srunner_add_suite( runner, create_suite_ReadMathML       () );
   srunner_add_suite( runner, create_suite_WriteMathML      () );
+  srunner_add_suite( runner, create_suite_WriteMathMLFromAST      () );
 
   srunner_add_suite( runner, create_suite_TestReadFromFile1() );
   srunner_add_suite( runner, create_suite_TestReadFromFile2() );

Added: trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp	                        (rev 0)
+++ trunk/libsbml/src/sbml/math/test/TestWriteMathMLFromAST.cpp	2012-03-22 11:55:45 UTC (rev 15550)
@@ -0,0 +1,1187 @@
+/**
+ * \file    TestWriteMathMLFromASTFromAST.cpp
+ * \brief   Write MathML unit tests starting from ASTNodes
+ * \author  Sarah Keating
+ * 
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML.  Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2009-2012 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ *  
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ *     Pasadena, CA, USA 
+ *  
+ * Copyright (C) 2002-2005 jointly by the following organizations: 
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. Japan Science and Technology Agency, Japan
+ * 
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation.  A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as http://sbml.org/software/libsbml/license.html
+ * ---------------------------------------------------------------------- -->*/
+
+#include <limits>
+#include <iostream>
+#include <cstring>
+#include <cstdio>
+
+#include <check.h>
+
+#include <sbml/math/FormulaParser.h>
+#include <sbml/math/ASTNode.h>
+#include <sbml/math/MathML.h>
+
+#include <sbml/xml/XMLToken.h>
+#include <sbml/xml/XMLNode.h>
+
+/** @cond doxygen-ignored */
+
+using namespace std;
+LIBSBML_CPP_NAMESPACE_USE
+
+/** @endcond */
+
+
+/**
+ * Wraps the string s in the appropriate XML boilerplate.
+ */
+#define XML_HEADER    "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+#define MATHML_HEADER "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
+#define MATHML_HEADER_UNITS  "<math xmlns=\"http://www.w3.org/1998/Math/MathML\""
+#define MATHML_HEADER_UNITS2  " xmlns:sbml=\"http://www.sbml.org/sbml/level3/version1/core\">\n"
+#define MATHML_FOOTER "</math>"
+
+#define wrapMathML(s)   XML_HEADER MATHML_HEADER s MATHML_FOOTER
+#define wrapMathMLUnits(s)  XML_HEADER MATHML_HEADER_UNITS MATHML_HEADER_UNITS2 s MATHML_FOOTER
+
+
+static ASTNode* N;
+static char*    S;
+
+
+void
+WriteMathMLFromAST_setup ()
+{
+  N = NULL;
+  S = NULL;
+}
+
+
+void
+WriteMathMLFromAST_teardown ()
+{
+  delete N;
+  free(S);
+}
+
+
+static bool
+equals (const char* expected, const char* actual)
+{
+  if ( !strcmp(expected, actual) ) return true;
+
+  printf( "\nStrings are not equal:\n"  );
+  printf( "Expected:\n[%s]\n", expected );
+  printf( "Actual:\n[%s]\n"  , actual   );
+
+  return false;
+}
+
+
+CK_CPPSTART
+
+
+START_TEST (test_MathMLFromAST_cn_real_1)
+{
+  const char *expected = wrapMathML("  <cn> 1.2 </cn>\n");
+
+  N = SBML_parseFormula("1.2");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_real_2)
+{
+  const char* expected = wrapMathML("  <cn> 1234567.8 </cn>\n");
+
+  N = SBML_parseFormula("1234567.8");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_real_3)
+{
+  const char* expected = wrapMathML("  <cn> -3.14 </cn>\n");
+
+  N = SBML_parseFormula("-3.14");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_real_locale)
+{
+  const char* expected = wrapMathML("  <cn> 2.72 </cn>\n");
+
+
+  setlocale(LC_NUMERIC, "de_DE");
+
+  N = SBML_parseFormula("2.72");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+
+  setlocale(LC_NUMERIC, "C");
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_1)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 0 <sep/> 3 </cn>\n"
+  );
+
+  N = SBML_parseFormula("0e3");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_2)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 2 <sep/> 3 </cn>\n"
+  );
+
+  N = SBML_parseFormula("2e3");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_3)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 1234567.8 <sep/> 3 </cn>\n"
+  );
+
+  N = SBML_parseFormula("1234567.8e3");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_4)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 6.0221367 <sep/> 23 </cn>\n"
+  );
+
+  N = SBML_parseFormula("6.0221367e+23");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_5)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 4 <sep/> -6 </cn>\n"
+  );
+
+  N = SBML_parseFormula(".000004");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_6)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> 4 <sep/> -12 </cn>\n"
+  );
+
+  N = SBML_parseFormula(".000004e-6");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_e_notation_7)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"e-notation\"> -1 <sep/> -6 </cn>\n"
+  );
+
+  N = SBML_parseFormula("-1e-6");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_integer)
+{
+  const char* expected = wrapMathML("  <cn type=\"integer\"> 5 </cn>\n");
+
+  N = SBML_parseFormula("5");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_rational)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"rational\"> 1 <sep/> 3 </cn>\n"
+  );
+
+  N = new ASTNode;
+  N->setValue(static_cast<long>(1), 3);
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_ci)
+{
+  const char* expected = wrapMathML("  <ci> foo </ci>\n");
+
+  N = SBML_parseFormula("foo");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_csymbol_delay)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <csymbol encoding=\"text\" definitionURL=\"http://www.sbml.org/sbml/"
+    "symbols/delay\"> my_delay </csymbol>\n"
+    "    <ci> x </ci>\n"
+    "    <cn> 0.1 </cn>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("delay(x, 0.1)");
+  N->setName("my_delay");
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_csymbol_time)
+{
+  const char* expected = wrapMathML
+  (
+    "  <csymbol encoding=\"text\" "
+    "definitionURL=\"http://www.sbml.org/sbml/symbols/time\"> t </csymbol>\n"
+  );
+
+  N = new ASTNode(AST_NAME_TIME);
+  N->setName("t");
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_true)
+{
+  const char* expected = wrapMathML("  <true/>\n");
+
+  N = new ASTNode(AST_CONSTANT_TRUE);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_false)
+{
+  const char* expected = wrapMathML("  <false/>\n");
+
+  N = new ASTNode(AST_CONSTANT_FALSE);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_notanumber)
+{
+  const char* expected = wrapMathML("  <notanumber/>\n");
+
+  N = new ASTNode(AST_REAL);
+  N->setValue( numeric_limits<double>::quiet_NaN() );
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_infinity)
+{
+  const char* expected = wrapMathML("  <infinity/>\n");
+
+  N = new ASTNode;
+  N->setValue( numeric_limits<double>::infinity() );
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_infinity_neg)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply> <minus/> <infinity/> </apply>\n"
+  );
+
+  N = new ASTNode;
+  N->setValue( - numeric_limits<double>::infinity() );
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_constant_exponentiale)
+{
+  const char* expected = wrapMathML("  <exponentiale/>\n");
+
+  N = new ASTNode(AST_CONSTANT_E);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_plus_binary)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <plus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "  </apply>\n"
+  );
+
+//  N = SBML_parseFormula("1 + 2");
+
+  N = new ASTNode(AST_PLUS);
+  
+  ASTNode *c1 = new ASTNode(AST_INTEGER);
+  c1->setValue(1);
+  ASTNode *c2 = new ASTNode(AST_INTEGER);
+  c2->setValue(2);
+  
+  N->addChild(c1);
+  N->addChild(c2);
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_plus_nary_1)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <plus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <cn type=\"integer\"> 3 </cn>\n"
+    "  </apply>\n"
+  );
+ 
+  //N = SBML_parseFormula("1 + 2 + 3");
+
+  N = new ASTNode(AST_PLUS);
+  
+  ASTNode *c1 = new ASTNode(AST_INTEGER);
+  c1->setValue(1);
+  ASTNode *c2 = new ASTNode(AST_INTEGER);
+  c2->setValue(2);
+  ASTNode *c3 = new ASTNode(AST_INTEGER);
+  c3->setValue(3);
+  
+  N->addChild(c1);
+  N->addChild(c2);
+  N->addChild(c3);
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_plus_nary_2)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <plus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <cn type=\"integer\"> 3 </cn>\n"
+    "  </apply>\n"
+  );
+  
+  //N = SBML_parseFormula("(1 + 2) + 3");
+
+  N = new ASTNode(AST_PLUS);
+  
+  ASTNode *c1 = new ASTNode(AST_INTEGER);
+  c1->setValue(1);
+  ASTNode *c2 = new ASTNode(AST_INTEGER);
+  c2->setValue(2);
+  ASTNode *c3 = new ASTNode(AST_INTEGER);
+  c3->setValue(3);
+  
+  ASTNode *plus = new ASTNode(AST_PLUS);
+  plus->addChild(c1);
+  plus->addChild(c2);
+  
+  N->addChild(plus);
+  N->addChild(c3);
+  
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_plus_nary_3)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <plus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <cn type=\"integer\"> 3 </cn>\n"
+    "  </apply>\n"
+  );
+
+//  N = SBML_parseFormula("1 + (2 + 3)");
+  
+  N = new ASTNode(AST_PLUS);
+  
+  ASTNode *c1 = new ASTNode(AST_INTEGER);
+  c1->setValue(1);
+  ASTNode *c2 = new ASTNode(AST_INTEGER);
+  c2->setValue(2);
+  ASTNode *c3 = new ASTNode(AST_INTEGER);
+  c3->setValue(3);
+  
+  ASTNode *plus = new ASTNode(AST_PLUS);
+  plus->addChild(c2);
+  plus->addChild(c3);
+  
+  N->addChild(c1);
+  N->addChild(plus);
+  
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_plus_nary_4)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <plus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <apply>\n"
+    "      <times/>\n"
+    "      <ci> x </ci>\n"
+    "      <ci> y </ci>\n"
+    "      <ci> z </ci>\n"
+    "    </apply>\n"
+    "    <cn type=\"integer\"> 3 </cn>\n"
+    "  </apply>\n"
+  );
+
+//  N = SBML_parseFormula("1 + 2 + x * y * z + 3");
+  
+  N = new ASTNode(AST_PLUS);
+  
+  ASTNode *c1 = new ASTNode(AST_INTEGER);
+  c1->setValue(1);
+  ASTNode *c2 = new ASTNode(AST_INTEGER);
+  c2->setValue(2);
+  ASTNode *c3 = new ASTNode(AST_INTEGER);
+  c3->setValue(3);
+  ASTNode *cx = new ASTNode(AST_NAME);
+  cx->setName("x");
+  ASTNode *cy = new ASTNode(AST_NAME);
+  cy->setName("y");
+  ASTNode *cz = new ASTNode(AST_NAME);
+  cz->setName("z");
+  
+  ASTNode *times = new ASTNode(AST_TIMES);
+  times->addChild(cx);
+  times->addChild(cy);
+  times->addChild(cz);
+  
+  N->addChild(c1);
+  N->addChild(c2);
+  N->addChild(times);
+  N->addChild(c3);
+  
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_minus)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <minus/>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("1 - 2");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_minus_unary_1)
+{
+  const char* expected = wrapMathML
+  (
+    "  <cn type=\"integer\"> -2 </cn>\n"
+  );
+
+  N = SBML_parseFormula("-2");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_minus_unary_2)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <minus/>\n"
+    "    <ci> a </ci>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("-a");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_function_1)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <ci> foo </ci>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <cn type=\"integer\"> 3 </cn>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("foo(1, 2, 3)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_function_2)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <ci> foo </ci>\n"
+    "    <cn type=\"integer\"> 1 </cn>\n"
+    "    <cn type=\"integer\"> 2 </cn>\n"
+    "    <apply>\n"
+    "      <ci> bar </ci>\n"
+    "      <ci> z </ci>\n"
+    "    </apply>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("foo(1, 2, bar(z))");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_sin)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <sin/>\n"
+    "    <ci> x </ci>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("sin(x)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_log)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <log/>\n"
+    "    <logbase>\n"
+    "      <cn type=\"integer\"> 2 </cn>\n"
+    "    </logbase>\n"
+    "    <ci> N </ci>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("log(2, N)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_root)
+{
+  const char* expected = wrapMathML
+  (
+    "  <apply>\n"
+    "    <root/>\n"
+    "    <degree>\n"
+    "      <cn type=\"integer\"> 3 </cn>\n"
+    "    </degree>\n"
+    "    <ci> x </ci>\n"
+    "  </apply>\n"
+  );
+
+  N = SBML_parseFormula("root(3, x)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_lambda)
+{
+  const char* expected = wrapMathML
+  (
+    "  <lambda>\n"
+    "    <bvar>\n"
+    "      <ci> x </ci>\n"
+    "    </bvar>\n"
+    "    <bvar>\n"
+    "      <ci> y </ci>\n"
+    "    </bvar>\n"
+    "    <apply>\n"
+    "      <root/>\n"
+    "      <degree>\n"
+    "        <cn type=\"integer\"> 2 </cn>\n"
+    "      </degree>\n"
+    "      <apply>\n"
+    "        <plus/>\n"
+    "        <apply>\n"
+    "          <power/>\n"
+    "          <ci> x </ci>\n"
+    "          <cn type=\"integer\"> 2 </cn>\n"
+    "        </apply>\n"
+    "        <apply>\n"
+    "          <power/>\n"
+    "          <ci> y </ci>\n"
+    "          <cn type=\"integer\"> 2 </cn>\n"
+    "        </apply>\n"
+    "      </apply>\n"
+    "    </apply>\n"
+    "  </lambda>\n"
+  );
+
+  N = SBML_parseFormula("lambda(x, y, root(2, x^2 + y^2))");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_lambda_no_bvars)
+{
+  const char* expected = wrapMathML
+  (
+    "  <lambda>\n"
+    "    <apply>\n"
+    "      <plus/>\n"
+    "      <cn type=\"integer\"> 2 </cn>\n"
+    "      <cn type=\"integer\"> 2 </cn>\n"
+    "    </apply>\n"
+    "  </lambda>\n"
+  );
+
+  N = SBML_parseFormula("lambda(2 + 2)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_piecewise)
+{
+  const char* expected = wrapMathML
+  (
+    "  <piecewise>\n"
+    "    <piece>\n"
+    "      <apply>\n"
+    "        <minus/>\n"
+    "        <ci> x </ci>\n"
+    "      </apply>\n"
+    "      <apply>\n"
+    "        <lt/>\n"
+    "        <ci> x </ci>\n"
+    "        <cn type=\"integer\"> 0 </cn>\n"
+    "      </apply>\n"
+    "    </piece>\n"
+    "    <piece>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "      <apply>\n"
+    "        <eq/>\n"
+    "        <ci> x </ci>\n" 
+    "        <cn type=\"integer\"> 0 </cn>\n"
+    "      </apply>\n"
+    "    </piece>\n"
+    "    <piece>\n"
+    "      <ci> x </ci>\n"
+    "      <apply>\n"
+    "        <gt/>\n"
+    "        <ci> x </ci>\n" 
+    "        <cn type=\"integer\"> 0 </cn>\n"
+    "      </apply>\n"
+    "    </piece>\n"
+    "  </piecewise>\n"
+  );
+
+  const char *f = "piecewise(-x, lt(x, 0), 0, eq(x, 0), x, gt(x, 0))";
+
+  N = SBML_parseFormula(f);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_piecewise_otherwise)
+{
+  const char* expected = wrapMathML
+  (
+    "  <piecewise>\n"
+    "    <piece>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "      <apply>\n"
+    "        <lt/>\n"
+    "        <ci> x </ci>\n"
+    "        <cn type=\"integer\"> 0 </cn>\n"
+    "      </apply>\n"
+    "    </piece>\n"
+    "    <otherwise>\n"
+    "      <ci> x </ci>\n" 
+    "    </otherwise>\n"
+    "  </piecewise>\n"
+  );
+
+  N = SBML_parseFormula("piecewise(0, lt(x, 0), x)");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_semantics)
+{
+  const char* expected = wrapMathML
+  (
+    "  <semantics>\n"
+    "    <apply>\n"
+    "      <lt/>\n"
+    "      <ci> x </ci>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "    </apply>\n"
+    "  </semantics>\n"
+  );
+
+  N = SBML_parseFormula("lt(x, 0)");
+  N->setSemanticsFlag();
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_semantics_url)
+{
+  const char* expected = wrapMathML
+  (
+    "  <semantics definitionURL=\"foobar\">\n"
+    "    <apply>\n"
+    "      <lt/>\n"
+    "      <ci> x </ci>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "    </apply>\n"
+    "  </semantics>\n"
+  );
+
+  XMLAttributes *xa = new XMLAttributes();
+  xa->add("definitionURL", "foobar");
+  
+  N = SBML_parseFormula("lt(x, 0)");
+  N->setSemanticsFlag();
+  N->setDefinitionURL(*xa);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_semantics_ann)
+{
+  const char* expected = wrapMathML
+  (
+    "  <semantics>\n"
+    "    <apply>\n"
+    "      <lt/>\n"
+    "      <ci> x </ci>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "    </apply>\n"
+    "    <annotation encoding=\"bar\">foo</annotation>\n"
+    "  </semantics>\n"
+  );
+
+  XMLAttributes xa = XMLAttributes();
+  xa.add("encoding", "bar");
+  
+  XMLTriple triple = XMLTriple("annotation", "", "");
+  
+  XMLToken ann_token = XMLToken(triple, xa);
+  
+  XMLNode *ann = new XMLNode(ann_token);
+  XMLToken text = XMLToken("foo");
+  XMLNode textNode = XMLNode(text);
+  ann->addChild(textNode);
+  
+  N = SBML_parseFormula("lt(x, 0)");
+  N->setSemanticsFlag();
+  N->addSemanticsAnnotation(ann);
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_semantics_annxml)
+{
+  const char* expected = wrapMathML
+  (
+    "  <semantics>\n"
+    "    <apply>\n"
+    "      <lt/>\n"
+    "      <ci> x </ci>\n"
+    "      <cn type=\"integer\"> 0 </cn>\n"
+    "    </apply>\n"
+    "    <annotation-xml encoding=\"bar\">\n"
+    "      <foobar>\n"
+    "        <bar id=\"c\"/>\n"
+    "      </foobar>\n"
+    "    </annotation-xml>\n"
+    "  </semantics>\n"
+  );
+
+  XMLAttributes xa = XMLAttributes();
+  xa.add("encoding", "bar");
+  
+  XMLAttributes xa1 = XMLAttributes();
+  xa1.add("id", "c");
+
+  XMLAttributes blank = XMLAttributes();
+
+  XMLTriple triple = XMLTriple("annotation-xml", "", "");
+  XMLTriple foo_triple = XMLTriple("foobar", "", "");
+  XMLTriple bar_triple = XMLTriple("bar", "", "");
+  
+  XMLToken ann_token = XMLToken(triple, xa);
+  XMLToken foo_token = XMLToken(foo_triple, blank);
+  XMLToken bar_token = XMLToken(bar_triple, xa1);
+  
+  XMLNode bar = XMLNode(bar_token);
+  XMLNode foo = XMLNode(foo_token);
+  XMLNode *ann = new XMLNode(ann_token);
+
+  foo.addChild(bar);
+  ann->addChild(foo);
+  
+  N = SBML_parseFormula("lt(x, 0)");
+  N->setSemanticsFlag();
+  N->addSemanticsAnnotation(ann);
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_cn_units)
+{
+  const char *expected = wrapMathMLUnits("  <cn sbml:units=\"mole\"> 1.2 </cn>\n");
+
+  N = SBML_parseFormula("1.2");
+  N->setUnits("mole");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_csymbol_avogadro)
+{
+  const char* expected = wrapMathML
+  (
+    "  <csymbol encoding=\"text\" "
+    "definitionURL=\"http://www.sbml.org/sbml/symbols/avogadro\"> NA </csymbol>\n"
+  );
+
+  N = new ASTNode(AST_NAME_AVOGADRO);
+  N->setName("NA");
+
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+START_TEST (test_MathMLFromAST_ci_definitionURL)
+{
+  const char* expected = wrapMathML("  <ci definitionURL=\"http://someurl\"> foo </ci>\n");
+
+  N = SBML_parseFormula("foo");
+  XMLAttributes xml;
+  xml.add("", "http://someurl");
+  N->setDefinitionURL(xml);
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+START_TEST (test_MathMLFromAST_ci_id)
+{
+  const char* expected = wrapMathML("  <ci id=\"test\"> foo </ci>\n");
+
+  N = SBML_parseFormula("foo");
+  N->setId("test");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+START_TEST (test_MathMLFromAST_ci_class)
+{
+  const char* expected = wrapMathML("  <ci class=\"test\"> foo </ci>\n");
+
+  N = SBML_parseFormula("foo");
+  N->setClass("test");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+START_TEST (test_MathMLFromAST_ci_style)
+{
+  const char* expected = wrapMathML("  <ci style=\"test\"> foo </ci>\n");
+
+  N = SBML_parseFormula("foo");
+  N->setStyle("test");
+  S = writeMathMLToString(N);
+
+  fail_unless( equals(expected, S) );
+}
+END_TEST
+
+
+Suite *
+create_suite_WriteMathMLFromAST ()
+{
+  Suite *suite = suite_create("WriteMathMLFromAST");
+  TCase *tcase = tcase_create("WriteMathMLFromAST");
+
+  tcase_add_checked_fixture(tcase, WriteMathMLFromAST_setup, WriteMathMLFromAST_teardown);
+
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_real_1             );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_real_2             );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_real_3             );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_real_locale        );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_1       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_2       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_3       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_4       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_5       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_6       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_e_notation_7       );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_integer            );
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_rational           );
+
+  //tcase_add_test( tcase, test_MathMLFromAST_ci                    );
+  //tcase_add_test( tcase, test_MathMLFromAST_csymbol_delay         );
+  //tcase_add_test( tcase, test_MathMLFromAST_csymbol_time          );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_true         );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_false        );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_notanumber   );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_infinity     );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_infinity_neg );
+  //tcase_add_test( tcase, test_MathMLFromAST_constant_exponentiale );
+  tcase_add_test( tcase, test_MathMLFromAST_plus_binary           );
+  tcase_add_test( tcase, test_MathMLFromAST_plus_nary_1           );
+  tcase_add_test( tcase, test_MathMLFromAST_plus_nary_2           );
+  tcase_add_test( tcase, test_MathMLFromAST_plus_nary_3           );
+  tcase_add_test( tcase, test_MathMLFromAST_plus_nary_4           );
+  //tcase_add_test( tcase, test_MathMLFromAST_minus                 );
+  //tcase_add_test( tcase, test_MathMLFromAST_minus_unary_1         );
+  //tcase_add_test( tcase, test_MathMLFromAST_minus_unary_2         );
+  //tcase_add_test( tcase, test_MathMLFromAST_function_1            );
+  //tcase_add_test( tcase, test_MathMLFromAST_function_2            );
+  //tcase_add_test( tcase, test_MathMLFromAST_sin                   );
+  //tcase_add_test( tcase, test_MathMLFromAST_log                   );
+  //tcase_add_test( tcase, test_MathMLFromAST_root                  );
+  //tcase_add_test( tcase, test_MathMLFromAST_lambda                );
+  //tcase_add_test( tcase, test_MathMLFromAST_lambda_no_bvars       );
+  //tcase_add_test( tcase, test_MathMLFromAST_piecewise             );
+  //tcase_add_test( tcase, test_MathMLFromAST_piecewise_otherwise   );
+
+  //tcase_add_test( tcase, test_MathMLFromAST_semantics             );
+  //tcase_add_test( tcase, test_MathMLFromAST_semantics_url         );
+  //tcase_add_test( tcase, test_MathMLFromAST_semantics_ann         );
+  //tcase_add_test( tcase, test_MathMLFromAST_semantics_annxml      );
+
+  ///* L3 additions */
+  //tcase_add_test( tcase, test_MathMLFromAST_cn_units           );
+
+  //tcase_add_test( tcase, test_MathMLFromAST_csymbol_avogadro         );
+  //tcase_add_test( tcase, test_MathMLFromAST_ci_definitionURL         );
+  //tcase_add_test( tcase, test_MathMLFromAST_ci_id                    );
+  //tcase_add_test( tcase, test_MathMLFromAST_ci_class                 );
+  //tcase_add_test( tcase, test_MathMLFromAST_ci_style                 );
+
+  suite_add_tcase(suite, tcase);
+
+  return suite;
+}
+
+
+CK_CPPEND

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Revision: 15640
          http://sbml.svn.sourceforge.net/sbml/?rev=15640&view=rev
Author:   sarahkeating
Date:     2012-04-22 12:20:20 +0000 (Sun, 22 Apr 2012)
Log Message:
-----------
added the new L3 parser files to the makefiles

until we properly decommission the gnumake we need to maintain it; pain though it is as I'm currently debugging the tests that fail because they cannot find things

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/Makefile.in
    trunk/libsbml/src/sbml/math/test/Makefile.in

Modified: trunk/libsbml/src/sbml/math/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/math/Makefile.in	2012-04-22 12:17:17 UTC (rev 15639)
+++ trunk/libsbml/src/sbml/math/Makefile.in	2012-04-22 12:20:20 UTC (rev 15640)
@@ -55,6 +55,8 @@
   FormulaFormatter.h \
   FormulaParser.h    \
   FormulaTokenizer.h \
+  L3Parser.h         \
+  L3ParserSettings.h \
   MathML.h
 
 header_inst_prefix = math
@@ -64,6 +66,9 @@
   FormulaFormatter.c \
   FormulaParser.c    \
   FormulaTokenizer.c \
+  L3Parser.tab.cpp   \
+  L3Parser.ypp       \
+  L3ParserSettings.cpp \
   MathML.cpp
 
 

Modified: trunk/libsbml/src/sbml/math/test/Makefile.in
===================================================================
--- trunk/libsbml/src/sbml/math/test/Makefile.in	2012-04-22 12:17:17 UTC (rev 15639)
+++ trunk/libsbml/src/sbml/math/test/Makefile.in	2012-04-22 12:20:20 UTC (rev 15640)
@@ -61,6 +61,7 @@
   TestReadFromFile1.cpp  \
   TestReadFromFile2.cpp  \
   TestValidASTNode.cpp   \
+  TestL3FormulaParser.c \
   TestRunner.c
 
 extra_CPPFLAGS = -I.. -I../..

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Revision: 15659
          http://sbml.svn.sourceforge.net/sbml/?rev=15659&view=rev
Author:   mhucka
Date:     2012-04-24 00:42:19 +0000 (Tue, 24 Apr 2012)
Log Message:
-----------
Fixed up doxygen references to a couple of functions.  This fixes
dangling references reported by Bruce Shapiro.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/FormulaFormatter.h
    trunk/libsbml/src/sbml/math/FormulaParser.h
    trunk/libsbml/src/sbml/math/FormulaTokenizer.h
    trunk/libsbml/src/sbml/math/L3Parser.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2012-04-23 18:54:32 UTC (rev 15658)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2012-04-24 00:42:19 UTC (rev 15659)
@@ -139,8 +139,8 @@
  * 
  * <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@... csharp 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()@endif@... csharp SBML_parseFormula()@else <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()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
+ * read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.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&nbsp;1.  A
  * formula in this text-string form can be handed to a program that
  * understands SBML Level&nbsp;1 mathematical expressions, or used as part
@@ -1220,7 +1220,8 @@
    * 
    * For numbers, unary minus nodes can be "collapsed" by negating the
    * number.  In fact, 
-   * @if clike SBML_parseFormula() @endif@... csharp SBML_parseFormula() @else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif does this during its parsing process.
+   * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.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@...) cannot
    * be "collapsed", so this predicate function is necessary.
@@ -2314,7 +2315,8 @@
  * otherwise.
  *
  * For numbers, unary minus nodes can be "collapsed" by negating the
- * number.  In fact, SBML_parseFormula() does this during its parse.
+ * number.  In fact, @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * does this during its parse.
  * However, unary minus nodes for symbols (@c AST_NAMES) cannot be
  * "collapsed", so this predicate function is necessary.
  *

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-04-23 18:54:32 UTC (rev 15658)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-04-24 00:42:19 UTC (rev 15659)
@@ -42,29 +42,14 @@
  * Converts an AST to a string representation of a formula using a syntax
  * basically derived from SBML Level&nbsp;1.
  *
- * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level&nbsp;1.  A formula in
- * this text-string form therefore can be handed to a program that
- * understands SBML Level&nbsp;1 mathematical expressions, or used as part
- * of a formula translation system.  The syntax is described in detail in
- * the documentation for ASTNode. @endif@... csharp The text-string form of
- * mathematical formulas produced by SBML_formulaToString() and read by
- * SBML_parseFormula() are simple C-inspired infix notation taken from SBML
- * Level&nbsp;1.  A formula in this text-string form therefore can be
- * handed to a program that understands SBML Level&nbsp;1 mathematical
- * expressions, or used as part of a formula translation system.  The
- * syntax is described in detail in 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 <code><a
- * href="libsbml.html#parseFormula(java.lang.String)">
- * libsbml.parseFormula()</a></code> are simple C-inspired infix notation
- * taken from SBML Level&nbsp;1.  A formula in this text-string form
- * therefore can be handed to a program that understands SBML Level&nbsp;1
- * mathematical expressions, or used as part of a formula translation
- * system.  The syntax is described in detail in the documentation for
- * ASTNode.  @endif
+ * The text-string form of mathematical formulas produced by
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * formula in this text-string form therefore can be handed to a program
+ * that understands SBML Level&nbsp;1 mathematical expressions, or used as
+ * part of a formula translation system.  The syntax is described in detail
+ * in the documentation for ASTNode. 
  *
  * Note that this facility is provided as a convenience by libSBML&mdash;the
  * MathML standard does not actually define a "string-form" equivalent to
@@ -121,6 +106,7 @@
  *
  * @if clike @see SBML_parseFormula()@endif
  * @if csharp @see SBML_parseFormula()@endif
+ * @if python @see libsbml.parseFormula()@endif
  * @if java @see parseFormula(java.lang.String)@endif
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.h	2012-04-23 18:54:32 UTC (rev 15658)
+++ trunk/libsbml/src/sbml/math/FormulaParser.h	2012-04-24 00:42:19 UTC (rev 15659)
@@ -43,27 +43,14 @@
  * Parses the given SBML formula and returns a representation of it as an
  * Abstract Syntax Tree (AST).
  *
- * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level&nbsp;1.  A formula in
- * this text-string form therefore can be handed to a program that
- * understands SBML Level&nbsp;1 mathematical expressions, or used as part
- * of a formula translation system.  The syntax is described in detail in
- * the documentation for ASTNode. @endif@... csharp The text-string form of
- * mathematical formulas produced by SBML_formulaToString() and read by
- * SBML_parseFormula() are simple C-inspired infix notation taken from SBML
- * Level&nbsp;1.  A formula in this text-string form therefore can be
- * handed to a program that understands SBML Level&nbsp;1 mathematical
- * expressions, or used as part of a formula translation system.  The
- * syntax is described in detail in 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
- * simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * The text-string form of mathematical formulas produced by
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form therefore can be handed to a program
  * that understands SBML Level&nbsp;1 mathematical expressions, or used as
  * part of a formula translation system.  The syntax is described in detail
- * in the documentation for ASTNode.  @endif
+ * in the documentation for ASTNode. 
  *
  * This returns the root node of the AST corresponding to the formula.  If
  * the formula contains a syntax error, @c NULL is returned instead.
@@ -122,6 +109,7 @@
  *
  * @if clike @see SBML_formulaToString()@endif
  * @if csharp @see SBML_formulaToString()@endif
+ * @if python @see libsbml.formulaToString()@endif
  * @if java @see formulaToString(ASTNode tree)@endif
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaTokenizer.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-04-23 18:54:32 UTC (rev 15658)
+++ trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-04-24 00:42:19 UTC (rev 15659)
@@ -76,8 +76,8 @@
  * Levels&nbsp;2 and&nbsp;3.  LibSBML implements a parser and converter to
  * translate formulas between this text-string representation and MathML.
  * The principal entry points to the translation system are
- * @if java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@else SBML_formulaToString()@endif
- * and @if java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@else SBML_parseFormula()@endif.
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  *
  * LibSBML also provides a lower-level interface to the formula parser.
  * This takes the form of the C functions

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-23 18:54:32 UTC (rev 15658)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-24 00:42:19 UTC (rev 15659)
@@ -300,6 +300,7 @@
  *
  * @if clike @see SBML_formulaToString()@endif
  * @if csharp @see SBML_formulaToString()@endif
+ * @if python @see libsbml.formulaToString()@endif
  * @if java @see formulaToString(ASTNode tree)@endif
  */
 LIBSBML_EXTERN

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Revision: 15661
          http://sbml.svn.sourceforge.net/sbml/?rev=15661&view=rev
Author:   mhucka
Date:     2012-04-24 02:30:56 +0000 (Tue, 24 Apr 2012)
Log Message:
-----------
Argh, the previous fix for the doxygen links broke the docs for C++.
Now fixed.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/FormulaFormatter.h
    trunk/libsbml/src/sbml/math/FormulaParser.h
    trunk/libsbml/src/sbml/math/FormulaTokenizer.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2012-04-24 01:05:20 UTC (rev 15660)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2012-04-24 02:30:56 UTC (rev 15661)
@@ -139,8 +139,8 @@
  * 
  * <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@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
- * read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <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()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif and
+ * read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  * are simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form can be handed to a program that
  * understands SBML Level&nbsp;1 mathematical expressions, or used as part
@@ -1220,7 +1220,7 @@
    * 
    * For numbers, unary minus nodes can be "collapsed" by negating the
    * number.  In fact, 
-   * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+   * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <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@...) cannot
@@ -2315,7 +2315,7 @@
  * otherwise.
  *
  * For numbers, unary minus nodes can be "collapsed" by negating the
- * number.  In fact, @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * number.  In fact, @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  * does this during its parse.
  * However, unary minus nodes for symbols (@c AST_NAMES) cannot be
  * "collapsed", so this predicate function is necessary.

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-04-24 01:05:20 UTC (rev 15660)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-04-24 02:30:56 UTC (rev 15661)
@@ -43,8 +43,8 @@
  * basically derived from SBML Level&nbsp;1.
  *
  * The text-string form of mathematical formulas produced by
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
- * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form therefore can be handed to a program
  * that understands SBML Level&nbsp;1 mathematical expressions, or used as

Modified: trunk/libsbml/src/sbml/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.h	2012-04-24 01:05:20 UTC (rev 15660)
+++ trunk/libsbml/src/sbml/math/FormulaParser.h	2012-04-24 02:30:56 UTC (rev 15661)
@@ -44,8 +44,8 @@
  * Abstract Syntax Tree (AST).
  *
  * The text-string form of mathematical formulas produced by
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
- * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form therefore can be handed to a program
  * that understands SBML Level&nbsp;1 mathematical expressions, or used as

Modified: trunk/libsbml/src/sbml/math/FormulaTokenizer.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-04-24 01:05:20 UTC (rev 15660)
+++ trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-04-24 02:30:56 UTC (rev 15661)
@@ -76,8 +76,8 @@
  * Levels&nbsp;2 and&nbsp;3.  LibSBML implements a parser and converter to
  * translate formulas between this text-string representation and MathML.
  * The principal entry points to the translation system are
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@else <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@else <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif
  *
  * LibSBML also provides a lower-level interface to the formula parser.
  * This takes the form of the C functions

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Revision: 15704
          http://sbml.svn.sourceforge.net/sbml/?rev=15704&view=rev
Author:   luciansmith
Date:     2012-04-26 21:35:53 +0000 (Thu, 26 Apr 2012)
Log Message:
-----------
One functional change:  you can now set the L3ParserSettings object used as a default for subsequent SBML_parseL3Function calls.
 - Wrapped the entire L3Parser class in '#ifndef SWIG', /** @cond doxygen-libsbml-internal */, and flagged the class itself '@internal'.
 - Moved all the documentation to the C functions, as they're the only ones exposed.
 - Removed the L3ParserSettings::L3ParserSettings(Model*) constructor and replaced it with an explicit function instead.  This allows the SBML_parseL3FunctionWithModel function to use the default L3ParserSettings even if it's been changed by the new function.
 - Cleaned up the documentation itself to better reflect its C-ness, and fixed a couple bits here and there.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.h
    trunk/libsbml/src/sbml/math/L3Parser.tab.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/L3ParserSettings.cpp
    trunk/libsbml/src/sbml/math/L3ParserSettings.h

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-26 14:53:48 UTC (rev 15703)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-04-26 21:35:53 UTC (rev 15704)
@@ -26,21 +26,6 @@
  * also available online as http://sbml.org/software/libsbml/license.html
  * ---------------------------------------------------------------------- -->*/
 
-/** @cond doxygen-libsbml-internal */
-/**
- * The L3Parser class is an internal class designed to hold the guts of the bison parser, plus
- * the lexer.  It is designed to be a global singleton object, because that's the cleanest way
- * I could find to incorporate functions into the bison framework.
- *
- * The functions declared in this file are defined in the file L3Parser.ypp, which
- * must be compiled by bison to create L3Parser.tab.cpp, the file included in
- * libsbml.  For more details, see the L3Parser.ypp file.
- *
- * Within the various 'sbml_yylex*' functions that bison creates, functions
- * from the global 'l3p' object (of the L3Parser class) are used to calculate
- * necessary information for the parsing of the string, and to determine appropriate
- * error messages when things go wrong.
- */
 #ifndef L3Parser_h
 #define L3Parser_h
 
@@ -60,11 +45,30 @@
 class SBMLVisitor;
 class FormulaUnitsData;
 
+#ifndef SWIG //Hide the entire class from SWIG
+/** @cond doxygen-libsbml-internal */
+/**
+ * @class L3Parser
+ * @brief Class providing functionality for the bison-generated parser.
+ *
+ * The L3Parser class is an internal class designed to hold the guts of the bison parser, plus
+ * the lexer.  It is designed to be a global singleton object, because that's the cleanest way
+ * I could find to incorporate functions into the bison framework.
+ *
+ * The functions declared in this file are defined in the file L3Parser.ypp, which
+ * must be compiled by bison to create L3Parser.tab.cpp, the file included in
+ * libsbml.  For more details, see the L3Parser.ypp file.
+ *
+ * Within the various 'sbml_yylex*' functions that bison creates, functions
+ * from the global 'l3p' object (of the L3Parser class) are used to calculate
+ * necessary information for the parsing of the string, and to determine appropriate
+ * error messages when things go wrong.
+ * @internal
+ */
 class LIBSBML_EXTERN L3Parser
 {
 public:
 
-#ifndef SWIG
   std::stringstream input;
   ASTNode* outputNode;
   std::string error;
@@ -73,15 +77,13 @@
   long denominator;
 
   //settings:
-  const L3ParserSettings defaultParserSettings;
+  L3ParserSettings defaultParserSettings;
   Model* model;
   l3p_log_type parselog;
   bool collapseminus;
   bool parseunits;
   bool avocsymbol;
 
-#endif
-  
   L3Parser();
   ~L3Parser();
 
@@ -165,9 +167,6 @@
    */
   std::string getError();
   
-  
-#ifndef SWIG
-  
   /**
    * The bison parser needs string pointers to pass around from function to
    * function.  In order to not create too many of these objects, and to
@@ -182,8 +181,6 @@
    */
   std::string* addWord(const std::string& word);
   
-#endif 
-  
   /**
    * This function checks the provided ASTNode function to see if it is a 
    * known function with the wrong number of arguments.  If so, an error is set
@@ -196,122 +193,7 @@
    */
   L3ParserSettings getDefaultParserSettings();
 
-  /** @endcond */
-
   /**
-   * Parses the given SBML formula and returns a representation of it as an
-   * Abstract Syntax Tree (AST).
-   *
- * The text-string form of mathematical formulas produced by
-   * SBML_l3FormulaToString() and read by SBML_parseL3Formula() are expanded
-   * versions of the SBML_formulaToString() and SBML_parseFormula() functions
-   * that worked to produce and consume the defined L1-infix syntax, with the
-   * following differences:
-   *
-   * @li Bare numbers may be assigned units, using the syntax "[number] [unit string]".
-       The number may be in any form (an integer, real, or rational number), and the
-       unit string must conform to the syntax of an SBML ID.
-   * @li Boolean function symbols '&&', '||', '!', and '!=' may be used.
-   * @li The 'modulo' symbol '%' is allowed, and will produce a piecewise function
-       in the MathML (thanks to Copasi and Frank Bergmann for the code providing this functionality).
-   * @li All 'arc-' trigonometric functions may be defined in the infix either
-       using 'arc' as a prefix or simply 'a':  'arccsc' and 'acsc' both define
-       the MathML-defined arc-cosecant.  Many functions in the L1 infix parser
-       were defined this way as well, but not all.
-   * @li "([integer]/[integer])" is parsed as a rational number instead of as a
-       'divide' function with two arguments.  No spaces are allowed in this construct.
-       This allows you to assign units to a rational number with formulas like
-       "(3/4) ml"  "(3 / 4)" will parse as a 'divide' function and thus may not be
-       assigned units.
-   * @li Various settings may be altered by passing in an L3ParserSettings object to
-       this function in addition to the infix string, including:
-   * @li @li The function 'log' with a single argument ("log(x)") can be parsed as
-       log10(x), ln(x), or as an error.
-   * @li @li Unary minuses may be collapsed or expanded.
-   * @li @li Unit parsing can be turned off.
-   * @li @li The string 'avogadro' can be parsed as a csymbol or as a name.
-   * @li @li A Model object may be provided to the parser.  When it is, 
-       SIds from that model are used
-       in preference to pre-defined MathML definitions:  if the translator is
-       given a model with a species 'pi', and a formula '3*pi', the produced
-       MathML will contain the construct '<ci> pi </ci>' instead of the
-       construct '<pi/>'.
-   * @li @li Similarly, when a model object is provided, SIds of function 
-       definitions present in the model are used
-       preferentially over pre-defined MathML functions:  if the passed-in Model
-       contains a FunctionDefinition 'sin', that function will be used instead
-       of the predefined MathML <sin/>.
-   *
-   * The function returns the root node of the AST corresponding to the formula.  If
-   * the formula contains a syntax error, @c NULL is returned instead.  When NULL
-   * is returned, an error is set:  @see SBML_getLastParseL3Error()
-   *
-   * Note that this facility (and the L1-based SBML_parseFormula) is provided as a convenience by libSBML—the
-   * MathML standard does not actually define a "string-form" equivalent to
-   * MathML expression trees, so the choice of formula syntax is somewhat
-   * arbitrary.  The approach taken by libSBML is to start with the syntax defined by
-   * SBML Level 1 (which in fact used a text-string representation of
-   * formulas and not MathML), and expand it to include the above functionality.  This formula syntax is based mostly on C
-   * programming syntax, and may contain operators, function calls, symbols,
-   * and white space characters.  The following table provides the precedence
-   * rules for the different entities that may appear in formula strings.
-   *
-   * @htmlinclude math-precedence-table.html
-   * 
-   * In the table above, @em operand implies the construct is an operand, @em
-   * prefix implies the operation is applied to the following arguments, @em
-   * unary implies there is one argument, and @em binary implies there are
-   * two arguments.  The values in the <b>Precedence</b> column show how the
-   * order of different types of operation are determined.  For example, the
-   * expression <code>a * b + c</code> is evaluated as <code>(a * b) +
-   * c</code> because the @c * operator has higher precedence.  The
-   * <b>Associates</b> column shows how the order of similar precedence
-   * operations is determined; for example, <code>a && b || c</code> is
-   * evaluated as <code>(a && b) || c</code> because the @c && and @c ||
-   * operators are left-associative.
-   *
-   * The function call syntax consists of a function name, followed by optional
-   * white space, followed by an opening parenthesis token, followed by a
-   * sequence of zero or more arguments separated by commas (with each comma
-   * optionally preceded and/or followed by zero or more white space
-   * characters, followed by a closing parenthesis token.  The function name
-   * must be chosen from one of the pre-defined functions in SBML or a
-   * user-defined function in the model.  The following table lists the names
-   * of certain common mathematical functions; this table corresponds to
-   * Table&nbsp;6 in the <a target="_blank" href="http://sbml.org/Documents/Specifications#SBML_Level_1_Version_2">SBML Level&nbsp;1 Version&nbsp;2 specification</a> with additions based on the 
-   * functions adding in SBML Level 2 and Level 3:
-   *
-   * @htmlinclude string-functions-table-l3.html
-   *
-   * Note that this function's interpretation of the string 'log' as a function with a single 
-   * argument can be changed through the use of an L3ParserSettings object.
-   * By default, unlike the Level 1 parser, 'log' is interpreted as log base-10, and
-   * not as the natural log.  However, you can change the interpretation to
-   * be log base-10, natural log, or as an error:  since the string is
-   * ambiguous, you require the use of 'log10' or 'ln' instead, which 
-   * are more clear.
-   * 
-   * In addition, the following symbols will be translated to MathML concepts,
-   * if no symbol with that SId is found in the provided Model object:
-   *
-   * @htmlinclude string-values-table-l3.html
-   * 
-   * @param formula the text-string formula expression to be parsed
- * @param settings the settings for the parser behavior
-   *
-   * @return the root node of the AST, or NULL if an error occurred in
-   * parsing the formula
-   *
- * @if clike @see SBML_formulaToString()@endif@~
- * @if csharp @see SBML_formulaToString()@endif@~
- * @if python @see libsbml.formulaToString()@endif@~
- * @if java @see formulaToString(ASTNode tree)@endif@~
-   */
-  static ASTNode * parseL3Formula(const std::string formula,
-                                  L3ParserSettings settings);
-
-
-  /**
    * Parses the provided string to an ASTNode, using the default settings, namely:
    * @li No 'Model' object to compare strings against.
    * @li Parses "log(x)" as the log base-10 of x.
@@ -324,6 +206,34 @@
   static ASTNode * parseL3Formula(const std::string formula);
 
   /**
+   * Parses the provided string to an ASTNode, using the provided settings.
+   */
+  static ASTNode * parseL3Formula(const std::string formula,
+                                  L3ParserSettings settings);
+
+
+  /**
+   * Parses the provided string to an ASTNode, using the default setting but the provided Model* object.
+   */
+  static ASTNode * parseL3Formula(const std::string formula,
+                                  Model* model);
+
+
+  /*
+   * Change the default settings for this parser to the settings provided.  All subsequent
+   * calls to parseL3Formula with no 'settings' argument will use these settings
+   * instead of the defaults.
+   */
+  void setDefaultSettings(L3ParserSettings settings);
+
+  /*
+   * Change the default settings for the global 'l3p' parser to the settings provided.  All subsequent
+   * calls to parseL3Formula with no 'settings' argument will use these settings
+   * instead of the defaults.
+   */
+  static void setGlobalDefaultSettings(L3ParserSettings settings);
+
+  /**
    * If the either versions of the function @see SBML_parseL3Formula() returns NULL, an error 
    * is set internally which is accessible via this function.  The returned error will 
    * report the string it was trying to parse, which character it had parsed when it 
@@ -332,19 +242,9 @@
    */
   static char* getLastParseL3Error();
 };
+/** @endcond */ //The entire class should be invisible to the documentation.
+#endif //The entire class should be invisible to SWIG, too.
 
-#ifndef SWIG
-/** @cond doxygen-libsbml-internal */
-
-/**
- * The global l3p object is defined in the L3Parser.ypp file. This 'extern' 
- * declaration lets others interact with it, if they so desire.
- */
-extern L3Parser* l3p;
-/** @endcond */
-
-#endif
-
 LIBSBML_CPP_NAMESPACE_END
 
 #endif  /* __cplusplus */
@@ -353,21 +253,210 @@
 BEGIN_C_DECLS
 
 
+/**
+ * Parses the given SBML formula and returns a representation of it as an
+ * Abstract Syntax Tree (AST).
+ *
+ * The text-string form of mathematical formulas produced by
+ * SBML_l3FormulaToString() and read by SBML_parseL3Formula() are expanded
+ * versions of the SBML_formulaToString() and SBML_parseFormula() functions
+ * that worked to produce and consume the defined L1-infix syntax, with the
+ * following differences:
+ *
+ * @li Bare numbers may be assigned units, using the syntax "[number] [unit string]".
+ The number may be in any form (an integer, real, or rational number), and the
+ unit string must conform to the syntax of an SBML ID.
+ * @li Boolean function symbols '&&', '||', '!', and '!=' may be used.
+ * @li The 'modulo' symbol '%' is allowed, and will produce a piecewise function
+ in the MathML (thanks to Copasi and Frank Bergmann for the code providing this functionality).
+ * @li All 'arc-' trigonometric functions may be defined in the infix either
+ using 'arc' as a prefix or simply 'a':  'arccsc' and 'acsc' both define
+ the MathML-defined arc-cosecant.  Many functions in the L1 infix parser
+ were defined this way as well, but not all.
+ * @li "([integer]/[integer])" is parsed as a rational number instead of as a
+ 'divide' function with two arguments.  No spaces are allowed in this construct.
+ This allows you to assign units to a rational number with formulas like
+ "(3/4) ml"  "(3 / 4)" will parse as a 'divide' function and thus may not be
+ assigned units.
+ * @li Various settings may be altered by using an L3ParserSettings object, including:
+ * @li @li The function 'log' with a single argument ("log(x)") can be parsed as
+ log10(x), ln(x), or as an error.
+ * @li @li Unary minuses may be collapsed or expanded.
+ * @li @li Unit parsing can be turned off.
+ * @li @li The string 'avogadro' can be parsed as a csymbol or as a name.
+ * @li @li A Model object may be provided to the parser.  When it is, 
+ SIds from that model are used
+ in preference to pre-defined MathML definitions:  if the translator is
+ given a model with a species 'pi', and a formula '3*pi', the produced
+ MathML will contain the construct '&lt;ci&gt; pi &lt;/ci&gt;' instead of the
+ construct '&lt;pi/&gt;'.
+ * @li @li Similarly, when a model object is provided, SIds of function 
+ definitions present in the model are used
+ preferentially over pre-defined MathML functions:  if the passed-in Model
+ contains a FunctionDefinition 'sin', that function will be used instead
+ of the predefined MathML &lt;sin/&gt;.
+ *
+ * These settings can be set once for all subsequent calls to this function
+ * by calling SBML_setDefaultL3ParserSettings, or these settings can be changed
+ * on an as-needed basis by using the function SBML_parseL3FormulaWithSettings.
+ *
+ * The function returns the root node of the AST corresponding to the formula.  If
+ * the formula contains a syntax error, @c NULL is returned instead.  When NULL
+ * is returned, an error is set:  @see SBML_getLastParseL3Error()
+ *
+ * Note that this facility (and the L1-based SBML_parseFormula) is provided as a convenience by libSBML&mdash;the
+ * MathML standard does not actually define a "string-form" equivalent to
+ * MathML expression trees, so the choice of formula syntax is somewhat
+ * arbitrary.  The approach taken by libSBML is to start with the syntax defined by
+ * SBML Level&nbsp;1 (which in fact used a text-string representation of
+ * formulas and not MathML), and expand it to include the above functionality.  
+ * This formula syntax is based mostly on C
+ * programming syntax, and may contain operators, function calls, symbols,
+ * and white space characters.  The following table provides the precedence
+ * rules for the different entities that may appear in formula strings.
+ *
+ * @htmlinclude math-precedence-table-l3.html
+ * 
+ * In the table above, @em operand implies the construct is an operand, @em
+ * prefix implies the operation is applied to the following arguments, @em
+ * unary implies there is one argument, and @em binary implies there are
+ * two arguments.  The values in the <b>Precedence</b> column show how the
+ * order of different types of operation are determined.  For example, the
+ * expression <code>a + b * c</code> is evaluated as <code>a + (b * c)</code> 
+ * because the @c * operator has higher precedence.  The
+ * <b>Associates</b> column shows how the order of similar precedence
+ * operations is determined; for example, <code>a && b || c</code> is
+ * evaluated as <code>(a && b) || c</code> because the @c && and @c ||
+ * operators are left-associative and have the same precedence.
+ *
+ * The function call syntax consists of a function name, followed by optional
+ * white space, followed by an opening parenthesis token, followed by a
+ * sequence of zero or more arguments separated by commas (with each comma
+ * optionally preceded and/or followed by zero or more white space
+ * characters, followed by a closing parenthesis token.  The function name
+ * must be chosen from one of the pre-defined functions in SBML or a
+ * user-defined function in the model.  The following table lists the names
+ * of certain common mathematical functions; this table corresponds to
+ * Table&nbsp;6 in the <a target="_blank" href="http://sbml.org/Documents/Specifications#SBML_Level_1_Version_2">SBML Level&nbsp;1 Version&nbsp;2 specification</a> with additions based on the 
+ * functions added in SBML Level 2 and Level 3:
+ *
+ * @htmlinclude string-functions-table-l3.html
+ *
+ * Note that this function's interpretation of the string 'log' as a function with a single 
+ * argument can be changed through the use of an L3ParserSettings object.
+ * By default, unlike the Level 1 parser, 'log' is interpreted as log base-10, and
+ * not as the natural log.  However, you can change the interpretation to
+ * be log base-10, natural log, or as an error:  since the string is
+ * ambiguous, you require the use of 'log10' or 'ln' instead, which 
+ * are more clear.
+ * 
+ * In addition, the following symbols will be translated to MathML concepts,
+ * if no symbol with that SId is found in the provided Model object:
+ *
+ * @htmlinclude string-values-table-l3.html
+ * 
+ * Note that whether or not 'avogadro' is parsed as AST_NAME_AVOGADRO or
+ * AST_NAME is settable through the use of an L3ParserSettings object.  This
+ * functionality is provided because SBML Level 2 models may not use
+ * AST_NAME_AVOGADRO ASTNodes.
+ *
+ * @param formula the text-string formula expression to be parsed
+ * @param settings the settings for the parser behavior
+ *
+ * @return the root node of the AST, or NULL if an error occurred in
+ * parsing the formula
+ *
+ * @if clike @see SBML_formulaToString()@endif@~
+ * @if csharp @see SBML_formulaToString()@endif@~
+ * @if python @see libsbml.formulaToString()@endif@~
+ * @if java @see formulaToString()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3Formula (const char *formula);
 
-
+/**
+ * Parses the given SBML formula and returns a representation of it as an
+ * Abstract Syntax Tree (AST), using the default L3ParserSettings, but with the Model
+ * object provided.  If the default settings have been changed by SBML_setDefaultL3ParserSettings,
+ * those settings are all used, but the model is changed for parsing this string only.
+ *
+ * For more details, see the SBML_parseL3Formula() function:
+ * 
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
-SBML_parseL3FormulaWithSettings (const char *formula, L3ParserSettings_t *settings);
+SBML_parseL3FormulaWithModel (const char *formula, Model_t * model);
 
 
+/**
+ * Parses the given SBML formula and returns a representation of it as an
+ * Abstract Syntax Tree (AST), using the provided L3ParserSettings object.  This
+ * object allows you to change the following behaviors:
+ * @li Set a Model object to compare strings against.
+ * @li Parse "log(x)" as the log base-10 of x, natural log of x, or as an error.
+ * @li Parses "[number] [id]' by setting id to the unit of the number or as an error.
+ * @li Parses "avogadro" to an ASTNode of type AST_NAME_AVOGADRO or as type AST_NAME.
+ * @li Always creates explicit ASTNodes of type AST_MINUS for all unary minuses, or collapse them when possible.
+ *
+ * For more details, see the L3ParserSettings class, and the SBML_parseL3Formula() function:
+ * 
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
-SBML_parseL3FormulaWithModel (const char *formula, Model_t * model);
+SBML_parseL3FormulaWithSettings (const char *formula, L3ParserSettings_t *settings);
 
+/*
+ * Changes the default settings for the SBML_parseL3Formula function.  All
+ * subsequent calls to SBML_parseL3Formula() and SBML_parseL3FormulaWithModel() 
+ * will use the settings provided here, instead of the defaults.
+ * 
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ */
+LIBSBML_EXTERN
+void
+SBML_setDefaultL3ParserSettings (L3ParserSettings_t *settings);
 
+
+/**
+ * If @see SBML_parseL3Formula(), @see SBML_parseL3FormulaWithSettings(), or 
+ * @see SBML_parseL3FormulaWithModel() return NULL, an error 
+ * is set internally which is accessible via this function.  The returned error will 
+ * report the string it was trying to parse, which character it had parsed when it 
+ * encountered the error, and what the error was.
+ * 
+ */
 LIBSBML_EXTERN
 char*
 SBML_getLastParseL3Error();

Modified: trunk/libsbml/src/sbml/math/L3Parser.tab.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.tab.cpp	2012-04-26 14:53:48 UTC (rev 15703)
+++ trunk/libsbml/src/sbml/math/L3Parser.tab.cpp	2012-04-26 21:35:53 UTC (rev 15704)
@@ -2542,6 +2542,18 @@
 
 
 ASTNode *
+L3Parser::parseL3Formula (std::string formula, Model* model)
+{
+  if (l3p==NULL) {
+    l3p = new L3Parser();
+  }
+  L3ParserSettings l3ps = l3p->getDefaultParserSettings();
+  l3ps.setModel(model);
+  return L3Parser::parseL3Formula(formula, l3ps);
+}
+
+
+ASTNode *
 L3Parser::parseL3Formula (std::string formula, L3ParserSettings settings)
 {
   if (l3p==NULL) {
@@ -2559,7 +2571,21 @@
   
 }
 
+void
+L3Parser::setDefaultSettings(L3ParserSettings settings)
+{
+  defaultParserSettings = settings;
+}
 
+void
+L3Parser::setGlobalDefaultSettings(L3ParserSettings settings)
+{
+  if (l3p==NULL) {
+    l3p = new L3Parser();
+  }
+  l3p->setDefaultSettings(settings);
+}
+
 char* 
 L3Parser::getLastParseL3Error()
 {
@@ -2593,6 +2619,13 @@
 
 
 LIBSBML_EXTERN
+void 
+SBML_setDefaultL3ParserSettings (L3ParserSettings_t *settings)
+{
+  return L3Parser::setGlobalDefaultSettings(*(settings));
+}
+
+LIBSBML_EXTERN
 char*
 SBML_getLastParseL3Error()
 {

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-04-26 14:53:48 UTC (rev 15703)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-04-26 21:35:53 UTC (rev 15704)
@@ -809,6 +809,18 @@
 
 
 ASTNode *
+L3Parser::parseL3Formula (std::string formula, Model* model)
+{
+  if (l3p==NULL) {
+    l3p = new L3Parser();
+  }
+  L3ParserSettings l3ps = l3p->getDefaultParserSettings();
+  l3ps.setModel(model);
+  return L3Parser::parseL3Formula(formula, l3ps);
+}
+
+
+ASTNode *
 L3Parser::parseL3Formula (std::string formula, L3ParserSettings settings)
 {
   if (l3p==NULL) {
@@ -826,7 +838,21 @@
   
 }
 
+void
+L3Parser::setDefaultSettings(L3ParserSettings settings)
+{
+  defaultParserSettings = settings;
+}
 
+void
+L3Parser::setGlobalDefaultSettings(L3ParserSettings settings)
+{
+  if (l3p==NULL) {
+    l3p = new L3Parser();
+  }
+  l3p->setDefaultSettings(settings);
+}
+
 char* 
 L3Parser::getLastParseL3Error()
 {
@@ -860,6 +886,13 @@
 
 
 LIBSBML_EXTERN
+void 
+SBML_setDefaultL3ParserSettings (L3ParserSettings_t *settings)
+{
+  return L3Parser::setGlobalDefaultSettings(*(settings));
+}
+
+LIBSBML_EXTERN
 char*
 SBML_getLastParseL3Error()
 {

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.cpp	2012-04-26 14:53:48 UTC (rev 15703)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.cpp	2012-04-26 21:35:53 UTC (rev 15704)
@@ -46,15 +46,6 @@
 {
 }
 
-L3ParserSettings::L3ParserSettings(Model* model)
-  : mModel (model)
-  , mParselog(L3P_PARSE_LOG_AS_LOG10)
-  , mCollapseminus(L3P_EXPAND_UNARY_MINUS)
-  , mParseunits(L3P_PARSE_UNITS)
-  , mAvoCsymbol(L3P_AVOGADRO_IS_CSYMBOL)
-{
-}
-
 L3ParserSettings::L3ParserSettings(Model* model, l3p_log_type parselog, bool collapseminus, bool parseunits, bool avocsymbol)
   : mModel (model)
   , mParselog(parselog)

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-04-26 14:53:48 UTC (rev 15703)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-04-26 21:35:53 UTC (rev 15704)
@@ -113,14 +113,6 @@
    */
   L3ParserSettings(Model* model, l3p_log_type parselog, bool collapseminus, bool parseunits, bool avocsymbol);
 
-  /** 
-   * Creates a new L3ParserSettings object sets with provided Model pointer, and setting everything else to the default (L3P_PARSE_LOG_AS_LOG10, L3P_EXPAND_UNARY_MINUS, L3P_PARSE_UNITS, and L3P_AVOGADRO_IS_CSYMBOL).  This constructor allows the use of a Model* pointer instead of an actual L3ParserSettings object when using the function SBML_parseL3formula().
-   *
-   * @param model a Model pointer, to use in parsing infix functions.
-   *
-   */
-  L3ParserSettings(Model* model);
-
   /**
    * Destroys this L3ParserSettings.
    */

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15777
          http://sbml.svn.sourceforge.net/sbml/?rev=15777&view=rev
Author:   luciansmith
Date:     2012-05-02 22:33:54 +0000 (Wed, 02 May 2012)
Log Message:
-----------
Copying in the documentation from the .h file into the .ypp/cpp file for the C documentation.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-02 22:25:32 UTC (rev 15776)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-02 22:33:54 UTC (rev 15777)
@@ -65,7 +65,7 @@
 /* "%code top" blocks.  */
 
 /* Line 171 of yacc.c  */
-#line 52 "L3Parser.ypp"
+#line 52 "L3parser.ypp"
 
 
  /** @cond doxygen-libsbml-internal */
@@ -87,7 +87,7 @@
 /* Copy the first part of user declarations.  */
 
 /* Line 189 of yacc.c  */
-#line 57 "L3Parser.ypp"
+#line 57 "L3parser.ypp"
 
 /**
  *
@@ -339,7 +339,7 @@
 {
 
 /* Line 214 of yacc.c  */
-#line 263 "L3Parser.ypp"
+#line 263 "L3parser.ypp"
 
   ASTNode* astnode;
   char character;
@@ -1632,35 +1632,35 @@
         case 3:
 
 /* Line 1464 of yacc.c  */
-#line 297 "L3Parser.ypp"
+#line 297 "L3parser.ypp"
     {l3p->outputNode = (yyvsp[(1) - (1)].astnode);}
     break;
 
   case 4:
 
 /* Line 1464 of yacc.c  */
-#line 298 "L3Parser.ypp"
+#line 298 "L3parser.ypp"
     {;}
     break;
 
   case 5:
 
 /* Line 1464 of yacc.c  */
-#line 299 "L3Parser.ypp"
+#line 299 "L3parser.ypp"
     {delete (yyvsp[(1) - (2)].astnode);;}
     break;
 
   case 6:
 
 /* Line 1464 of yacc.c  */
-#line 302 "L3Parser.ypp"
+#line 302 "L3parser.ypp"
     {(yyval.astnode) = (yyvsp[(1) - (1)].astnode);;}
     break;
 
   case 7:
 
 /* Line 1464 of yacc.c  */
-#line 303 "L3Parser.ypp"
+#line 303 "L3parser.ypp"
     {
                    (yyval.astnode) = new ASTNode();
                    string name(*(yyvsp[(1) - (1)].word));
@@ -1692,21 +1692,21 @@
   case 8:
 
 /* Line 1464 of yacc.c  */
-#line 329 "L3Parser.ypp"
+#line 329 "L3parser.ypp"
     {(yyval.astnode) = (yyvsp[(2) - (3)].astnode);;}
     break;
 
   case 9:
 
 /* Line 1464 of yacc.c  */
-#line 330 "L3Parser.ypp"
+#line 330 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_POWER); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 10:
 
 /* Line 1464 of yacc.c  */
-#line 331 "L3Parser.ypp"
+#line 331 "L3parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_TIMES) {
                     (yyval.astnode) = (yyvsp[(1) - (3)].astnode);
@@ -1723,7 +1723,7 @@
   case 11:
 
 /* Line 1464 of yacc.c  */
-#line 342 "L3Parser.ypp"
+#line 342 "L3parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_PLUS) {
                     (yyval.astnode) = (yyvsp[(1) - (3)].astnode);
@@ -1740,42 +1740,42 @@
   case 12:
 
 /* Line 1464 of yacc.c  */
-#line 353 "L3Parser.ypp"
+#line 353 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_DIVIDE); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 13:
 
 /* Line 1464 of yacc.c  */
-#line 354 "L3Parser.ypp"
+#line 354 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_MINUS); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 14:
 
 /* Line 1464 of yacc.c  */
-#line 355 "L3Parser.ypp"
+#line 355 "L3parser.ypp"
     {(yyval.astnode) = l3p->createModuloTree((yyvsp[(1) - (3)].astnode), (yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 15:
 
 /* Line 1464 of yacc.c  */
-#line 356 "L3Parser.ypp"
+#line 356 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 16:
 
 /* Line 1464 of yacc.c  */
-#line 357 "L3Parser.ypp"
+#line 357 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 17:
 
 /* Line 1464 of yacc.c  */
-#line 358 "L3Parser.ypp"
+#line 358 "L3parser.ypp"
     {
                   if (l3p->collapseminus) {
                     if ((yyvsp[(2) - (2)].astnode)->getType()==AST_REAL) {
@@ -1814,70 +1814,70 @@
   case 18:
 
 /* Line 1464 of yacc.c  */
-#line 391 "L3Parser.ypp"
+#line 391 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 19:
 
 /* Line 1464 of yacc.c  */
-#line 392 "L3Parser.ypp"
+#line 392 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 20:
 
 /* Line 1464 of yacc.c  */
-#line 393 "L3Parser.ypp"
+#line 393 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_EQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 21:
 
 /* Line 1464 of yacc.c  */
-#line 394 "L3Parser.ypp"
+#line 394 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 22:
 
 /* Line 1464 of yacc.c  */
-#line 395 "L3Parser.ypp"
+#line 395 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 23:
 
 /* Line 1464 of yacc.c  */
-#line 396 "L3Parser.ypp"
+#line 396 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 24:
 
 /* Line 1464 of yacc.c  */
-#line 397 "L3Parser.ypp"
+#line 397 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_LOGICAL_AND); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 25:
 
 /* Line 1464 of yacc.c  */
-#line 398 "L3Parser.ypp"
+#line 398 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_LOGICAL_OR); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 26:
 
 /* Line 1464 of yacc.c  */
-#line 399 "L3Parser.ypp"
+#line 399 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_LOGICAL_NOT); (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));;}
     break;
 
   case 27:
 
 /* Line 1464 of yacc.c  */
-#line 400 "L3Parser.ypp"
+#line 400 "L3parser.ypp"
     {
                    (yyval.astnode) = new ASTNode(AST_FUNCTION);
                    string name(*(yyvsp[(1) - (3)].word));
@@ -1894,7 +1894,7 @@
   case 28:
 
 /* Line 1464 of yacc.c  */
-#line 411 "L3Parser.ypp"
+#line 411 "L3parser.ypp"
     {
                    (yyval.astnode) = (yyvsp[(3) - (4)].astnode);
                    string name(*(yyvsp[(1) - (4)].word));
@@ -1949,35 +1949,35 @@
   case 29:
 
 /* Line 1464 of yacc.c  */
-#line 462 "L3Parser.ypp"
+#line 462 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));;}
     break;
 
   case 30:
 
 /* Line 1464 of yacc.c  */
-#line 463 "L3Parser.ypp"
+#line 463 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);;}
     break;
 
   case 31:
 
 /* Line 1464 of yacc.c  */
-#line 464 "L3Parser.ypp"
+#line 464 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));;}
     break;
 
   case 32:
 
 /* Line 1464 of yacc.c  */
-#line 465 "L3Parser.ypp"
+#line 465 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);;}
     break;
 
   case 33:
 
 /* Line 1464 of yacc.c  */
-#line 466 "L3Parser.ypp"
+#line 466 "L3parser.ypp"
     {
                   (yyval.astnode) = (yyvsp[(1) - (2)].astnode);
                   if ((yyval.astnode)->getUnits() != "") {
@@ -1995,14 +1995,14 @@
   case 34:
 
 /* Line 1464 of yacc.c  */
-#line 480 "L3Parser.ypp"
+#line 480 "L3parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));;}
     break;
 
   case 35:
 
 /* Line 1464 of yacc.c  */
-#line 481 "L3Parser.ypp"
+#line 481 "L3parser.ypp"
     {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
@@ -2221,7 +2221,7 @@
 
 
 /* Line 1684 of yacc.c  */
-#line 484 "L3Parser.ypp"
+#line 484 "L3parser.ypp"
 
 
 
@@ -2737,7 +2737,194 @@
 /** Everything above this point is internal. */
 /** @endcond */
 
-
+/** @cond doxygen-c-only */
+/**
+ * Parses the given mathematical formula and returns a representation of it
+ * as an Abstract Syntax Tree (AST).
+ *
+ * The text-string form of mathematical formulas read by this function
+ * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * respectively.  The latter two libSBML functions were originally
+ * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
+ * and were focused on the syntax of mathematical formulas used in SBML
+ * Level&nbsp;1.  With time, and the use of MathML in SBML Levels&nbsp;2
+ * and&nbsp;3, it became clear that supporting Level&nbsp;2 and&nbsp;3's
+ * expanded mathematical syntax would be useful for software developers.
+ * To maintain backwards compatibility, the original
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * have been left untouched, and instead, the new functionality is
+ * provided in the form of
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ *
+ * The following are the differences in the formula syntax supported by
+ * this function, compared to what is supported by  @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~:
+ *
+ * @li Units may be asociated with bare numbers, using the following syntax:
+ * <div style="margin: 10px auto 10px 25px; display: block">
+ * <span class="code" style="background-color: #d0d0ee">number</span>
+ * <span class="code" style="background-color: #edd">unit</span>
+ * </div>
+ * The <span class="code" style="background-color: #d0d0ee">number</span>
+ * may be in any form (an integer, real, or rational
+ * number), and the 
+ * <span class="code" style="background-color: #edd">unit</span>
+ * must conform to the syntax of an SBML identifier (technically, the
+ * type defined as @c SId in the SBML specifications).  The whitespace between
+ * <span class="code" style="background-color: #d0d0ee">number</span>
+ * and <span class="code" style="background-color: #edd">unit</span>
+ * is optional.
+ * @li The Boolean function symbols @c &&, @c ||, @c !, and @c != may be used.
+ * @li The @em modulo operation is allowed as the symbol @c @% and 
+ * will produce a piecewise function in the MathML.
+ * @li All inverse trigonometric functions may be defined in the infix
+ * either using @c arc as a prefix or simply @c a; in other words, both
+ * @c arccsc and @c acsc are interpreted as the operator @em arccosecant
+ * defined in MathML.  (Many functions in the SBML Level&nbsp;1 infix-notation
+ * parser implemented by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * are defined this way as well, but not all.)
+ * @li The following expression is parsed as a rational number instead of
+ * as a numerical division:
+ * <pre style="display: block; margin-left: 25px">
+ * (<span class="code" style="background-color: #d0d0ee">integer</span>/<span class="code" style="background-color: #d0d0ee">integer</span>)</pre>
+ * No spaces are allowed in this construct; in other words,
+ * &quot;<code>(3 / 4)</code>&quot; will be parsed into the MathML
+ * <code>&lt;divide&gt;</code> construct rather than a rational number.  The 
+ * general number syntax allows you to assign units to a rational number, e.g.,
+ * &quot;<code>(3/4) ml</code>&quot;.  (If the string is a division, units
+ * are not interpreted in this way.)
+ * @li Various settings may be altered by using an L3ParserSettings object
+ * in conjunction with the alternative function call
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, including the following:
+ * <ul>
+ * <li> The function @c log with a single argument (&quot;<code>log(x)</code>&quot;) 
+ * can be parsed as <code>log10(x)</code>, <code>ln(x)</code>, or treated
+ * as an error based on the settings.
+ * <li> Unary minuses may be collapsed or expanded.
+ * <li> Parsing of units can be turned on and off.
+ * <li> The string @c avogadro can be parsed as a MathML @em csymbol or
+ * as an identifier.
+ * <li> A Model object may optionally be provided to the parser using
+ * the variant function call @if clike  SBML_parseL3FormulaWithModel()@endif@... csharp  SBML_parseL3FormulaWithModel()@endif@... python  libsbml.SBML_parseL3FormulaWithModel()@endif@... java  SBML_parseL3FormulaWithModel()@endif@~.
+ * When this is done, identifiers (values of type @c SId) from that model
+ * are used in preference to pre-defined MathML definitions.  More
+ * precisely, the Model entities whose identifiers will shadow identical
+ * symbols in the mathematical formula are: Species, Compartment,
+ * Parameter, Reaction, and SpeciesReference.  For instance, if the parser
+ * is given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * <li> Similarly, when a Model object is provided, @c SId values of
+ * user-defined functions present in the model will be used preferentially
+ * over pre-defined MathML functions.  For example, if the passed-in Model
+ * contains a FunctionDefinition with the identifier
+ * &quot;<code>sin</code>&quot;, that function will be used instead of the
+ * predefined MathML function <code>&lt;sin/&gt;</code>.
+ * </ul>
+ * These configuration settings cannot be changed using @em this function
+ * (i.e., @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~), 
+ * but they can be change on a per-call basis by using the alternative function 
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ *
+ * This function returns the root node of the AST corresponding to the
+ * formula given as the argument.  If the formula contains a syntax error,
+ * this function will return @c NULL instead.  When @c NULL is returned, an
+ * error is set; information about the error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ *
+ * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></scode>@endif@~
+ * are provided as a convenience by libSBML&mdash;the MathML standard does not
+ * actually define a "string-form" equivalent to MathML expressions, so the
+ * choice of formula syntax is arbitrary.  The approach taken by libSBML is
+ * to start with the syntax defined by SBML Level&nbsp;1 (which in fact
+ * used a text-string representation of formulas, and not MathML), and
+ * expand it to include the above functionality.  This formula syntax is
+ * based mostly on C programming syntax, and may contain operators,
+ * function calls, symbols, and white space characters.  The following
+ * table provides the precedence rules for the different entities that may
+ * appear in formula strings.
+ *
+ * @htmlinclude math-precedence-table-l3.html
+ * 
+ * In the table above, @em operand implies the construct is an operand, @em
+ * prefix implies the operation is applied to the following arguments, @em
+ * unary implies there is one argument, and @em binary implies there are
+ * two arguments.  The values in the <b>Precedence</b> column show how the
+ * order of different types of operation are determined.  For example, the
+ * expression <code>a + b * c</code> is evaluated as <code>a + (b * c)</code> 
+ * because the @c * operator has higher precedence.  The
+ * <b>Associates</b> column shows how the order of similar precedence
+ * operations is determined; for example, <code>a && b || c</code> is
+ * evaluated as <code>(a && b) || c</code> because the @c && and @c ||
+ * operators are left-associative and have the same precedence.
+ *
+ * The function call syntax consists of a function name, followed by optional
+ * white space, followed by an opening parenthesis token, followed by a
+ * sequence of zero or more arguments separated by commas (with each comma
+ * optionally preceded and/or followed by zero or more white space
+ * characters), followed by a closing parenthesis token.  The function name
+ * must be chosen from one of the pre-defined functions in SBML or a
+ * user-defined function in the model.  The following table lists the names
+ * of certain common mathematical functions; this table corresponds to
+ * Table&nbsp;6 in the <a target="_blank" href="http://sbml.org/Documents/Specifications#SBML_Level_1_Version_2">SBML Level&nbsp;1 Version&nbsp;2 specification</a> with additions based on the 
+ * functions added in SBML Level 2 and Level 3:
+ *
+ * @htmlinclude string-functions-table-l3.html
+ *
+ * Note that this function's interpretation of the string
+ * &quot;<code>log</code>&quot; as a function with a single argument can be
+ * changed; use the function @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ * instead of this function and pass it an appropriate L3ParserSettings
+ * object.  By default, unlike the SBML Level&nbsp;1 parser implemented by
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * the string &quot;<code>log</code>&quot; is interpreted as the base&nbsp;10
+ * logarithm, and @em not as the natural logarithm.  However, you can change
+ * the interpretation to be base-10 log, natural log, or as an error; since
+ * the name "log" by itself is ambiguous, you require that the parser uses
+ * @c log10 or @c ln instead, which are more clear.  Please refer to
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * 
+ * In addition, the following symbols will be translated to their MathML
+ * equivalents, if no symbol with the same @c SId identifier string exists
+ * in the Model object provided:
+ *
+ * @htmlinclude string-values-table-l3.html
+ * 
+ * Note that whether the string &quot;<code>avogadro</code>&quot; is parsed
+ * as an AST node of type @c AST_NAME_AVOGADRO or @c AST_NAME is
+ * configurable; use the alternate version of this function, called
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * This functionality is provided because SBML Level&nbsp;2 models may not
+ * use @c AST_NAME_AVOGADRO AST nodes.
+ *
+ * @param formula the text-string formula expression to be parsed
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using 
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ *
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_formulaToString()@endif@~
+ * @if csharp @see SBML_formulaToString()@endif@~
+ * @if python @see libsbml.formulaToString()@endif@~
+ * @if java @see formulaToString()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3Formula (const char *formula)
@@ -2750,6 +2937,40 @@
 }
 
 
+/**
+ * Parses the given mathematical formula using specific a specific Model to
+ * resolve symbols, and returns an Abstract Syntax Tree (AST)
+ * representation of the result.
+ *
+ * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * except that this function uses the given model in the argument @p model
+ * to check against identifiers that appear in the @p formula.
+ *
+ * For more details about the parser, please see the definition of
+ * the function SBML_parseL3Formula().
+ *
+ * @param formula the mathematical formula expression to be parsed
+ * @param model the Model object to use for checking identifiers
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3FormulaWithModel (const char *formula, const Model_t * model)
@@ -2763,6 +2984,66 @@
 }
 
 
+/**
+ * Parses the given mathematical formula using specific parser settings and
+ * returns an Abstract Syntax Tree (AST) representation of the result.
+ *
+ * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * except that this function uses the parser settings given in the argument
+ * @p settings.  The settings override the default parsing behavior.
+ *
+ * The parameter @p settings allows callers to change the following parsing
+ * behaviors:
+ *
+ * @li Use a specific Model object against which identifiers to compare
+ * identifiers.  This causes the parser to search the Model for identifiers
+ * that the parser encounters in the formula.  If a given symbol in the
+ * formula matches the identifier of a Species, Compartment, Parameter,
+ * Reaction, SpeciesReference or FunctionDefinition in the Model, then the
+ * symbol is assumed to refer to that model entity instead of any possible
+ * mathematical terms with the same symbol.  For example, if the parser is
+ * given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * @li Whether to parse &quot;<code>log(x)</code>&quot; with a single
+ * argument as the base 10
+ * logarithm of x, the natural logarithm of x, or treat the case as an
+ * error.
+ * @li Whether to parse &quot;<code>number id</code>&quot; by interpreting
+ * @c id as the identifier of a unit of measurement associated with the
+ * number, or whether to treat the case as an error.
+ * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
+ * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
+ * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
+ * all unary minuses, or collapse them when possible.
+ *
+ * For more details about the parser, please see the definition of
+ * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ *
+ * @param formula the mathematical formula expression to be parsed
+ * @param settings the settings to be used for this parser invocation
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3FormulaWithSettings (const char *formula, const L3ParserSettings_t * settings)
@@ -2782,6 +3063,52 @@
 }
 
 
+/**
+ * Returns a copy of the default parser settings used by @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * 
+ * The settings structure allows callers to change the following parsing
+ * behaviors:
+ * 
+ * @li Use a specific Model object against which identifiers to compare
+ * identifiers.  This causes the parser to search the Model for identifiers
+ * that the parser encounters in the formula.  If a given symbol in the
+ * formula matches the identifier of a Species, Compartment, Parameter,
+ * Reaction, SpeciesReference or FunctionDefinition in the Model, then the
+ * symbol is assumed to refer to that model entity instead of any possible
+ * mathematical terms with the same symbol.  For example, if the parser is
+ * given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * @li Whether to parse &quot;<code>log(x)</code>&quot; with a single
+ * argument as the base 10
+ * logarithm of x, the natural logarithm of x, or treat the case as an
+ * error.
+ * @li Whether to parse &quot;<code>number id</code>&quot; by interpreting
+ * @c id as the identifier of a unit of measurement associated with the
+ * number, or whether to treat the case as an error.
+ * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
+ * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
+ * @li Whether to always create explicit ASTNode objects of type @c AST_MINUS
+ * for all unary minus operators in a formula, or collapse them when possible.
+ *
+ * For more details about the parser, please see the definition of
+ * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 L3ParserSettings_t* 
 SBML_getDefaultL3ParserSettings ()
@@ -2792,6 +3119,31 @@
   return new L3ParserSettings(l3p->getDefaultL3ParserSettings());
 }
 
+/**
+ * Returns the last error reported by the parser.
+ *
+ * If @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~, 
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, or
+ * @if clike SBML_parseL3FormulaWithModel()@endif@... csharp SBML_parseL3FormulaWithModel()@endif@... python libsbml.parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String)">libsbml.parseL3FormulaWithModel()</a></code>@endif@~ return @c NULL, an error is set internally which is accessible
+ * via this function. 
+ *
+ * @return a string describing the error that occurred.  This will contain
+ * the string the parser was trying to parse, which character it had parsed
+ * when it encountered the error, and a description of the error.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 char*
 SBML_getLastParseL3Error()
@@ -2801,4 +3153,5 @@
   }
   return safe_strdup(l3p->getError().c_str());
 }
+/** @endcond */ //C-only documentation bit.
 

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-02 22:25:32 UTC (rev 15776)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-02 22:33:54 UTC (rev 15777)
@@ -996,7 +996,194 @@
 /** Everything above this point is internal. */
 /** @endcond */
 
-
+/** @cond doxygen-c-only */
+/**
+ * Parses the given mathematical formula and returns a representation of it
+ * as an Abstract Syntax Tree (AST).
+ *
+ * The text-string form of mathematical formulas read by this function
+ * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * respectively.  The latter two libSBML functions were originally
+ * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
+ * and were focused on the syntax of mathematical formulas used in SBML
+ * Level&nbsp;1.  With time, and the use of MathML in SBML Levels&nbsp;2
+ * and&nbsp;3, it became clear that supporting Level&nbsp;2 and&nbsp;3's
+ * expanded mathematical syntax would be useful for software developers.
+ * To maintain backwards compatibility, the original
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * have been left untouched, and instead, the new functionality is
+ * provided in the form of
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ *
+ * The following are the differences in the formula syntax supported by
+ * this function, compared to what is supported by  @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~:
+ *
+ * @li Units may be asociated with bare numbers, using the following syntax:
+ * <div style="margin: 10px auto 10px 25px; display: block">
+ * <span class="code" style="background-color: #d0d0ee">number</span>
+ * <span class="code" style="background-color: #edd">unit</span>
+ * </div>
+ * The <span class="code" style="background-color: #d0d0ee">number</span>
+ * may be in any form (an integer, real, or rational
+ * number), and the 
+ * <span class="code" style="background-color: #edd">unit</span>
+ * must conform to the syntax of an SBML identifier (technically, the
+ * type defined as @c SId in the SBML specifications).  The whitespace between
+ * <span class="code" style="background-color: #d0d0ee">number</span>
+ * and <span class="code" style="background-color: #edd">unit</span>
+ * is optional.
+ * @li The Boolean function symbols @c &&, @c ||, @c !, and @c != may be used.
+ * @li The @em modulo operation is allowed as the symbol @c @% and 
+ * will produce a piecewise function in the MathML.
+ * @li All inverse trigonometric functions may be defined in the infix
+ * either using @c arc as a prefix or simply @c a; in other words, both
+ * @c arccsc and @c acsc are interpreted as the operator @em arccosecant
+ * defined in MathML.  (Many functions in the SBML Level&nbsp;1 infix-notation
+ * parser implemented by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * are defined this way as well, but not all.)
+ * @li The following expression is parsed as a rational number instead of
+ * as a numerical division:
+ * <pre style="display: block; margin-left: 25px">
+ * (<span class="code" style="background-color: #d0d0ee">integer</span>/<span class="code" style="background-color: #d0d0ee">integer</span>)</pre>
+ * No spaces are allowed in this construct; in other words,
+ * &quot;<code>(3 / 4)</code>&quot; will be parsed into the MathML
+ * <code>&lt;divide&gt;</code> construct rather than a rational number.  The 
+ * general number syntax allows you to assign units to a rational number, e.g.,
+ * &quot;<code>(3/4) ml</code>&quot;.  (If the string is a division, units
+ * are not interpreted in this way.)
+ * @li Various settings may be altered by using an L3ParserSettings object
+ * in conjunction with the alternative function call
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, including the following:
+ * <ul>
+ * <li> The function @c log with a single argument (&quot;<code>log(x)</code>&quot;) 
+ * can be parsed as <code>log10(x)</code>, <code>ln(x)</code>, or treated
+ * as an error based on the settings.
+ * <li> Unary minuses may be collapsed or expanded.
+ * <li> Parsing of units can be turned on and off.
+ * <li> The string @c avogadro can be parsed as a MathML @em csymbol or
+ * as an identifier.
+ * <li> A Model object may optionally be provided to the parser using
+ * the variant function call @if clike  SBML_parseL3FormulaWithModel()@endif@... csharp  SBML_parseL3FormulaWithModel()@endif@... python  libsbml.SBML_parseL3FormulaWithModel()@endif@... java  SBML_parseL3FormulaWithModel()@endif@~.
+ * When this is done, identifiers (values of type @c SId) from that model
+ * are used in preference to pre-defined MathML definitions.  More
+ * precisely, the Model entities whose identifiers will shadow identical
+ * symbols in the mathematical formula are: Species, Compartment,
+ * Parameter, Reaction, and SpeciesReference.  For instance, if the parser
+ * is given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * <li> Similarly, when a Model object is provided, @c SId values of
+ * user-defined functions present in the model will be used preferentially
+ * over pre-defined MathML functions.  For example, if the passed-in Model
+ * contains a FunctionDefinition with the identifier
+ * &quot;<code>sin</code>&quot;, that function will be used instead of the
+ * predefined MathML function <code>&lt;sin/&gt;</code>.
+ * </ul>
+ * These configuration settings cannot be changed using @em this function
+ * (i.e., @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~), 
+ * but they can be change on a per-call basis by using the alternative function 
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ *
+ * This function returns the root node of the AST corresponding to the
+ * formula given as the argument.  If the formula contains a syntax error,
+ * this function will return @c NULL instead.  When @c NULL is returned, an
+ * error is set; information about the error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ *
+ * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></scode>@endif@~
+ * are provided as a convenience by libSBML&mdash;the MathML standard does not
+ * actually define a "string-form" equivalent to MathML expressions, so the
+ * choice of formula syntax is arbitrary.  The approach taken by libSBML is
+ * to start with the syntax defined by SBML Level&nbsp;1 (which in fact
+ * used a text-string representation of formulas, and not MathML), and
+ * expand it to include the above functionality.  This formula syntax is
+ * based mostly on C programming syntax, and may contain operators,
+ * function calls, symbols, and white space characters.  The following
+ * table provides the precedence rules for the different entities that may
+ * appear in formula strings.
+ *
+ * @htmlinclude math-precedence-table-l3.html
+ * 
+ * In the table above, @em operand implies the construct is an operand, @em
+ * prefix implies the operation is applied to the following arguments, @em
+ * unary implies there is one argument, and @em binary implies there are
+ * two arguments.  The values in the <b>Precedence</b> column show how the
+ * order of different types of operation are determined.  For example, the
+ * expression <code>a + b * c</code> is evaluated as <code>a + (b * c)</code> 
+ * because the @c * operator has higher precedence.  The
+ * <b>Associates</b> column shows how the order of similar precedence
+ * operations is determined; for example, <code>a && b || c</code> is
+ * evaluated as <code>(a && b) || c</code> because the @c && and @c ||
+ * operators are left-associative and have the same precedence.
+ *
+ * The function call syntax consists of a function name, followed by optional
+ * white space, followed by an opening parenthesis token, followed by a
+ * sequence of zero or more arguments separated by commas (with each comma
+ * optionally preceded and/or followed by zero or more white space
+ * characters), followed by a closing parenthesis token.  The function name
+ * must be chosen from one of the pre-defined functions in SBML or a
+ * user-defined function in the model.  The following table lists the names
+ * of certain common mathematical functions; this table corresponds to
+ * Table&nbsp;6 in the <a target="_blank" href="http://sbml.org/Documents/Specifications#SBML_Level_1_Version_2">SBML Level&nbsp;1 Version&nbsp;2 specification</a> with additions based on the 
+ * functions added in SBML Level 2 and Level 3:
+ *
+ * @htmlinclude string-functions-table-l3.html
+ *
+ * Note that this function's interpretation of the string
+ * &quot;<code>log</code>&quot; as a function with a single argument can be
+ * changed; use the function @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ * instead of this function and pass it an appropriate L3ParserSettings
+ * object.  By default, unlike the SBML Level&nbsp;1 parser implemented by
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * the string &quot;<code>log</code>&quot; is interpreted as the base&nbsp;10
+ * logarithm, and @em not as the natural logarithm.  However, you can change
+ * the interpretation to be base-10 log, natural log, or as an error; since
+ * the name "log" by itself is ambiguous, you require that the parser uses
+ * @c log10 or @c ln instead, which are more clear.  Please refer to
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * 
+ * In addition, the following symbols will be translated to their MathML
+ * equivalents, if no symbol with the same @c SId identifier string exists
+ * in the Model object provided:
+ *
+ * @htmlinclude string-values-table-l3.html
+ * 
+ * Note that whether the string &quot;<code>avogadro</code>&quot; is parsed
+ * as an AST node of type @c AST_NAME_AVOGADRO or @c AST_NAME is
+ * configurable; use the alternate version of this function, called
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * This functionality is provided because SBML Level&nbsp;2 models may not
+ * use @c AST_NAME_AVOGADRO AST nodes.
+ *
+ * @param formula the text-string formula expression to be parsed
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using 
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ *
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_formulaToString()@endif@~
+ * @if csharp @see SBML_formulaToString()@endif@~
+ * @if python @see libsbml.formulaToString()@endif@~
+ * @if java @see formulaToString()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3Formula (const char *formula)
@@ -1009,6 +1196,40 @@
 }
 
 
+/**
+ * Parses the given mathematical formula using specific a specific Model to
+ * resolve symbols, and returns an Abstract Syntax Tree (AST)
+ * representation of the result.
+ *
+ * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * except that this function uses the given model in the argument @p model
+ * to check against identifiers that appear in the @p formula.
+ *
+ * For more details about the parser, please see the definition of
+ * the function SBML_parseL3Formula().
+ *
+ * @param formula the mathematical formula expression to be parsed
+ * @param model the Model object to use for checking identifiers
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3FormulaWithModel (const char *formula, const Model_t * model)
@@ -1022,6 +1243,66 @@
 }
 
 
+/**
+ * Parses the given mathematical formula using specific parser settings and
+ * returns an Abstract Syntax Tree (AST) representation of the result.
+ *
+ * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * except that this function uses the parser settings given in the argument
+ * @p settings.  The settings override the default parsing behavior.
+ *
+ * The parameter @p settings allows callers to change the following parsing
+ * behaviors:
+ *
+ * @li Use a specific Model object against which identifiers to compare
+ * identifiers.  This causes the parser to search the Model for identifiers
+ * that the parser encounters in the formula.  If a given symbol in the
+ * formula matches the identifier of a Species, Compartment, Parameter,
+ * Reaction, SpeciesReference or FunctionDefinition in the Model, then the
+ * symbol is assumed to refer to that model entity instead of any possible
+ * mathematical terms with the same symbol.  For example, if the parser is
+ * given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * @li Whether to parse &quot;<code>log(x)</code>&quot; with a single
+ * argument as the base 10
+ * logarithm of x, the natural logarithm of x, or treat the case as an
+ * error.
+ * @li Whether to parse &quot;<code>number id</code>&quot; by interpreting
+ * @c id as the identifier of a unit of measurement associated with the
+ * number, or whether to treat the case as an error.
+ * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
+ * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
+ * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
+ * all unary minuses, or collapse them when possible.
+ *
+ * For more details about the parser, please see the definition of
+ * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ *
+ * @param formula the mathematical formula expression to be parsed
+ * @param settings the settings to be used for this parser invocation
+ *
+ * @return the root node of an AST representing the mathematical formula,
+ * or @c NULL if an error occurred while parsing the formula.  When @c NULL
+ * is returned, an error is recorded internally; information about the
+ * error can be retrieved using
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_getLastParseL3Error()@endif@~
+ * @if csharp @see SBML_getLastParseL3Error()@endif@~
+ * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if java @see SBML_getLastParseL3Error()@endif@~
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ */
 LIBSBML_EXTERN
 ASTNode_t *
 SBML_parseL3FormulaWithSettings (const char *formula, const L3ParserSettings_t * settings)
@@ -1041,6 +1322,52 @@
 }
 
 
+/**
+ * Returns a copy of the default parser settings used by @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * 
+ * The settings structure allows callers to change the following parsing
+ * behaviors:
+ * 
+ * @li Use a specific Model object against which identifiers to compare
+ * identifiers.  This causes the parser to search the Model for identifiers
+ * that the parser encounters in the formula.  If a given symbol in the
+ * formula matches the identifier of a Species, Compartment, Parameter,
+ * Reaction, SpeciesReference or FunctionDefinition in the Model, then the
+ * symbol is assumed to refer to that model entity instead of any possible
+ * mathematical terms with the same symbol.  For example, if the parser is
+ * given a Model containing a Species with the identifier
+ * &quot;<code>pi</code>&quot;, and the formula to be parsed is
+ * &quot;<code>3*pi</code>&quot;, the MathML produced will contain the
+ * construct <code>&lt;ci&gt; pi &lt;/ci&gt;</code> instead of the
+ * construct <code>&lt;pi/&gt;</code>.
+ * @li Whether to parse &quot;<code>log(x)</code>&quot; with a single
+ * argument as the base 10
+ * logarithm of x, the natural logarithm of x, or treat the case as an
+ * error.
+ * @li Whether to parse &quot;<code>number id</code>&quot; by interpreting
+ * @c id as the identifier of a unit of measurement associated with the
+ * number, or whether to treat the case as an error.
+ * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
+ * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
+ * @li Whether to always create explicit ASTNode objects of type @c AST_MINUS
+ * for all unary minus operators in a formula, or collapse them when possible.
+ *
+ * For more details about the parser, please see the definition of
+ * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * 
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 L3ParserSettings_t* 
 SBML_getDefaultL3ParserSettings ()
@@ -1051,6 +1378,31 @@
   return new L3ParserSettings(l3p->getDefaultL3ParserSettings());
 }
 
+/**
+ * Returns the last error reported by the parser.
+ *
+ * If @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~, 
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, or
+ * @if clike SBML_parseL3FormulaWithModel()@endif@... csharp SBML_parseL3FormulaWithModel()@endif@... python libsbml.parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String)">libsbml.parseL3FormulaWithModel()</a></code>@endif@~ return @c NULL, an error is set internally which is accessible
+ * via this function. 
+ *
+ * @return a string describing the error that occurred.  This will contain
+ * the string the parser was trying to parse, which character it had parsed
+ * when it encountered the error, and a description of the error.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if java @see SBML_parseL3FormulaWithModel()@endif@~
+ * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
+ */
 LIBSBML_EXTERN
 char*
 SBML_getLastParseL3Error()
@@ -1060,3 +1412,4 @@
   }
   return safe_strdup(l3p->getError().c_str());
 }
+/** @endcond */ //C-only documentation bit.

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15785
          http://sbml.svn.sourceforge.net/sbml/?rev=15785&view=rev
Author:   mhucka
Date:     2012-05-03 17:37:54 +0000 (Thu, 03 May 2012)
Log Message:
-----------
Corrected the descriptions of how the parser behaves w.r.t. minus signs.
Thanks to Lucian for realizing that my previous interpretations were
completely bogus.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.h
    trunk/libsbml/src/sbml/math/L3ParserSettings.h

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-03 16:15:00 UTC (rev 15784)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-03 17:37:54 UTC (rev 15785)
@@ -98,10 +98,13 @@
  * <li> The function @c log with a single argument (&quot;<code>log(x)</code>&quot;) 
  * can be parsed as <code>log10(x)</code>, <code>ln(x)</code>, or treated
  * as an error, as desired.
- * <li> Multiple unary minuses in a row (e.g., &quot;<code>- -3</code>&quot;)
- * can be turned into a single minus in the AST representation, or the multiple
- * minuses can be preserved.
- * <li> Parsing of units can be turned on and off.
+ * <li> Unary minus signs can be collapsed or preserved; that is,
+ * sequential pairs of unary minuses (e.g., &quot;<code>- -3</code>&quot;)
+ * can be removed from the input entirely and single unary minuses can be
+ * incorporated into the number node, or all minuses can be preserved in
+ * the AST node structure.
+ * <li> Parsing of units embedded in the input string can be turned on and
+ * off.
  * <li> The string @c avogadro can be parsed as a MathML @em csymbol or
  * as an identifier.
  * <li> A Model object may optionally be provided to the parser using
@@ -304,7 +307,7 @@
  * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
  * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
  * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
- * all unary minuses, or collapse them when possible.
+ * all unary minuses, or collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
@@ -368,8 +371,8 @@
  * number, or whether to treat the case as an error.
  * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
  * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
- * @li Whether to always create explicit ASTNode objects of type @c AST_MINUS
- * for all unary minus operators in a formula, or collapse them when possible.
+ * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
+ * all unary minuses, or collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-03 16:15:00 UTC (rev 15784)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-03 17:37:54 UTC (rev 15785)
@@ -53,10 +53,13 @@
  * <li> The function @c log with a single argument (&quot;<code>log(x)</code>&quot;) 
  * can be parsed as <code>log10(x)</code>, <code>ln(x)</code>, or treated
  * as an error, as desired.
- * <li> Pairs of multiple unary minuses in a row
- * (e.g., &quot;<code>- -3</code>&quot;) can be turned into a single minus
- * in the AST representation, or the multiple minuses can be preserved.
- * <li> Parsing of units can be turned on and off.
+ * <li> Unary minus signs can be collapsed or preserved; that is,
+ * sequential pairs of unary minuses (e.g., &quot;<code>- -3</code>&quot;)
+ * can be removed from the input entirely and single unary minuses can be
+ * incorporated into the number node, or all minuses can be preserved in
+ * the AST node structure.
+ * <li> Parsing of units embedded in the input string can be turned on and
+ * off.
  * <li> The string @c avogadro can be parsed as a MathML @em csymbol or
  * as an identifier.
  * <li> A Model object may optionally be provided to the parser using
@@ -177,7 +180,7 @@
    * the symbol @c log in formulas
    *
    * @param collapseminus a flag that controls how the parser will handle
-   * multiple minus signs in a row
+   * minus signs
    *
    * @param parseunits a flag that controls how the parser will handle
    * apparent references to units of measurement associated with raw
@@ -185,6 +188,18 @@
    *
    * @param avocsymbol a flag that controls how the parser will handle
    * the appearance of the symbol @c avogadro in a formula
+   *
+   * @see getModel()
+   * @see setModel()
+   * @see unsetModel()
+   * @see getParseLog()
+   * @see setParseLog()
+   * @see getParseUnits()
+   * @see setParseUnits()
+   * @see getParseCollapseMinus()
+   * @see setParseCollapseMinus()
+   * @see getParseAvogadroCsymbol()
+   * @see setParseAvogadroCsymbol()
    */
   L3ParserSettings(Model* model, ParseLogType_t parselog,
                    bool collapseminus, bool parseunits, bool avocsymbol);
@@ -283,36 +298,33 @@
   ParseLogType_t getParseLog() const;
 
 
-/* Need figure out what this bit about numbers means:
-
-   * Unary minuses found in infix will always be translated into
-   * an AST node of type AST_MINUS in the latter case, and subsequent pairs
-   * will disappear entirely in the former case, as well as numbers
-   * (AST_INTEGER, AST_REAL, AST_REAL_E, and AST_RATIONAL) nodes being
-   * given negative values.
-*/
-
   /**
-   * Sets the behavior for handling multiple unary minuses appearing 
-   * in mathematical formulas.
+   * Sets the behavior for handling unary minuses appearing in mathematical
+   * formulas.
    *
-   * Pairs of multiple unary minuses in a row (e.g., &quot;<code>-
-   * -3</code>&quot;) can be turned into a single minus in the AST
-   * representation, or the multiple minuses can be preserved.  This method
-   * lets you tell the parser which behavior to use.  The two possibilities
-   * are represented using the following constants:
+   * This setting affects two behaviors.  First, pairs of multiple unary
+   * minuses in a row (e.g., &quot;<code>- -3</code>&quot;) can be
+   * collapsed and ignored in the input, or the multiple minuses can be
+   * preserved in the AST node tree that is generated by the parser.
+   * Second, minus signs in front of numbers can be collapsed into the
+   * number node itself; for example, a &quot;<code>- 4.1</code>&quot; can
+   * be turned into a single ASTNode of type @c AST_NODE with a value of
+   * <code>-4.1</code>, or it can be turned into a node of type @c
+   * AST_MINUS having a child node of type @c AST_REAL.  This method lets
+   * you tell the parser which behavior to use&mdash;either collapse
+   * minuses or always preserve them.  The two possibilities are
+   * represented using the following constants:
    *
    * @li @link L3P_COLLAPSE_UNARY_MINUS@... (value = @c true): collapse
-   * pairs of multiple unary minuses into a single AST node of type @c
-   * AST_MINUS.
+   * unary minuses where possible.
    * @li @link L3P_EXPAND_UNARY_MINUS@... (value = @c false): do not
-   * collapse pairs of unary minuses, and instead translate each one into
-   * an AST node of type @c AST_MINUS.
+   * collapse unary minuses, and instead translate each one into an AST
+   * node of type @c AST_MINUS.
    *
    * @param collapseminus a boolean value (one of the constants
    * @link L3P_COLLAPSE_UNARY_MINUS@... or
-   * @link L3P_EXPAND_UNARY_MINUS@...) indicating how multiple
-   * unary minuses should be handled.
+   * @link L3P_EXPAND_UNARY_MINUS@...) indicating how unary minus
+   * signs in the input should be handled.
    *
    * @see getParseCollapseMinus()
    */
@@ -323,18 +335,24 @@
    * Returns a flag indicating the current behavior set for handling
    * multiple unary minuses in formulas.
    *
-   * Pairs of multiple unary minuses in a row (e.g., &quot;<code>-
-   * -3</code>&quot;) can be turned into a single minus in the AST
-   * representation, or the multiple minuses can be preserved.  This method
-   * lets you tell the parser which behavior to use.  The two possibilities
-   * are represented using the following constants:
+   * This setting affects two behaviors.  First, pairs of multiple unary
+   * minuses in a row (e.g., &quot;<code>- -3</code>&quot;) can be
+   * collapsed and ignored in the input, or the multiple minuses can be
+   * preserved in the AST node tree that is generated by the parser.
+   * Second, minus signs in front of numbers can be collapsed into the
+   * number node itself; for example, a &quot;<code>- 4.1</code>&quot; can
+   * be turned into a single ASTNode of type @c AST_NODE with a value of
+   * <code>-4.1</code>, or it can be turned into a node of type @c
+   * AST_MINUS having a child node of type @c AST_REAL.  This method lets
+   * you tell the parser which behavior to use&mdash;either collapse
+   * minuses or always preserve them.  The two possibilities are
+   * represented using the following constants:
    *
    * @li @link L3P_COLLAPSE_UNARY_MINUS@... (value = @c true): collapse
-   * pairs of multiple unary minuses into a single AST node of type @c
-   * AST_MINUS.
+   * unary minuses where possible.
    * @li @link L3P_EXPAND_UNARY_MINUS@... (value = @c false): do not
-   * collapse pairs of unary minuses, and instead translate each one into
-   * an AST node of type @c AST_MINUS.
+   * collapse unary minuses, and instead translate each one into an AST
+   * node of type @c AST_MINUS.
    *
    * @return A boolean, one of @link L3P_COLLAPSE_UNARY_MINUS@... or
    * @link L3P_EXPAND_UNARY_MINUS@....

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Revision: 15786
          http://sbml.svn.sourceforge.net/sbml/?rev=15786&view=rev
Author:   mhucka
Date:     2012-05-03 22:45:40 +0000 (Thu, 03 May 2012)
Log Message:
-----------
Linked references to AST_ constants to their definitions.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.h
    trunk/libsbml/src/sbml/math/L3ParserSettings.h

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-03 17:37:54 UTC (rev 15785)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-03 22:45:40 UTC (rev 15786)
@@ -198,11 +198,13 @@
  * @htmlinclude string-values-table-l3.html
  * 
  * Note that whether the string &quot;<code>avogadro</code>&quot; is parsed
- * as an AST node of type @c AST_NAME_AVOGADRO or @c AST_NAME is
- * configurable; use the alternate version of this function, called
+ * as an AST node of type @link ASTNodeType_t#AST_NAME_AVOGADRO
+ * AST_NAME_AVOGADRO@... or @link ASTNodeType_t#AST_NAME
+ * AST_NAME@... is configurable; use the alternate version of this
+ * function, called
  * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
  * This functionality is provided because SBML Level&nbsp;2 models may not
- * use @c AST_NAME_AVOGADRO AST nodes.
+ * use @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@... AST nodes.
  *
  * @param formula the text-string formula expression to be parsed
  *
@@ -305,9 +307,11 @@
  * @c id as the identifier of a unit of measurement associated with the
  * number, or whether to treat the case as an error.
  * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
- * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
- * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
- * all unary minuses, or collapse and remove minuses where possible.
+ * type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@... or
+ * as type @link ASTNodeType_t#AST_NAME AST_NAME@....
+ * @li Whether to always create explicit ASTNodes of type @link
+ * ASTNodeType_t#AST_MINUS AST_MINUS@... for all unary minuses, or
+ * collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
@@ -370,9 +374,11 @@
  * @c id as the identifier of a unit of measurement associated with the
  * number, or whether to treat the case as an error.
  * @li Whether to parse &quot;<code>avogadro</code>&quot; as an ASTNode of
- * type @c AST_NAME_AVOGADRO or as type @c AST_NAME.
- * @li Whether to always create explicit ASTNodes of type @c AST_MINUS for
- * all unary minuses, or collapse and remove minuses where possible.
+ * type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@... or
+ * as type @link ASTNodeType_t#AST_NAME AST_NAME@....
+ * @li Whether to always create explicit ASTNodes of type @link
+ * ASTNodeType_t#AST_MINUS AST_MINUS@... for all unary minuses, or
+ * collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-03 17:37:54 UTC (rev 15785)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-03 22:45:40 UTC (rev 15786)
@@ -133,13 +133,43 @@
 
 
 #define L3P_COLLAPSE_UNARY_MINUS true
+/*!<
+ * Collapse unary minuses where possible.
+ * @see @link getParseCollapseMinus()@endlink
+ * @see @link setParseCollapseMinus()@endlink
+ */
 #define L3P_EXPAND_UNARY_MINUS   false
+/*!<
+ * Retain unary minuses in the AST representation.
+ * @see @link getParseCollapseMinus()@endlink
+ * @see @link setParseCollapseMinus()@endlink
+ */
 
 #define L3P_PARSE_UNITS  true
+/*!<
+ * Parse units in text-string formulas.
+ * @see @link setParseCollapseMinus()@endlink
+ * @see @link getParseCollapseMinus()@endlink
+ */
 #define L3P_NO_UNITS false
+/*!<
+ * Do not recognize units in text-string formulas -- treat them as errors.
+ * @see @link setParseCollapseMinus()@endlink
+ * @see @link getParseCollapseMinus()@endlink
+ */
 
 #define L3P_AVOGADRO_IS_CSYMBOL true
+/*!<
+ * Recognize 'avogadro' as an SBML Level 3 symbol.
+ * @see @link getParseAvogadroCsymbol()@endlink
+ * @see @link setParseAvogadroCsymbol()@endlink
+ */
 #define L3P_AVOGADRO_IS_NAME    false
+/*!<
+ * Do not treat 'avogadro' specially -- consider it a plain symbol name.
+ * @see @link getParseAvogadroCsymbol()@endlink
+ * @see @link setParseAvogadroCsymbol()@endlink
+ */
 
 #ifdef __cplusplus
 
@@ -308,18 +338,20 @@
    * preserved in the AST node tree that is generated by the parser.
    * Second, minus signs in front of numbers can be collapsed into the
    * number node itself; for example, a &quot;<code>- 4.1</code>&quot; can
-   * be turned into a single ASTNode of type @c AST_NODE with a value of
-   * <code>-4.1</code>, or it can be turned into a node of type @c
-   * AST_MINUS having a child node of type @c AST_REAL.  This method lets
-   * you tell the parser which behavior to use&mdash;either collapse
-   * minuses or always preserve them.  The two possibilities are
-   * represented using the following constants:
+   * be turned into a single ASTNode of type @link ASTNodeType_t#AST_REAL
+   * AST_REAL@... with a value of <code>-4.1</code>, or it can be
+   * turned into a node of type @link ASTNodeType_t#AST_MINUS
+   * AST_MINUS@... having a child node of type @link
+   * ASTNodeType_t#AST_REAL AST_REAL@....  This method lets you tell
+   * the parser which behavior to use&mdash;either collapse minuses or
+   * always preserve them.  The two possibilities are represented using the
+   * following constants:
    *
    * @li @link L3P_COLLAPSE_UNARY_MINUS@... (value = @c true): collapse
    * unary minuses where possible.
    * @li @link L3P_EXPAND_UNARY_MINUS@... (value = @c false): do not
    * collapse unary minuses, and instead translate each one into an AST
-   * node of type @c AST_MINUS.
+   * node of type @link ASTNodeType_t#AST_MINUS AST_MINUS@....
    *
    * @param collapseminus a boolean value (one of the constants
    * @link L3P_COLLAPSE_UNARY_MINUS@... or
@@ -341,18 +373,20 @@
    * preserved in the AST node tree that is generated by the parser.
    * Second, minus signs in front of numbers can be collapsed into the
    * number node itself; for example, a &quot;<code>- 4.1</code>&quot; can
-   * be turned into a single ASTNode of type @c AST_NODE with a value of
-   * <code>-4.1</code>, or it can be turned into a node of type @c
-   * AST_MINUS having a child node of type @c AST_REAL.  This method lets
-   * you tell the parser which behavior to use&mdash;either collapse
-   * minuses or always preserve them.  The two possibilities are
-   * represented using the following constants:
+   * be turned into a single ASTNode of type @link ASTNodeType_t#AST_REAL
+   * AST_REAL@... with a value of <code>-4.1</code>, or it can be
+   * turned into a node of type @link ASTNodeType_t#AST_MINUS
+   * AST_MINUS@... having a child node of type @link
+   * ASTNodeType_t#AST_REAL AST_REAL@....  This method lets you tell
+   * the parser which behavior to use&mdash;either collapse minuses or
+   * always preserve them.  The two possibilities are represented using the
+   * following constants:
    *
    * @li @link L3P_COLLAPSE_UNARY_MINUS@... (value = @c true): collapse
    * unary minuses where possible.
    * @li @link L3P_EXPAND_UNARY_MINUS@... (value = @c false): do not
    * collapse unary minuses, and instead translate each one into an AST
-   * node of type @c AST_MINUS.
+   * node of type @link ASTNodeType_t#AST_MINUS AST_MINUS@....
    *
    * @return A boolean, one of @link L3P_COLLAPSE_UNARY_MINUS@... or
    * @link L3P_EXPAND_UNARY_MINUS@....
@@ -379,8 +413,9 @@
    * The consequence of these differences is that if SBML Level&nbsp;2 is
    * the target, (1) parsing of formula strings containing units needs to
    * be treated as an error, and (2) the string @c avogadro must be
-   * converted to an ASTNode of type @c AST_NAME instead of @c
-   * AST_NAME_AVOGADRO.
+   * converted to an ASTNode of type @link ASTNodeType_t#AST_NAME
+   * AST_NAME@... instead of @link ASTNodeType_t#AST_NAME_AVOGADRO
+   * AST_NAME_AVOGADRO@....
    *
    * @see getTargetL3()
    * @see getTargetL2()
@@ -406,7 +441,7 @@
    * The consequence of these differences is that if SBML Level&nbsp;3 is
    * the target, (1) formula strings are allowed to specify units after
    * numbers, and (2) the string @c avogadro is converted to an ASTNode of
-   * type @c AST_NAME_AVOGADRO.
+   * type @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@....
    *
    * @see getTargetL3()
    * @see getTargetL2()
@@ -422,8 +457,9 @@
    * @return @c true if this L3ParserSettings object is set up to produce
    * AST nodes appropriate for inclusion in SBML Level&nbsp;2 documents:
    * units on numbers are treated as errors, and the string @c avogadro is
-   * interpreted as @c AST_NAME and not @c AST_NAME_AVOGADRO.  (Both must
-   * be true, or this routine will return @c false.)
+   * interpreted as @link ASTNodeType_t#AST_NAME AST_NAME@... and not
+   * @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@....
+   * (Both must be true, or this routine will return @c false.)
    *
    * @see getTargetL3()
    * @see setTargetL2()
@@ -439,8 +475,10 @@
    * @return @c true if this L3ParserSettings object is set up to produce
    * AST nodes that take full advantage of properties present in SBML
    * Level&nbsp;3 documents: units are properly interpreted, and @c
-   * avogadro is interpreted as @c AST_NAME_AVOGADRO and not @c AST_NAME.
-   * (Both must be true, or this routine will return @c false.)
+   * avogadro is interpreted as @link ASTNodeType_t#AST_NAME_AVOGADRO
+   * AST_NAME_AVOGADRO@... and not @link ASTNodeType_t#AST_NAME
+   * AST_NAME@....  (Both must be true, or this routine will return @c
+   * false.)
    *
    * @see getTargetL2()
    * @see setTargetL3()
@@ -523,10 +561,11 @@
    *
    * @li @link L3P_AVOGADRO_IS_CSYMBOL@... (value = @c true): tells the
    * parser to translate the string @c avogadro (in any capitalization)
-   * into an AST node of type @c AST_NAME_AVOGADRO.
+   * into an AST node of type @link ASTNodeType_t#AST_NAME_AVOGADRO
+   * AST_NAME_AVOGADRO@....
    * @li @link L3P_AVOGADRO_IS_NAME@... (value = @c false): tells the
-   * parser to translate the string @c avogadro into an AST of type @c
-   * AST_NAME.
+   * parser to translate the string @c avogadro into an AST of type @link
+   * ASTNodeType_t#AST_NAME AST_NAME@....
    *
    * Since SBML Level&nbsp;2 does not define a symbol for Avogadro's
    * constant, the value should be set to @c false when parsing text-string
@@ -555,10 +594,11 @@
    * one of the following possibilities:
    * @li @link L3P_AVOGADRO_IS_CSYMBOL@... (value = @c true): tells the
    * parser to translate the string @c avogadro (in any capitalization)
-   * into an AST node of type @c AST_NAME_AVOGADRO.
+   * into an AST node of type @link ASTNodeType_t#AST_NAME_AVOGADRO
+   * AST_NAME_AVOGADRO@....
    * @li @link L3P_AVOGADRO_IS_NAME@... (value = @c false): tells the
-   * parser to translate the string @c avogadro into an AST of type @c
-   * AST_NAME.
+   * parser to translate the string @c avogadro into an AST of type @link
+   * ASTNodeType_t#AST_NAME AST_NAME@....
    *
    * @see setParseAvogadroCsymbol()
    */

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Revision: 15789
          http://sbml.svn.sourceforge.net/sbml/?rev=15789&view=rev
Author:   mhucka
Date:     2012-05-04 00:01:21 +0000 (Fri, 04 May 2012)
Log Message:
-----------
More corrections and expansions for the L3 infix formula parser.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/FormulaFormatter.c
    trunk/libsbml/src/sbml/math/FormulaFormatter.h
    trunk/libsbml/src/sbml/math/FormulaParser.c
    trunk/libsbml/src/sbml/math/FormulaParser.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 00:00:40 UTC (rev 15788)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 00:01:21 UTC (rev 15789)
@@ -141,9 +141,10 @@
  * 
  * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~ and
  * read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
- * are simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~
+ * are in a simple C-inspired infix notation.  A
  * formula in this text-string form can be handed to a program that
- * understands SBML Level&nbsp;1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
  * of a translation system.  The libSBML distribution comes with an example
  * program in the @c "examples" subdirectory called @c translateMath that
  * implements an interactive command-line demonstration of translating
@@ -200,6 +201,15 @@
  * @htmlinclude math-functions.html
  * 
  * @warning @htmlinclude L1-math-syntax-warning.html
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
+ * @if clike @see SBML_parseFormula()@endif@~
+ * @if csharp @see SBML_parseFormula()@endif@~
+ * @if python @see libsbml.SBML_parseFormula()@endif@~
+ * @if java @see SBML_parseFormula()@endif@~
  */
 
 #ifndef ASTNode_h
@@ -798,6 +808,7 @@
   LIBSBML_EXTERN
   char getCharacter () const;
 
+
   /**
    * Get the id of this ASTNode.  
    * 
@@ -806,6 +817,7 @@
   LIBSBML_EXTERN
   std::string getId () const;
 
+
   /**
    * Get the class of this ASTNode.  
    * 
@@ -814,6 +826,7 @@
   LIBSBML_EXTERN
   std::string getClass () const;
 
+
   /**
    * Get the style of this ASTNode.  
    * 
@@ -822,6 +835,7 @@
   LIBSBML_EXTERN
   std::string getStyle () const;
 
+
   /**
    * Get the value of this node as an integer. This function should be
    * called only when
@@ -963,6 +977,10 @@
    * @note The <code>sbml:units</code> attribute is only available in SBML
    * Level&nbsp;3.  It may not be used in Levels 1&ndash;2 of SBML.
    * 
+   * @if clike @see SBML_parseL3Formula()@endif@~
+   * @if csharp @see SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if java @see SBML_parseL3Formula()@endif@~
    */
   LIBSBML_EXTERN
   std::string getUnits () const;
@@ -973,6 +991,11 @@
    * symbol @c avogadro.  The predicate returns @c false (zero) otherwise.
    * 
    * @return @c true if this ASTNode is the special symbol avogadro.
+   *
+   * @if clike @see SBML_parseL3Formula()@endif@~
+   * @if csharp @see SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if java @see SBML_parseL3Formula()@endif@~
    */
   LIBSBML_EXTERN
   bool isAvogadro () const;
@@ -1076,6 +1099,11 @@
    * 
    * @return @c true if the given ASTNode represents a log10() function, @c
    * false otherwise.
+   *
+   * @if clike @see SBML_parseL3Formula()@endif@~
+   * @if csharp @see SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if java @see SBML_parseL3Formula()@endif@~
    */
   LIBSBML_EXTERN
   bool isLog10 () const;
@@ -1221,16 +1249,24 @@
    * For numbers, unary minus nodes can be "collapsed" by negating the
    * number.  In fact, 
    * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <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
+   * does this during its parsing process, and 
+   * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~
+   * has a configuration option that allows this behavior to be turned
+   * on or off.  However, unary minus nodes for symbols
    * (@link ASTNodeType_t#AST_NAME AST_NAME@...) cannot
    * be "collapsed", so this predicate function is necessary.
    * 
    * @return @c true if this ASTNode is a unary minus, @c false otherwise.
+   *
+   * @if clike @see SBML_parseL3Formula()@endif@~
+   * @if csharp @see SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if java @see SBML_parseL3Formula()@endif@~
    */
   LIBSBML_EXTERN
   bool isUMinus () const;
 
+
   /**
    * Predicate returning @c true (non-zero) if this node is a unary plus
    * operator, @c false (zero) otherwise.  A node is defined as a unary
@@ -1242,6 +1278,7 @@
   LIBSBML_EXTERN
   bool isUPlus () const;
 
+
   /**
    * Predicate returning @c true (non-zero) if this node has an unknown type.
    * 
@@ -1260,6 +1297,7 @@
   LIBSBML_EXTERN
   bool isUnknown () const;
 
+
   /**
    * Predicate returning @c true (non-zero) if this node has the mathml attribute
    * <code>id</code>.
@@ -1268,6 +1306,7 @@
    */
   LIBSBML_EXTERN
   bool isSetId() const;
+
   
   /**
    * Predicate returning @c true (non-zero) if this node has the mathml attribute
@@ -1278,6 +1317,7 @@
   LIBSBML_EXTERN
   bool isSetClass() const;
 
+
   /**
    * Predicate returning @c true (non-zero) if this node has the mathml attribute
    * <code>style</code>.
@@ -1286,6 +1326,7 @@
    */
   LIBSBML_EXTERN
   bool isSetStyle() const;
+
     
   /**
    * Predicate returning @c true (non-zero) if this node has the attribute
@@ -1557,6 +1598,7 @@
   virtual void replaceIDWithFunction(const std::string& id, const ASTNode* function);
   /** @endcond */
 
+
   /** @cond doxygen-libsbml-internal */
   /**
    * Replaces any 'AST_NAME_TIME' nodes with a node that multiplies time by the given function.
@@ -1590,6 +1632,7 @@
   LIBSBML_EXTERN
   int unsetId ();
 
+
   /**
    * Unsets the mathml class of this ASTNode.
    *
@@ -1601,6 +1644,7 @@
   LIBSBML_EXTERN
   int unsetClass ();
 
+
   /**
    * Unsets the mathml style of this ASTNode.
    *
@@ -1612,6 +1656,7 @@
   LIBSBML_EXTERN
   int unsetStyle ();
 
+
   /** @cond doxygen-libsbml-internal */
 
   /**
@@ -2205,6 +2250,11 @@
  *
  * More precisley, the node type is @c AST_FUNCTION_LOG with two children
  * the first of which is an @c AST_INTEGER equal to 10.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
  */
 LIBSBML_EXTERN
 int
@@ -2316,12 +2366,19 @@
  *
  * For numbers, unary minus nodes can be "collapsed" by negating the
  * number.  In fact, @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
- * does this during its parse.
- * However, unary minus nodes for symbols (@c AST_NAMES) cannot be
- * "collapsed", so this predicate function is necessary.
+ * does this during its parse, and 
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~
+ * has a configuration option that allows this behavior to be turned
+ * on or off.  However, unary minus nodes for symbols (@c AST_NAMES) 
+ * cannot be "collapsed", so this predicate function is necessary.
  *
  * A node is defined as a unary minus node if it is of type @c AST_MINUS
  * and has exactly one child.
+ *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
  */
 LIBSBML_EXTERN
 int

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-05-04 00:00:40 UTC (rev 15788)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.c	2012-05-04 00:01:21 UTC (rev 15789)
@@ -41,20 +41,22 @@
  * basically derived from SBML Level&nbsp;1.
  *
  * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level&nbsp;1.  A formula in
+ * SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula() 
+ * are in a C-inspired infix notation.  A formula in
  * this text-string form therefore can be handed to a program that
- * understands SBML Level&nbsp;1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
  * of a formula translation system.  The syntax is described in detail in
  * the documentation for ASTNode. @endif@... java 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
  * <code><a href="libsbml.html#parseFormula(java.lang.String)">
- * libsbml.parseFormula()</a></code> are
- * simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * libsbml.parseFormula()</a></code> and
+ * <code><a href="libsbml.html#parseL3Formula(java.lang.String)">
+ * libsbml.parseL3Formula()</a></code> are in a 
+ * simple C-inspired infix notation.  A
  * formula in this text-string form therefore can be handed to a program
- * that understands SBML Level&nbsp;1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
  * part of a formula translation system.  The syntax is described in detail
  * in the documentation for ASTNode.   @endif
  *
@@ -112,6 +114,7 @@
  * responsible for freeing it when it is no longer needed.
  *
  * @see SBML_parseFormula()
+ * @see SBML_parseL3Formula()
  */
 LIBSBML_EXTERN
 char *

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-04 00:00:40 UTC (rev 15788)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-04 00:01:21 UTC (rev 15789)
@@ -108,6 +108,10 @@
  * @if csharp @see SBML_parseFormula()@endif@~
  * @if python @see libsbml.parseFormula()@endif@~
  * @if java @see parseFormula(java.lang.String)@endif@~
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
  */
 LIBSBML_EXTERN
 char *

Modified: trunk/libsbml/src/sbml/math/FormulaParser.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.c	2012-05-04 00:00:40 UTC (rev 15788)
+++ trunk/libsbml/src/sbml/math/FormulaParser.c	2012-05-04 00:01:21 UTC (rev 15789)
@@ -299,18 +299,19 @@
  * Abstract Syntax Tree (AST).
  *
  * @if clike The text-string form of mathematical formulas produced by
- * SBML_formulaToString() and read by SBML_parseFormula() are simple
- * C-inspired infix notation taken from SBML Level&nbsp;1.  A formula in
+ * SBML_formulaToString() and read by SBML_parseFormula() and SBML_parseL3Formula() 
+ * are in a simple C-inspired infix notation.  A formula in
  * this text-string form therefore can be handed to a program that
- * understands SBML Level&nbsp;1 mathematical expressions, or used as part
+ * understands SBML mathematical expressions, or used as part
  * of a formula translation system.  The syntax is described in detail in
  * the documentation for ASTNode. @endif@... java 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
- * simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * <code><a href="libsbml.html">libsbml.parseFormula()</a></code> and
+ * <code><a href="libsbml.html">libsbml.parseL3Formula()</a></code> 
+ * are in a simple C-inspired infix notation.  A
  * formula in this text-string form therefore can be handed to a program
- * that understands SBML Level&nbsp;1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
  * part of a formula translation system.  The syntax is described in detail
  * in the documentation for ASTNode.   @endif
  *
@@ -370,6 +371,10 @@
  * parsing the formula
  *
  * @see SBML_formulaToString()
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
  */
 LIBSBML_EXTERN
 ASTNode_t *

Modified: trunk/libsbml/src/sbml/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-04 00:00:40 UTC (rev 15788)
+++ trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-04 00:01:21 UTC (rev 15789)
@@ -46,9 +46,10 @@
  * The text-string form of mathematical formulas produced by
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
  * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
- * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
+ * and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~
+ * use a simple C-inspired infix notation.  A
  * formula in this text-string form therefore can be handed to a program
- * that understands SBML Level&nbsp;1 mathematical expressions, or used as
+ * that understands SBML mathematical expressions, or used as
  * part of a formula translation system.  The syntax is described in detail
  * in the documentation for ASTNode. 
  *
@@ -107,6 +108,10 @@
  * @return the root node of the AST, or NULL if an error occurred in
  * parsing the formula
  *
+ * @if clike @see SBML_parseL3Formula()@endif@~
+ * @if csharp @see SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_formulaToString()@endif@~
  * @if csharp @see SBML_formulaToString()@endif@~
  * @if python @see libsbml.formulaToString()@endif@~

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15805
          http://sbml.svn.sourceforge.net/sbml/?rev=15805&view=rev
Author:   mhucka
Date:     2012-05-04 18:51:58 +0000 (Fri, 04 May 2012)
Log Message:
-----------
Fixed some cross-reference errors and made a few hacks for Doxygen
tag-handling weirdnesses.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.h
    trunk/libsbml/src/sbml/math/FormulaFormatter.h
    trunk/libsbml/src/sbml/math/FormulaParser.c
    trunk/libsbml/src/sbml/math/FormulaParser.h
    trunk/libsbml/src/sbml/math/FormulaTokenizer.h
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.h
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/L3ParserSettings.h

Modified: trunk/libsbml/src/sbml/math/ASTNode.h
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/ASTNode.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -141,7 +141,8 @@
  * 
  * The text-string form of mathematical formulas produced by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~ and
  * read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
- * and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * and
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * are in a simple C-inspired infix notation.  A
  * formula in this text-string form can be handed to a program that
  * understands SBML mathematical expressions, or used as part
@@ -204,11 +205,11 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseFormula()@endif@~
  * @if csharp @see SBML_parseFormula()@endif@~
- * @if python @see libsbml.SBML_parseFormula()@endif@~
+ * @if python @see libsbml.parseFormula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseFormula(String formula)">libsbml.parseFormula(String formula)</a></code>@endif@~
  */
 
@@ -979,7 +980,7 @@
    * 
    * @if clike @see SBML_parseL3Formula()@endif@~
    * @if csharp @see SBML_parseL3Formula()@endif@~
-   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.parseL3Formula()@endif@~
    * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
    */
   LIBSBML_EXTERN
@@ -994,7 +995,7 @@
    *
    * @if clike @see SBML_parseL3Formula()@endif@~
    * @if csharp @see SBML_parseL3Formula()@endif@~
-   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.parseL3Formula()@endif@~
    * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
    */
   LIBSBML_EXTERN
@@ -1102,7 +1103,7 @@
    *
    * @if clike @see SBML_parseL3Formula()@endif@~
    * @if csharp @see SBML_parseL3Formula()@endif@~
-   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.parseL3Formula()@endif@~
    * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
    */
   LIBSBML_EXTERN
@@ -1260,7 +1261,7 @@
    *
    * @if clike @see SBML_parseL3Formula()@endif@~
    * @if csharp @see SBML_parseL3Formula()@endif@~
-   * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+   * @if python @see libsbml.parseL3Formula()@endif@~
    * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
    */
   LIBSBML_EXTERN
@@ -2253,7 +2254,7 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  */
 LIBSBML_EXTERN
@@ -2377,7 +2378,7 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -110,7 +110,7 @@
  * @if java @see parseFormula(java.lang.String)@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaParser.c
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.c	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/FormulaParser.c	2012-05-04 18:51:58 UTC (rev 15805)
@@ -373,7 +373,7 @@
  * @see SBML_formulaToString()
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -46,7 +46,8 @@
  * The text-string form of mathematical formulas produced by
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
  * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
- * and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * and
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * use a simple C-inspired infix notation.  A
  * formula in this text-string form therefore can be handed to a program
  * that understands SBML mathematical expressions, or used as
@@ -110,7 +111,7 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_formulaToString()@endif@~
  * @if csharp @see SBML_formulaToString()@endif@~

Modified: trunk/libsbml/src/sbml/math/FormulaTokenizer.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/FormulaTokenizer.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -77,7 +77,8 @@
  * translate formulas between this text-string representation and MathML.
  * The principal entry points to the translation system are
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~.
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~.
  *
  * LibSBML also provides a lower-level interface to the formula parser.
  * This takes the form of the C functions

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-04 18:51:58 UTC (rev 15805)
@@ -2744,7 +2744,8 @@
  *
  * The text-string form of mathematical formulas read by this function
  * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
  * respectively.  The latter two libSBML functions were originally
  * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
  * and were focused on the syntax of mathematical formulas used in SBML
@@ -2753,7 +2754,8 @@
  * expanded mathematical syntax would be useful for software developers.
  * To maintain backwards compatibility, the original
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
  * have been left untouched, and instead, the new functionality is
  * provided in the form of
  * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
@@ -2910,7 +2912,7 @@
  *
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see SBML_getLastParseL3Error()@endif@~
  * @if clike @see SBML_formulaToString()@endif@~
  * @if csharp @see SBML_formulaToString()@endif@~
@@ -2918,11 +2920,11 @@
  * @if java @see formulaToString()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -2942,7 +2944,8 @@
  * resolve symbols, and returns an Abstract Syntax Tree (AST)
  * representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * This is identical to
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
  * except that this function uses the given model in the argument @p model
  * to check against identifiers that appear in the @p formula.
  *
@@ -2960,15 +2963,15 @@
  * 
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see SBML_getLastParseL3Error()@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -2988,7 +2991,8 @@
  * Parses the given mathematical formula using specific parser settings and
  * returns an Abstract Syntax Tree (AST) representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * This is identical to
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
  * except that this function uses the parser settings given in the argument
  * @p settings.  The settings override the default parsing behavior.
  *
@@ -3020,7 +3024,7 @@
  * all unary minuses, or collapse them when possible.
  *
  * For more details about the parser, please see the definition of
- * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * L3ParserSettings and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
  *
  * @param formula the mathematical formula expression to be parsed
  * @param settings the settings to be used for this parser invocation
@@ -3033,15 +3037,15 @@
  * 
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see SBML_getLastParseL3Error()@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  */
 LIBSBML_EXTERN
@@ -3094,19 +3098,19 @@
  * for all unary minus operators in a formula, or collapse them when possible.
  *
  * For more details about the parser, please see the definition of
- * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * L3ParserSettings and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
  * 
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -3133,15 +3137,15 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -41,7 +41,8 @@
  *
  * The text-string form of mathematical formulas read by this function
  * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
  * respectively.  The latter two libSBML functions were originally
  * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
  * and were focused on the syntax of mathematical formulas used in SBML
@@ -50,7 +51,8 @@
  * expanded mathematical syntax would be useful for software developers.
  * To maintain backwards compatibility, the original
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
  * have been left untouched, and instead, the new functionality is
  * provided in the form of
  * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
@@ -224,11 +226,11 @@
  * @if java @see formulaToString(ASTNode tree)@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see  <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  */
 LIBSBML_EXTERN
@@ -241,7 +243,8 @@
  * resolve symbols, and returns an Abstract Syntax Tree (AST)
  * representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
+ * This is identical to
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
  * except that this function uses the given model in the argument @p model
  * to check against identifiers that appear in the @p formula.
  *
@@ -260,15 +263,15 @@
  * 
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error</a></code>@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  */
 LIBSBML_EXTERN
@@ -280,7 +283,8 @@
  * Parses the given mathematical formula using specific parser settings and
  * returns an Abstract Syntax Tree (AST) representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * This is identical to
+ @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
  * except that this function uses the parser settings given in the argument
  * @p settings.  The settings override the default parsing behavior.
  *
@@ -314,7 +318,8 @@
  * collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
- * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * L3ParserSettings and
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
  *
  * @param formula the mathematical formula expression to be parsed
  *
@@ -328,19 +333,19 @@
  * 
  * @if clike @see SBML_getDefaultL3ParserSettings()@endif@~
  * @if csharp @see SBML_getDefaultL3ParserSettings()@endif@~
- * @if python @see libsbml.SBML_getDefaultL3ParserSettings()@endif@~
+ * @if python @see libsbml.getDefaultL3ParserSettings()@endif@~
  * @if java @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">libsbml.getDefaultL3ParserSettings</a></code>@endif@~
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error</a></code>@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
  */
 LIBSBML_EXTERN
@@ -381,19 +386,20 @@
  * collapse and remove minuses where possible.
  *
  * For more details about the parser, please see the definition of
- * L3ParserSettings_t and @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * L3ParserSettings and
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
  * 
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  */
 LIBSBML_EXTERN
@@ -415,15 +421,15 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-04 18:51:58 UTC (rev 15805)
@@ -1003,7 +1003,8 @@
  *
  * The text-string form of mathematical formulas read by this function
  * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
  * respectively.  The latter two libSBML functions were originally
  * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
  * and were focused on the syntax of mathematical formulas used in SBML
@@ -1012,7 +1013,8 @@
  * expanded mathematical syntax would be useful for software developers.
  * To maintain backwards compatibility, the original
  * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * and
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
  * have been left untouched, and instead, the new functionality is
  * provided in the form of
  * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
@@ -1177,11 +1179,11 @@
  * @if java @see formulaToString()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -1201,7 +1203,8 @@
  * resolve symbols, and returns an Abstract Syntax Tree (AST)
  * representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * This is identical to
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
  * except that this function uses the given model in the argument @p model
  * to check against identifiers that appear in the @p formula.
  *
@@ -1219,15 +1222,15 @@
  * 
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see SBML_getLastParseL3Error()@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -1247,7 +1250,8 @@
  * Parses the given mathematical formula using specific parser settings and
  * returns an Abstract Syntax Tree (AST) representation of the result.
  *
- * This is identical to @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ * This is identical to
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
  * except that this function uses the parser settings given in the argument
  * @p settings.  The settings override the default parsing behavior.
  *
@@ -1292,15 +1296,15 @@
  * 
  * @if clike @see SBML_getLastParseL3Error()@endif@~
  * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
+ * @if python @see libsbml.getLastParseL3Error()@endif@~
  * @if java @see SBML_getLastParseL3Error()@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  */
 LIBSBML_EXTERN
@@ -1357,15 +1361,15 @@
  * 
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN
@@ -1392,15 +1396,15 @@
  *
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see SBML_parseL3Formula()@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see SBML_parseL3FormulaWithModel()@endif@~
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see SBML_parseL3FormulaWithSettings()@endif@~
  */
 LIBSBML_EXTERN

Modified: trunk/libsbml/src/sbml/math/L3ParserSettings.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-04 18:20:07 UTC (rev 15804)
+++ trunk/libsbml/src/sbml/math/L3ParserSettings.h	2012-05-04 18:51:58 UTC (rev 15805)
@@ -93,15 +93,15 @@
  *
  * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithSettings()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  * @if clike @see SBML_parseL3Formula()@endif@~
  * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.SBML_parseL3Formula()@endif@~
+ * @if python @see libsbml.parseL3Formula()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
  * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.SBML_parseL3FormulaWithModel()@endif@~
+ * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
  * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
  */
 

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Revision: 15839
          http://sbml.svn.sourceforge.net/sbml/?rev=15839&view=rev
Author:   fbergmann
Date:     2012-05-08 20:13:21 +0000 (Tue, 08 May 2012)
Log Message:
-----------
- fix parsing of real numbers

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-08 16:52:24 UTC (rev 15838)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-08 20:13:21 UTC (rev 15839)
@@ -2290,7 +2290,7 @@
         streampos numbegin = l3p->input.tellg();
         l3p->input >> numlong;
         streampos numend = l3p->input.tellg();
-        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
+        double fraction = numlong/pow(10.0, ( numend != -1 ? static_cast<long>(numend-numbegin) : 1 ));
         number += fraction;
       }
     }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-08 16:52:24 UTC (rev 15838)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-08 20:13:21 UTC (rev 15839)
@@ -548,7 +548,7 @@
         streampos numbegin = l3p->input.tellg();
         l3p->input >> numlong;
         streampos numend = l3p->input.tellg();
-        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
+        double fraction = numlong/pow(10.0, ( numend != -1 ? static_cast<long>(numend-numbegin) : 1 ));
         number += fraction;
       }
     }

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Revision: 15840
          http://sbml.svn.sourceforge.net/sbml/?rev=15840&view=rev
Author:   fbergmann
Date:     2012-05-08 20:52:55 +0000 (Tue, 08 May 2012)
Log Message:
-----------
- need to actually take the whole length into account

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-08 20:13:21 UTC (rev 15839)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-08 20:52:55 UTC (rev 15840)
@@ -2290,7 +2290,9 @@
         streampos numbegin = l3p->input.tellg();
         l3p->input >> numlong;
         streampos numend = l3p->input.tellg();
-        double fraction = numlong/pow(10.0, ( numend != -1 ? static_cast<long>(numend-numbegin) : 1 ));
+        if (numend < 0)
+            numend = l3p->input.str().length();
+        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
         number += fraction;
       }
     }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-08 20:13:21 UTC (rev 15839)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-08 20:52:55 UTC (rev 15840)
@@ -547,8 +547,9 @@
       if (isdigit(l3p->input.peek())) {
         streampos numbegin = l3p->input.tellg();
         l3p->input >> numlong;
-        streampos numend = l3p->input.tellg();
-        double fraction = numlong/pow(10.0, ( numend != -1 ? static_cast<long>(numend-numbegin) : 1 ));
+        if (numend < 0)
+            numend = l3p->input.str().length();
+        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
         number += fraction;
       }
     }

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Revision: 15860
          http://sbml.svn.sourceforge.net/sbml/?rev=15860&view=rev
Author:   mhucka
Date:     2012-05-15 00:20:14 +0000 (Tue, 15 May 2012)
Log Message:
-----------
A lot of cross-references for the Java case were just plain wrong or
incomplete.  Hopefully they're all fixed now.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/FormulaFormatter.h
    trunk/libsbml/src/sbml/math/FormulaParser.h
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.h

Modified: trunk/libsbml/src/sbml/math/FormulaFormatter.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-14 23:53:42 UTC (rev 15859)
+++ trunk/libsbml/src/sbml/math/FormulaFormatter.h	2012-05-15 00:20:14 UTC (rev 15860)
@@ -43,8 +43,8 @@
  * basically derived from SBML Level 1.
  *
  * The text-string form of mathematical formulas produced by
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
  * use a simple C-inspired infix notation taken from SBML Level&nbsp;1.  A
  * formula in this text-string form therefore can be handed to a program
  * that understands SBML Level&nbsp;1 mathematical expressions, or used as
@@ -104,14 +104,34 @@
  * mathematical formula.  The caller owns the returned string and is
  * responsible for freeing it when it is no longer needed.
  *
- * @if clike @see SBML_parseFormula()@endif@~
- * @if csharp @see SBML_parseFormula()@endif@~
- * @if python @see libsbml.parseFormula()@endif@~
- * @if java @see parseFormula(java.lang.String)@endif@~
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 char *

Modified: trunk/libsbml/src/sbml/math/FormulaParser.h
===================================================================
--- trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-14 23:53:42 UTC (rev 15859)
+++ trunk/libsbml/src/sbml/math/FormulaParser.h	2012-05-15 00:20:14 UTC (rev 15860)
@@ -44,8 +44,8 @@
  * Abstract Syntax Tree (AST).
  *
  * The text-string form of mathematical formulas produced by
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
- * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
+ * and read by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
  * and
  * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
  * use a simple C-inspired infix notation.  A
@@ -109,14 +109,34 @@
  * @return the root node of the AST, or NULL if an error occurred in
  * parsing the formula
  *
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
- * @if clike @see SBML_formulaToString()@endif@~
- * @if csharp @see SBML_formulaToString()@endif@~
- * @if python @see libsbml.formulaToString()@endif@~
- * @if java @see formulaToString(ASTNode tree)@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 ASTNode_t *

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-14 23:53:42 UTC (rev 15859)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-15 00:20:14 UTC (rev 15860)
@@ -2845,7 +2845,7 @@
  * error is set; information about the error can be retrieved using
  * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
  *
- * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></scode>@endif@~
+ * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
  * are provided as a convenience by libSBML&mdash;the MathML standard does not
  * actually define a "string-form" equivalent to MathML expressions, so the
  * choice of formula syntax is arbitrary.  The approach taken by libSBML is

Modified: trunk/libsbml/src/sbml/math/L3Parser.h
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-14 23:53:42 UTC (rev 15859)
+++ trunk/libsbml/src/sbml/math/L3Parser.h	2012-05-15 00:20:14 UTC (rev 15860)
@@ -40,9 +40,9 @@
  * as an Abstract Syntax Tree (AST).
  *
  * The text-string form of mathematical formulas read by this function
- * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * are expanded versions of the formats produced and read by @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
  * and
- * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~, 
  * respectively.  The latter two libSBML functions were originally
  * developed to support conversion between SBML Levels&nbsp;1 and&nbsp;2,
  * and were focused on the syntax of mathematical formulas used in SBML
@@ -50,15 +50,15 @@
  * and&nbsp;3, it became clear that supporting Level&nbsp;2 and&nbsp;3's
  * expanded mathematical syntax would be useful for software developers.
  * To maintain backwards compatibility, the original
- * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString()</a></code>@endif@~
+ * @if clike SBML_formulaToString()@endif@... csharp SBML_formulaToString()@endif@... python libsbml.formulaToString()@endif@... java <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode)">libsbml.formulaToString(ASTNode tree)</a></code>@endif@~
  * and
- * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
  * have been left untouched, and instead, the new functionality is
  * provided in the form of
  * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
  *
  * The following are the differences in the formula syntax supported by
- * this function, compared to what is supported by  @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~:
+ * this function, compared to what is supported by  @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~:
  *
  * @li Units may be asociated with bare numbers, using the following syntax:
  * <div style="margin: 10px auto 10px 25px; display: block">
@@ -81,7 +81,7 @@
  * either using @c arc as a prefix or simply @c a; in other words, both
  * @c arccsc and @c acsc are interpreted as the operator @em arccosecant
  * defined in MathML.  (Many functions in the SBML Level&nbsp;1 infix-notation
- * parser implemented by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * parser implemented by @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
  * are defined this way as well, but not all.)
  * @li The following expression is parsed as a rational number instead of
  * as a numerical division:
@@ -95,7 +95,7 @@
  * are not interpreted in this way.)
  * @li Various settings may be altered by using an L3ParserSettings object
  * in conjunction with the alternative function call
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, including the following:
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~, including the following:
  * <ul>
  * <li> The function @c log with a single argument (&quot;<code>log(x)</code>&quot;) 
  * can be parsed as <code>log10(x)</code>, <code>ln(x)</code>, or treated
@@ -110,9 +110,9 @@
  * <li> The string @c avogadro can be parsed as a MathML @em csymbol or
  * as an identifier.
  * <li> A Model object may optionally be provided to the parser using
- * the variant function call @if clike  SBML_parseL3FormulaWithModel()@endif@... csharp  SBML_parseL3FormulaWithModel()@endif@... python  libsbml.SBML_parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String)">libsbml.parseL3FormulaWithModel()</a></code>@endif@~.
+ * the variant function call @if clike  SBML_parseL3FormulaWithModel()@endif@... csharp  SBML_parseL3FormulaWithModel()@endif@... python  libsbml.SBML_parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~.
  * or stored in a L3ParserSettings object passed to the variant function
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~.
  * When a Model object is provided, identifiers (values of type @c SId)
  * from that model are used in preference to pre-defined MathML
  * definitions.  More precisely, the Model entities whose identifiers will
@@ -133,15 +133,15 @@
  * These configuration settings cannot be changed using @em this function
  * (i.e., @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~), 
  * but they can be change on a per-call basis by using the alternative function 
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  *
  * This function returns the root node of the AST corresponding to the
  * formula given as the argument.  If the formula contains a syntax error,
  * this function will return @c NULL instead.  When @c NULL is returned, an
  * error is set; information about the error can be retrieved using
- * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
  *
- * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></scode>@endif@~
+ * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~
  * are provided as a convenience by libSBML&mdash;the MathML standard does not
  * actually define a "string-form" equivalent to MathML expressions, so the
  * choice of formula syntax is arbitrary.  The approach taken by libSBML is
@@ -182,16 +182,16 @@
  *
  * Note that this function's interpretation of the string
  * &quot;<code>log</code>&quot; as a function with a single argument can be
- * changed; use the function @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~
+ * changed; use the function @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
  * instead of this function and pass it an appropriate L3ParserSettings
  * object.  By default, unlike the SBML Level&nbsp;1 parser implemented by
- * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~, 
+ * @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula(String formula)</a></code>@endif@~, 
  * the string &quot;<code>log</code>&quot; is interpreted as the base&nbsp;10
  * logarithm, and @em not as the natural logarithm.  However, you can change
  * the interpretation to be base-10 log, natural log, or as an error; since
  * the name "log" by itself is ambiguous, you require that the parser uses
  * @c log10 or @c ln instead, which are more clear.  Please refer to
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~.
  * 
  * In addition, the following symbols will be translated to their MathML
  * equivalents, if no symbol with the same @c SId identifier string exists
@@ -204,7 +204,7 @@
  * AST_NAME_AVOGADRO@... or @link ASTNodeType_t#AST_NAME
  * AST_NAME@... is configurable; use the alternate version of this
  * function, called
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~.
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~.
  * This functionality is provided because SBML Level&nbsp;2 models may not
  * use @link ASTNodeType_t#AST_NAME_AVOGADRO AST_NAME_AVOGADRO@... AST nodes.
  *
@@ -214,24 +214,36 @@
  * or @c NULL if an error occurred while parsing the formula.  When @c NULL
  * is returned, an error is recorded internally; information about the
  * error can be retrieved using 
- * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
  *
- * @if clike @see SBML_getLastParseL3Error()@endif@~
- * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python libsbml.getLastParseL3Error()@endif@~
- * @if java @see <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error</a></code>@endif@~
- * @if clike @see SBML_formulaToString()@endif@~
- * @if csharp @see SBML_formulaToString()@endif@~
- * @if python @see libsbml.formulaToString()@endif@~
- * @if java @see formulaToString(ASTNode tree)@endif@~
- * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
- * @if java @see  <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 ASTNode_t *
@@ -244,12 +256,12 @@
  * representation of the result.
  *
  * This is identical to
- * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
  * except that this function uses the given model in the argument @p model
  * to check against identifiers that appear in the @p formula.
  *
  * For more details about the parser, please see the definition of
- * the function @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
+ * the function @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
  *
  * @param formula the mathematical formula expression to be parsed
  *
@@ -259,20 +271,32 @@
  * or @c NULL if an error occurred while parsing the formula.  When @c NULL
  * is returned, an error is recorded internally; information about the
  * error can be retrieved using
- * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
  * 
- * @if clike @see SBML_getLastParseL3Error()@endif@~
- * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python @see libsbml.getLastParseL3Error()@endif@~
- * @if java @see <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error</a></code>@endif@~
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 ASTNode_t *
@@ -284,7 +308,7 @@
  * returns an Abstract Syntax Tree (AST) representation of the result.
  *
  * This is identical to
- @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(org.sbml.libsbml.ASTNode)">libsbml.parseL3Formula()</a></code>@endif@~,
+ @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~,
  * except that this function uses the parser settings given in the argument
  * @p settings.  The settings override the default parsing behavior.
  *
@@ -319,7 +343,7 @@
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings and
- * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
  *
  * @param formula the mathematical formula expression to be parsed
  *
@@ -329,24 +353,32 @@
  * or @c NULL if an error occurred while parsing the formula.  When @c NULL
  * is returned, an error is recorded internally; information about the
  * error can be retrieved using
- * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
+ * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error()</a></code>@endif@~.
  * 
- * @if clike @see SBML_getDefaultL3ParserSettings()@endif@~
- * @if csharp @see SBML_getDefaultL3ParserSettings()@endif@~
- * @if python @see libsbml.getDefaultL3ParserSettings()@endif@~
- * @if java @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">libsbml.getDefaultL3ParserSettings</a></code>@endif@~
- * @if clike @see SBML_getLastParseL3Error()@endif@~
- * @if csharp @see SBML_getLastParseL3Error()@endif@~
- * @if python @see libsbml.getLastParseL3Error()@endif@~
- * @if java @see <code><a href="libsbml.html#getLastParseL3Error()">libsbml.getLastParseL3Error</a></code>@endif@~
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 ASTNode_t *
@@ -354,7 +386,7 @@
 
 
 /**
- * Returns a copy of the default parser settings used by @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * Returns a copy of the default parser settings used by @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
  * 
  * The settings structure allows callers to change the following parsing
  * behaviors:
@@ -387,20 +419,32 @@
  *
  * For more details about the parser, please see the definition of
  * L3ParserSettings and
- * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~.
+ * @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~.
  * 
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getLastParseL3Error()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getLastParseL3Error()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getLastParseL3Error()">getLastParseL3Error()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 L3ParserSettings_t*
@@ -410,27 +454,39 @@
 /**
  * Returns the last error reported by the parser.
  *
- * If @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula()</a></code>@endif@~, 
- * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String)">libsbml.parseL3FormulaWithSettings()</a></code>@endif@~, or
- * @if clike SBML_parseL3FormulaWithModel()@endif@... csharp SBML_parseL3FormulaWithModel()@endif@... python libsbml.parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String)">libsbml.parseL3FormulaWithModel()</a></code>@endif@~ return @c NULL, an error is set internally which is accessible
+ * If @if clike SBML_parseL3Formula()@endif@... csharp SBML_parseL3Formula()@endif@... python libsbml.parseL3Formula()@endif@... java <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>@endif@~, 
+ * @if clike SBML_parseL3FormulaWithSettings()@endif@... csharp SBML_parseL3FormulaWithSettings()@endif@... python libsbml.parseL3FormulaWithSettings()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~, or
+ * @if clike SBML_parseL3FormulaWithModel()@endif@... csharp SBML_parseL3FormulaWithModel()@endif@... python libsbml.parseL3FormulaWithModel()@endif@... java <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~ return @c NULL, an error is set internally which is accessible
  * via this function. 
  *
  * @return a string describing the error that occurred.  This will contain
  * the string the parser was trying to parse, which character it had parsed
  * when it encountered the error, and a description of the error.
  *
- * @if clike @see SBML_parseL3Formula()@endif@~
- * @if csharp @see SBML_parseL3Formula()@endif@~
- * @if python @see libsbml.parseL3Formula()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3Formula(String formula)">libsbml.parseL3Formula(String formula)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithModel()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithModel()@endif@~
- * @if python @see libsbml.parseL3FormulaWithModel()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithModel(String formula, Model model)">libsbml.parseL3FormulaWithModel(String formula, Model model)</a></code>@endif@~
- * @if clike @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if csharp @see SBML_parseL3FormulaWithSettings()@endif@~
- * @if python @see libsbml.parseL3FormulaWithSettings()@endif@~
- * @if java @see <code><a href="libsbml.html#parseL3FormulaWithSettings(String formula, L3ParserSettings settings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>@endif@~
+ * @if clike @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if csharp @see SBML_formulaToString()
+ * @see SBML_parseL3FormulaWithSettings()
+ * @see SBML_parseL3Formula()
+ * @see SBML_parseL3FormulaWithModel()
+ * @see SBML_getDefaultL3ParserSettings()
+ * @endif@~
+ * @if python @see libsbml.formulaToString()
+ * @see libsbml.parseL3FormulaWithSettings()
+ * @see libsbml.parseL3Formula()
+ * @see libsbml.parseL3FormulaWithModel()
+ * @see libsbml.getDefaultL3ParserSettings()
+ * @endif@~
+ * @if java @see <code><a href="libsbml.html#formulaToString(org.sbml.libsbml.ASTNode tree)">libsbml.formulaToString(ASTNode tree)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithSettings(java.lang.String, org.sbml.libsbml.L3ParserSettings)">libsbml.parseL3FormulaWithSettings(String formula, L3ParserSettings settings)</a></code>
+ * @see <code><a href="libsbml.html#parseL3Formula(java.lang.String)">libsbml.parseL3Formula(String formula)</a></code>
+ * @see <code><a href="libsbml.html#parseL3FormulaWithModel(java.lang.String, org.sbml.libsbml.Model)">parseL3FormulaWithModel(String formula, Model model)</a></code>
+ * @see <code><a href="libsbml.html#getDefaultL3ParserSettings()">getDefaultL3ParserSettings()</a></code>
+ * @endif@~
  */
 LIBSBML_EXTERN
 char*

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Revision: 15876
          http://sbml.svn.sourceforge.net/sbml/?rev=15876&view=rev
Author:   luciansmith
Date:     2012-05-21 07:54:19 +0000 (Mon, 21 May 2012)
Log Message:
-----------
Added 'pow' to mean 'power'.
Fixed 'replaceIDWithFunction'  (was looking at 'id' instead of 'name'.  Arrrrgh)

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/ASTNode.cpp
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/ASTNode.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/ASTNode.cpp	2012-05-18 19:53:11 UTC (rev 15875)
+++ trunk/libsbml/src/sbml/math/ASTNode.cpp	2012-05-21 07:54:19 UTC (rev 15876)
@@ -1976,7 +1976,7 @@
   for (unsigned int i=0; i<getNumChildren(); i++) {
     ASTNode* child = getChild(i);
     if (child->getType() == AST_NAME &&
-        child->getId() == id) {
+        child->getName() == id) {
       replaceChild(i, function->deepCopy());
     }
     else {

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-18 19:53:11 UTC (rev 15875)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-05-21 07:54:19 UTC (rev 15876)
@@ -2445,6 +2445,7 @@
   if (caselessStrCmp(name, "log10"))    return AST_FUNCTION_LOG;
   if (caselessStrCmp(name, "piecewise")) return AST_FUNCTION_PIECEWISE;
   if (caselessStrCmp(name, "power"))    return AST_POWER;
+  if (caselessStrCmp(name, "pow"))      return AST_POWER;
   if (caselessStrCmp(name, "sqr"))      return AST_FUNCTION_POWER;
   if (caselessStrCmp(name, "sqrt"))     return AST_FUNCTION_ROOT;
   if (caselessStrCmp(name, "root"))     return AST_FUNCTION_ROOT;
@@ -2845,7 +2846,7 @@
  * error is set; information about the error can be retrieved using
  * @if clike SBML_getLastParseL3Error()@endif@... csharp SBML_getLastParseL3Error()@endif@... python libsbml.getLastParseL3Error()@endif@... java <code><a href="libsbml.html#getLastParseL3Error(java.lang.String)">libsbml.getLastParseL3Error()</a></code>@endif@~.
  *
- * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></code>@endif@~
+ * Note that this facility and the SBML Level&nbsp;1-based @if clike SBML_parseFormula()@endif@... csharp SBML_parseFormula()@endif@... python libsbml.parseFormula()@endif@... java <code><a href="libsbml.html#parseFormula(java.lang.String)">libsbml.parseFormula()</a></scode>@endif@~
  * are provided as a convenience by libSBML&mdash;the MathML standard does not
  * actually define a "string-form" equivalent to MathML expressions, so the
  * choice of formula syntax is arbitrary.  The approach taken by libSBML is

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-18 19:53:11 UTC (rev 15875)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-05-21 07:54:19 UTC (rev 15876)
@@ -703,6 +703,7 @@
   if (caselessStrCmp(name, "log10"))    return AST_FUNCTION_LOG;
   if (caselessStrCmp(name, "piecewise")) return AST_FUNCTION_PIECEWISE;
   if (caselessStrCmp(name, "power"))    return AST_POWER;
+  if (caselessStrCmp(name, "pow"))      return AST_POWER;
   if (caselessStrCmp(name, "sqr"))      return AST_FUNCTION_POWER;
   if (caselessStrCmp(name, "sqrt"))     return AST_FUNCTION_ROOT;
   if (caselessStrCmp(name, "root"))     return AST_FUNCTION_ROOT;

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Revision: 15922
          http://sbml.svn.sourceforge.net/sbml/?rev=15922&view=rev
Author:   luciansmith
Date:     2012-06-26 04:41:18 +0000 (Tue, 26 Jun 2012)
Log Message:
-----------
Fix for parsing long strings of digits, plus new tests for 'em.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
    trunk/libsbml/src/sbml/math/test/TestRunner.c

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-06-24 20:17:20 UTC (rev 15921)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-06-26 04:41:18 UTC (rev 15922)
@@ -2274,64 +2274,68 @@
   if (isdigit(cc) || (cc=='.' && isdigit(l3p->input.peek()))) {
     double number;
     long numlong;
-    bool isdouble = false;
     l3p->input.unget();
-    if (cc != '.') {
-      l3p->input >> numlong;
+    streampos numbegin = l3p->input.tellg();
+    l3p->input >> numlong;
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    l3p->input >> number;
+    streampos numend = l3p->input.tellg();
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    bool decimal = false;
+    bool e = false;
+    while (l3p->input.tellg() != numend) {
+      cc = l3p->input.get();
+      if (cc=='.') {
+        decimal = true;
+      }
+      if (cc=='e' || cc=='E') {
+        e = true;
+      }
     }
-    else {
-      numlong = 0;
+    if (!decimal && !e && number == static_cast<double>(numlong)) {
+      sbml_yylval.numlong = numlong;
+      return INTEGER;
     }
-    if (l3p->input.peek() == '.') {
-      isdouble = true;
-      number = numlong;
-      l3p->input.get();
-      if (isdigit(l3p->input.peek())) {
-        streampos numbegin = l3p->input.tellg();
-        l3p->input >> numlong;
-        streampos numend = l3p->input.tellg();
-        if (numend < 0)
-            numend = l3p->input.str().length();
-        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
-        number += fraction;
-      }
+    if (!e) {
+      sbml_yylval.numdouble = number;
+      return DOUBLE;
     }
-    if (l3p->input.peek() == 'e' || l3p->input.peek() == 'E') {
-      l3p->input.get();
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    string mantissa = "";
+    while (l3p->input.tellg() != numend && (isdigit(cc) || cc=='.')) {
       cc = l3p->input.get();
-      if (!(isdigit(cc) || cc=='-' || cc=='+')) {
-        l3p->input.unget();
-        l3p->input.unget();
+      mantissa += cc;
+    }
+    if (cc=='e' || cc=='E') {
+      mantissa.pop_back();
+      if (l3p->input.peek()=='+') {
+        cc = l3p->input.get();
       }
-      else {
-        if (!isdouble) {
-          //It is now!
-          number = numlong;
-        }
-        bool isneg = false;
-        if (cc=='-') {
-          isneg = true;
-        }
-        else if (isdigit(cc)) {
-          l3p->input.unget();
-        }
-        l3p->input >> numlong;
-        if (isneg) {
-          numlong = -numlong;
-        }
-        l3p->exponent = numlong;
-        sbml_yylval.mantissa = number;
-        return E_NOTATION;
+      bool isneg = false;
+      if (l3p->input.peek()=='-') {
+        cc = l3p->input.get();
+        isneg = true;
       }
+      l3p->input >> numlong;
+      if (isneg) {
+        numlong = -numlong;
+      }
+      stringstream mantissastr;
+      mantissastr.str(mantissa);
+      mantissastr >> number;
+      l3p->exponent = numlong;
+      sbml_yylval.mantissa = number;
+      return E_NOTATION;
     }
-    if (isdouble) {
+    else {
+      assert(false); //How did this happen?
+      //This is an error condition, but parsing the value as a double should be sufficient.
       sbml_yylval.numdouble = number;
       return DOUBLE;
     }
-    else {
-      sbml_yylval.numlong = numlong;
-      return INTEGER;
-    }
   }
   else if (cc=='(') {
     streampos rationalbegin = l3p->input.tellg();
@@ -2357,6 +2361,7 @@
         }
       }
     }
+	l3p->input.clear();
     l3p->input.seekg(rationalbegin, ios::beg); // Not actually a rational number.
     return '(';
   }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-06-24 20:17:20 UTC (rev 15921)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-06-26 04:41:18 UTC (rev 15922)
@@ -532,64 +532,68 @@
   if (isdigit(cc) || (cc=='.' && isdigit(l3p->input.peek()))) {
     double number;
     long numlong;
-    bool isdouble = false;
     l3p->input.unget();
-    if (cc != '.') {
-      l3p->input >> numlong;
+    streampos numbegin = l3p->input.tellg();
+    l3p->input >> numlong;
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    l3p->input >> number;
+    streampos numend = l3p->input.tellg();
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    bool decimal = false;
+    bool e = false;
+    while (l3p->input.tellg() != numend) {
+      cc = l3p->input.get();
+      if (cc=='.') {
+        decimal = true;
+      }
+      if (cc=='e' || cc=='E') {
+        e = true;
+      }
     }
-    else {
-      numlong = 0;
+    if (!decimal && !e && number == static_cast<double>(numlong)) {
+      sbml_yylval.numlong = numlong;
+      return INTEGER;
     }
-    if (l3p->input.peek() == '.') {
-      isdouble = true;
-      number = numlong;
-      l3p->input.get();
-      if (isdigit(l3p->input.peek())) {
-        streampos numbegin = l3p->input.tellg();
-        l3p->input >> numlong;
-        streampos numend = l3p->input.tellg();
-        if (numend < 0)
-            numend = l3p->input.str().length();
-        double fraction = numlong/pow(10.0, static_cast<long>(numend-numbegin));
-        number += fraction;
-      }
+    if (!e) {
+      sbml_yylval.numdouble = number;
+      return DOUBLE;
     }
-    if (l3p->input.peek() == 'e' || l3p->input.peek() == 'E') {
-      l3p->input.get();
+    l3p->input.clear();
+    l3p->input.seekg(numbegin);
+    string mantissa = "";
+    while (l3p->input.tellg() != numend && (isdigit(cc) || cc=='.')) {
       cc = l3p->input.get();
-      if (!(isdigit(cc) || cc=='-' || cc=='+')) {
-        l3p->input.unget();
-        l3p->input.unget();
+      mantissa += cc;
+    }
+    if (cc=='e' || cc=='E') {
+      mantissa.pop_back();
+      if (l3p->input.peek()=='+') {
+        cc = l3p->input.get();
       }
-      else {
-        if (!isdouble) {
-          //It is now!
-          number = numlong;
-        }
-        bool isneg = false;
-        if (cc=='-') {
-          isneg = true;
-        }
-        else if (isdigit(cc)) {
-          l3p->input.unget();
-        }
-        l3p->input >> numlong;
-        if (isneg) {
-          numlong = -numlong;
-        }
-        l3p->exponent = numlong;
-        sbml_yylval.mantissa = number;
-        return E_NOTATION;
+      bool isneg = false;
+      if (l3p->input.peek()=='-') {
+        cc = l3p->input.get();
+        isneg = true;
       }
+      l3p->input >> numlong;
+      if (isneg) {
+        numlong = -numlong;
+      }
+      stringstream mantissastr;
+      mantissastr.str(mantissa);
+      mantissastr >> number;
+      l3p->exponent = numlong;
+      sbml_yylval.mantissa = number;
+      return E_NOTATION;
     }
-    if (isdouble) {
+    else {
+      assert(false); //How did this happen?
+      //This is an error condition, but parsing the value as a double should be sufficient.
       sbml_yylval.numdouble = number;
       return DOUBLE;
     }
-    else {
-      sbml_yylval.numlong = numlong;
-      return INTEGER;
-    }
   }
   else if (cc=='(') {
     streampos rationalbegin = l3p->input.tellg();
@@ -615,6 +619,7 @@
         }
       }
     }
+	l3p->input.clear();
     l3p->input.seekg(rationalbegin, ios::beg); // Not actually a rational number.
     return '(';
   }

Modified: trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-06-24 20:17:20 UTC (rev 15921)
+++ trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-06-26 04:41:18 UTC (rev 15922)
@@ -1842,6 +1842,62 @@
 END_TEST
 
 
+START_TEST (test_SBML_parseL3Formula_longint)
+{
+  ASTNode_t *r = SBML_parseL3Formula("166112956810631");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 166112956810631.0, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longdecimal)
+{
+  ASTNode_t *r = SBML_parseL3Formula("0.00166112956810631");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 0.00166112956810631, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longnumberparen)
+{
+  ASTNode_t *r = SBML_parseL3Formula("(0.00166112956810631)");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 0.00166112956810631, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_crazylong)
+{
+  ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890)");
+
+  fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
+  fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
+  fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
 Suite *
 create_suite_L3FormulaParser (void) 
 { 
@@ -1917,7 +1973,10 @@
   tcase_add_test( tcase, test_SBML_parseL3Formula_avogadrosettings);
   tcase_add_test( tcase, test_SBML_parseL3Formula_unitssettings);
   tcase_add_test( tcase, test_SBML_parseL3Formula_power);
-
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longint);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longdecimal);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longnumberparen);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_crazylong);
   suite_add_tcase(suite, tcase);
 
   return suite;

Modified: trunk/libsbml/src/sbml/math/test/TestRunner.c
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestRunner.c	2012-06-24 20:17:20 UTC (rev 15921)
+++ trunk/libsbml/src/sbml/math/test/TestRunner.c	2012-06-26 04:41:18 UTC (rev 15922)
@@ -55,7 +55,7 @@
 Suite *create_suite_ASTNode          (void);
 Suite *create_suite_FormulaFormatter (void);
 Suite *create_suite_FormulaParser    (void);
-//Suite *create_suite_L3FormulaParser  (void);
+Suite *create_suite_L3FormulaParser  (void);
 Suite *create_suite_L3FormulaParserC (void);
 Suite *create_suite_FormulaTokenizer (void);
 Suite *create_suite_ReadMathML       (void);
@@ -115,7 +115,7 @@
 
   srunner_add_suite( runner, create_suite_FormulaFormatter () );
   srunner_add_suite( runner, create_suite_FormulaParser    () );
-//  srunner_add_suite( runner, create_suite_L3FormulaParser  () );
+  srunner_add_suite( runner, create_suite_L3FormulaParser  () );
   srunner_add_suite( runner, create_suite_L3FormulaParserC () );
   srunner_add_suite( runner, create_suite_FormulaTokenizer () );
   srunner_add_suite( runner, create_suite_ReadMathML       () );

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15932
          http://sbml.svn.sourceforge.net/sbml/?rev=15932&view=rev
Author:   luciansmith
Date:     2012-06-29 22:59:29 +0000 (Fri, 29 Jun 2012)
Log Message:
-----------
Removed 'pop_back' since that's a c++11 thing (bah).  Also, better handling of stringstream number parsing failure, which happens when reading a number with an 'e' after it, like "10e"  (which *doesn't* happen with strings like "10x" for some dumb reason.  Sigh.)

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-06-29 14:35:30 UTC (rev 15931)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-06-29 22:59:29 UTC (rev 15932)
@@ -2280,6 +2280,32 @@
     l3p->input.clear();
     l3p->input.seekg(numbegin);
     l3p->input >> number;
+    if (l3p->input.fail()) {
+      //The only reason I know of for this to happen is that there was a number followed by an 'e'.
+      l3p->input.clear(); //clear the error.
+      l3p->input.seekg(numbegin);
+      string failnum = "";
+      cc = l3p->input.get();
+      bool decimal = false;
+      while (l3p->input.good() && (isdigit(cc) || cc=='.')) {
+        failnum += cc;
+        cc = l3p->input.get();
+      }
+      if (cc=='e' || cc=='E') {
+        l3p->input.unget();
+        //We're going to call yylex recursively here, so we need to swap out l3p->input
+        streampos numend = l3p->input.tellg();
+        string tempinput = l3p->input.str();
+        l3p->input.str(failnum);
+        int ret = sbml_yylex();
+        l3p->input.str(tempinput);
+        l3p->input.clear();
+        l3p->input.seekg(numend);
+        return ret;
+      }
+      //Something weird went wrong; give up.
+      return -1;
+    }
     streampos numend = l3p->input.tellg();
     l3p->input.clear();
     l3p->input.seekg(numbegin);
@@ -2304,13 +2330,13 @@
     }
     l3p->input.clear();
     l3p->input.seekg(numbegin);
+    cc = l3p->input.get();
     string mantissa = "";
     while (l3p->input.tellg() != numend && (isdigit(cc) || cc=='.')) {
+      mantissa += cc;
       cc = l3p->input.get();
-      mantissa += cc;
     }
     if (cc=='e' || cc=='E') {
-      mantissa.pop_back();
       if (l3p->input.peek()=='+') {
         cc = l3p->input.get();
       }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-06-29 14:35:30 UTC (rev 15931)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-06-29 22:59:29 UTC (rev 15932)
@@ -538,6 +538,32 @@
     l3p->input.clear();
     l3p->input.seekg(numbegin);
     l3p->input >> number;
+    if (l3p->input.fail()) {
+      //The only reason I know of for this to happen is that there was a number followed by an 'e'.
+      l3p->input.clear(); //clear the error.
+      l3p->input.seekg(numbegin);
+      string failnum = "";
+      cc = l3p->input.get();
+      bool decimal = false;
+      while (l3p->input.good() && (isdigit(cc) || cc=='.')) {
+        failnum += cc;
+        cc = l3p->input.get();
+      }
+      if (cc=='e' || cc=='E') {
+        l3p->input.unget();
+        //We're going to call yylex recursively here, so we need to swap out l3p->input
+        streampos numend = l3p->input.tellg();
+        string tempinput = l3p->input.str();
+        l3p->input.str(failnum);
+        int ret = sbml_yylex();
+        l3p->input.str(tempinput);
+        l3p->input.clear();
+        l3p->input.seekg(numend);
+        return ret;
+      }
+      //Something weird went wrong; give up.
+      return -1;
+    }
     streampos numend = l3p->input.tellg();
     l3p->input.clear();
     l3p->input.seekg(numbegin);
@@ -562,13 +588,13 @@
     }
     l3p->input.clear();
     l3p->input.seekg(numbegin);
+    cc = l3p->input.get();
     string mantissa = "";
     while (l3p->input.tellg() != numend && (isdigit(cc) || cc=='.')) {
+      mantissa += cc;
       cc = l3p->input.get();
-      mantissa += cc;
     }
     if (cc=='e' || cc=='E') {
-      mantissa.pop_back();
       if (l3p->input.peek()=='+') {
         cc = l3p->input.get();
       }

Modified: trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-06-29 14:35:30 UTC (rev 15931)
+++ trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-06-29 22:59:29 UTC (rev 15932)
@@ -1898,6 +1898,146 @@
 END_TEST
 
 
+START_TEST (test_SBML_parseL3Formula_easunit)
+{
+  ASTNode_t *r = SBML_parseL3Formula("1.01e");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 1.01, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_easunitparen)
+{
+  ASTNode_t *r = SBML_parseL3Formula("(1.01e)");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 1.01, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_easunitint)
+{
+  ASTNode_t *r = SBML_parseL3Formula("101e");
+
+  fail_unless( ASTNode_getType       (r) == AST_INTEGER, NULL );
+  fail_unless( ASTNode_getInteger    (r) == 101, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "e"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_ergunit)
+{
+  ASTNode_t *r = SBML_parseL3Formula("101erg");
+
+  fail_unless( ASTNode_getType       (r) == AST_INTEGER, NULL );
+  fail_unless( ASTNode_getInteger    (r) == 101, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longinterg)
+{
+  ASTNode_t *r = SBML_parseL3Formula("166112956810631erg");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 166112956810631.0, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longdecimalerg)
+{
+  ASTNode_t *r = SBML_parseL3Formula("0.00166112956810631erg");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 0.00166112956810631, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_longnumberparenerg)
+{
+  ASTNode_t *r = SBML_parseL3Formula("(0.00166112956810631erg)");
+
+  fail_unless( ASTNode_getType       (r) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (r) == 0.00166112956810631, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 0  , NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_crazylongerg)
+{
+  ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890erg)");
+
+  fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
+  fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
+  fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
+  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+
+  ASTNode_free(r);
+
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_wrongnum)
+{
+  ASTNode_t *r = SBML_parseL3Formula("1.2.4");
+
+  fail_unless(r == NULL, NULL);
+  fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1.2.4' at position 5:  syntax error, unexpected number"), NULL);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_wrongnum2)
+{
+  ASTNode_t *r = SBML_parseL3Formula("1.2.");
+
+  fail_unless(r == NULL, NULL);
+  fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '1.2.' at position 4:  syntax error, unexpected $undefined"), NULL);
+}
+END_TEST
+
+
 Suite *
 create_suite_L3FormulaParser (void) 
 { 
@@ -1977,6 +2117,16 @@
   tcase_add_test( tcase, test_SBML_parseL3Formula_longdecimal);
   tcase_add_test( tcase, test_SBML_parseL3Formula_longnumberparen);
   tcase_add_test( tcase, test_SBML_parseL3Formula_crazylong);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_easunit);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_easunitparen);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_easunitint);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_ergunit);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longinterg);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longdecimalerg);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_longnumberparenerg);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_crazylongerg);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum2);
   suite_add_tcase(suite, tcase);
 
   return suite;

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 15973
          http://sbml.svn.sourceforge.net/sbml/?rev=15973&view=rev
Author:   luciansmith
Date:     2012-07-10 19:26:26 +0000 (Tue, 10 Jul 2012)
Log Message:
-----------
Fix for (perhaps) 64-bit OSes and parsing long strings of numbers; also different tests depending on whether parsing ridiculously long strings of numbers with stringstream results in inf (windows) or an error (ubuntu).

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-10 13:58:46 UTC (rev 15972)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-10 19:26:26 UTC (rev 15973)
@@ -1,9 +1,8 @@
-/* A Bison parser, made by GNU Bison 2.4.2.  */
+/* A Bison parser, made by GNU Bison 2.5.  */
 
-/* Skeleton implementation for Bison's Yacc-like parsers in C
+/* Bison implementation for Yacc-like parsers in C
    
-      Copyright (C) 1984, 1989-1990, 2000-2006, 2009-2010 Free Software
-   Foundation, Inc.
+      Copyright (C) 1984, 1989-1990, 2000-2011 Free Software Foundation, Inc.
    
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -45,7 +44,7 @@
 #define YYBISON 1
 
 /* Bison version.  */
-#define YYBISON_VERSION "2.4.2"
+#define YYBISON_VERSION "2.5"
 
 /* Skeleton name.  */
 #define YYSKELETON_NAME "yacc.c"
@@ -64,7 +63,7 @@
 
 /* "%code top" blocks.  */
 
-/* Line 171 of yacc.c  */
+/* Line 250 of yacc.c  */
 #line 52 "L3Parser.ypp"
 
 
@@ -72,8 +71,8 @@
 
 
 
-/* Line 171 of yacc.c  */
-#line 77 "L3Parser.cpp"
+/* Line 250 of yacc.c  */
+#line 76 "L3Parser.cpp"
 /* Substitute the variable and function names.  */
 #define yyparse         sbml_yyparse
 #define yylex           sbml_yylex
@@ -86,7 +85,7 @@
 
 /* Copy the first part of user declarations.  */
 
-/* Line 189 of yacc.c  */
+/* Line 268 of yacc.c  */
 #line 57 "L3Parser.ypp"
 
 /**
@@ -296,8 +295,8 @@
   int sbml_yylloc_last_position = 1;
 
 
-/* Line 189 of yacc.c  */
-#line 301 "L3Parser.cpp"
+/* Line 268 of yacc.c  */
+#line 300 "L3Parser.cpp"
 
 /* Enabling traces.  */
 #ifndef YYDEBUG
@@ -341,7 +340,7 @@
 typedef union YYSTYPE
 {
 
-/* Line 214 of yacc.c  */
+/* Line 293 of yacc.c  */
 #line 266 "L3Parser.ypp"
 
   ASTNode* astnode;
@@ -354,8 +353,8 @@
 
 
 
-/* Line 214 of yacc.c  */
-#line 359 "L3Parser.cpp"
+/* Line 293 of yacc.c  */
+#line 358 "L3Parser.cpp"
 } YYSTYPE;
 # define YYSTYPE_IS_TRIVIAL 1
 # define yystype YYSTYPE /* obsolescent; will be withdrawn */
@@ -366,8 +365,8 @@
 /* Copy the second part of user declarations.  */
 
 
-/* Line 264 of yacc.c  */
-#line 371 "L3Parser.cpp"
+/* Line 343 of yacc.c  */
+#line 370 "L3Parser.cpp"
 
 #ifdef short
 # undef short
@@ -470,11 +469,11 @@
 #    define alloca _alloca
 #   else
 #    define YYSTACK_ALLOC alloca
-#    if ! defined _ALLOCA_H && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
+#    if ! defined _ALLOCA_H && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 #     include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
-#     ifndef _STDLIB_H
-#      define _STDLIB_H 1
+#     ifndef EXIT_SUCCESS
+#      define EXIT_SUCCESS 0
 #     endif
 #    endif
 #   endif
@@ -497,24 +496,24 @@
 #  ifndef YYSTACK_ALLOC_MAXIMUM
 #   define YYSTACK_ALLOC_MAXIMUM YYSIZE_MAXIMUM
 #  endif
-#  if (defined __cplusplus && ! defined _STDLIB_H \
+#  if (defined __cplusplus && ! defined EXIT_SUCCESS \
        && ! ((defined YYMALLOC || defined malloc) \
 	     && (defined YYFREE || defined free)))
 #   include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
-#   ifndef _STDLIB_H
-#    define _STDLIB_H 1
+#   ifndef EXIT_SUCCESS
+#    define EXIT_SUCCESS 0
 #   endif
 #  endif
 #  ifndef YYMALLOC
 #   define YYMALLOC malloc
-#   if ! defined malloc && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
+#   if ! defined malloc && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 void *malloc (YYSIZE_T); /* INFRINGES ON USER NAME SPACE */
 #   endif
 #  endif
 #  ifndef YYFREE
 #   define YYFREE free
-#   if ! defined free && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
+#   if ! defined free && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 void free (void *); /* INFRINGES ON USER NAME SPACE */
 #   endif
@@ -543,23 +542,7 @@
      ((N) * (sizeof (yytype_int16) + sizeof (YYSTYPE)) \
       + YYSTACK_GAP_MAXIMUM)
 
-/* Copy COUNT objects from FROM to TO.  The source and destination do
-   not overlap.  */
-# ifndef YYCOPY
-#  if defined __GNUC__ && 1 < __GNUC__
-#   define YYCOPY(To, From, Count) \
-      __builtin_memcpy (To, From, (Count) * sizeof (*(From)))
-#  else
-#   define YYCOPY(To, From, Count)		\
-      do					\
-	{					\
-	  YYSIZE_T yyi;				\
-	  for (yyi = 0; yyi < (Count); yyi++)	\
-	    (To)[yyi] = (From)[yyi];		\
-	}					\
-      while (YYID (0))
-#  endif
-# endif
+# define YYCOPY_NEEDED 1
 
 /* Relocate STACK from its old location to the new one.  The
    local variables YYSIZE and YYSTACKSIZE give the old and new number of
@@ -579,6 +562,26 @@
 
 #endif
 
+#if defined YYCOPY_NEEDED && YYCOPY_NEEDED
+/* Copy COUNT objects from FROM to TO.  The source and destination do
+   not overlap.  */
+# ifndef YYCOPY
+#  if defined __GNUC__ && 1 < __GNUC__
+#   define YYCOPY(To, From, Count) \
+      __builtin_memcpy (To, From, (Count) * sizeof (*(From)))
+#  else
+#   define YYCOPY(To, From, Count)		\
+      do					\
+	{					\
+	  YYSIZE_T yyi;				\
+	  for (yyi = 0; yyi < (Count); yyi++)	\
+	    (To)[yyi] = (From)[yyi];		\
+	}					\
+      while (YYID (0))
+#  endif
+# endif
+#endif /* !YYCOPY_NEEDED */
+
 /* YYFINAL -- State number of the termination state.  */
 #define YYFINAL  17
 /* YYLAST -- Last index in YYTABLE.  */
@@ -713,8 +716,8 @@
        1,     1,     1,     2,     1,     3
 };
 
-/* YYDEFACT[STATE-NAME] -- Default rule to reduce with in state
-   STATE-NUM when YYTABLE doesn't specify something else to do.  Zero
+/* YYDEFACT[STATE-NAME] -- Default reduction number in state STATE-NUM.
+   Performed when YYTABLE doesn't specify something else to do.  Zero
    means the default is an error.  */
 static const yytype_uint8 yydefact[] =
 {
@@ -755,8 +758,7 @@
 
 /* YYTABLE[YYPACT[STATE-NUM]].  What to do in state STATE-NUM.  If
    positive, shift that token.  If negative, reduce the rule which
-   number is the opposite.  If zero, do what YYDEFACT says.
-   If YYTABLE_NINF, syntax error.  */
+   number is the opposite.  If YYTABLE_NINF, syntax error.  */
 #define YYTABLE_NINF -4
 static const yytype_int8 yytable[] =
 {
@@ -780,6 +782,12 @@
       30
 };
 
+#define yypact_value_is_default(yystate) \
+  ((yystate) == (-17))
+
+#define yytable_value_is_error(yytable_value) \
+  YYID (0)
+
 static const yytype_int8 yycheck[] =
 {
        2,     3,    12,    13,    14,    15,    22,     9,    23,    24,
@@ -848,7 +856,6 @@
     {								\
       yychar = (Token);						\
       yylval = (Value);						\
-      yytoken = YYTRANSLATE (yychar);				\
       YYPOPSTACK (1);						\
       goto yybackup;						\
     }								\
@@ -890,19 +897,10 @@
 #endif
 
 
-/* YY_LOCATION_PRINT -- Print the location on the stream.
-   This macro was not mandated originally: define only if we know
-   we won't break user code: when these are the locations we know.  */
+/* This macro is provided for backward compatibility. */
 
 #ifndef YY_LOCATION_PRINT
-# if defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL
-#  define YY_LOCATION_PRINT(File, Loc)			\
-     fprintf (File, "%d.%d-%d.%d",			\
-	      (Loc).first_line, (Loc).first_column,	\
-	      (Loc).last_line,  (Loc).last_column)
-# else
-#  define YY_LOCATION_PRINT(File, Loc) ((void) 0)
-# endif
+# define YY_LOCATION_PRINT(File, Loc) ((void) 0)
 #endif
 
 
@@ -1094,7 +1092,6 @@
 # define YYMAXDEPTH 10000
 #endif
 
-
 
 #if YYERROR_VERBOSE
 
@@ -1197,115 +1194,142 @@
 }
 # endif
 
-/* Copy into YYRESULT an error message about the unexpected token
-   YYCHAR while in state YYSTATE.  Return the number of bytes copied,
-   including the terminating null byte.  If YYRESULT is null, do not
-   copy anything; just return the number of bytes that would be
-   copied.  As a special case, return 0 if an ordinary "syntax error"
-   message will do.  Return YYSIZE_MAXIMUM if overflow occurs during
-   size calculation.  */
-static YYSIZE_T
-yysyntax_error (char *yyresult, int yystate, int yychar)
+/* Copy into *YYMSG, which is of size *YYMSG_ALLOC, an error message
+   about the unexpected token YYTOKEN for the state stack whose top is
+   YYSSP.
+
+   Return 0 if *YYMSG was successfully written.  Return 1 if *YYMSG is
+   not large enough to hold the message.  In that case, also set
+   *YYMSG_ALLOC to the required number of bytes.  Return 2 if the
+   required number of bytes is too large to store.  */
+static int
+yysyntax_error (YYSIZE_T *yymsg_alloc, char **yymsg,
+                yytype_int16 *yyssp, int yytoken)
 {
-  int yyn = yypact[yystate];
+  YYSIZE_T yysize0 = yytnamerr (0, yytname[yytoken]);
+  YYSIZE_T yysize = yysize0;
+  YYSIZE_T yysize1;
+  enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
+  /* Internationalized format string. */
+  const char *yyformat = 0;
+  /* Arguments of yyformat. */
+  char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
+  /* Number of reported tokens (one for the "unexpected", one per
+     "expected"). */
+  int yycount = 0;
 
-  if (! (YYPACT_NINF < yyn && yyn <= YYLAST))
-    return 0;
-  else
+  /* There are many possibilities here to consider:
+     - Assume YYFAIL is not used.  It's too flawed to consider.  See
+       <http://lists.gnu.org/archive/html/bison-patches/2009-12/msg00024.html>
+       for details.  YYERROR is fine as it does not invoke this
+       function.
+     - If this state is a consistent state with a default action, then
+       the only way this function was invoked is if the default action
+       is an error action.  In that case, don't check for expected
+       tokens because there are none.
+     - The only way there can be no lookahead present (in yychar) is if
+       this state is a consistent state with a default action.  Thus,
+       detecting the absence of a lookahead is sufficient to determine
+       that there is no unexpected or expected token to report.  In that
+       case, just report a simple "syntax error".
+     - Don't assume there isn't a lookahead just because this state is a
+       consistent state with a default action.  There might have been a
+       previous inconsistent state, consistent state with a non-default
+       action, or user semantic action that manipulated yychar.
+     - Of course, the expected token list depends on states to have
+       correct lookahead information, and it depends on the parser not
+       to perform extra reductions after fetching a lookahead from the
+       scanner and before detecting a syntax error.  Thus, state merging
+       (from LALR or IELR) and default reductions corrupt the expected
+       token list.  However, the list is correct for canonical LR with
+       one exception: it will still contain any token that will not be
+       accepted due to an error action in a later state.
+  */
+  if (yytoken != YYEMPTY)
     {
-      int yytype = YYTRANSLATE (yychar);
-      YYSIZE_T yysize0 = yytnamerr (0, yytname[yytype]);
-      YYSIZE_T yysize = yysize0;
-      YYSIZE_T yysize1;
-      int yysize_overflow = 0;
-      enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
-      char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
-      int yyx;
+      int yyn = yypact[*yyssp];
+      yyarg[yycount++] = yytname[yytoken];
+      if (!yypact_value_is_default (yyn))
+        {
+          /* Start YYX at -YYN if negative to avoid negative indexes in
+             YYCHECK.  In other words, skip the first -YYN actions for
+             this state because they are default actions.  */
+          int yyxbegin = yyn < 0 ? -yyn : 0;
+          /* Stay within bounds of both yycheck and yytname.  */
+          int yychecklim = YYLAST - yyn + 1;
+          int yyxend = yychecklim < YYNTOKENS ? yychecklim : YYNTOKENS;
+          int yyx;
 
-# if 0
-      /* This is so xgettext sees the translatable formats that are
-	 constructed on the fly.  */
-      YY_("syntax error, unexpected %s");
-      YY_("syntax error, unexpected %s, expecting %s");
-      YY_("syntax error, unexpected %s, expecting %s or %s");
-      YY_("syntax error, unexpected %s, expecting %s or %s or %s");
-      YY_("syntax error, unexpected %s, expecting %s or %s or %s or %s");
-# endif
-      char *yyfmt;
-      char const *yyf;
-      static char const yyunexpected[] = "syntax error, unexpected %s";
-      static char const yyexpecting[] = ", expecting %s";
-      static char const yyor[] = " or %s";
-      char yyformat[sizeof yyunexpected
-		    + sizeof yyexpecting - 1
-		    + ((YYERROR_VERBOSE_ARGS_MAXIMUM - 2)
-		       * (sizeof yyor - 1))];
-      char const *yyprefix = yyexpecting;
+          for (yyx = yyxbegin; yyx < yyxend; ++yyx)
+            if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR
+                && !yytable_value_is_error (yytable[yyx + yyn]))
+              {
+                if (yycount == YYERROR_VERBOSE_ARGS_MAXIMUM)
+                  {
+                    yycount = 1;
+                    yysize = yysize0;
+                    break;
+                  }
+                yyarg[yycount++] = yytname[yyx];
+                yysize1 = yysize + yytnamerr (0, yytname[yyx]);
+                if (! (yysize <= yysize1
+                       && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+                  return 2;
+                yysize = yysize1;
+              }
+        }
+    }
 
-      /* Start YYX at -YYN if negative to avoid negative indexes in
-	 YYCHECK.  */
-      int yyxbegin = yyn < 0 ? -yyn : 0;
+  switch (yycount)
+    {
+# define YYCASE_(N, S)                      \
+      case N:                               \
+        yyformat = S;                       \
+      break
+      YYCASE_(0, YY_("syntax error"));
+      YYCASE_(1, YY_("syntax error, unexpected %s"));
+      YYCASE_(2, YY_("syntax error, unexpected %s, expecting %s"));
+      YYCASE_(3, YY_("syntax error, unexpected %s, expecting %s or %s"));
+      YYCASE_(4, YY_("syntax error, unexpected %s, expecting %s or %s or %s"));
+      YYCASE_(5, YY_("syntax error, unexpected %s, expecting %s or %s or %s or %s"));
+# undef YYCASE_
+    }
 
-      /* Stay within bounds of both yycheck and yytname.  */
-      int yychecklim = YYLAST - yyn + 1;
-      int yyxend = yychecklim < YYNTOKENS ? yychecklim : YYNTOKENS;
-      int yycount = 1;
+  yysize1 = yysize + yystrlen (yyformat);
+  if (! (yysize <= yysize1 && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
+    return 2;
+  yysize = yysize1;
 
-      yyarg[0] = yytname[yytype];
-      yyfmt = yystpcpy (yyformat, yyunexpected);
+  if (*yymsg_alloc < yysize)
+    {
+      *yymsg_alloc = 2 * yysize;
+      if (! (yysize <= *yymsg_alloc
+             && *yymsg_alloc <= YYSTACK_ALLOC_MAXIMUM))
+        *yymsg_alloc = YYSTACK_ALLOC_MAXIMUM;
+      return 1;
+    }
 
-      for (yyx = yyxbegin; yyx < yyxend; ++yyx)
-	if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR)
-	  {
-	    if (yycount == YYERROR_VERBOSE_ARGS_MAXIMUM)
-	      {
-		yycount = 1;
-		yysize = yysize0;
-		yyformat[sizeof yyunexpected - 1] = '\0';
-		break;
-	      }
-	    yyarg[yycount++] = yytname[yyx];
-	    yysize1 = yysize + yytnamerr (0, yytname[yyx]);
-	    yysize_overflow |= (yysize1 < yysize);
-	    yysize = yysize1;
-	    yyfmt = yystpcpy (yyfmt, yyprefix);
-	    yyprefix = yyor;
-	  }
-
-      yyf = YY_(yyformat);
-      yysize1 = yysize + yystrlen (yyf);
-      yysize_overflow |= (yysize1 < yysize);
-      yysize = yysize1;
-
-      if (yysize_overflow)
-	return YYSIZE_MAXIMUM;
-
-      if (yyresult)
-	{
-	  /* Avoid sprintf, as that infringes on the user's name space.
-	     Don't have undefined behavior even if the translation
-	     produced a string with the wrong number of "%s"s.  */
-	  char *yyp = yyresult;
-	  int yyi = 0;
-	  while ((*yyp = *yyf) != '\0')
-	    {
-	      if (*yyp == '%' && yyf[1] == 's' && yyi < yycount)
-		{
-		  yyp += yytnamerr (yyp, yyarg[yyi++]);
-		  yyf += 2;
-		}
-	      else
-		{
-		  yyp++;
-		  yyf++;
-		}
-	    }
-	}
-      return yysize;
-    }
+  /* Avoid sprintf, as that infringes on the user's name space.
+     Don't have undefined behavior even if the translation
+     produced a string with the wrong number of "%s"s.  */
+  {
+    char *yyp = *yymsg;
+    int yyi = 0;
+    while ((*yyp = *yyformat) != '\0')
+      if (*yyp == '%' && yyformat[1] == 's' && yyi < yycount)
+        {
+          yyp += yytnamerr (yyp, yyarg[yyi++]);
+          yyformat += 2;
+        }
+      else
+        {
+          yyp++;
+          yyformat++;
+        }
+  }
+  return 0;
 }
 #endif /* YYERROR_VERBOSE */
-
 
 /*-----------------------------------------------.
 | Release the memory associated to this symbol.  |
@@ -1338,6 +1362,7 @@
     }
 }
 
+
 /* Prevent warnings from -Wmissing-prototypes.  */
 #ifdef YYPARSE_PARAM
 #if defined __STDC__ || defined __cplusplus
@@ -1364,11 +1389,10 @@
 int yynerrs;
 
 
+/*----------.
+| yyparse.  |
+`----------*/
 
-/*-------------------------.
-| yyparse or yypush_parse.  |
-`-------------------------*/
-
 #ifdef YYPARSE_PARAM
 #if (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
@@ -1391,8 +1415,6 @@
 #endif
 #endif
 {
-
-
     int yystate;
     /* Number of tokens to shift before error messages enabled.  */
     int yyerrstatus;
@@ -1547,7 +1569,7 @@
 
   /* First try to decide what to do without reference to lookahead token.  */
   yyn = yypact[yystate];
-  if (yyn == YYPACT_NINF)
+  if (yypact_value_is_default (yyn))
     goto yydefault;
 
   /* Not known => get a lookahead token if don't already have one.  */
@@ -1578,8 +1600,8 @@
   yyn = yytable[yyn];
   if (yyn <= 0)
     {
-      if (yyn == 0 || yyn == YYTABLE_NINF)
-	goto yyerrlab;
+      if (yytable_value_is_error (yyn))
+        goto yyerrlab;
       yyn = -yyn;
       goto yyreduce;
     }
@@ -1634,35 +1656,35 @@
     {
         case 3:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 299 "L3Parser.ypp"
     {l3p->outputNode = (yyvsp[(1) - (1)].astnode);}
     break;
 
   case 4:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 300 "L3Parser.ypp"
-    {;}
+    {}
     break;
 
   case 5:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 301 "L3Parser.ypp"
-    {delete (yyvsp[(1) - (2)].astnode);;}
+    {delete (yyvsp[(1) - (2)].astnode);}
     break;
 
   case 6:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 304 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(1) - (1)].astnode);;}
+    {(yyval.astnode) = (yyvsp[(1) - (1)].astnode);}
     break;
 
   case 7:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 305 "L3Parser.ypp"
     {
                    (yyval.astnode) = new ASTNode();
@@ -1689,26 +1711,26 @@
                        (yyval.astnode)->setType(AST_NAME);
                      }
                    }
-        ;}
+        }
     break;
 
   case 8:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 331 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(2) - (3)].astnode);;}
+    {(yyval.astnode) = (yyvsp[(2) - (3)].astnode);}
     break;
 
   case 9:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 332 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_POWER); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_POWER); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
   case 10:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 333 "L3Parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_TIMES) {
@@ -1720,12 +1742,12 @@
                     (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode));
                     (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));
                   }
-                ;}
+                }
     break;
 
   case 11:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 344 "L3Parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_PLUS) {
@@ -1737,47 +1759,47 @@
                     (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode));
                     (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));
                   }
-                ;}
+                }
     break;
 
   case 12:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 355 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_DIVIDE); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_DIVIDE); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
   case 13:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 356 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_MINUS); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_MINUS); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
   case 14:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 357 "L3Parser.ypp"
-    {(yyval.astnode) = l3p->createModuloTree((yyvsp[(1) - (3)].astnode), (yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = l3p->createModuloTree((yyvsp[(1) - (3)].astnode), (yyvsp[(3) - (3)].astnode));}
     break;
 
   case 15:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 358 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
   case 16:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 359 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
   case 17:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 360 "L3Parser.ypp"
     {
                   if (l3p->collapseminus) {
@@ -1811,75 +1833,75 @@
                     (yyval.astnode) = new ASTNode(AST_MINUS);
                     (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));
                   }
-                ;}
+                }
     break;
 
   case 18:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 393 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 19:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 394 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 20:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 395 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_EQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_EQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 21:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 396 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 22:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 397 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 23:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 398 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 24:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 399 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_AND); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_AND); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 25:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 400 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_OR); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_OR); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
     break;
 
   case 26:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 401 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_NOT); (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_NOT); (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));}
     break;
 
   case 27:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 402 "L3Parser.ypp"
     {
                    (yyval.astnode) = new ASTNode(AST_FUNCTION);
@@ -1891,12 +1913,12 @@
                      if (type != AST_UNKNOWN) (yyval.astnode)->setType(type);
                      if (l3p->checkNumArguments((yyval.astnode))) YYABORT;
                    }
-        ;}
+        }
     break;
 
   case 28:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 413 "L3Parser.ypp"
     {
                    (yyval.astnode) = (yyvsp[(3) - (4)].astnode);
@@ -1946,40 +1968,40 @@
                      }
                    }
                    if (l3p->checkNumArguments((yyval.astnode))) YYABORT;
-        ;}
+        }
     break;
 
   case 29:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 464 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));;}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));}
     break;
 
   case 30:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 465 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);;}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);}
     break;
 
   case 31:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 466 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));;}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));}
     break;
 
   case 32:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 467 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);;}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);}
     break;
 
   case 33:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 468 "L3Parser.ypp"
     {
                   (yyval.astnode) = (yyvsp[(1) - (2)].astnode);
@@ -1992,29 +2014,40 @@
                     YYERROR;
                   }
                   (yyval.astnode)->setUnits(*(yyvsp[(2) - (2)].word));
-               ;}
+               }
     break;
 
   case 34:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 482 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));;}
+    {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));}
     break;
 
   case 35:
 
-/* Line 1464 of yacc.c  */
+/* Line 1806 of yacc.c  */
 #line 483 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
+    {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
     break;
 
 
 
-/* Line 1464 of yacc.c  */
-#line 2016 "L3Parser.cpp"
+/* Line 1806 of yacc.c  */
+#line 2038 "L3Parser.cpp"
       default: break;
     }
+  /* User semantic actions sometimes alter yychar, and that requires
+     that yytoken be updated with the new translation.  We take the
+     approach of translating immediately before every use of yytoken.
+     One alternative is translating here after every semantic action,
+     but that translation would be missed if the semantic action invokes
+     YYABORT, YYACCEPT, or YYERROR immediately after altering yychar or
+     if it invokes YYBACKUP.  In the case of YYABORT or YYACCEPT, an
+     incorrect destructor might then be invoked immediately.  In the
+     case of YYERROR or YYBACKUP, subsequent parser actions might lead
+     to an incorrect destructor call or verbose syntax error message
+     before the lookahead is translated.  */
   YY_SYMBOL_PRINT ("-> $$ =", yyr1[yyn], &yyval, &yyloc);
 
   YYPOPSTACK (yylen);
@@ -2042,6 +2075,10 @@
 | yyerrlab -- here on detecting error |
 `------------------------------------*/
 yyerrlab:
+  /* Make sure we have latest lookahead translation.  See comments at
+     user semantic actions for why this is necessary.  */
+  yytoken = yychar == YYEMPTY ? YYEMPTY : YYTRANSLATE (yychar);
+
   /* If not already recovering from an error, report this error.  */
   if (!yyerrstatus)
     {
@@ -2049,37 +2086,36 @@
 #if ! YYERROR_VERBOSE
       yyerror (YY_("syntax error"));
 #else
+# define YYSYNTAX_ERROR yysyntax_error (&yymsg_alloc, &yymsg, \
+                                        yyssp, yytoken)
       {
-	YYSIZE_T yysize = yysyntax_error (0, yystate, yychar);
-	if (yymsg_alloc < yysize && yymsg_alloc < YYSTACK_ALLOC_MAXIMUM)
-	  {
-	    YYSIZE_T yyalloc = 2 * yysize;
-	    if (! (yysize <= yyalloc && yyalloc <= YYSTACK_ALLOC_MAXIMUM))
-	      yyalloc = YYSTACK_ALLOC_MAXIMUM;
-	    if (yymsg != yymsgbuf)
-	      YYSTACK_FREE (yymsg);
-	    yymsg = (char *) YYSTACK_ALLOC (yyalloc);
-	    if (yymsg)
-	      yymsg_alloc = yyalloc;
-	    else
-	      {
-		yymsg = yymsgbuf;
-		yymsg_alloc = sizeof yymsgbuf;
-	      }
-	  }
-
-	if (0 < yysize && yysize <= yymsg_alloc)
-	  {
-	    (void) yysyntax_error (yymsg, yystate, yychar);
-	    yyerror (yymsg);
-	  }
-	else
-	  {
-	    yyerror (YY_("syntax error"));
-	    if (yysize != 0)
-	      goto yyexhaustedlab;
-	  }
+        char const *yymsgp = YY_("syntax error");
+        int yysyntax_error_status;
+        yysyntax_error_status = YYSYNTAX_ERROR;
+        if (yysyntax_error_status == 0)
+          yymsgp = yymsg;
+        else if (yysyntax_error_status == 1)
+          {
+            if (yymsg != yymsgbuf)
+              YYSTACK_FREE (yymsg);
+            yymsg = (char *) YYSTACK_ALLOC (yymsg_alloc);
+            if (!yymsg)
+              {
+                yymsg = yymsgbuf;
+                yymsg_alloc = sizeof yymsgbuf;
+                yysyntax_error_status = 2;
+              }
+            else
+              {
+                yysyntax_error_status = YYSYNTAX_ERROR;
+                yymsgp = yymsg;
+              }
+          }
+        yyerror (yymsgp);
+        if (yysyntax_error_status == 2)
+          goto yyexhaustedlab;
       }
+# undef YYSYNTAX_ERROR
 #endif
     }
 
@@ -2138,7 +2174,7 @@
   for (;;)
     {
       yyn = yypact[yystate];
-      if (yyn != YYPACT_NINF)
+      if (!yypact_value_is_default (yyn))
 	{
 	  yyn += YYTERROR;
 	  if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
@@ -2197,8 +2233,13 @@
 
 yyreturn:
   if (yychar != YYEMPTY)
-     yydestruct ("Cleanup: discarding lookahead",
-		 yytoken, &yylval);
+    {
+      /* Make sure we have latest lookahead translation.  See comments at
+         user semantic actions for why this is necessary.  */
+      yytoken = YYTRANSLATE (yychar);
+      yydestruct ("Cleanup: discarding lookahead",
+                  yytoken, &yylval);
+    }
   /* Do not reclaim the symbols of the rule which action triggered
      this YYABORT or YYACCEPT.  */
   YYPOPSTACK (yylen);
@@ -2223,7 +2264,7 @@
 
 
 
-/* Line 1684 of yacc.c  */
+/* Line 2067 of yacc.c  */
 #line 486 "L3Parser.ypp"
 
 
@@ -2320,7 +2361,7 @@
         e = true;
       }
     }
-    if (!decimal && !e && number == static_cast<double>(numlong)) {
+    if (!decimal && !e && number == static_cast<double>(numlong) && numlong <= SBML_INT_MAX) {
       sbml_yylval.numlong = numlong;
       return INTEGER;
     }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-10 13:58:46 UTC (rev 15972)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-10 19:26:26 UTC (rev 15973)
@@ -296,7 +296,7 @@
 %% /* The grammar: */
 
 input:          /* empty */
-        |       node {l3p->outputNode = $1}
+        |       node {l3p->outputNode = $1;}
         |       error {}
         |       node error {delete $1;}
         ;
@@ -578,7 +578,7 @@
         e = true;
       }
     }
-    if (!decimal && !e && number == static_cast<double>(numlong)) {
+    if (!decimal && !e && number == static_cast<double>(numlong) && numlong <= SBML_INT_MAX) {
       sbml_yylval.numlong = numlong;
       return INTEGER;
     }

Modified: trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-07-10 13:58:46 UTC (rev 15972)
+++ trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-07-10 19:26:26 UTC (rev 15973)
@@ -1888,12 +1888,16 @@
 {
   ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890)");
 
-  fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
-  fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
-  fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
+  if (r==NULL) {
+    fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890)' at position 312:  syntax error, unexpected end of string"), NULL);
+  }
+  else {
+    fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
+    fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
+    fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
 
-  ASTNode_free(r);
-
+    ASTNode_free(r);
+  }
 }
 END_TEST
 
@@ -2007,13 +2011,17 @@
 {
   ASTNode_t *r = SBML_parseL3Formula("(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890erg)");
 
-  fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
-  fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
-  fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
-  fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
+  if (r==NULL) {
+    fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input '(1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890erg)' at position 311:  syntax error, unexpected end of string"), NULL);
+  }
+  else {
+    fail_unless( ASTNode_getType(r)             == AST_REAL, NULL );
+    fail_unless( util_isInf(ASTNode_getReal(r)) ==  1, NULL );
+    fail_unless( ASTNode_getNumChildren(r)      ==  0, NULL );
+    fail_unless( !strcmp(ASTNode_getUnits(r), "erg"), NULL );
 
-  ASTNode_free(r);
-
+    ASTNode_free(r);
+  }
 }
 END_TEST
 

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16022
          http://sbml.svn.sourceforge.net/sbml/?rev=16022&view=rev
Author:   luciansmith
Date:     2012-07-18 21:13:11 +0000 (Wed, 18 Jul 2012)
Log Message:
-----------
Fix for gcc stringstream on MacOS eating a trailing 'e' for numbers.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-18 12:58:01 UTC (rev 16021)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-18 21:13:11 UTC (rev 16022)
@@ -1,8 +1,9 @@
-/* A Bison parser, made by GNU Bison 2.5.  */
+/* A Bison parser, made by GNU Bison 2.4.2.  */
 
-/* Bison implementation for Yacc-like parsers in C
+/* Skeleton implementation for Bison's Yacc-like parsers in C
    
-      Copyright (C) 1984, 1989-1990, 2000-2011 Free Software Foundation, Inc.
+      Copyright (C) 1984, 1989-1990, 2000-2006, 2009-2010 Free Software
+   Foundation, Inc.
    
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
@@ -44,7 +45,7 @@
 #define YYBISON 1
 
 /* Bison version.  */
-#define YYBISON_VERSION "2.5"
+#define YYBISON_VERSION "2.4.2"
 
 /* Skeleton name.  */
 #define YYSKELETON_NAME "yacc.c"
@@ -63,7 +64,7 @@
 
 /* "%code top" blocks.  */
 
-/* Line 250 of yacc.c  */
+/* Line 171 of yacc.c  */
 #line 52 "L3Parser.ypp"
 
 
@@ -71,8 +72,8 @@
 
 
 
-/* Line 250 of yacc.c  */
-#line 76 "L3Parser.cpp"
+/* Line 171 of yacc.c  */
+#line 77 "L3Parser.cpp"
 /* Substitute the variable and function names.  */
 #define yyparse         sbml_yyparse
 #define yylex           sbml_yylex
@@ -85,7 +86,7 @@
 
 /* Copy the first part of user declarations.  */
 
-/* Line 268 of yacc.c  */
+/* Line 189 of yacc.c  */
 #line 57 "L3Parser.ypp"
 
 /**
@@ -295,8 +296,8 @@
   int sbml_yylloc_last_position = 1;
 
 
-/* Line 268 of yacc.c  */
-#line 300 "L3Parser.cpp"
+/* Line 189 of yacc.c  */
+#line 301 "L3Parser.cpp"
 
 /* Enabling traces.  */
 #ifndef YYDEBUG
@@ -340,7 +341,7 @@
 typedef union YYSTYPE
 {
 
-/* Line 293 of yacc.c  */
+/* Line 214 of yacc.c  */
 #line 266 "L3Parser.ypp"
 
   ASTNode* astnode;
@@ -353,8 +354,8 @@
 
 
 
-/* Line 293 of yacc.c  */
-#line 358 "L3Parser.cpp"
+/* Line 214 of yacc.c  */
+#line 359 "L3Parser.cpp"
 } YYSTYPE;
 # define YYSTYPE_IS_TRIVIAL 1
 # define yystype YYSTYPE /* obsolescent; will be withdrawn */
@@ -365,8 +366,8 @@
 /* Copy the second part of user declarations.  */
 
 
-/* Line 343 of yacc.c  */
-#line 370 "L3Parser.cpp"
+/* Line 264 of yacc.c  */
+#line 371 "L3Parser.cpp"
 
 #ifdef short
 # undef short
@@ -469,11 +470,11 @@
 #    define alloca _alloca
 #   else
 #    define YYSTACK_ALLOC alloca
-#    if ! defined _ALLOCA_H && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
+#    if ! defined _ALLOCA_H && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 #     include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
-#     ifndef EXIT_SUCCESS
-#      define EXIT_SUCCESS 0
+#     ifndef _STDLIB_H
+#      define _STDLIB_H 1
 #     endif
 #    endif
 #   endif
@@ -496,24 +497,24 @@
 #  ifndef YYSTACK_ALLOC_MAXIMUM
 #   define YYSTACK_ALLOC_MAXIMUM YYSIZE_MAXIMUM
 #  endif
-#  if (defined __cplusplus && ! defined EXIT_SUCCESS \
+#  if (defined __cplusplus && ! defined _STDLIB_H \
        && ! ((defined YYMALLOC || defined malloc) \
 	     && (defined YYFREE || defined free)))
 #   include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
-#   ifndef EXIT_SUCCESS
-#    define EXIT_SUCCESS 0
+#   ifndef _STDLIB_H
+#    define _STDLIB_H 1
 #   endif
 #  endif
 #  ifndef YYMALLOC
 #   define YYMALLOC malloc
-#   if ! defined malloc && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
+#   if ! defined malloc && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 void *malloc (YYSIZE_T); /* INFRINGES ON USER NAME SPACE */
 #   endif
 #  endif
 #  ifndef YYFREE
 #   define YYFREE free
-#   if ! defined free && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
+#   if ! defined free && ! defined _STDLIB_H && (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
 void free (void *); /* INFRINGES ON USER NAME SPACE */
 #   endif
@@ -542,7 +543,23 @@
      ((N) * (sizeof (yytype_int16) + sizeof (YYSTYPE)) \
       + YYSTACK_GAP_MAXIMUM)
 
-# define YYCOPY_NEEDED 1
+/* Copy COUNT objects from FROM to TO.  The source and destination do
+   not overlap.  */
+# ifndef YYCOPY
+#  if defined __GNUC__ && 1 < __GNUC__
+#   define YYCOPY(To, From, Count) \
+      __builtin_memcpy (To, From, (Count) * sizeof (*(From)))
+#  else
+#   define YYCOPY(To, From, Count)		\
+      do					\
+	{					\
+	  YYSIZE_T yyi;				\
+	  for (yyi = 0; yyi < (Count); yyi++)	\
+	    (To)[yyi] = (From)[yyi];		\
+	}					\
+      while (YYID (0))
+#  endif
+# endif
 
 /* Relocate STACK from its old location to the new one.  The
    local variables YYSIZE and YYSTACKSIZE give the old and new number of
@@ -562,26 +579,6 @@
 
 #endif
 
-#if defined YYCOPY_NEEDED && YYCOPY_NEEDED
-/* Copy COUNT objects from FROM to TO.  The source and destination do
-   not overlap.  */
-# ifndef YYCOPY
-#  if defined __GNUC__ && 1 < __GNUC__
-#   define YYCOPY(To, From, Count) \
-      __builtin_memcpy (To, From, (Count) * sizeof (*(From)))
-#  else
-#   define YYCOPY(To, From, Count)		\
-      do					\
-	{					\
-	  YYSIZE_T yyi;				\
-	  for (yyi = 0; yyi < (Count); yyi++)	\
-	    (To)[yyi] = (From)[yyi];		\
-	}					\
-      while (YYID (0))
-#  endif
-# endif
-#endif /* !YYCOPY_NEEDED */
-
 /* YYFINAL -- State number of the termination state.  */
 #define YYFINAL  17
 /* YYLAST -- Last index in YYTABLE.  */
@@ -716,8 +713,8 @@
        1,     1,     1,     2,     1,     3
 };
 
-/* YYDEFACT[STATE-NAME] -- Default reduction number in state STATE-NUM.
-   Performed when YYTABLE doesn't specify something else to do.  Zero
+/* YYDEFACT[STATE-NAME] -- Default rule to reduce with in state
+   STATE-NUM when YYTABLE doesn't specify something else to do.  Zero
    means the default is an error.  */
 static const yytype_uint8 yydefact[] =
 {
@@ -758,7 +755,8 @@
 
 /* YYTABLE[YYPACT[STATE-NUM]].  What to do in state STATE-NUM.  If
    positive, shift that token.  If negative, reduce the rule which
-   number is the opposite.  If YYTABLE_NINF, syntax error.  */
+   number is the opposite.  If zero, do what YYDEFACT says.
+   If YYTABLE_NINF, syntax error.  */
 #define YYTABLE_NINF -4
 static const yytype_int8 yytable[] =
 {
@@ -782,12 +780,6 @@
       30
 };
 
-#define yypact_value_is_default(yystate) \
-  ((yystate) == (-17))
-
-#define yytable_value_is_error(yytable_value) \
-  YYID (0)
-
 static const yytype_int8 yycheck[] =
 {
        2,     3,    12,    13,    14,    15,    22,     9,    23,    24,
@@ -856,6 +848,7 @@
     {								\
       yychar = (Token);						\
       yylval = (Value);						\
+      yytoken = YYTRANSLATE (yychar);				\
       YYPOPSTACK (1);						\
       goto yybackup;						\
     }								\
@@ -897,10 +890,19 @@
 #endif
 
 
-/* This macro is provided for backward compatibility. */
+/* YY_LOCATION_PRINT -- Print the location on the stream.
+   This macro was not mandated originally: define only if we know
+   we won't break user code: when these are the locations we know.  */
 
 #ifndef YY_LOCATION_PRINT
-# define YY_LOCATION_PRINT(File, Loc) ((void) 0)
+# if defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL
+#  define YY_LOCATION_PRINT(File, Loc)			\
+     fprintf (File, "%d.%d-%d.%d",			\
+	      (Loc).first_line, (Loc).first_column,	\
+	      (Loc).last_line,  (Loc).last_column)
+# else
+#  define YY_LOCATION_PRINT(File, Loc) ((void) 0)
+# endif
 #endif
 
 
@@ -1092,6 +1094,7 @@
 # define YYMAXDEPTH 10000
 #endif
 
+
 
 #if YYERROR_VERBOSE
 
@@ -1194,142 +1197,115 @@
 }
 # endif
 
-/* Copy into *YYMSG, which is of size *YYMSG_ALLOC, an error message
-   about the unexpected token YYTOKEN for the state stack whose top is
-   YYSSP.
-
-   Return 0 if *YYMSG was successfully written.  Return 1 if *YYMSG is
-   not large enough to hold the message.  In that case, also set
-   *YYMSG_ALLOC to the required number of bytes.  Return 2 if the
-   required number of bytes is too large to store.  */
-static int
-yysyntax_error (YYSIZE_T *yymsg_alloc, char **yymsg,
-                yytype_int16 *yyssp, int yytoken)
+/* Copy into YYRESULT an error message about the unexpected token
+   YYCHAR while in state YYSTATE.  Return the number of bytes copied,
+   including the terminating null byte.  If YYRESULT is null, do not
+   copy anything; just return the number of bytes that would be
+   copied.  As a special case, return 0 if an ordinary "syntax error"
+   message will do.  Return YYSIZE_MAXIMUM if overflow occurs during
+   size calculation.  */
+static YYSIZE_T
+yysyntax_error (char *yyresult, int yystate, int yychar)
 {
-  YYSIZE_T yysize0 = yytnamerr (0, yytname[yytoken]);
-  YYSIZE_T yysize = yysize0;
-  YYSIZE_T yysize1;
-  enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
-  /* Internationalized format string. */
-  const char *yyformat = 0;
-  /* Arguments of yyformat. */
-  char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
-  /* Number of reported tokens (one for the "unexpected", one per
-     "expected"). */
-  int yycount = 0;
+  int yyn = yypact[yystate];
 
-  /* There are many possibilities here to consider:
-     - Assume YYFAIL is not used.  It's too flawed to consider.  See
-       <http://lists.gnu.org/archive/html/bison-patches/2009-12/msg00024.html>
-       for details.  YYERROR is fine as it does not invoke this
-       function.
-     - If this state is a consistent state with a default action, then
-       the only way this function was invoked is if the default action
-       is an error action.  In that case, don't check for expected
-       tokens because there are none.
-     - The only way there can be no lookahead present (in yychar) is if
-       this state is a consistent state with a default action.  Thus,
-       detecting the absence of a lookahead is sufficient to determine
-       that there is no unexpected or expected token to report.  In that
-       case, just report a simple "syntax error".
-     - Don't assume there isn't a lookahead just because this state is a
-       consistent state with a default action.  There might have been a
-       previous inconsistent state, consistent state with a non-default
-       action, or user semantic action that manipulated yychar.
-     - Of course, the expected token list depends on states to have
-       correct lookahead information, and it depends on the parser not
-       to perform extra reductions after fetching a lookahead from the
-       scanner and before detecting a syntax error.  Thus, state merging
-       (from LALR or IELR) and default reductions corrupt the expected
-       token list.  However, the list is correct for canonical LR with
-       one exception: it will still contain any token that will not be
-       accepted due to an error action in a later state.
-  */
-  if (yytoken != YYEMPTY)
+  if (! (YYPACT_NINF < yyn && yyn <= YYLAST))
+    return 0;
+  else
     {
-      int yyn = yypact[*yyssp];
-      yyarg[yycount++] = yytname[yytoken];
-      if (!yypact_value_is_default (yyn))
-        {
-          /* Start YYX at -YYN if negative to avoid negative indexes in
-             YYCHECK.  In other words, skip the first -YYN actions for
-             this state because they are default actions.  */
-          int yyxbegin = yyn < 0 ? -yyn : 0;
-          /* Stay within bounds of both yycheck and yytname.  */
-          int yychecklim = YYLAST - yyn + 1;
-          int yyxend = yychecklim < YYNTOKENS ? yychecklim : YYNTOKENS;
-          int yyx;
+      int yytype = YYTRANSLATE (yychar);
+      YYSIZE_T yysize0 = yytnamerr (0, yytname[yytype]);
+      YYSIZE_T yysize = yysize0;
+      YYSIZE_T yysize1;
+      int yysize_overflow = 0;
+      enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
+      char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
+      int yyx;
 
-          for (yyx = yyxbegin; yyx < yyxend; ++yyx)
-            if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR
-                && !yytable_value_is_error (yytable[yyx + yyn]))
-              {
-                if (yycount == YYERROR_VERBOSE_ARGS_MAXIMUM)
-                  {
-                    yycount = 1;
-                    yysize = yysize0;
-                    break;
-                  }
-                yyarg[yycount++] = yytname[yyx];
-                yysize1 = yysize + yytnamerr (0, yytname[yyx]);
-                if (! (yysize <= yysize1
-                       && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
-                  return 2;
-                yysize = yysize1;
-              }
-        }
-    }
+# if 0
+      /* This is so xgettext sees the translatable formats that are
+	 constructed on the fly.  */
+      YY_("syntax error, unexpected %s");
+      YY_("syntax error, unexpected %s, expecting %s");
+      YY_("syntax error, unexpected %s, expecting %s or %s");
+      YY_("syntax error, unexpected %s, expecting %s or %s or %s");
+      YY_("syntax error, unexpected %s, expecting %s or %s or %s or %s");
+# endif
+      char *yyfmt;
+      char const *yyf;
+      static char const yyunexpected[] = "syntax error, unexpected %s";
+      static char const yyexpecting[] = ", expecting %s";
+      static char const yyor[] = " or %s";
+      char yyformat[sizeof yyunexpected
+		    + sizeof yyexpecting - 1
+		    + ((YYERROR_VERBOSE_ARGS_MAXIMUM - 2)
+		       * (sizeof yyor - 1))];
+      char const *yyprefix = yyexpecting;
 
-  switch (yycount)
-    {
-# define YYCASE_(N, S)                      \
-      case N:                               \
-        yyformat = S;                       \
-      break
-      YYCASE_(0, YY_("syntax error"));
-      YYCASE_(1, YY_("syntax error, unexpected %s"));
-      YYCASE_(2, YY_("syntax error, unexpected %s, expecting %s"));
-      YYCASE_(3, YY_("syntax error, unexpected %s, expecting %s or %s"));
-      YYCASE_(4, YY_("syntax error, unexpected %s, expecting %s or %s or %s"));
-      YYCASE_(5, YY_("syntax error, unexpected %s, expecting %s or %s or %s or %s"));
-# undef YYCASE_
-    }
+      /* Start YYX at -YYN if negative to avoid negative indexes in
+	 YYCHECK.  */
+      int yyxbegin = yyn < 0 ? -yyn : 0;
 
-  yysize1 = yysize + yystrlen (yyformat);
-  if (! (yysize <= yysize1 && yysize1 <= YYSTACK_ALLOC_MAXIMUM))
-    return 2;
-  yysize = yysize1;
+      /* Stay within bounds of both yycheck and yytname.  */
+      int yychecklim = YYLAST - yyn + 1;
+      int yyxend = yychecklim < YYNTOKENS ? yychecklim : YYNTOKENS;
+      int yycount = 1;
 
-  if (*yymsg_alloc < yysize)
-    {
-      *yymsg_alloc = 2 * yysize;
-      if (! (yysize <= *yymsg_alloc
-             && *yymsg_alloc <= YYSTACK_ALLOC_MAXIMUM))
-        *yymsg_alloc = YYSTACK_ALLOC_MAXIMUM;
-      return 1;
-    }
+      yyarg[0] = yytname[yytype];
+      yyfmt = yystpcpy (yyformat, yyunexpected);
 
-  /* Avoid sprintf, as that infringes on the user's name space.
-     Don't have undefined behavior even if the translation
-     produced a string with the wrong number of "%s"s.  */
-  {
-    char *yyp = *yymsg;
-    int yyi = 0;
-    while ((*yyp = *yyformat) != '\0')
-      if (*yyp == '%' && yyformat[1] == 's' && yyi < yycount)
-        {
-          yyp += yytnamerr (yyp, yyarg[yyi++]);
-          yyformat += 2;
-        }
-      else
-        {
-          yyp++;
-          yyformat++;
-        }
-  }
-  return 0;
+      for (yyx = yyxbegin; yyx < yyxend; ++yyx)
+	if (yycheck[yyx + yyn] == yyx && yyx != YYTERROR)
+	  {
+	    if (yycount == YYERROR_VERBOSE_ARGS_MAXIMUM)
+	      {
+		yycount = 1;
+		yysize = yysize0;
+		yyformat[sizeof yyunexpected - 1] = '\0';
+		break;
+	      }
+	    yyarg[yycount++] = yytname[yyx];
+	    yysize1 = yysize + yytnamerr (0, yytname[yyx]);
+	    yysize_overflow |= (yysize1 < yysize);
+	    yysize = yysize1;
+	    yyfmt = yystpcpy (yyfmt, yyprefix);
+	    yyprefix = yyor;
+	  }
+
+      yyf = YY_(yyformat);
+      yysize1 = yysize + yystrlen (yyf);
+      yysize_overflow |= (yysize1 < yysize);
+      yysize = yysize1;
+
+      if (yysize_overflow)
+	return YYSIZE_MAXIMUM;
+
+      if (yyresult)
+	{
+	  /* Avoid sprintf, as that infringes on the user's name space.
+	     Don't have undefined behavior even if the translation
+	     produced a string with the wrong number of "%s"s.  */
+	  char *yyp = yyresult;
+	  int yyi = 0;
+	  while ((*yyp = *yyf) != '\0')
+	    {
+	      if (*yyp == '%' && yyf[1] == 's' && yyi < yycount)
+		{
+		  yyp += yytnamerr (yyp, yyarg[yyi++]);
+		  yyf += 2;
+		}
+	      else
+		{
+		  yyp++;
+		  yyf++;
+		}
+	    }
+	}
+      return yysize;
+    }
 }
 #endif /* YYERROR_VERBOSE */
+
 
 /*-----------------------------------------------.
 | Release the memory associated to this symbol.  |
@@ -1362,7 +1338,6 @@
     }
 }
 
-
 /* Prevent warnings from -Wmissing-prototypes.  */
 #ifdef YYPARSE_PARAM
 #if defined __STDC__ || defined __cplusplus
@@ -1389,10 +1364,11 @@
 int yynerrs;
 
 
-/*----------.
-| yyparse.  |
-`----------*/
 
+/*-------------------------.
+| yyparse or yypush_parse.  |
+`-------------------------*/
+
 #ifdef YYPARSE_PARAM
 #if (defined __STDC__ || defined __C99__FUNC__ \
      || defined __cplusplus || defined _MSC_VER)
@@ -1415,6 +1391,8 @@
 #endif
 #endif
 {
+
+
     int yystate;
     /* Number of tokens to shift before error messages enabled.  */
     int yyerrstatus;
@@ -1569,7 +1547,7 @@
 
   /* First try to decide what to do without reference to lookahead token.  */
   yyn = yypact[yystate];
-  if (yypact_value_is_default (yyn))
+  if (yyn == YYPACT_NINF)
     goto yydefault;
 
   /* Not known => get a lookahead token if don't already have one.  */
@@ -1600,8 +1578,8 @@
   yyn = yytable[yyn];
   if (yyn <= 0)
     {
-      if (yytable_value_is_error (yyn))
-        goto yyerrlab;
+      if (yyn == 0 || yyn == YYTABLE_NINF)
+	goto yyerrlab;
       yyn = -yyn;
       goto yyreduce;
     }
@@ -1656,35 +1634,35 @@
     {
         case 3:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 299 "L3Parser.ypp"
-    {l3p->outputNode = (yyvsp[(1) - (1)].astnode);}
+    {l3p->outputNode = (yyvsp[(1) - (1)].astnode);;}
     break;
 
   case 4:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 300 "L3Parser.ypp"
-    {}
+    {;}
     break;
 
   case 5:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 301 "L3Parser.ypp"
-    {delete (yyvsp[(1) - (2)].astnode);}
+    {delete (yyvsp[(1) - (2)].astnode);;}
     break;
 
   case 6:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 304 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(1) - (1)].astnode);}
+    {(yyval.astnode) = (yyvsp[(1) - (1)].astnode);;}
     break;
 
   case 7:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 305 "L3Parser.ypp"
     {
                    (yyval.astnode) = new ASTNode();
@@ -1711,26 +1689,26 @@
                        (yyval.astnode)->setType(AST_NAME);
                      }
                    }
-        }
+        ;}
     break;
 
   case 8:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 331 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(2) - (3)].astnode);}
+    {(yyval.astnode) = (yyvsp[(2) - (3)].astnode);;}
     break;
 
   case 9:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 332 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_POWER); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_POWER); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 10:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 333 "L3Parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_TIMES) {
@@ -1742,12 +1720,12 @@
                     (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode));
                     (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));
                   }
-                }
+                ;}
     break;
 
   case 11:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 344 "L3Parser.ypp"
     {
                   if ((yyvsp[(1) - (3)].astnode)->getType()==AST_PLUS) {
@@ -1759,47 +1737,47 @@
                     (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode));
                     (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));
                   }
-                }
+                ;}
     break;
 
   case 12:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 355 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_DIVIDE); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_DIVIDE); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 13:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 356 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_MINUS); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_MINUS); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 14:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 357 "L3Parser.ypp"
-    {(yyval.astnode) = l3p->createModuloTree((yyvsp[(1) - (3)].astnode), (yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = l3p->createModuloTree((yyvsp[(1) - (3)].astnode), (yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 15:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 358 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 16:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 359 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LT); (yyval.astnode)->addChild((yyvsp[(1) - (3)].astnode)); (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
   case 17:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 360 "L3Parser.ypp"
     {
                   if (l3p->collapseminus) {
@@ -1833,75 +1811,75 @@
                     (yyval.astnode) = new ASTNode(AST_MINUS);
                     (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));
                   }
-                }
+                ;}
     break;
 
   case 18:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 393 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_GEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 19:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 394 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_LEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 20:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 395 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_EQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_EQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 21:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 396 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 22:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 397 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 23:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 398 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_RELATIONAL_NEQ); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 24:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 399 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_AND); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_AND); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 25:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 400 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_OR); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_OR); (yyval.astnode)->addChild((yyvsp[(1) - (4)].astnode)); (yyval.astnode)->addChild((yyvsp[(4) - (4)].astnode));;}
     break;
 
   case 26:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 401 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_LOGICAL_NOT); (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_LOGICAL_NOT); (yyval.astnode)->addChild((yyvsp[(2) - (2)].astnode));;}
     break;
 
   case 27:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 402 "L3Parser.ypp"
     {
                    (yyval.astnode) = new ASTNode(AST_FUNCTION);
@@ -1913,12 +1891,12 @@
                      if (type != AST_UNKNOWN) (yyval.astnode)->setType(type);
                      if (l3p->checkNumArguments((yyval.astnode))) YYABORT;
                    }
-        }
+        ;}
     break;
 
   case 28:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 413 "L3Parser.ypp"
     {
                    (yyval.astnode) = (yyvsp[(3) - (4)].astnode);
@@ -1968,40 +1946,40 @@
                      }
                    }
                    if (l3p->checkNumArguments((yyval.astnode))) YYABORT;
-        }
+        ;}
     break;
 
   case 29:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 464 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));;}
     break;
 
   case 30:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 465 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);;}
     break;
 
   case 31:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 466 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));;}
     break;
 
   case 32:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 467 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);}
+    {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);;}
     break;
 
   case 33:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 468 "L3Parser.ypp"
     {
                   (yyval.astnode) = (yyvsp[(1) - (2)].astnode);
@@ -2014,40 +1992,29 @@
                     YYERROR;
                   }
                   (yyval.astnode)->setUnits(*(yyvsp[(2) - (2)].word));
-               }
+               ;}
     break;
 
   case 34:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 482 "L3Parser.ypp"
-    {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));}
+    {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));;}
     break;
 
   case 35:
 
-/* Line 1806 of yacc.c  */
+/* Line 1464 of yacc.c  */
 #line 483 "L3Parser.ypp"
-    {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));}
+    {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
 
 
-/* Line 1806 of yacc.c  */
-#line 2038 "L3Parser.cpp"
+/* Line 1464 of yacc.c  */
+#line 2016 "L3Parser.cpp"
       default: break;
     }
-  /* User semantic actions sometimes alter yychar, and that requires
-     that yytoken be updated with the new translation.  We take the
-     approach of translating immediately before every use of yytoken.
-     One alternative is translating here after every semantic action,
-     but that translation would be missed if the semantic action invokes
-     YYABORT, YYACCEPT, or YYERROR immediately after altering yychar or
-     if it invokes YYBACKUP.  In the case of YYABORT or YYACCEPT, an
-     incorrect destructor might then be invoked immediately.  In the
-     case of YYERROR or YYBACKUP, subsequent parser actions might lead
-     to an incorrect destructor call or verbose syntax error message
-     before the lookahead is translated.  */
   YY_SYMBOL_PRINT ("-> $$ =", yyr1[yyn], &yyval, &yyloc);
 
   YYPOPSTACK (yylen);
@@ -2075,10 +2042,6 @@
 | yyerrlab -- here on detecting error |
 `------------------------------------*/
 yyerrlab:
-  /* Make sure we have latest lookahead translation.  See comments at
-     user semantic actions for why this is necessary.  */
-  yytoken = yychar == YYEMPTY ? YYEMPTY : YYTRANSLATE (yychar);
-
   /* If not already recovering from an error, report this error.  */
   if (!yyerrstatus)
     {
@@ -2086,36 +2049,37 @@
 #if ! YYERROR_VERBOSE
       yyerror (YY_("syntax error"));
 #else
-# define YYSYNTAX_ERROR yysyntax_error (&yymsg_alloc, &yymsg, \
-                                        yyssp, yytoken)
       {
-        char const *yymsgp = YY_("syntax error");
-        int yysyntax_error_status;
-        yysyntax_error_status = YYSYNTAX_ERROR;
-        if (yysyntax_error_status == 0)
-          yymsgp = yymsg;
-        else if (yysyntax_error_status == 1)
-          {
-            if (yymsg != yymsgbuf)
-              YYSTACK_FREE (yymsg);
-            yymsg = (char *) YYSTACK_ALLOC (yymsg_alloc);
-            if (!yymsg)
-              {
-                yymsg = yymsgbuf;
-                yymsg_alloc = sizeof yymsgbuf;
-                yysyntax_error_status = 2;
-              }
-            else
-              {
-                yysyntax_error_status = YYSYNTAX_ERROR;
-                yymsgp = yymsg;
-              }
-          }
-        yyerror (yymsgp);
-        if (yysyntax_error_status == 2)
-          goto yyexhaustedlab;
+	YYSIZE_T yysize = yysyntax_error (0, yystate, yychar);
+	if (yymsg_alloc < yysize && yymsg_alloc < YYSTACK_ALLOC_MAXIMUM)
+	  {
+	    YYSIZE_T yyalloc = 2 * yysize;
+	    if (! (yysize <= yyalloc && yyalloc <= YYSTACK_ALLOC_MAXIMUM))
+	      yyalloc = YYSTACK_ALLOC_MAXIMUM;
+	    if (yymsg != yymsgbuf)
+	      YYSTACK_FREE (yymsg);
+	    yymsg = (char *) YYSTACK_ALLOC (yyalloc);
+	    if (yymsg)
+	      yymsg_alloc = yyalloc;
+	    else
+	      {
+		yymsg = yymsgbuf;
+		yymsg_alloc = sizeof yymsgbuf;
+	      }
+	  }
+
+	if (0 < yysize && yysize <= yymsg_alloc)
+	  {
+	    (void) yysyntax_error (yymsg, yystate, yychar);
+	    yyerror (yymsg);
+	  }
+	else
+	  {
+	    yyerror (YY_("syntax error"));
+	    if (yysize != 0)
+	      goto yyexhaustedlab;
+	  }
       }
-# undef YYSYNTAX_ERROR
 #endif
     }
 
@@ -2174,7 +2138,7 @@
   for (;;)
     {
       yyn = yypact[yystate];
-      if (!yypact_value_is_default (yyn))
+      if (yyn != YYPACT_NINF)
 	{
 	  yyn += YYTERROR;
 	  if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
@@ -2233,13 +2197,8 @@
 
 yyreturn:
   if (yychar != YYEMPTY)
-    {
-      /* Make sure we have latest lookahead translation.  See comments at
-         user semantic actions for why this is necessary.  */
-      yytoken = YYTRANSLATE (yychar);
-      yydestruct ("Cleanup: discarding lookahead",
-                  yytoken, &yylval);
-    }
+     yydestruct ("Cleanup: discarding lookahead",
+		 yytoken, &yylval);
   /* Do not reclaim the symbols of the rule which action triggered
      this YYABORT or YYACCEPT.  */
   YYPOPSTACK (yylen);
@@ -2264,7 +2223,7 @@
 
 
 
-/* Line 2067 of yacc.c  */
+/* Line 1684 of yacc.c  */
 #line 486 "L3Parser.ypp"
 
 
@@ -2352,6 +2311,7 @@
     l3p->input.seekg(numbegin);
     bool decimal = false;
     bool e = false;
+    bool last_e = false;
     while (l3p->input.tellg() != numend) {
       cc = l3p->input.get();
       if (cc=='.') {
@@ -2359,8 +2319,16 @@
       }
       if (cc=='e' || cc=='E') {
         e = true;
+        last_e = true;
       }
+      else {
+        last_e = false;
+      }
     }
+    if (last_e) {
+       e = false;
+       l3p->input.unget();
+    }
     if (!decimal && !e && number == static_cast<double>(numlong) && numlong <= SBML_INT_MAX) {
       sbml_yylval.numlong = numlong;
       return INTEGER;
@@ -2428,7 +2396,7 @@
         }
       }
     }
-	l3p->input.clear();
+    l3p->input.clear();
     l3p->input.seekg(rationalbegin, ios::beg); // Not actually a rational number.
     return '(';
   }

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-18 12:58:01 UTC (rev 16021)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-18 21:13:11 UTC (rev 16022)
@@ -569,6 +569,7 @@
     l3p->input.seekg(numbegin);
     bool decimal = false;
     bool e = false;
+    bool last_e = false;
     while (l3p->input.tellg() != numend) {
       cc = l3p->input.get();
       if (cc=='.') {
@@ -576,8 +577,16 @@
       }
       if (cc=='e' || cc=='E') {
         e = true;
+        last_e = true;
       }
+      else {
+        last_e = false;
+      }
     }
+    if (last_e) {
+       e = false;
+       l3p->input.unget();
+    }
     if (!decimal && !e && number == static_cast<double>(numlong) && numlong <= SBML_INT_MAX) {
       sbml_yylval.numlong = numlong;
       return INTEGER;
@@ -645,7 +654,7 @@
         }
       }
     }
-	l3p->input.clear();
+    l3p->input.clear();
     l3p->input.seekg(rationalbegin, ios::beg); // Not actually a rational number.
     return '(';
   }

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16085
          http://sbml.svn.sourceforge.net/sbml/?rev=16085&view=rev
Author:   luciansmith
Date:     2012-07-25 22:29:14 +0000 (Wed, 25 Jul 2012)
Log Message:
-----------
Removed errant unused variable (the function is now recursive instead of trying to figure everything out separately in an error condition).

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-25 22:27:20 UTC (rev 16084)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-25 22:29:14 UTC (rev 16085)
@@ -2286,7 +2286,6 @@
       l3p->input.seekg(numbegin);
       string failnum = "";
       cc = l3p->input.get();
-      bool decimal = false;
       while (l3p->input.good() && (isdigit(cc) || cc=='.')) {
         failnum += cc;
         cc = l3p->input.get();

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-25 22:27:20 UTC (rev 16084)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-25 22:29:14 UTC (rev 16085)
@@ -544,7 +544,6 @@
       l3p->input.seekg(numbegin);
       string failnum = "";
       cc = l3p->input.get();
-      bool decimal = false;
       while (l3p->input.good() && (isdigit(cc) || cc=='.')) {
         failnum += cc;
         cc = l3p->input.get();

This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 16155
          http://sbml.svn.sourceforge.net/sbml/?rev=16155&view=rev
Author:   luciansmith
Date:     2012-07-30 20:55:43 +0000 (Mon, 30 Jul 2012)
Log Message:
-----------
Add in parsing of lambda functions to L3 Parser.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-30 18:01:51 UTC (rev 16154)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-07-30 20:55:43 UTC (rev 16155)
@@ -2479,6 +2479,7 @@
   if (caselessStrCmp(name, "exp"))      return AST_FUNCTION_EXP;
   if (caselessStrCmp(name, "factorial")) return AST_FUNCTION_FACTORIAL;
   if (caselessStrCmp(name, "floor"))    return AST_FUNCTION_FLOOR;
+  if (caselessStrCmp(name, "lambda"))   return AST_LAMBDA;
   if (caselessStrCmp(name, "log"))      return AST_FUNCTION_LOG;
   if (caselessStrCmp(name, "ln"))       return AST_FUNCTION_LN;
   if (caselessStrCmp(name, "log10"))    return AST_FUNCTION_LOG;
@@ -2747,6 +2748,7 @@
     return false;
 
   case AST_FUNCTION_PIECEWISE:
+  case AST_LAMBDA:
     if (children == 0) {
       error << "at least one argument, but none were found.";
       l3p->setError(error.str());

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-30 18:01:51 UTC (rev 16154)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-07-30 20:55:43 UTC (rev 16155)
@@ -737,6 +737,7 @@
   if (caselessStrCmp(name, "exp"))      return AST_FUNCTION_EXP;
   if (caselessStrCmp(name, "factorial")) return AST_FUNCTION_FACTORIAL;
   if (caselessStrCmp(name, "floor"))    return AST_FUNCTION_FLOOR;
+  if (caselessStrCmp(name, "lambda"))   return AST_LAMBDA;
   if (caselessStrCmp(name, "log"))      return AST_FUNCTION_LOG;
   if (caselessStrCmp(name, "ln"))       return AST_FUNCTION_LN;
   if (caselessStrCmp(name, "log10"))    return AST_FUNCTION_LOG;
@@ -1005,6 +1006,7 @@
     return false;
 
   case AST_FUNCTION_PIECEWISE:
+  case AST_LAMBDA:
     if (children == 0) {
       error << "at least one argument, but none were found.";
       l3p->setError(error.str());

Modified: trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-07-30 18:01:51 UTC (rev 16154)
+++ trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-07-30 20:55:43 UTC (rev 16155)
@@ -2046,6 +2046,116 @@
 END_TEST
 
 
+START_TEST (test_SBML_parseL3Formula_lambda1)
+{
+  ASTNode_t *r = SBML_parseL3Formula("lambda(3.3)");
+
+  fail_unless( ASTNode_getType       (r) == AST_LAMBDA, NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 1  , NULL );
+
+  ASTNode_t *c = ASTNode_getLeftChild(r);
+
+  fail_unless( ASTNode_getType       (c) == AST_REAL, NULL );
+  fail_unless( ASTNode_getReal       (c) == 3.3, NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+  ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambda2)
+{
+  ASTNode_t *r = SBML_parseL3Formula("lambda(x,x^3)");
+  ASTNode_t *c;
+
+
+  fail_unless( ASTNode_getType(r) == AST_LAMBDA , NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 2     , NULL );
+
+  c = ASTNode_getLeftChild(r);
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0     , NULL );
+
+  c = ASTNode_getRightChild(r);
+
+  fail_unless( ASTNode_getType       (c) == AST_POWER, NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 2     , NULL );
+
+  c = ASTNode_getLeftChild(c);
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0     , NULL );
+
+  c = ASTNode_getRightChild(r->getRightChild());
+
+  fail_unless( ASTNode_getType       (c) == AST_INTEGER, NULL );
+  fail_unless( ASTNode_getInteger    (c) == 3, NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+
+  ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambda3)
+{
+  ASTNode_t *r = SBML_parseL3Formula("lambda(x, y, x+y)");
+  ASTNode_t *c;
+
+
+  fail_unless( ASTNode_getType(r) == AST_LAMBDA , NULL );
+  fail_unless( ASTNode_getNumChildren(r) == 3     , NULL );
+
+  c = ASTNode_getChild(r, 0);
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0     , NULL );
+
+  c = ASTNode_getChild(r, 1);
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "y") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0     , NULL );
+
+  c = ASTNode_getChild(r, 2);
+
+  fail_unless( ASTNode_getType       (c) == AST_PLUS, NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 2     , NULL );
+
+  c = ASTNode_getLeftChild(c);
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "x") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0     , NULL );
+
+  c = ASTNode_getRightChild(r->getChild(2));
+
+  fail_unless( ASTNode_getType       (c) == AST_NAME, NULL );
+  fail_unless( !strcmp(ASTNode_getName(c), "y") , NULL );
+  fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
+
+
+  ASTNode_free(r);
+}
+END_TEST
+
+
+START_TEST (test_SBML_parseL3Formula_lambdaerr)
+{
+  ASTNode_t *r = SBML_parseL3Formula("lambda()");
+
+  fail_unless(r == NULL, NULL);
+  fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'lambda()' at position 8:  The function 'lambda' takes at least one argument, but none were found."), NULL);
+}
+END_TEST
+
+
 Suite *
 create_suite_L3FormulaParser (void) 
 { 
@@ -2136,6 +2246,10 @@
   tcase_add_test( tcase, test_SBML_parseL3Formula_crazylongerg);
   tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum);
   tcase_add_test( tcase, test_SBML_parseL3Formula_wrongnum2);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_lambda1);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_lambda2);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_lambda3);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_lambdaerr);
   suite_add_tcase(suite, tcase);
 
   return suite;

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Revision: 16603
          http://sbml.svn.sourceforge.net/sbml/?rev=16603&view=rev
Author:   luciansmith
Date:     2012-12-17 19:54:26 +0000 (Mon, 17 Dec 2012)
Log Message:
-----------
The function 'sqrt' should take exactly one argument.  If there were 2 arguments, the old code added in '2' as the root, and then complained that there were three arguments, which didn't match user input.  The new code just notices that it was wrong from the get-go.

Modified Paths:
--------------
    trunk/libsbml/src/sbml/math/L3Parser.cpp
    trunk/libsbml/src/sbml/math/L3Parser.ypp
    trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp

Modified: trunk/libsbml/src/sbml/math/L3Parser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-12-17 19:31:03 UTC (rev 16602)
+++ trunk/libsbml/src/sbml/math/L3Parser.cpp	2012-12-17 19:54:26 UTC (rev 16603)
@@ -666,8 +666,8 @@
 {
        0,   298,   298,   299,   300,   301,   304,   305,   331,   332,
      333,   344,   355,   356,   357,   358,   359,   360,   393,   394,
-     395,   396,   397,   398,   399,   400,   401,   402,   413,   464,
-     465,   466,   467,   468,   482,   483
+     395,   396,   397,   398,   399,   400,   401,   402,   413,   469,
+     470,   471,   472,   473,   487,   488
 };
 #endif
 
@@ -1908,6 +1908,11 @@
                      ASTNodeType_t type = l3p->getFunctionFor(name);
                      if (type != AST_UNKNOWN) (yyval.astnode)->setType(type);
                      if (type==AST_FUNCTION_ROOT && l3p->caselessStrCmp(name, "sqrt")) {
+                       //If the number of arguments is wrong, set an error now instead of waiting for later.
+                       if ((yyval.astnode)->getNumChildren() != 1) {
+                         l3p->setError("The function 'sqrt' takes exactly one argument.");
+                         YYABORT;
+                       }
                        //Add a '2' node before the existing child.
                        ASTNode* int2 = new ASTNode(AST_INTEGER);
                        int2->setValue(2);
@@ -1952,35 +1957,35 @@
   case 29:
 
 /* Line 1464 of yacc.c  */
-#line 464 "L3Parser.ypp"
+#line 469 "L3Parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numdouble));;}
     break;
 
   case 30:
 
 /* Line 1464 of yacc.c  */
-#line 465 "L3Parser.ypp"
+#line 470 "L3Parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].mantissa), l3p->exponent);;}
     break;
 
   case 31:
 
 /* Line 1464 of yacc.c  */
-#line 466 "L3Parser.ypp"
+#line 471 "L3Parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].numlong));;}
     break;
 
   case 32:
 
 /* Line 1464 of yacc.c  */
-#line 467 "L3Parser.ypp"
+#line 472 "L3Parser.ypp"
     {(yyval.astnode) = new ASTNode(); (yyval.astnode)->setValue((yyvsp[(1) - (1)].rational), l3p->denominator);;}
     break;
 
   case 33:
 
 /* Line 1464 of yacc.c  */
-#line 468 "L3Parser.ypp"
+#line 473 "L3Parser.ypp"
     {
                   (yyval.astnode) = (yyvsp[(1) - (2)].astnode);
                   if ((yyval.astnode)->getUnits() != "") {
@@ -1998,21 +2003,21 @@
   case 34:
 
 /* Line 1464 of yacc.c  */
-#line 482 "L3Parser.ypp"
+#line 487 "L3Parser.ypp"
     {(yyval.astnode) = new ASTNode(AST_FUNCTION); (yyval.astnode)->addChild((yyvsp[(1) - (1)].astnode));;}
     break;
 
   case 35:
 
 /* Line 1464 of yacc.c  */
-#line 483 "L3Parser.ypp"
+#line 488 "L3Parser.ypp"
     {(yyval.astnode) = (yyvsp[(1) - (3)].astnode);  (yyval.astnode)->addChild((yyvsp[(3) - (3)].astnode));;}
     break;
 
 
 
 /* Line 1464 of yacc.c  */
-#line 2016 "L3Parser.cpp"
+#line 2021 "L3Parser.cpp"
       default: break;
     }
   YY_SYMBOL_PRINT ("-> $$ =", yyr1[yyn], &yyval, &yyloc);
@@ -2224,7 +2229,7 @@
 
 
 /* Line 1684 of yacc.c  */
-#line 486 "L3Parser.ypp"
+#line 491 "L3Parser.ypp"
 
 
 

Modified: trunk/libsbml/src/sbml/math/L3Parser.ypp
===================================================================
--- trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-12-17 19:31:03 UTC (rev 16602)
+++ trunk/libsbml/src/sbml/math/L3Parser.ypp	2012-12-17 19:54:26 UTC (rev 16603)
@@ -275,13 +275,13 @@
 
 %type <astnode> node nodelist number
 
-%left '&' '|' /* Boolean functions and, or */
+%left '&' '|'         /* Boolean functions and, or */
 %left '<' '>' '=' '!' /* Boolean comparison functions (gt, lt, eq, etc.) */
-%left NOT /* boolean negation--unary not */
+%left NOT             /* Boolean negation--unary not */
 %left '-' '+'
 %left '*' '/' '%'
-%right '^'    /* exponentiation        */
-%left NEG     /* negation--unary minus */
+%right '^'            /* exponentiation        */
+%left NEG             /* negation--unary minus */
 
 %token YYEOF 0 "end of string"
 %token  <numdouble> DOUBLE "number"
@@ -420,6 +420,11 @@
                      ASTNodeType_t type = l3p->getFunctionFor(name);
                      if (type != AST_UNKNOWN) $$->setType(type);
                      if (type==AST_FUNCTION_ROOT && l3p->caselessStrCmp(name, "sqrt")) {
+                       //If the number of arguments is wrong, set an error now instead of waiting for later.
+                       if ($$->getNumChildren() != 1) {
+                         l3p->setError("The function 'sqrt' takes exactly one argument.");
+                         YYABORT;
+                       }
                        //Add a '2' node before the existing child.
                        ASTNode* int2 = new ASTNode(AST_INTEGER);
                        int2->setValue(2);

Modified: trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp
===================================================================
--- trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-12-17 19:31:03 UTC (rev 16602)
+++ trunk/libsbml/src/sbml/math/test/TestL3FormulaParser.cpp	2012-12-17 19:54:26 UTC (rev 16603)
@@ -2154,6 +2154,16 @@
 END_TEST
 
 
+START_TEST (test_SBML_parseL3Formula_sqrterr)
+{
+  ASTNode_t *r = SBML_parseL3Formula("sqrt(x,y)");
+
+  fail_unless(r == NULL, NULL);
+  fail_unless( !strcmp(SBML_getLastParseL3Error(), "Error when parsing input 'sqrt(x,y)' at position 9:  The function 'sqrt' takes exactly one argument."), NULL);
+}
+END_TEST
+
+
 Suite *
 create_suite_L3FormulaParser (void) 
 { 
@@ -2248,6 +2258,7 @@
   tcase_add_test( tcase, test_SBML_parseL3Formula_lambda2);
   tcase_add_test( tcase, test_SBML_parseL3Formula_lambda3);
   tcase_add_test( tcase, test_SBML_parseL3Formula_lambdaerr);
+  tcase_add_test( tcase, test_SBML_parseL3Formula_sqrterr);
   suite_add_tcase(suite, tcase);
 
   return suite;

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