Menu
▾
▴
[sbml-svn] SF.net SVN: sbml:[20928] branches/libsbml-dev-l2v5-l3v2
|
From: <sar...@us...> - 2014-07-28 08:46:04
|
Revision: 20928
http://sourceforge.net/p/sbml/code/20928
Author: sarahkeating
Date: 2014-07-28 08:45:51 +0000 (Mon, 28 Jul 2014)
Log Message:
-----------
Merged revision(s) 20884-20927 from trunk/libsbml:
Modified Paths:
--------------
branches/libsbml-dev-l2v5-l3v2/src/bindings/matlab/OutputSBML.c
branches/libsbml-dev-l2v5-l3v2/src/bindings/matlab/TranslateSBML.c
branches/libsbml-dev-l2v5-l3v2/src/bindings/swig/swigdoc.py
branches/libsbml-dev-l2v5-l3v2/src/sbml/SBase.cpp
branches/libsbml-dev-l2v5-l3v2/src/sbml/math-legacy/ASTNode.cpp
branches/libsbml-dev-l2v5-l3v2/src/sbml/math-legacy/MathML.cpp
branches/libsbml-dev-l2v5-l3v2/src/sbml/test/TestRunner.c
Property Changed:
----------------
branches/libsbml-dev-l2v5-l3v2/
Index: branches/libsbml-dev-l2v5-l3v2
===================================================================
--- branches/libsbml-dev-l2v5-l3v2 2014-07-28 08:43:57 UTC (rev 20927)
+++ branches/libsbml-dev-l2v5-l3v2 2014-07-28 08:45:51 UTC (rev 20928)
Property changes on: branches/libsbml-dev-l2v5-l3v2
___________________________________________________________________
Modified: svn:mergeinfo
## -2,4 +2,4 ##
/branches/libsbml-4:9056-10118
/branches/libsbml-5-conversion:14155-14227
/branches/libsbml-ast-plugin:16251-19654
-/trunk/libsbml:20289-20883
+/trunk/libsbml:20289-20927
\ No newline at end of property
Modified: branches/libsbml-dev-l2v5-l3v2/src/bindings/matlab/OutputSBML.c
===================================================================
--- branches/libsbml-dev-l2v5-l3v2/src/bindings/matlab/OutputSBML.c 2014-07-28 08:43:57 UTC (rev 20927)
+++ branches/libsbml-dev-l2v5-l3v2/src/bindings/matlab/OutputSBML.c 2014-07-28 08:45:51 UTC (rev 20928)
@@ -55,6 +55,108 @@
#endif
+
+#if defined(WIN32) && !defined(CYGWIN) && !defined(USE_OCTAVE)
+#define FILE_CHAR wchar_t*
+#define FILE_FOPEN(file) _wfopen(file, L"r")
+#define USE_FILE_WCHAR 1
+#else
+#define FILE_CHAR char*
+#define FILE_FOPEN(file) fopen(file, "r")
+#endif
+
+#ifndef uint16_t
+#define uint16_t unsigned short
+#endif
+
+FILE_CHAR readUnicodeString(const mxArray *prhs, mwSize length)
+{
+#ifdef USE_OCTAVE
+ char* ansii = (char *) mxCalloc(length, sizeof(char));
+ mxGetString(prhs, ansii, length);
+ return ansii;
+#else
+ wchar_t* utf16 = (wchar_t *) mxCalloc(length, sizeof(wchar_t));
+ char* utf8 = NULL;
+ uint16_T *ch = (uint16_T *) mxGetData(prhs);
+ wchar_t* p = utf16;
+ mwSize i;
+ for ( i = 0; i < length-1; ++i)
+ *p++ = *ch++;
+ *p = 0;
+
+#if USE_FILE_WCHAR
+ return utf16;
+#else
+
+ utf8 = (char*)mxCalloc(length*2, sizeof(char));
+
+ wcstombs(utf8, utf16, length*2);
+
+ /*mxFree(utf16);*/
+
+ if (utf8 != NULL && strlen(utf8) == 0 && length > 0)
+ {
+ mexErrMsgTxt("This string uses characters that cannot be expressed in UTF8, please rename the file.");
+ }
+
+ return utf8;
+#endif /* USE_FILE_WCHAR */
+
+#endif /* USE_OCTAVE*/
+
+}
+
+
+FILE_CHAR readUnicodeStringFromArrays(mxArray *mxFilename[2])
+
+{
+ mwSize nBuflen = (mxGetM(mxFilename[0])*mxGetN(mxFilename[0])+1);
+ FILE_CHAR pacTempString1 = readUnicodeString(mxFilename[0],nBuflen);
+
+ mwSize nBufferLen = (mxGetM(mxFilename[1])*mxGetN(mxFilename[1])+1);
+ FILE_CHAR pacTempString2 = readUnicodeString(mxFilename[1],nBufferLen);
+
+#if USE_FILE_WCHAR
+ FILE_CHAR pacFilename = (wchar_t *) mxCalloc(nBufferLen+nBuflen, sizeof(wchar_t));
+ wcscpy(pacFilename, pacTempString2);
+ wcscpy(pacFilename, pacTempString1);
+#else
+ FILE_CHAR pacFilename = (char *) mxCalloc(nBufferLen+nBuflen, sizeof(char));
+ strcpy(pacFilename, pacTempString2);
+ strcat(pacFilename, pacTempString1);
+#endif
+
+ /*mxFree(pacTempString1);*/
+ /*mxFree(pacTempString2);*/
+ return pacFilename;
+}
+
+#if USE_FILE_WCHAR
+
+int endsWith(const wchar_t* fileName, const char* ext)
+{
+ size_t len = wcslen(fileName), i;
+ size_t targetLen = strlen(ext);
+ wchar_t* temp1 = (wchar_t*)mxCalloc(targetLen, sizeof(wchar_t));
+ char* temp2 = (char*)mxCalloc(targetLen, sizeof(char));
+ int result = 0;
+
+ for (i = 0; i < targetLen; ++i)
+ {
+ temp1[i] = fileName[len - targetLen + i];
+ }
+
+ wcstombs(temp2,temp1, targetLen);
+ result = strcmp_insensitive(temp2, ext);
+
+ /*mxFree(temp1);*/
+ /*mxFree(temp2);*/
+ return result;
+}
+
+#endif
+
static char * timeSymbol = NULL;
static char * delaySymbol = NULL;
static char * avoSymbol = NULL;
@@ -136,36 +238,37 @@
mexFunction (int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
- mxArray * mxCheckStructure[2];
- mxArray * mxFilename[2], * mxExt[1];
- int nStatus;
- char *pacFilename = NULL, *pacTempString1 = NULL, *pacTempString2 = NULL;
+ mxArray * mxCheckStructure[2];
+ mxArray * mxFilename[2], * mxExt[1];
+ int nStatus;
+ FILE_CHAR pacFilename = NULL;
+ char *pacTempString1 = NULL, *pacTempString2 = NULL;
size_t nBuflen, nBufferLen;
-
- SBMLDocument_t *sbmlDocument;
+
+ SBMLDocument_t *sbmlDocument;
SBMLNamespaces_t *ns;
XMLNamespaces_t *xmlns;
- Model_t *sbmlModel;
+ Model_t *sbmlModel;
- mxArray * mxLevel, * mxVersion, * mxNotes, * mxAnnotations, * mxFBCVersion;
+ mxArray * mxLevel, * mxVersion, * mxNotes, * mxAnnotations, * mxFBCVersion;
mxArray * mxName, * mxId, *mxNamespaces, *mxMetaid, *mxTimeSymbol;
mxArray * mxSubstanceUnits, * mxTimeUnits, *mxLengthUnits, *mxAreaUnits;
mxArray * mxVolumeUnits, * mxExtentUnits, *mxConversionFactor;
mxArray * mxDelaySymbol, *mxAvoSymbol, *mxActiveObjective;
- unsigned int nLevel, nVersion, nFBCVersion;
- char * pacNotes, * pacAnnotations;
+ unsigned int nLevel, nVersion, nFBCVersion;
+ char * pacNotes, * pacAnnotations;
char * pacName, * pacId, *pacMetaid;
char * pacSubstanceUnits, * pacTimeUnits, *pacLengthUnits, *pacAreaUnits;
char * pacVolumeUnits, * pacExtentUnits, *pacConversionFactor, *pacActiveObjective;
int nSBOTerm;
-
+
SBasePlugin_t * plugin;
- mxArray * mxParameters, * mxCompartments, * mxFunctionDefinitions;
+ mxArray * mxParameters, * mxCompartments, * mxFunctionDefinitions;
mxArray * mxUnitDefinitions, *mxSBOTerm;
- mxArray * mxSpecies, * mxRules, * mxReactions, * mxEvents, * mxConstraints;
- mxArray * mxSpeciesTypes, * mxCompartmentTypes, * mxInitialAssignments;
+ mxArray * mxSpecies, * mxRules, * mxReactions, * mxEvents, * mxConstraints;
+ mxArray * mxSpeciesTypes, * mxCompartmentTypes, * mxInitialAssignments;
mxArray * mxFluxBounds, *mxObjectives, *mxFluxObjectives;
unsigned int usingOctave = 0;
mxArray * mxOctave[1];
@@ -176,136 +279,130 @@
/* determine whether we are in octave or matlab */
mexCallMATLAB(1, mxOctave, 0, NULL, "isoctave");
-
+
nBuflen = (mxGetM(mxOctave[0])*mxGetN(mxOctave[0])+1);
pacTempString1 = (char *) mxCalloc(nBuflen, sizeof(char));
nStatus = mxGetString(mxOctave[0], pacTempString1, (mwSize)(nBuflen));
if (nStatus != 0)
{
- mexErrMsgTxt("Could not determine platform");
+ mexErrMsgTxt("Could not determine platform");
}
if (!(strcmp_insensitive(pacTempString1, "0") == 0))
usingOctave = 1;
-/*************************************************************************************
- * validate inputs and outputs
- **********************************************************************************/
+ /*************************************************************************************
+ * validate inputs and outputs
+ **********************************************************************************/
if (nrhs < 1)
{
- mexErrMsgTxt("Must supply at least the model as an output argument\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
+ mexErrMsgTxt("Must supply at least the model as an output argument\n"
+ "USAGE: OutputSBML(SBMLModel, (filename))");
}
if (usingOctave == 1 && nrhs < 2)
{
- mexErrMsgTxt("Octave requires the filename to be specified\n"
- "USAGE: OutputSBML(SBMLModel, filename)");
+ mexErrMsgTxt("Octave requires the filename to be specified\n"
+ "USAGE: OutputSBML(SBMLModel, filename)");
}
if (nrhs > 3)
{
inInstaller = 1;
}
-/**
- * create a copy of the input
- */
- mxModel[0] = mxDuplicateArray(prhs[0]);
- mexMakeArrayPersistent(mxModel[0]);
- mexAtExit(FreeMem);
+ /**
+ * create a copy of the input
+ */
+ mxModel[0] = mxDuplicateArray(prhs[0]);
+ mexMakeArrayPersistent(mxModel[0]);
+ mexAtExit(FreeMem);
-/**
- * we know have the option of a third argument that indicates that we
- * want the structure to ONLY contain expected fields or not
- */
-if (nrhs > 2)
-{
- mxModel[1] = (mxArray *)prhs[2];
-}
-else
-{
- mxModel[1] = mxCreateDoubleScalar(1);
-}
-
-/**
- * check number and type of output arguments
- * SHOULDNT BE ANY
- */
- if (nlhs > 0)
- {
- mexErrMsgTxt("Too many output arguments\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
- }
+ /**
+ * we know have the option of a third argument that indicates that we
+ * want the structure to ONLY contain expected fields or not
+ */
+ if (nrhs > 2)
+ {
+ mxModel[1] = (mxArray *)prhs[2];
+ }
+ else
+ {
+ mxModel[1] = mxCreateDoubleScalar(1);
+ }
-/**
- * check number and type of input arguments
- * must be a valid MATLAB_SBML structure
- * and optionally the filename
- */
-
- if (nrhs > 4)
- {
- mexErrMsgTxt("Too many input arguments\n"
- "USAGE: OutputSBML(SBMLModel, (filename), (exclusive))");
- }
-
- nStatus = mexCallMATLAB(2, mxCheckStructure, 2, mxModel, "isSBML_Model");
-
- if ((nStatus != 0) || (mxIsLogicalScalarTrue(mxCheckStructure[0]) != 1))
- {
- /* there are errors - use the pacFilename char * to list these to the user */
+ /**
+ * check number and type of output arguments
+ * SHOULDNT BE ANY
+ */
+ if (nlhs > 0)
+ {
+ mexErrMsgTxt("Too many output arguments\n"
+ "USAGE: OutputSBML(SBMLModel, (filename))");
+ }
+
+ /**
+ * check number and type of input arguments
+ * must be a valid MATLAB_SBML structure
+ * and optionally the filename
+ */
+
+ if (nrhs > 4)
+ {
+ mexErrMsgTxt("Too many input arguments\n"
+ "USAGE: OutputSBML(SBMLModel, (filename), (exclusive))");
+ }
+
+ nStatus = mexCallMATLAB(2, mxCheckStructure, 2, mxModel, "isSBML_Model");
+
+ if ((nStatus != 0) || (mxIsLogicalScalarTrue(mxCheckStructure[0]) != 1))
+ {
+ /* there are errors - use the pacTempString1 char * to list these to the user */
nBuflen = (mxGetM(mxCheckStructure[1])*mxGetN(mxCheckStructure[1])+1);
- pacFilename = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxCheckStructure[1], pacFilename, (mwSize)(nBuflen));
+ pacTempString1 = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxCheckStructure[1], pacTempString1, (mwSize)(nBuflen));
if (nStatus == 0)
{
msgTxt = (char *) mxCalloc(200+nBuflen, sizeof(char));
sprintf(msgTxt, "\n%s\n\nErrors reported: %s%s\n", "First input must be a valid MATLAB_SBML Structure",
- pacFilename, "USAGE: OutputSBML(SBMLModel, (filename))");
+ pacTempString1, "USAGE: OutputSBML(SBMLModel, (filename))");
mexErrMsgTxt(msgTxt);
}
else
{
msgTxt = (char *) mxCalloc(200, sizeof(char));
sprintf(msgTxt, "%s\n%s", "First input must be a valid MATLAB_SBML Structure",
- "USAGE: OutputSBML(SBMLModel, (filename))");
+ "USAGE: OutputSBML(SBMLModel, (filename))");
mexErrMsgTxt(msgTxt);
}
- }
+ }
if (nrhs >= 2)
{
-
- if (mxIsChar(prhs[1]) != 1)
- {
- mexErrMsgTxt("Second input must be a filename\n"
- "USAGE: OutputSBML(SBMLModel, (filename))");
- }
- nBuflen = (mxGetM(prhs[1])*mxGetN(prhs[1])+1);
- pacFilename = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(prhs[1], pacFilename, (mwSize)(nBuflen));
-
- if (nStatus != 0)
+ if (mxIsChar(prhs[1]) != 1)
{
- mexErrMsgTxt("Cannot copy filename");
+ mexErrMsgTxt("Second input must be a filename\n"
+ "USAGE: OutputSBML(SBMLModel, (filename))");
}
+ nBuflen = (mxGetM(prhs[1])*mxGetN(prhs[1])+1);
+ pacFilename = readUnicodeString(prhs[1], (mwSize)nBuflen);
+
}
-/*********************************************************************************************************
- * get the details of the model
- ***********************************************************************************************************/
+ /*********************************************************************************************************
+ * get the details of the model
+ ***********************************************************************************************************/
-/**
- * get the SBML level and version from the structure
- * and create the document with these
- */
+ /**
+ * get the SBML level and version from the structure
+ * and create the document with these
+ */
- mxLevel = mxGetField(mxModel[0], 0, "SBML_level");
- nLevel = (unsigned int) mxGetScalar(mxLevel);
+ mxLevel = mxGetField(mxModel[0], 0, "SBML_level");
+ nLevel = (unsigned int) mxGetScalar(mxLevel);
- mxVersion = mxGetField(mxModel[0], 0, "SBML_version");
- nVersion = (unsigned int) mxGetScalar(mxVersion);
+ mxVersion = mxGetField(mxModel[0], 0, "SBML_version");
+ nVersion = (unsigned int) mxGetScalar(mxVersion);
if (nLevel > 1)
{
@@ -313,7 +410,7 @@
nBuflen = (mxGetM(mxTimeSymbol)*mxGetN(mxTimeSymbol)+1);
timeSymbol = (char *)mxCalloc(nBuflen, sizeof(char));
nStatus = mxGetString(mxTimeSymbol, timeSymbol, (mwSize)(nBuflen));
-
+
mxDelaySymbol = mxGetField(mxModel[0], 0, "delay_symbol");
nBuflen = (mxGetM(mxDelaySymbol)*mxGetN(mxDelaySymbol)+1);
delaySymbol = (char *)mxCalloc(nBuflen, sizeof(char));
@@ -340,7 +437,7 @@
/* add any saved namespaces */
ns = SBMLNamespaces_create(nLevel, nVersion);
- mxNamespaces = mxGetField(mxModel[0], 0, "namespaces");
+ mxNamespaces = mxGetField(mxModel[0], 0, "namespaces");
GetNamespaces(mxNamespaces, ns);
/* look for fbc */
@@ -349,10 +446,10 @@
{
fbcPresent = 1;
}
-
+
/* the fbc namespace may not be set
- * but thet fbc package may still be used
- */
+ * but thet fbc package may still be used
+ */
if (fbcPresent == 0)
{
nStatus = mxGetFieldNumber(mxModel[0], "fbc_version");
@@ -370,104 +467,104 @@
if (fbcPresent == 1)
{
SBMLDocument_setPkgRequired(sbmlDocument, "fbc", 0);
- mxFBCVersion = mxGetField(mxModel[0], 0, "fbc_version");
- nFBCVersion = (unsigned int) mxGetScalar(mxFBCVersion);
+ mxFBCVersion = mxGetField(mxModel[0], 0, "fbc_version");
+ nFBCVersion = (unsigned int) mxGetScalar(mxFBCVersion);
}
- /* create a model within the document */
+ /* create a model within the document */
sbmlModel = SBMLDocument_createModel(sbmlDocument);
- /* get notes */
- mxNotes = mxGetField(mxModel[0], 0, "notes");
+ /* get notes */
+ mxNotes = mxGetField(mxModel[0], 0, "notes");
nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
-
+
if (nStatus != 0)
{
- mexErrMsgTxt("Cannot copy notes");
+ mexErrMsgTxt("Cannot copy notes");
}
- SBase_setNotesString((SBase_t *)(sbmlModel), pacNotes);
-
- /* get name */
- mxName = mxGetField(mxModel[0], 0, "name");
+ SBase_setNotesString((SBase_t *)(sbmlModel), pacNotes);
+
+ /* get name */
+ mxName = mxGetField(mxModel[0], 0, "name");
nBuflen = (mxGetM(mxName)*mxGetN(mxName)+1);
pacName = (char *)mxCalloc(nBuflen, sizeof(char));
nStatus = mxGetString(mxName, pacName, (mwSize)(nBuflen));
-
+
if (nStatus != 0)
{
- mexErrMsgTxt("Cannot copy name");
+ mexErrMsgTxt("Cannot copy name");
}
- Model_setName(sbmlModel, pacName);
+ Model_setName(sbmlModel, pacName);
- mxUnitDefinitions = mxGetField(mxModel[0], 0, "unitDefinition");
- GetUnitDefinition(mxUnitDefinitions, nLevel, nVersion, sbmlModel);
+ mxUnitDefinitions = mxGetField(mxModel[0], 0, "unitDefinition");
+ GetUnitDefinition(mxUnitDefinitions, nLevel, nVersion, sbmlModel);
- mxCompartments = mxGetField(mxModel[0], 0, "compartment");
- GetCompartment(mxCompartments, nLevel, nVersion, sbmlModel);
+ mxCompartments = mxGetField(mxModel[0], 0, "compartment");
+ GetCompartment(mxCompartments, nLevel, nVersion, sbmlModel);
mxSpecies = mxGetField(mxModel[0], 0, "species");
- GetSpecies(mxSpecies, nLevel, nVersion, sbmlModel);
-
- mxParameters = mxGetField(mxModel[0], 0, "parameter");
- GetParameter(mxParameters, nLevel, nVersion, sbmlModel);
-
+ GetSpecies(mxSpecies, nLevel, nVersion, sbmlModel);
+
+ mxParameters = mxGetField(mxModel[0], 0, "parameter");
+ GetParameter(mxParameters, nLevel, nVersion, sbmlModel);
+
mxRules = mxGetField(mxModel[0], 0, "rule");
- GetRule(mxRules, nLevel, nVersion, sbmlModel);
+ GetRule(mxRules, nLevel, nVersion, sbmlModel);
mxReactions = mxGetField(mxModel[0], 0, "reaction");
- GetReaction(mxReactions, nLevel, nVersion, sbmlModel);
+ GetReaction(mxReactions, nLevel, nVersion, sbmlModel);
- /* level 2 and 3 only */
- if (nLevel > 1)
- {
- /* get id */
- mxId = mxGetField(mxModel[0], 0, "id");
- nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
- pacId = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy id");
- }
+ /* level 2 and 3 only */
+ if (nLevel > 1)
+ {
+ /* get id */
+ mxId = mxGetField(mxModel[0], 0, "id");
+ nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
+ pacId = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
- Model_setId(sbmlModel, pacId);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy id");
+ }
- /* get metaid */
- mxMetaid = mxGetField(mxModel[0], 0, "metaid");
- nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
- pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy metaid");
- }
+ Model_setId(sbmlModel, pacId);
- SBase_setMetaId((SBase_t *) (sbmlModel), pacMetaid);
+ /* get metaid */
+ mxMetaid = mxGetField(mxModel[0], 0, "metaid");
+ nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
+ pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
- mxFunctionDefinitions = mxGetField(mxModel[0], 0, "functionDefinition");
- GetFunctionDefinition(mxFunctionDefinitions, nLevel, nVersion, sbmlModel);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy metaid");
+ }
+ SBase_setMetaId((SBase_t *) (sbmlModel), pacMetaid);
+
+ mxFunctionDefinitions = mxGetField(mxModel[0], 0, "functionDefinition");
+ GetFunctionDefinition(mxFunctionDefinitions, nLevel, nVersion, sbmlModel);
+
mxEvents = mxGetField(mxModel[0], 0, "event");
- GetEvent(mxEvents, nLevel, nVersion, sbmlModel);
+ GetEvent(mxEvents, nLevel, nVersion, sbmlModel);
- }
+ }
- /* level 2 version 2-4 */
- if (nLevel == 2)
- {
+ /* level 2 version 2-4 */
+ if (nLevel == 2)
+ {
if (nVersion > 1)
{
- /* get sboTerm */
- mxSBOTerm = mxGetField(mxModel[0], 0, "sboTerm");
- nSBOTerm = (int)mxGetScalar(mxSBOTerm);
+ /* get sboTerm */
+ mxSBOTerm = mxGetField(mxModel[0], 0, "sboTerm");
+ nSBOTerm = (int)mxGetScalar(mxSBOTerm);
- SBase_setSBOTerm((SBase_t *) (sbmlModel), nSBOTerm);
+ SBase_setSBOTerm((SBase_t *) (sbmlModel), nSBOTerm);
mxCompartmentTypes = mxGetField(mxModel[0], 0, "compartmentType");
GetCompartmentType(mxCompartmentTypes, nLevel, nVersion, sbmlModel);
@@ -481,241 +578,243 @@
mxConstraints = mxGetField(mxModel[0], 0, "constraint");
GetConstraint(mxConstraints, nLevel, nVersion, sbmlModel);
}
- }
+ }
- /* level 3 */
- if (nLevel == 3)
- {
+ /* level 3 */
+ if (nLevel == 3)
+ {
/* get sboTerm */
mxSBOTerm = mxGetField(mxModel[0], 0, "sboTerm");
- nSBOTerm = (int)mxGetScalar(mxSBOTerm);
+ nSBOTerm = (int)mxGetScalar(mxSBOTerm);
- SBase_setSBOTerm((SBase_t *) (sbmlModel), nSBOTerm);
+ SBase_setSBOTerm((SBase_t *) (sbmlModel), nSBOTerm);
mxInitialAssignments = mxGetField(mxModel[0], 0, "initialAssignment");
GetInitialAssignment(mxInitialAssignments, nLevel, nVersion, sbmlModel);
-
+
mxConstraints = mxGetField(mxModel[0], 0, "constraint");
GetConstraint(mxConstraints, nLevel, nVersion, sbmlModel);
/* get substanceUnits */
- mxSubstanceUnits = mxGetField(mxModel[0], 0, "substanceUnits");
- nBuflen = (mxGetM(mxSubstanceUnits)*mxGetN(mxSubstanceUnits)+1);
- pacSubstanceUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxSubstanceUnits, pacSubstanceUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy substanceUnits");
- }
+ mxSubstanceUnits = mxGetField(mxModel[0], 0, "substanceUnits");
+ nBuflen = (mxGetM(mxSubstanceUnits)*mxGetN(mxSubstanceUnits)+1);
+ pacSubstanceUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxSubstanceUnits, pacSubstanceUnits, (mwSize)(nBuflen));
- Model_setSubstanceUnits(sbmlModel, pacSubstanceUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy substanceUnits");
+ }
+ Model_setSubstanceUnits(sbmlModel, pacSubstanceUnits);
+
/* get timeUnits */
- mxTimeUnits = mxGetField(mxModel[0], 0, "timeUnits");
- nBuflen = (mxGetM(mxTimeUnits)*mxGetN(mxTimeUnits)+1);
- pacTimeUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxTimeUnits, pacTimeUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy timeUnits");
- }
+ mxTimeUnits = mxGetField(mxModel[0], 0, "timeUnits");
+ nBuflen = (mxGetM(mxTimeUnits)*mxGetN(mxTimeUnits)+1);
+ pacTimeUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxTimeUnits, pacTimeUnits, (mwSize)(nBuflen));
- Model_setTimeUnits(sbmlModel, pacTimeUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy timeUnits");
+ }
+ Model_setTimeUnits(sbmlModel, pacTimeUnits);
+
/* get lengthUnits */
- mxLengthUnits = mxGetField(mxModel[0], 0, "lengthUnits");
- nBuflen = (mxGetM(mxLengthUnits)*mxGetN(mxLengthUnits)+1);
- pacLengthUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxLengthUnits, pacLengthUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy lengthUnits");
- }
+ mxLengthUnits = mxGetField(mxModel[0], 0, "lengthUnits");
+ nBuflen = (mxGetM(mxLengthUnits)*mxGetN(mxLengthUnits)+1);
+ pacLengthUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxLengthUnits, pacLengthUnits, (mwSize)(nBuflen));
- Model_setLengthUnits(sbmlModel, pacLengthUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy lengthUnits");
+ }
+ Model_setLengthUnits(sbmlModel, pacLengthUnits);
+
/* get areaUnits */
- mxAreaUnits = mxGetField(mxModel[0], 0, "areaUnits");
- nBuflen = (mxGetM(mxAreaUnits)*mxGetN(mxAreaUnits)+1);
- pacAreaUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxAreaUnits, pacAreaUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy areaUnits");
- }
+ mxAreaUnits = mxGetField(mxModel[0], 0, "areaUnits");
+ nBuflen = (mxGetM(mxAreaUnits)*mxGetN(mxAreaUnits)+1);
+ pacAreaUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxAreaUnits, pacAreaUnits, (mwSize)(nBuflen));
- Model_setAreaUnits(sbmlModel, pacAreaUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy areaUnits");
+ }
+ Model_setAreaUnits(sbmlModel, pacAreaUnits);
+
/* get volumeUnits */
- mxVolumeUnits = mxGetField(mxModel[0], 0, "volumeUnits");
- nBuflen = (mxGetM(mxVolumeUnits)*mxGetN(mxVolumeUnits)+1);
- pacVolumeUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxVolumeUnits, pacVolumeUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy volumeUnits");
- }
+ mxVolumeUnits = mxGetField(mxModel[0], 0, "volumeUnits");
+ nBuflen = (mxGetM(mxVolumeUnits)*mxGetN(mxVolumeUnits)+1);
+ pacVolumeUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxVolumeUnits, pacVolumeUnits, (mwSize)(nBuflen));
- Model_setVolumeUnits(sbmlModel, pacVolumeUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy volumeUnits");
+ }
+ Model_setVolumeUnits(sbmlModel, pacVolumeUnits);
+
/* get extentUnits */
- mxExtentUnits = mxGetField(mxModel[0], 0, "extentUnits");
- nBuflen = (mxGetM(mxExtentUnits)*mxGetN(mxExtentUnits)+1);
- pacExtentUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxExtentUnits, pacExtentUnits, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy extentUnits");
- }
+ mxExtentUnits = mxGetField(mxModel[0], 0, "extentUnits");
+ nBuflen = (mxGetM(mxExtentUnits)*mxGetN(mxExtentUnits)+1);
+ pacExtentUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxExtentUnits, pacExtentUnits, (mwSize)(nBuflen));
- Model_setExtentUnits(sbmlModel, pacExtentUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy extentUnits");
+ }
+ Model_setExtentUnits(sbmlModel, pacExtentUnits);
+
/* get conversionFactor */
- mxConversionFactor = mxGetField(mxModel[0], 0, "conversionFactor");
- nBuflen = (mxGetM(mxConversionFactor)*mxGetN(mxConversionFactor)+1);
- pacConversionFactor = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxConversionFactor, pacConversionFactor, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy conversionFactor");
- }
+ mxConversionFactor = mxGetField(mxModel[0], 0, "conversionFactor");
+ nBuflen = (mxGetM(mxConversionFactor)*mxGetN(mxConversionFactor)+1);
+ pacConversionFactor = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxConversionFactor, pacConversionFactor, (mwSize)(nBuflen));
- Model_setConversionFactor(sbmlModel, pacConversionFactor);
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy conversionFactor");
+ }
+ Model_setConversionFactor(sbmlModel, pacConversionFactor);
+ }
- /* get annotations */
+
+ /* get annotations */
mxAnnotations = mxGetField(mxModel[0], 0, "annotation");
nBuflen = (mxGetM(mxAnnotations)*mxGetN(mxAnnotations)+1);
pacAnnotations = (char *)mxCalloc(nBuflen, sizeof(char));
-
+
nStatus = mxGetString(mxAnnotations, pacAnnotations, (mwSize)(nBuflen));
-
+
if (nStatus != 0)
{
- mexErrMsgTxt("Cannot copy annotations");
+ mexErrMsgTxt("Cannot copy annotations");
}
SBase_setAnnotationString((SBase_t *) (sbmlModel), pacAnnotations);
- if (fbcPresent == 1)
+ if (fbcPresent == 1)
+ {
+#ifdef USE_FBC
+ mxFluxBounds = mxGetField(mxModel[0], 0, "fbc_fluxBound");
+ GetFluxBound(mxFluxBounds, nLevel, nVersion, nFBCVersion, sbmlModel);
+
+ mxObjectives = mxGetField(mxModel[0], 0, "fbc_objective");
+ GetObjective(mxObjectives, nLevel, nVersion, nFBCVersion, sbmlModel);
+
+ /* get conversionFactor */
+ mxActiveObjective = mxGetField(mxModel[0], 0, "fbc_activeObjective");
+ nBuflen = (mxGetM(mxActiveObjective)*mxGetN(mxActiveObjective)+1);
+ pacActiveObjective = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxActiveObjective, pacActiveObjective, (mwSize)(nBuflen));
+
+ if (nStatus != 0)
{
-#ifdef USE_FBC
- mxFluxBounds = mxGetField(mxModel[0], 0, "fbc_fluxBound");
- GetFluxBound(mxFluxBounds, nLevel, nVersion, nFBCVersion, sbmlModel);
-
- mxObjectives = mxGetField(mxModel[0], 0, "fbc_objective");
- GetObjective(mxObjectives, nLevel, nVersion, nFBCVersion, sbmlModel);
-
- /* get conversionFactor */
- mxActiveObjective = mxGetField(mxModel[0], 0, "fbc_activeObjective");
- nBuflen = (mxGetM(mxActiveObjective)*mxGetN(mxActiveObjective)+1);
- pacActiveObjective = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxActiveObjective, pacActiveObjective, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy ActiveObjective");
- }
-
- FbcModelPlugin_setActiveObjectiveId(SBase_getPlugin((SBase_t *)(sbmlModel), "fbc"),
- pacActiveObjective);
-#endif
+ mexErrMsgTxt("Cannot copy ActiveObjective");
}
-
-/************************************************************************************************************
- * output the resulting model to specified file
- *********************************************************************************************************/
+ FbcModelPlugin_setActiveObjectiveId(SBase_getPlugin((SBase_t *)(sbmlModel), "fbc"),
+ pacActiveObjective);
+#endif
+ }
- if (nrhs == 1)
- {
- /**
- * prompt user for a filename
- * and write the document to this
- */
- /* extension to look for */
+ /************************************************************************************************************
+ * output the resulting model to specified file
+ *********************************************************************************************************/
+
+ if (nrhs == 1)
+ {
+ /**
+ * prompt user for a filename
+ * and write the document to this
+ */
+
+ /* extension to look for */
mxExt[0] = mxCreateString(".xml");
nStatus = mexCallMATLAB(2, mxFilename, 1, mxExt, "uiputfile");
-
+
if (nStatus != 0)
{
mexErrMsgTxt("Failed to read filename");
}
- /* get the filename returned */
- nBuflen = (mxGetM(mxFilename[0])*mxGetN(mxFilename[0])+1);
- pacTempString1 = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxFilename[0], pacTempString1, (mwSize)(nBuflen));
-
- if (nStatus != 0)
+ pacFilename = readUnicodeStringFromArrays(mxFilename);
+
+#if USE_FILE_WCHAR
+ if (wcsstr(pacFilename, L".xml") == NULL)
{
- mexErrMsgTxt("Cannot copy filename");
+ wcscat(pacFilename, L".xml");
}
-
- /* get the full path */
- nBufferLen = (mxGetM(mxFilename[1])*mxGetN(mxFilename[1])+1);
- pacTempString2 = (char *)mxCalloc(nBufferLen, sizeof(char));
- nStatus = mxGetString(mxFilename[1], pacTempString2, (mwSize)(nBufferLen));
-
- if (nStatus != 0)
+#else
+ /* check that the extension has been used */
+ if (strstr(pacFilename, ".xml") == NULL)
{
- mexErrMsgTxt("Cannot copy path");
+ strcat(pacFilename, ".xml");
}
+#endif
+ }
+ else
+ {
+ /*
+ * user has specified a filename
+ * check that the extension has been used
+ */
+#if USE_FILE_WCHAR
+ if (wcsstr(pacFilename, L".xml") == NULL)
+ {
+ wcscat(pacFilename, L".xml");
+ }
+#else
+ /* check that the extension has been used */
+ if (strstr(pacFilename, ".xml") == NULL)
+ {
+ strcat(pacFilename, ".xml");
+ }
+#endif
+ }
- /* write full path and filename */
- pacFilename = (char *) mxCalloc(nBufferLen+nBuflen+4, sizeof(char));
- strcpy(pacFilename, pacTempString2);
- strcat(pacFilename, pacTempString1);
- /* check that the extension has been used */
- if (strstr(pacFilename, ".xml") == NULL)
- {
- strcat(pacFilename, ".xml");
- }
- }
- else
- {
- /*
- * user has specified a filename
- * check that the extension has been used
- */
- if (strstr(pacFilename, ".xml") == NULL)
- {
- strcat(pacFilename, ".xml");
- }
- }
-
-
/* write the SBML document to the filename specified */
- nStatus = writeSBML(sbmlDocument, pacFilename);
-
+#if USE_FILE_WCHAR
+ {
+ char* sbml = writeSBMLToString(sbmlDocument);
+ size_t len = strlen(sbml);
+ FILE* fp = _wfopen(pacFilename, L"w");
+ fwrite(sbml, sizeof(char), len, fp);
+ fclose(fp);
+ nStatus = 1;
+ }
+#else
+ nStatus = writeSBML(sbmlDocument, pacFilename);
+#endif
/* don't output messages from installer tests */
if (inInstaller == 0)
{
- if (nStatus != 1)
- {
- mexErrMsgTxt("Failed to write file");
- }
+ if (nStatus != 1)
+ {
+ mexErrMsgTxt("Failed to write file");
+ }
else
{
mexPrintf("Document written\n");
}
}
-
- /* free any memory allocated */
- mxFree(pacNotes);
- mxFree(pacAnnotations);
- mxFree(pacName);
+
+ /* free any memory allocated */
+ mxFree(pacNotes);
+ mxFree(pacAnnotations);
+ mxFree(pacName);
if (nLevel > 1)
{
mxFree(pacMetaid);
@@ -736,14 +835,14 @@
{
mxFree(pacTempString1);
mxFree(pacTempString2);
- mxFree(pacFilename);
+ mxFree(pacFilename);
mxDestroyArray(mxFilename[0]);
mxDestroyArray(mxFilename[1]);
mxDestroyArray(mxExt[0]);
}
- mxDestroyArray(mxCheckStructure[0]);
+ mxDestroyArray(mxCheckStructure[0]);
- SBMLDocument_free(sbmlDocument);
+ SBMLDocument_free(sbmlDocument);
}
/**
@@ -992,92 +1091,92 @@
*
*/
void
-GetCompartment (mxArray * mxCompartments,
- unsigned int unSBMLLevel,
- unsigned int unSBMLVersion,
- Model_t * sbmlModel)
+GetCompartment ( mxArray * mxCompartments,
+ unsigned int unSBMLLevel,
+ unsigned int unSBMLVersion,
+ Model_t * sbmlModel)
{
- size_t nNoCompartments = mxGetNumberOfElements(mxCompartments);
+ size_t nNoCompartments = mxGetNumberOfElements(mxCompartments);
- int nStatus;
- size_t nBuflen;
+ int nStatus;
+ size_t nBuflen;
- /* field values */
- char * pacNotes;
- char * pacAnnotations;
- char * pacName;
- char * pacId;
+ /* field values */
+ char * pacNotes;
+ char * pacAnnotations;
+ char * pacName;
+ char * pacId;
char * pacCompartmentType;
- double dVolume;
- unsigned int unSpatialDimensions;
+ double dVolume;
+ unsigned int unSpatialDimensions;
double dSpatialDimensions;
- double dSize;
- char * pacUnits;
- char * pacOutside;
- int nConstant;
- unsigned int unIsSetVolume;
- unsigned int unIsSetSize;
- unsigned int unIsSetSpatialDimensions;
+ double dSize;
+ char * pacUnits;
+ char * pacOutside;
+ int nConstant;
+ unsigned int unIsSetVolume;
+ unsigned int unIsSetSize;
+ unsigned int unIsSetSpatialDimensions;
int nSBOTerm;
- char * pacMetaid;
+ char * pacMetaid;
mxArray *mxMetaid, *mxIsSetSpatialDimensions;
- mxArray * mxNotes, * mxAnnotations, * mxName, * mxId, * mxUnits;
- mxArray * mxOutside, * mxVolume, * mxIsSetVolume, * mxSpatialDimensions;
+ mxArray * mxNotes, * mxAnnotations, * mxName, * mxId, * mxUnits;
+ mxArray * mxOutside, * mxVolume, * mxIsSetVolume, * mxSpatialDimensions;
mxArray * mxSize, * mxConstant, * mxIsSetSize, * mxCompartmentType, * mxSBOTerm;
-
- Compartment_t *pCompartment;
- int i;
- for (i = 0; i < nNoCompartments; i++) {
+ Compartment_t *pCompartment;
+ int i;
- pCompartment = Model_createCompartment(sbmlModel);
+ for (i = 0; i < nNoCompartments; i++) {
+ pCompartment = Model_createCompartment(sbmlModel);
- /* get notes */
- mxNotes = mxGetField(mxCompartments, i, "notes");
- nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
- pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy notes");
- }
+ /* get notes */
+ mxNotes = mxGetField(mxCompartments, i, "notes");
+ nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
+ pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
- SBase_setNotesString((SBase_t *) (pCompartment), pacNotes);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy notes");
+ }
+ SBase_setNotesString((SBase_t *) (pCompartment), pacNotes);
- /* get name */
- mxName = mxGetField(mxCompartments, i, "name");
- nBuflen = (mxGetM(mxName)*mxGetN(mxName)+1);
- pacName = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxName, pacName, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy name");
- }
+ /* get name */
+ mxName = mxGetField(mxCompartments, i, "name");
+ nBuflen = (mxGetM(mxName)*mxGetN(mxName)+1);
+ pacName = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxName, pacName, (mwSize)(nBuflen));
- Compartment_setName(pCompartment, pacName);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy name");
+ }
+ Compartment_setName(pCompartment, pacName);
- /* get units */
- mxUnits = mxGetField(mxCompartments, i, "units");
- nBuflen = (mxGetM(mxUnits)*mxGetN(mxUnits)+1);
- pacUnits = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxUnits, pacUnits, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy units");
- }
+ /* get units */
+ mxUnits = mxGetField(mxCompartments, i, "units");
+ nBuflen = (mxGetM(mxUnits)*mxGetN(mxUnits)+1);
+ pacUnits = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxUnits, pacUnits, (mwSize)(nBuflen));
- Compartment_setUnits(pCompartment, pacUnits);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy units");
+ }
+ Compartment_setUnits(pCompartment, pacUnits);
+
/* out of L3 */
-
+
if (unSBMLLevel < 3)
{
/* get outside */
@@ -1092,218 +1191,218 @@
}
Compartment_setOutside(pCompartment, pacOutside);
-
+
/* get isSetVolume */
mxIsSetVolume = mxGetField(mxCompartments, i, "isSetVolume");
unIsSetVolume = (unsigned int)mxGetScalar(mxIsSetVolume);
}
- /* level 1 only */
- if (unSBMLLevel == 1)
- {
- /* get volume */
- mxVolume = mxGetField(mxCompartments, i, "volume");
- dVolume = mxGetScalar(mxVolume);
+ /* level 1 only */
+ if (unSBMLLevel == 1)
+ {
+ /* get volume */
+ mxVolume = mxGetField(mxCompartments, i, "volume");
+ dVolume = mxGetScalar(mxVolume);
- if (unIsSetVolume == 1) {
- Compartment_setVolume(pCompartment, dVolume);
- }
-
- }
+ if (unIsSetVolume == 1) {
+ Compartment_setVolume(pCompartment, dVolume);
+ }
- /* level 2 only */
- if (unSBMLLevel == 2)
- {
- /* get metaid */
- mxMetaid = mxGetField(mxCompartments, i, "metaid");
- nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
- pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy metaid");
- }
+ }
- SBase_setMetaId((SBase_t *) (pCompartment), pacMetaid);
+ /* level 2 only */
+ if (unSBMLLevel == 2)
+ {
+ /* get metaid */
+ mxMetaid = mxGetField(mxCompartments, i, "metaid");
+ nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
+ pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy metaid");
+ }
+
+ SBase_setMetaId((SBase_t *) (pCompartment), pacMetaid);
+
/* get id */
- mxId = mxGetField(mxCompartments, i, "id");
- nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
- pacId = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
+ mxId = mxGetField(mxCompartments, i, "id");
+ nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
+ pacId = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy id");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy id");
+ }
- Compartment_setId(pCompartment, pacId);
-
-
- /* get constant */
- mxConstant = mxGetField(mxCompartments, i, "constant");
- nConstant = (int)mxGetScalar(mxConstant);
+ Compartment_setId(pCompartment, pacId);
- Compartment_setConstant(pCompartment, nConstant);
- /* get spatialdimensions */
- mxSpatialDimensions = mxGetField(mxCompartments, i, "spatialDimensions");
- unSpatialDimensions = (unsigned int)mxGetScalar(mxSpatialDimensions);
+ /* get constant */
+ mxConstant = mxGetField(mxCompartments, i, "constant");
+ nConstant = (int)mxGetScalar(mxConstant);
- Compartment_setSpatialDimensions(pCompartment, unSpatialDimensions);
+ Compartment_setConstant(pCompartment, nConstant);
- /* get isSetSize */
- mxIsSetSize = mxGetField(mxCompartments, i, "isSetSize");
- unIsSetSize = (unsigned int)mxGetScalar(mxIsSetSize);
+ /* get spatialdimensions */
+ mxSpatialDimensions = mxGetField(mxCompartments, i, "spatialDimensions");
+ unSpatialDimensions = (unsigned int)mxGetScalar(mxSpatialDimensions);
-
- /* get size */
- mxSize = mxGetField(mxCompartments, i, "size");
- dSize = mxGetScalar(mxSize);
+ Compartment_setSpatialDimensions(pCompartment, unSpatialDimensions);
- if (unIsSetSize == 1) {
- Compartment_setSize(pCompartment, dSize);
- }
+ /* get isSetSize */
+ mxIsSetSize = mxGetField(mxCompartments, i, "isSetSize");
+ unIsSetSize = (unsigned int)mxGetScalar(mxIsSetSize);
+
+ /* get size */
+ mxSize = mxGetField(mxCompartments, i, "size");
+ dSize = mxGetScalar(mxSize);
+
+ if (unIsSetSize == 1) {
+ Compartment_setSize(pCompartment, dSize);
+ }
+
/* level 2 version 2 onwards */
if (unSBMLVersion > 1)
{
- /* get compartmentType */
- mxCompartmentType = mxGetField(mxCompartments, i, "compartmentType");
- nBuflen = (mxGetM(mxCompartmentType)*mxGetN(mxCompartmentType)+1);
- pacCompartmentType = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxCompartmentType, pacCompartmentType, (mwSize)(nBuflen));
+ /* get compartmentType */
+ mxCompartmentType = mxGetField(mxCompartments, i, "compartmentType");
+ nBuflen = (mxGetM(mxCompartmentType)*mxGetN(mxCompartmentType)+1);
+ pacCompartmentType = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxCompartmentType, pacCompartmentType, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy compartmentType");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy compartmentType");
+ }
- Compartment_setCompartmentType(pCompartment, pacCompartmentType);
-
+ Compartment_setCompartmentType(pCompartment, pacCompartmentType);
+
}
/* level 2 version 3 + */
if (unSBMLVersion > 2)
{
- /* get sboTerm */
- mxSBOTerm = mxGetField(mxCompartments, i, "sboTerm");
- nSBOTerm = (int)mxGetScalar(mxSBOTerm);
+ /* get sboTerm */
+ mxSBOTerm = mxGetField(mxCompartments, i, "sboTerm");
+ nSBOTerm = (int)mxGetScalar(mxSBOTerm);
- SBase_setSBOTerm((SBase_t *) (pCompartment), nSBOTerm);
+ SBase_setSBOTerm((SBase_t *) (pCompartment), nSBOTerm);
}
- }
- /* level 3 only */
- else if (unSBMLLevel == 3)
- {
- /* get metaid */
- mxMetaid = mxGetField(mxCompartments, i, "metaid");
- nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
- pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy metaid");
- }
+ }
+ /* level 3 only */
+ else if (unSBMLLevel == 3)
+ {
+ /* get metaid */
+ mxMetaid = mxGetField(mxCompartments, i, "metaid");
+ nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
+ pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
- SBase_setMetaId((SBase_t *) (pCompartment), pacMetaid);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy metaid");
+ }
+ SBase_setMetaId((SBase_t *) (pCompartment), pacMetaid);
+
/* get id */
- mxId = mxGetField(mxCompartments, i, "id");
- nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
- pacId = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
+ mxId = mxGetField(mxCompartments, i, "id");
+ nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
+ pacId = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy id");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy id");
+ }
- Compartment_setId(pCompartment, pacId);
-
-
- /* get constant */
- mxConstant = mxGetField(mxCompartments, i, "constant");
- nConstant = (int)mxGetScalar(mxConstant);
+ Compartment_setId(pCompartment, pacId);
- Compartment_setConstant(pCompartment, nConstant);
- /* get isSetSpatialDimensions */
- mxIsSetSpatialDimensions = mxGetField(mxCompartments, i, "isSetSpatialDimensions");
- unIsSetSpatialDimensions = (unsigned int)mxGetScalar(mxIsSetSpatialDimensions);
+ /* get constant */
+ mxConstant = mxGetField(mxCompartments, i, "constant");
+ nConstant = (int)mxGetScalar(mxConstant);
+ Compartment_setConstant(pCompartment, nConstant);
+
+ /* get isSetSpatialDimensions */
+ mxIsSetSpatialDimensions = mxGetField(mxCompartments, i, "isSetSpatialDimensions");
+ unIsSetSpatialDimensions = (unsigned int)mxGetScalar(mxIsSetSpatialDimensions);
+
/* get spatialdimensions */
- mxSpatialDimensions = mxGetField(mxCompartments, i, "spatialDimensions");
- dSpatialDimensions = mxGetScalar(mxSpatialDimensions);
+ mxSpatialDimensions = mxGetField(mxCompartments, i, "spatialDimensions");
+ dSpatialDimensions = mxGetScalar(mxSpatialDimensions);
if (unIsSetSpatialDimensions == 1)
{
Compartment_setSpatialDimensionsAsDouble(pCompartment, dSpatialDimensions);
}
- /* get isSetSize */
- mxIsSetSize = mxGetField(mxCompartments, i, "isSetSize");
- unIsSetSize = (unsigned int)mxGetScalar(mxIsSetSize);
+ /* get isSetSize */
+ mxIsSetSize = mxGetField(mxCompartments, i, "isSetSize");
+ unIsSetSize = (unsigned int)mxGetScalar(mxIsSetSize);
-
- /* get size */
- mxSize = mxGetField(mxCompartments, i, "size");
- dSize = mxGetScalar(mxSize);
- if (unIsSetSize == 1) {
- Compartment_setSize(pCompartment, dSize);
- }
+ /* get size */
+ mxSize = mxGetField(mxCompartments, i, "size");
+ dSize = mxGetScalar(mxSize);
- /* get sboTerm */
- mxSBOTerm = mxGetField(mxCompartments, i, "sboTerm");
- nSBOTerm = (int)mxGetScalar(mxSBOTerm);
+ if (unIsSetSize == 1) {
+ Compartment_setSize(pCompartment, dSize);
+ }
- SBase_setSBOTerm((SBase_t *) (pCompartment), nSBOTerm);
- }
+ /* get sboTerm */
+ mxSBOTerm = mxGetField(mxCompartments, i, "sboTerm");
+ nSBOTerm = (int)mxGetScalar(mxSBOTerm);
- /* get annotations */
- mxAnnotations = mxGetField(mxCompartments, i, "annotation");
- nBuflen = (mxGetM(mxAnnotations)*mxGetN(mxAnnotations)+1);
- pacAnnotations = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxAnnotations, pacAnnotations, (mwSize)(nBuflen));
+ SBase_setSBOTerm((SBase_t *) (pCompartment), nSBOTerm);
+ }
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy annotations");
- }
+ /* get annotations */
+ mxAnnotations = mxGetField(mxCompartments, i, "annotation");
+ nBuflen = (mxGetM(mxAnnotations)*mxGetN(mxAnnotations)+1);
+ pacAnnotations = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxAnnotations, pacAnnotations, (mwSize)(nBuflen));
- SBase_setAnnotationString((SBase_t *) (pCompartment), pacAnnotations);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy annotations");
+ }
+ SBase_setAnnotationString((SBase_t *) (pCompartment), pacAnnotations);
+
/* free any memory allocated */
- mxFree(pacNotes);
- mxFree(pacAnnotations);
- mxFree(pacName);
- mxFree(pacUnits);
+ mxFree(pacNotes);
+ mxFree(pacAnnotations);
+ mxFree(pacName);
+ mxFree(pacUnits);
if (unSBMLLevel == 1)
{
- mxFree(pacOutside);
+ mxFree(pacOutside);
}
- /* level 2 only */
- else if (unSBMLLevel == 2)
- {
- mxFree(pacOutside);
- mxFree(pacId);
- mxFree(pacMetaid);
+ /* level 2 only */
+ else if (unSBMLLevel == 2)
+ {
+ mxFree(pacOutside);
+ mxFree(pacId);
+ mxFree(pacMetaid);
if (unSBMLVersion > 1)
{
mxFree(pacCompartmentType);
}
}
- else if (unSBMLLevel == 3)
- {
- mxFree(pacId);
- mxFree(pacMetaid);
+ else if (unSBMLLevel == 3)
+ {
+ mxFree(pacId);
+ mxFree(pacMetaid);
}
- }
+ }
}
/**
@@ -1321,133 +1420,133 @@
*/
void
GetUnitDefinition ( mxArray * mxUnitDefinitions,
- unsigned int unSBMLLevel,
- unsigned int unSBMLVersion,
- Model_t * sbmlModel )
+ unsigned int unSBMLLevel,
+ unsigned int unSBMLVersion,
+ Model_t * sbmlModel )
{
- size_t nNoUnitDefinitions = mxGetNumberOfElements(mxUnitDefinitions);
-
- int nStatus;
- size_t nBuflen;
+ size_t nNoUnitDefinitions = mxGetNumberOfElements(mxUnitDefinitions);
- /* values */
- char * pacNotes;
- char * pacAnnotations;
- char * pacName;
- char * pacId = NULL;
+ int nStatus;
+ size_t nBuflen;
+
+ /* values */
+ char * pacNotes;
+ char * pacAnnotations;
+ char * pacName;
+ char * pacId = NULL;
int nSBOTerm;
- char * pacMetaid;
+ char * pacMetaid;
mxArray *mxMetaid;
- mxArray * mxNotes, * mxAnnotations, * mxName, * mxId, * mxUnits, * mxSBOTerm;
+ mxArray * mxNotes, * mxAnnotations, * mxName, * mxId, * mxUnits, * mxSBOTerm;
- UnitDefinition_t *pUnitDefinition;
- int i;
+ UnitDefinition_t *pUnitDefinition;
+ int i;
- for (i = 0; i < nNoUnitDefinitions; i++)
- {
- pUnitDefinition = Model_createUnitDefinition(sbmlModel);
+ for (i = 0; i < nNoUnitDefinitions; i++)
+ {
+ pUnitDefinition = Model_createUnitDefinition(sbmlModel);
- /* get notes */
- mxNotes = mxGetField(mxUnitDefinitions, i, "notes");
- nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
- pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
+ /* get notes */
+ mxNotes = mxGetField(mxUnitDefinitions, i, "notes");
+ nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
+ pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy notes");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy notes");
+ }
- SBase_setNotesString((SBase_t *) (pUnitDefinition), pacNotes);
+ SBase_setNotesString((SBase_t *) (pUnitDefinition), pacNotes);
- /* get name */
- mxName = mxGetField(mxUnitDefinitions, i, "name");
- nBuflen = (mxGetM(mxName)*mxGetN(mxName)+1);
- pacName = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxName, pacName, (mwSize)(nBuflen));
+ /* get name */
+ mxName = mxGetField(mxUnitDefinitions, i, "name");
+ nBuflen = (mxGetM(mxName)*mxGetN(mxName)+1);
+ pacName = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxName, pacName, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy name");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy name");
+ }
- UnitDefinition_setName(pUnitDefinition, pacName);
+ UnitDefinition_setName(pUnitDefinition, pacName);
-
- /* get list of units */
- mxUnits = mxGetField(mxUnitDefinitions, i, "unit");
- GetUnit(mxUnits, unSBMLLevel, unSBMLVersion, pUnitDefinition);
+ /* get list of units */
+ mxUnits = mxGetField(mxUnitDefinitions, i, "unit");
+ GetUnit(mxUnits, unSBMLLevel, unSBMLVersion, pUnitDefinition);
- /* level 2 only */
- if (unSBMLLevel > 1)
- {
- /* get metaid */
- mxMetaid = mxGetField(mxUnitDefinitions, i, "metaid");
- nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
- pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy metaid");
- }
- SBase_setMetaId((SBase_t *) (pUnitDefinition), pacMetaid);
+ /* level 2 only */
+ if (unSBMLLevel > 1)
+ {
+ /* get metaid */
+ mxMetaid = mxGetField(mxUnitDefinitions, i, "metaid");
+ nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
+ pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
- /* get id */
- mxId = mxGetField(mxUnitDefinitions, i, "id");
- nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
- pacId = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy metaid");
+ }
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy id");
- }
+ SBase_setMetaId((SBase_t *) (pUnitDefinition), pacMetaid);
- UnitDefinition_setId(pUnitDefinition, pacId);
+ /* get id */
+ mxId = mxGetField(mxUnitDefinitions, i, "id");
+ nBuflen = (mxGetM(mxId)*mxGetN(mxId)+1);
+ pacId = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxId, pacId, (mwSize)(nBuflen));
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy id");
+ }
+
+ UnitDefinition_setId(pUnitDefinition, pacId);
+
/* level 2 version 3 only */
if ((unSBMLLevel == 2 && unSBMLVersion > 2) || unSBMLLevel > 2)
{
- /* get sboTerm */
- mxSBOTerm = mxGetField(mxUnitDefinitions, i, "sboTerm");
- nSBOTerm = (int)mxGetScalar(mxSBOTerm);
+ /* get sboTerm */
+ mxSBOTerm = mxGetField(mxUnitDefinitions, i, "sboTerm");
+ nSBOTerm = (int)mxGetScalar(mxSBOTerm);
- SBase_setSBOTerm((SBase_t *) (pUnitDefinition), nSBOTerm);
+ SBase_setSBOTerm((SBase_t *) (pUnitDefinition), nSBOTerm);
}
- }
+ }
- /* get annotations */
- mxAnnotations = mxGetField(mxUnitDefinitions, i, "annotation");
- nBuflen = (mxGetM(mxAnnotations)*mxGetN(mxAnnotations)+1);
- pacAnnotations = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxAnnotations, pacAnnotations, (mwSize)(nBuflen));
+ /* get annotations */
+ mxAnnotations = mxGetField(mxUnitDefinitions, i, "annotation");
+ nBuflen = (mxGetM(mxAnnotations)*mxGetN(mxAnnotations)+1);
+ pacAnnotations = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxAnnotations, pacAnnotations, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy annotations");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy annotations");
+ }
- SBase_setAnnotationString((SBase_t *) (pUnitDefinition), pacAnnotations);
+ SBase_setAnnotationString((SBase_t *) (pUnitDefinition), pacAnnotations);
/* free any memory allocated */
- mxFree(pacNotes);
- mxFree(pacAnnotations);
- mxFree(pacName);
- /* level 2 only */
- if (unSBMLLevel > 1)
- {
- mxFree(pacId);
- mxFree(pacMetaid);
+ mxFree(pacNotes);
+ mxFree(pacAnnotations);
+ mxFree(pacName);
+ /* level 2 only */
+ if (unSBMLLevel > 1)
+ {
+ mxFree(pacId);
+ mxFree(pacMetaid);
}
- }
+ }
}
/**
@@ -1467,142 +1566,142 @@
GetUnit ( mxArray * mxUnits,
unsigned int unSBMLLevel,
unsigned int unSBMLVersion,
- UnitDefinition_t * sbmlUnitDefinition )
+ UnitDefinition_t * sbmlUnitDefinition )
{
- size_t nNoUnits = mxGetNumberOfElements(mxUnits);
-
- int nStatus;
- size_t nBuflen;
+ size_t nNoUnits = mxGetNumberOfElements(mxUnits);
- /* values */
- char * pacNotes;
- char * pacAnnotations;
- char * pacKind;
- int nExponent;
- int nScale;
- double dMultiplier;
- double dOffset;
+ int nStatus;
+ size_t nBuflen;
+
+ /* values */
+ char * pacNotes;
+ char * pacAnnotations;
+ char * pacKind;
+ int nExponent;
+ int nScale;
+ double dMultiplier;
+ double dOffset;
double dExponent;
int nSBOTerm;
- char * pacMetaid;
+ char * pacMetaid;
mxArray *mxMetaid;
- mxArray * mxNotes, * mxAnnotations, * mxKind, *mxExponent;
- mxArray * mxScale, * mxMultiplier, * mxOffset, * mxSBOTerm;
+ mxArray * mxNotes, * mxAnnotations, * mxKind, *mxExponent;
+ mxArray * mxScale, * mxMultiplier, * mxOffset, * mxSBOTerm;
- Unit_t *pUnit;
- int i;
+ Unit_t *pUnit;
+ int i;
- for (i = 0; i < nNoUnits; i++)
- {
- pUnit = UnitDefinition_createUnit(sbmlUnitDefinition);
+ for (i = 0; i < nNoUnits; i++)
+ {
+ pUnit = UnitDefinition_createUnit(sbmlUnitDefinition);
- /* get notes */
- mxNotes = mxGetField(mxUnits, i, "notes");
- nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
- pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
+ /* get notes */
+ mxNotes = mxGetField(mxUnits, i, "notes");
+ nBuflen = (mxGetM(mxNotes)*mxGetN(mxNotes)+1);
+ pacNotes = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxNotes, pacNotes, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy notes");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy notes");
+ }
- SBase_setNotesString((SBase_t *) (pUnit), pacNotes);
+ SBase_setNotesString((SBase_t *) (pUnit), pacNotes);
- /* get kind */
- mxKind = mxGetField(mxUnits, i, "kind");
- nBuflen = (mxGetM(mxKind)*mxGetN(mxKind)+1);
- pacKind = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxKind, pacKind, (mwSize)(nBuflen));
+ /* get kind */
+ mxKind = mxGetField(mxUnits, i, "kind");
+ nBuflen = (mxGetM(mxKind)*mxGetN(mxKind)+1);
+ pacKind = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxKind, pacKind, (mwSize)(nBuflen));
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy kind");
- }
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy kind");
+ }
- Unit_setKind(pUnit, UnitKind_forName(pacKind));
+ Unit_setKind(pUnit, UnitKind_forName(pacKind));
- /* get scale */
- mxScale = mxGetField(mxUnits, i, "scale");
- nScale = (int)mxGetScalar(mxScale);
+ /* get scale */
+ mxScale = mxGetField(mxUnits, i, "scale");
+ nScale = (int)mxGetScalar(mxScale);
- Unit_setScale(pUnit, nScale);
+ Unit_setScale(pUnit, nScale);
- /* level 2 only */
- if (unSBMLLevel == 2)
- {
- /* get metaid */
- mxMetaid = mxGetField(mxUnits, i, "metaid");
- nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
- pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
- nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
-
- if (nStatus != 0)
- {
- mexErrMsgTxt("Cannot copy metaid");
- }
+ /* level 2 only */
+ if (unSBMLLevel == 2)
+ {
+ /* get metaid */
+ mxMetaid = mxGetField(mxUnits, i, "metaid");
+ nBuflen = (mxGetM(mxMetaid)*mxGetN(mxMetaid)+1);
+ pacMetaid = (char *)mxCalloc(nBuflen, sizeof(char));
+ nStatus = mxGetString(mxMetaid, pacMetaid, (mwSize)(nBuflen));
- SBase_setMetaId((SBase_t *) (pUnit), pacMetaid);
+ if (nStatus != 0)
+ {
+ mexErrMsgTxt("Cannot copy metaid");
+ }
- /* get multiplier */
- mxMultiplier = mxGetField(mxUnits, i, "multiplier");
- dMultiplier = mxGetScalar(mxMultiplier);
+ SBase_setMetaId((SBase_t *) (pUnit), pacMetaid);
- Unit_setMultiplier(pUnit, dMultiplier);
-
+ /* get multiplier */
+ mxMultiplier = mxGetField(mxUnits, i, "multiplier");
+ dMultiplier = mxGetScalar(mxMultiplier);
+
+ Unit_setMultiplier(pUnit, dMultiplier);
+
/* level 2 version 1 only */
if (unSBMLVersion == 1)
{
- /* get offset */
- mxOffset = mxGetField(mxUnits, i, "offset");
- dOffset = mxGetScalar(mxOffset);
+ /* get offset */
+ mxOffset = mxGetField(mxUnits, i, "offset");
+ dOffset = mxGetSca...
[truncated message content] |