void RTFDocVisitor::visitPre(DocDotFile *df)
{
DBG_RTF("{\\comment RTFDocVisitor::visitPre(DocDotFile)}\n");
writeDotFile(df->file());
// hide caption since it is not supported at the moment
pushEnabled();
m_hide=TRUE;
}
void HtmlDocVisitor::visitPre(DocDotFile *df)
{
if (m_hide) return;
m_t << "<div class=\"dotgraph\">" << endl;
writeDotFile(df->file(),df->relPath(),df->context());
if (df->hasCaption())
{
m_t << "<div class=\"caption\">" << endl;
}
}
void HtmlDocVisitor::visit(DocVerbatim *s)
{
if (m_hide) return;
switch(s->type())
{
case DocVerbatim::Code:
forceEndParagraph(s);
m_t << PREFRAG_START;
Doxygen::parserManager->getParser(m_langExt)
->parseCode(m_ci,s->context(),s->text(),
s->isExample(),s->exampleFile());
m_t << PREFRAG_END;
forceStartParagraph(s);
break;
case DocVerbatim::Verbatim:
forceEndParagraph(s);
m_t << PREFRAG_START;
filter(s->text());
m_t << PREFRAG_END;
forceStartParagraph(s);
break;
case DocVerbatim::HtmlOnly:
m_t << s->text();
break;
case DocVerbatim::ManOnly:
case DocVerbatim::LatexOnly:
case DocVerbatim::XmlOnly:
/* nothing */
break;
case DocVerbatim::Dot:
{
static int dotindex = 1;
QCString fileName(4096);
fileName.sprintf("%s%d%s",
(Config_getString("HTML_OUTPUT")+"/inline_dotgraph_").data(),
dotindex++,
".dot"
);
QFile file(fileName);
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s for writing\n",fileName.data());
}
file.writeBlock( s->text(), s->text().length() );
file.close();
forceEndParagraph(s);
m_t << "<div align=\"center\">" << endl;
writeDotFile(fileName,s->relPath(),s->context());
m_t << "</div>" << endl;
forceStartParagraph(s);
if (Config_getBool("DOT_CLEANUP")) file.remove();
}
break;
case DocVerbatim::Msc:
{
static int mscindex = 1;
QCString baseName(4096);
baseName.sprintf("%s%d",
(Config_getString("HTML_OUTPUT")+"/inline_mscgraph_").data(),
mscindex++
);
QFile file(baseName+".msc");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s.msc for writing\n",baseName.data());
}
QCString text = "msc {";
text+=s->text();
text+="}";
file.writeBlock( text, text.length() );
file.close();
forceEndParagraph(s);
m_t << "<div align=\"center\">" << endl;
writeMscFile(baseName+".msc",s->relPath(),s->context());
m_t << "</div>" << endl;
forceStartParagraph(s);
if (Config_getBool("DOT_CLEANUP")) file.remove();
}
break;
}
}
void RTFDocVisitor::visit(DocVerbatim *s)
{
if (m_hide) return;
DBG_RTF("{\\comment RTFDocVisitor::visit(DocVerbatim)}\n");
QCString lang = m_langExt;
if (!s->language().isEmpty()) // explicit language setting
{
lang = s->language();
}
switch(s->type())
{
case DocVerbatim::Code: // fall though
m_t << "{" << endl;
m_t << "\\par" << endl;
m_t << rtf_Style_Reset << getStyle("CodeExample");
Doxygen::parserManager->getParser(lang)
->parseCode(m_ci,s->context(),s->text(),
s->isExample(),s->exampleFile());
//m_t << "\\par" << endl;
m_t << "}" << endl;
break;
case DocVerbatim::Verbatim:
m_t << "{" << endl;
m_t << "\\par" << endl;
m_t << rtf_Style_Reset << getStyle("CodeExample");
filter(s->text(),TRUE);
//m_t << "\\par" << endl;
m_t << "}" << endl;
break;
case DocVerbatim::HtmlOnly:
case DocVerbatim::LatexOnly:
case DocVerbatim::XmlOnly:
case DocVerbatim::ManOnly:
/* nothing */
break;
case DocVerbatim::Dot:
{
static int dotindex = 1;
QCString fileName(4096);
fileName.sprintf("%s%d%s",
(Config_getString("RTF_OUTPUT")+"/inline_dotgraph_").data(),
dotindex++,
".dot"
);
QFile file(fileName);
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s for writing\n",fileName.data());
}
file.writeBlock( s->text(), s->text().length() );
file.close();
m_t << "\\par{\\qc "; // center picture
writeDotFile(fileName);
m_t << "} ";
if (Config_getBool("DOT_CLEANUP")) file.remove();
}
break;
case DocVerbatim::Msc:
{
static int mscindex = 1;
QCString baseName(4096);
baseName.sprintf("%s%d",
(Config_getString("RTF_OUTPUT")+"/inline_mscgraph_").data(),
mscindex++
);
QFile file(baseName+".msc");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s for writing\n",baseName.data());
}
QCString text = "msc {";
text+=s->text();
text+="}";
file.writeBlock( text, text.length() );
file.close();
m_t << "\\par{\\qc "; // center picture
writeMscFile(baseName);
m_t << "} ";
if (Config_getBool("DOT_CLEANUP")) file.remove();
}
break;
}
m_lastIsPara=FALSE;
}
void DocbookDocVisitor::visit(DocVerbatim *s)
{
if (m_hide) return;
SrcLangExt langExt = getLanguageFromFileName(m_langExt);
switch(s->type())
{
case DocVerbatim::Code: // fall though
m_t << "<literallayout><computeroutput>";
Doxygen::parserManager->getParser(m_langExt)
->parseCode(m_ci,s->context(),s->text(),langExt,
s->isExample(),s->exampleFile());
m_t << "</computeroutput></literallayout>";
break;
case DocVerbatim::Verbatim:
m_t << "<literallayout>";
filter(s->text());
m_t << "</literallayout>";
break;
case DocVerbatim::HtmlOnly:
break;
case DocVerbatim::RtfOnly:
break;
case DocVerbatim::ManOnly:
break;
case DocVerbatim::LatexOnly:
break;
case DocVerbatim::XmlOnly:
break;
case DocVerbatim::DocbookOnly:
break;
m_t << s->text();
break;
case DocVerbatim::Dot:
{
static int dotindex = 1;
QCString baseName(4096);
QCString name;
QCString stext = s->text();
m_t << "<para>" << endl;
name.sprintf("%s%d", "dot_inline_dotgraph_", dotindex);
baseName.sprintf("%s%d",
(Config_getString("DOCBOOK_OUTPUT")+"/inline_dotgraph_").data(),
dotindex++
);
QFile file(baseName+".dot");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s.msc for writing\n",baseName.data());
}
file.writeBlock( stext, stext.length() );
file.close();
m_t << " <figure>" << endl;
m_t << " <title>" << name << "</title>" << endl;
m_t << " <mediaobject>" << endl;
m_t << " <imageobject>" << endl;
writeDotFile(baseName);
m_t << " </imageobject>" << endl;
m_t << " </mediaobject>" << endl;
m_t << " </figure>" << endl;
m_t << "</para>" << endl;
}
break;
case DocVerbatim::Msc:
static int mscindex = 1;
QCString baseName(4096);
QCString name;
QCString stext = s->text();
m_t << "<para>" << endl;
name.sprintf("%s%d", "msc_inline_mscgraph_", mscindex);
baseName.sprintf("%s%d",
(Config_getString("DOCBOOK_OUTPUT")+"/inline_mscgraph_").data(),
mscindex++
);
QFile file(baseName+".msc");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s.msc for writing\n",baseName.data());
}
QCString text = "msc {";
text+=stext;
text+="}";
file.writeBlock( text, text.length() );
file.close();
m_t << " <figure>" << endl;
m_t << " <title>" << name << "</title>" << endl;
m_t << " <mediaobject>" << endl;
m_t << " <imageobject>" << endl;
writeMscFile(baseName);
m_t << " </imageobject>" << endl;
m_t << " </mediaobject>" << endl;
m_t << " </figure>" << endl;
m_t << "</para>" << endl;
break;
}
}
void DocbookDocVisitor::visit(DocVerbatim *s)
{
if (m_hide) return;
SrcLangExt langExt = getLanguageFromFileName(m_langExt);
switch(s->type())
{
case DocVerbatim::Code: // fall though
m_t << "<literallayout><computeroutput>";
Doxygen::parserManager->getParser(m_langExt)
->parseCode(m_ci,s->context(),s->text(),langExt,
s->isExample(),s->exampleFile());
m_t << "</computeroutput></literallayout>";
break;
case DocVerbatim::Verbatim:
m_t << "<literallayout>";
filter(s->text());
m_t << "</literallayout>";
break;
case DocVerbatim::HtmlOnly:
break;
case DocVerbatim::RtfOnly:
break;
case DocVerbatim::ManOnly:
break;
case DocVerbatim::LatexOnly:
break;
case DocVerbatim::XmlOnly:
break;
case DocVerbatim::DocbookOnly:
break;
m_t << s->text();
break;
case DocVerbatim::Dot:
{
static int dotindex = 1;
QCString baseName(4096);
QCString name;
QCString stext = s->text();
m_t << "<para>" << endl;
name.sprintf("%s%d", "dot_inline_dotgraph_", dotindex);
baseName.sprintf("%s%d",
(Config_getString(DOCBOOK_OUTPUT)+"/inline_dotgraph_").data(),
dotindex++
);
QFile file(baseName+".dot");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s.msc for writing\n",baseName.data());
}
file.writeBlock( stext, stext.length() );
file.close();
writeDotFile(baseName, s);
m_t << "</para>" << endl;
}
break;
case DocVerbatim::Msc:
{
static int mscindex = 1;
QCString baseName(4096);
QCString name;
QCString stext = s->text();
m_t << "<para>" << endl;
name.sprintf("%s%d", "msc_inline_mscgraph_", mscindex);
baseName.sprintf("%s%d",
(Config_getString(DOCBOOK_OUTPUT)+"/inline_mscgraph_").data(),
mscindex++
);
QFile file(baseName+".msc");
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s.msc for writing\n",baseName.data());
}
QCString text = "msc {";
text+=stext;
text+="}";
file.writeBlock( text, text.length() );
file.close();
writeMscFile(baseName,s);
m_t << "</para>" << endl;
}
break;
case DocVerbatim::PlantUML:
{
static QCString docbookOutput = Config_getString(DOCBOOK_OUTPUT);
QCString baseName = writePlantUMLSource(docbookOutput,s->exampleFile(),s->text());
QCString shortName = baseName;
int i;
if ((i=shortName.findRev('/'))!=-1)
{
shortName=shortName.right(shortName.length()-i-1);
}
m_t << "<para>" << endl;
writePlantUMLFile(baseName,s);
m_t << "</para>" << endl;
}
break;
}
}
void RTFDocVisitor::visit(DocVerbatim *s)
{
if (m_hide) return;
DBG_RTF("{\\comment RTFDocVisitor::visit(DocVerbatim)}\n");
QCString lang = m_langExt;
if (!s->language().isEmpty()) // explicit language setting
{
lang = s->language();
}
SrcLangExt langExt = getLanguageFromFileName(lang);
switch(s->type())
{
case DocVerbatim::Code: // fall though
m_t << "{" << endl;
m_t << "\\par" << endl;
m_t << rtf_Style_Reset << getStyle("CodeExample");
Doxygen::parserManager->getParser(lang)
->parseCode(m_ci,s->context(),s->text(),langExt,
s->isExample(),s->exampleFile());
//m_t << "\\par" << endl;
m_t << "}" << endl;
break;
case DocVerbatim::Verbatim:
m_t << "{" << endl;
m_t << "\\par" << endl;
m_t << rtf_Style_Reset << getStyle("CodeExample");
filter(s->text(),TRUE);
//m_t << "\\par" << endl;
m_t << "}" << endl;
break;
case DocVerbatim::RtfOnly:
m_t << s->text();
break;
case DocVerbatim::HtmlOnly:
case DocVerbatim::LatexOnly:
case DocVerbatim::XmlOnly:
case DocVerbatim::ManOnly:
case DocVerbatim::DocbookOnly:
/* nothing */
break;
case DocVerbatim::Dot:
{
static int dotindex = 1;
QCString fileName(4096);
fileName.sprintf("%s%d%s",
(Config_getString(RTF_OUTPUT)+"/inline_dotgraph_").data(),
dotindex++,
".dot"
);
QFile file(fileName);
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s for writing\n",fileName.data());
}
file.writeBlock( s->text(), s->text().length() );
file.close();
writeDotFile(fileName, s->hasCaption());
visitCaption(this, s->children());
includePicturePostRTF(true, s->hasCaption());
if (Config_getBool(DOT_CLEANUP)) file.remove();
}
break;
case DocVerbatim::Msc:
{
static int mscindex = 1;
QCString baseName(4096);
baseName.sprintf("%s%d%s",
(Config_getString(RTF_OUTPUT)+"/inline_mscgraph_").data(),
mscindex++,
".msc"
);
QFile file(baseName);
if (!file.open(IO_WriteOnly))
{
err("Could not open file %s for writing\n",baseName.data());
}
QCString text = "msc {";
text+=s->text();
text+="}";
file.writeBlock( text, text.length() );
file.close();
writeMscFile(baseName, s->hasCaption());
visitCaption(this, s->children());
includePicturePostRTF(true, s->hasCaption());
if (Config_getBool(DOT_CLEANUP)) file.remove();
}
break;
case DocVerbatim::PlantUML:
{
static QCString rtfOutput = Config_getString(RTF_OUTPUT);
QCString baseName = writePlantUMLSource(rtfOutput,s->exampleFile(),s->text());
writePlantUMLFile(baseName, s->hasCaption());
visitCaption(this, s->children());
includePicturePostRTF(true, s->hasCaption());
}
break;
}
m_lastIsPara=FALSE;
}
void RTFDocVisitor::writeDotFile(DocDotFile *df)
{
writeDotFile(df->file(), df->hasCaption());
}
void RTFDocVisitor::visitPre(DocDotFile *df)
{
DBG_RTF("{\\comment RTFDocVisitor::visitPre(DocDotFile)}\n");
writeDotFile(df);
}
int main(int argc, char* argv[] )
{
srand(time(NULL));
int verbose = 0;
char outputFile[256];
int doOutput = getWriteToFile( argc, argv, outputFile, 256);
if (argc == 1)
{
showUsageAndExit();
}
moleculizer* pMoleculizer = createNewMoleculizerObject();
setRateExtrapolation( pMoleculizer, 1 );
int result = loadModelFile( pMoleculizer, argc, argv);
switch(result)
{
case 0:
printf("Model loaded successfully.\n");
break;
case 1:
printf("Unknown error on load. Aborting\n");
return 1;
case 2:
printf("Document unparsable. Aborting.\n");
return 1;
case 3:
printf("Moleculizer has already loaded rules. Ignoring and continuing.\n");
return 1;
}
int numIter = getNumberOfIterations(argc, argv);
int maxSpecies = getMaxNumSpecies( argc, argv);
int maxRxns = getMaxNumReactions( argc, argv);
if (numIter > 0 && (maxSpecies > 0 || maxRxns > 0) )
{
// ANCHOR
printf("Error, if either (max species and/or max rxns) can be set or numIters. ");
showUsageAndExit();
}
verbose = getVerbose(argc, argv);
if(numIter == -1 )
{
int numRxns;
int numSpec;
species** speciesArray;
reaction** rxnArray;
int errorCode = \
getBoundedNetwork( pMoleculizer, maxSpecies, maxRxns, &speciesArray, &numSpec, &rxnArray, &numRxns );
if (errorCode)
{
printf("Unknown erorr. Check error messages for description. Exiting...\n");
exit(1);
}
else
{
numIter = 10;
printf("Network generated to %d species and %d reactions.\n", numSpec, numRxns);
}
}
else
{
int iter = 0;
for( iter = 0; iter != numIter; ++iter)
{
species** theSpecies;
int numSpecies = 0;
getAllExteriorSpecies( pMoleculizer, &theSpecies, &numSpecies);
if (numSpecies == 0)
{
printf("Entire network has been generated on the %dth iteration.\n", iter);
freeSpeciesArray( theSpecies, numSpecies);
break;
}
/* Get a random number in the range [0, numSpecies) */
int speciesNumber = rand() % numSpecies;
printf("Iteration %d: Expanding %s\n", iter + 1, theSpecies[speciesNumber]->name);
incrementSpecies( pMoleculizer, theSpecies[speciesNumber]->name);
freeSpeciesArray( theSpecies, numSpecies);
}
}
if (numIter == -1)
{
printf("Expanded entire network.\n");
}
else
{
printf("Expanded %d iterations.", numIter);
}
printf("\n##########################################\n");
printf("There are %d species and %d reactions.\n",
getNumberOfSpecies(pMoleculizer),
getNumberOfReactions(pMoleculizer) );
if ( verbose )
{
showAllSpecies( pMoleculizer );
showAllReactions( pMoleculizer);
}
if (doOutput)
{
writeDotFile(pMoleculizer, outputFile);
}
freeMoleculizerObject( pMoleculizer );
return 0;
}