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Searched refs:nexusFile (Results 1 – 4 of 4) sorted by relevance

/dports/biology/clustalw/clustalw-2.1/src/tree/
H A DClusterTree.h53 … clustalw::OutputFile* nexusFile, clustalw::TreeNames* treeNames, string* path);
55 … clustalw::OutputFile* distFile, clustalw::OutputFile* nexusFile, clustalw::OutputFile* pimFile,
58 ofstream* nexusFile, ofstream* pimFile,
62 ofstream* nexusFile, clustalw::Alignment* alignPtr,
H A DClusterTree.cpp761 … clustalw::OutputFile* nexusFile, clustalw::TreeNames* treeNames, string* path) in openFilesForBootstrap() argument
783 if(!nexusFile || !nexusFile->openFile(&(treeNames->nexusName), in openFilesForBootstrap()
793 …File* phylipFile, clustalw::OutputFile* distFile, clustalw::OutputFile* nexusFile, clustalw::Outpu… in openFilesForTreeFromAlignment() argument
828 if(!nexusFile || !nexusFile->openFile(&(treeNames->nexusName), in openFilesForTreeFromAlignment()
849 ofstream* nexusFile, ofstream* pimFile, ofstream* distFile, in calcQuickDistMatForAll() argument
855 overspill = calcQuickDistMatForSubSet(clustalFile, phylipFile, nexusFile, alignPtr); in calcQuickDistMatForAll()
889 ofstream* nexusFile, clustalw::Alignment* alignPtr, in calcQuickDistMatForSubSet() argument
928 if (nexusFile && clustalw::userParameters->getOutputTreeNexus()) in calcQuickDistMatForSubSet()
933 overspill = dnaDistanceMatrix(nexusFile, alignPtr); in calcQuickDistMatForSubSet()
937 overspill = protDistanceMatrix(nexusFile, alignPtr); in calcQuickDistMatForSubSet()
/dports/biology/clustalw/clustalw-2.1/src/general/
H A Dclustalw.h72 string nexusFile; member
/dports/biology/clustalw/clustalw-2.1/src/alignment/
H A DAlignmentOutput.cpp257 && fileNames.gdeFile == "" && fileNames.nexusFile == "" && fileNames.nrbfFile == "" in QTOpenFilesForOutput()
296 if(fileNames.nexusFile != "") in QTOpenFilesForOutput()
298 nexusOutName = fileNames.nexusFile; in QTOpenFilesForOutput()