| /dports/biology/mothur/mothur-1.46.1/source/read/ |
| H A D | splitmatrix.cpp | 112 string dupsFile = namefile; string dupsFormat = "name"; in createDistanceFilesFromTax() local
113 if (countfile != "") { dupsFile = countfile; dupsFormat = "count"; } in createDistanceFilesFromTax()
115 …Command* getCommand = new GetSeqsCommand(thisGroupsNames, "", "", dupsFile, dupsFormat, outputDir); in createDistanceFilesFromTax()
191 string dupsFile = namefile; string dupsFormat = "name"; in createDistanceFilesFromTax() local
192 if (countfile != "") { dupsFile = countfile; dupsFormat = "count"; } in createDistanceFilesFromTax()
197 …Command* removeCommand = new RemoveSeqsCommand(nonSingletonsFile, dupsFile, dupsFormat, outputDir); in createDistanceFilesFromTax()
269 string dupsFile = namefile; string dupsFormat = "name"; in createFastaFilesFromTax() local
270 if (countfile != "") { dupsFile = countfile; dupsFormat = "count"; } in createFastaFilesFromTax()
272 …Command* getCommand = new GetSeqsCommand(thisGroupsNames, "", "", dupsFile, dupsFormat, outputDir); in createFastaFilesFromTax()
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | removeseqscommand.h | 20 RemoveSeqsCommand(string, string dupsFile, string dupsFileType, string output);
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| H A D | getseqscommand.h | 21 …GetSeqsCommand(set<string>, string fasta, string list, string dupsFile, string dupsFileType, strin…
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| H A D | removeseqscommand.cpp | 107 RemoveSeqsCommand::RemoveSeqsCommand(string accnos, string dupsFile, string dupsFileType, string ou… in RemoveSeqsCommand() argument
117 if (dupsFile != "") { in RemoveSeqsCommand()
119 countfile = dupsFile; in RemoveSeqsCommand()
122 namefile = dupsFile; in RemoveSeqsCommand()
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| H A D | getseqscommand.cpp | 110 GetSeqsCommand::GetSeqsCommand(set<string> n, string ffile, string lfile, string dupsFile, string d… in GetSeqsCommand() argument
124 if (dupsFile != "") { in GetSeqsCommand()
126 countfile = dupsFile; in GetSeqsCommand()
129 namefile = dupsFile; in GetSeqsCommand()
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| H A D | clusterfitcommand.cpp | 345 string dupsFile = countfile; nameOrCount = "count"; in execute() local
346 if (namefile != "") { dupsFile = namefile; nameOrCount = "name"; } in execute()
366 …OptiData* matrix = new OptiRefMatrix(distfile, "column", dupsFile, nameOrCount, cutoff, fitPercent… in execute()
407 … OptiData* matrix = new OptiRefMatrix(distfile, "column", dupsFile, nameOrCount, cutoff, refNames); in execute()
452 …(refdistfile, refDupsFile, refNameOrCount, refformat, cutoff, distfile, dupsFile, nameOrCount, "co… in execute()
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| H A D | chimeraperseuscommand.cpp | 712 …ccnos, string newCountFile, vector<string> groups, string fasta, string dupsFile, int& numChimeras… in createProcessesGroups() argument
753 …s, dups, hasCount, alpha, beta, cutoff, (outputFName+extension), fasta, dupsFile, (accnos+extensi… in createProcessesGroups()
770 …psParsedFiles, dups, hasCount, alpha, beta, cutoff, outputFName, fasta, dupsFile, accnos, countli… in createProcessesGroups()
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| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | optirefmatrix.cpp | 13 OptiRefMatrix::OptiRefMatrix(string distFile, string distFormat, string dupsFile, string dupsFormat… in OptiRefMatrix() argument
31 readFiles(distFile, distFormat, dupsFile, dupsFormat, noRefNamesSet); in OptiRefMatrix()
34 OptiRefMatrix::OptiRefMatrix(string distFile, string distFormat, string dupsFile, string dupsFormat… in OptiRefMatrix() argument
47 readFiles(distFile, distFormat, dupsFile, dupsFormat, accnosRefFileNames); in OptiRefMatrix()
523 int OptiRefMatrix::readFiles(string distFile, string distFormat, string dupsFile, string dupsFormat… in readFiles() argument
526 if (dupsFormat == "name") { namefile = dupsFile; countfile = ""; } in readFiles()
527 else if (dupsFormat == "count") { countfile = dupsFile; namefile = ""; } in readFiles()
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