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Searched refs:mothurRemove (Results 1 – 25 of 131) sorted by relevance

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/dports/biology/mothur/mothur-1.46.1/source/read/
H A Dreadcluster.cpp132 … if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(tempFile); return 0; } in convertPhylip2Column()
149 … if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(tempFile); return 0; } in convertPhylip2Column()
171 … if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(tempFile); return 0; } in convertPhylip2Column()
186 … if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(tempFile); return 0; } in convertPhylip2Column()
224 …getControl_pressed()) { in2.close(); out2.close(); util.mothurRemove(tempFile); util.mothurRemove(… in convertPhylip2Column()
233 util.mothurRemove(tempFile); in convertPhylip2Column()
236 if (m->getControl_pressed()) { util.mothurRemove(outputFile); } in convertPhylip2Column()
310 … if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(tempFile); return 0; } in convertPhylip2Column()
399 …getControl_pressed()) { in2.close(); out2.close(); util.mothurRemove(tempFile); util.mothurRemove(… in convertPhylip2Column()
408 util.mothurRemove(tempFile); in convertPhylip2Column()
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H A Dsplitmatrix.cpp105 …); util.mothurRemove(nonSingletonsFile); for (int i = 0; i < dists.size(); i++) { util.mothurRemov… in createDistanceFilesFromTax()
179 util.mothurRemove(thisDistanceFile); in createDistanceFilesFromTax()
180 util.mothurRemove(outName); in createDistanceFilesFromTax()
226 util.mothurRemove(singleton); in createDistanceFilesFromTax()
230 util.mothurRemove(nonSingletonsFile); in createDistanceFilesFromTax()
232 … for (int i = 0; i < dists.size(); i++) { util.mothurRemove((dists[i].begin()->first)); util.mothu… in createDistanceFilesFromTax()
262 … for (int i = 0; i < dists.size(); i++) { util.mothurRemove((dists[i].begin()->first)); util.mothu… in createFastaFilesFromTax()
307 … for (int i = 0; i < dists.size(); i++) { util.mothurRemove((dists[i].begin()->first)); util.mothu… in createFastaFilesFromTax()
/dports/biology/mothur/mothur-1.46.1/source/datastructures/
H A Dblastdb.cpp118 util.mothurRemove(queryFileName); // let's clean stuff up and remove the temp files in ~BlastDB()
119 util.mothurRemove(dbFileName); // let's clean stuff up and remove the temp files in ~BlastDB()
120 util.mothurRemove((dbFileName+".nsq")); // let's clean stuff up and remove the temp files in ~BlastDB()
121 util.mothurRemove((dbFileName+".nsi")); // let's clean stuff up and remove the temp files in ~BlastDB()
122 util.mothurRemove((dbFileName+".nsd")); // let's clean stuff up and remove the temp files in ~BlastDB()
123 util.mothurRemove((dbFileName+".nin")); // let's clean stuff up and remove the temp files in ~BlastDB()
124 util.mothurRemove((dbFileName+".nhr")); // let's clean stuff up and remove the temp files in ~BlastDB()
185 util.mothurRemove((queryFileName+pid)); in findClosestSequences()
186 util.mothurRemove((blastFileName+pid)); in findClosestSequences()
247 util.mothurRemove((queryFileName+pid)); in findClosestMegaBlast()
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H A Dblastalign.cpp42 util.mothurRemove(candidateFileName); // files used to run bl2seq in ~BlastAlignment()
43 util.mothurRemove(templateFileName); in ~BlastAlignment()
44 util.mothurRemove(blastFileName); in ~BlastAlignment()
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dshhhseqscommand.cpp168 string rabundFileName = filenames["rabund"][0]; util.mothurRemove(rabundFileName); in driver()
174 …if (m->getControl_pressed()) { util.mothurRemove(distFileName); util.mothurRemove(listFileName); r… in driver()
178 util.mothurRemove(distFileName); in driver()
179 if (m->getControl_pressed()) { util.mothurRemove(listFileName); return 0; } in driver()
185 util.mothurRemove(listFileName); in driver()
333 if (m->getControl_pressed()) { util.mothurRemove(distFileName); return 0; } in execute()
573 util.mothurRemove(newFName+extension); in createProcessesGroups()
574 util.mothurRemove(newNName+extension); in createProcessesGroups()
582 util.mothurRemove(newFName); in createProcessesGroups()
583 util.mothurRemove(newNName); in createProcessesGroups()
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H A Dsortseqscommand.cpp273 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readFasta()
280 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readFasta()
360 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); retu… in readFasta()
451 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readFlow()
458 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readFlow()
540 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); retu… in readFlow()
632 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readQual()
639 … if (m->getControl_pressed()) { in2.close(); util.mothurRemove(outputFileName); return 0; } in readQual()
722 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); retu… in readQual()
804 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outputFileName); retu… in readName()
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H A Dchimeravsearchcommand.cpp412 if (fileToRemove != "") { params->util.mothurRemove(fileToRemove); } in driver()
438 params->util.mothurRemove(outputFNamec); in driver()
621 if (templatefile == "self") { util.mothurRemove(fastafile); } in execute()
675 …Control_pressed()) { in2.close(); out2.close(); util.mothurRemove(outputFileName); util.mothurRemo… in deconvoluteResults()
693 util.mothurRemove(accnosFileName); in deconvoluteResults()
753 util.mothurRemove(outputFileName); in deconvoluteResults()
801 …{ in3.close(); out3.close(); util.mothurRemove(outputFileName); util.mothurRemove((accnosFileName)… in deconvoluteResults()
846 util.mothurRemove(alnsFileName); in deconvoluteResults()
994 if (!params->m->getDebug()) { util.mothurRemove(params->formattedFastaFilename); } in driverGroups()
1128 util.mothurRemove((outputFName+extension)); in createProcessesGroups()
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H A Dmgclustercommand.cpp514 …lose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
537 …ose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
552 …ose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
570 …ose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
601 …ose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
629 …ose(); sabundFile.close(); util.mothurRemove(rabundFileName); util.mothurRemove(sabundFileName);… in runMothurCluster()
H A Dclustersplitcommand.cpp426 util.mothurRemove(thisNamefile); in execute()
427 util.mothurRemove(thisDistFile); in execute()
515 util.mothurRemove(singleton); in completeListFile()
598 util.mothurRemove(listNames[k]); in completeListFile()
879 params->util.mothurRemove(thisDistFile); in clusterClassicFile()
880 params->util.mothurRemove(thisNamefile); in clusterClassicFile()
953 params->util.mothurRemove(thisDistFile); in runOptiCluster()
954 params->util.mothurRemove(thisNamefile); in runOptiCluster()
1093 …trol_pressed()) { params->util.mothurRemove(ucVsearchFile); params->util.mothurRemove(logfile); p… in runVsearchCluster()
1113 …params->util.mothurRemove(ucVsearchFile); params->util.mothurRemove(logfile); params->util.mothur… in runVsearchCluster()
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H A Ddeuniqueseqscommand.cpp159 …tTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { o… in execute()
166 …tTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInfo()) { o… in execute()
215 … { outputTypes.clear(); util.mothurRemove(outFastaFile); if (countfile != "") { if (ct.hasGroupInf… in execute()
H A Dchimerauchimecommand.cpp723 …util.mothurRemove(outputFileName); rename((outputFileName+".temp").c_str(), outputFileName.c_str()… in execute()
728 if (templatefile == "self") { util.mothurRemove(fastafile); } in execute()
783 …Control_pressed()) { in2.close(); out2.close(); util.mothurRemove(outputFileName); util.mothurRemo… in deconvoluteResults()
800 util.mothurRemove(accnosFileName); in deconvoluteResults()
823 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove((outputFileName+".temp")… in deconvoluteResults()
889 util.mothurRemove(outputFileName); in deconvoluteResults()
937 …{ in3.close(); out3.close(); util.mothurRemove(outputFileName); util.mothurRemove((accnosFileName)… in deconvoluteResults()
991 util.mothurRemove(alnsFileName); in deconvoluteResults()
1132 if (!params->m->getDebug()) { params->util.mothurRemove(params->formattedFastaFilename); } in driverGroups()
1265 util.mothurRemove((outputFName+extension)); in createProcessesGroups()
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H A Dchimeraslayercommand.cpp375 util.mothurRemove(newCountFile); in execute()
459 …Control_pressed()) { in2.close(); out2.close(); util.mothurRemove(outputFileName); util.mothurRemo… in deconvoluteResults()
473 util.mothurRemove(accnosFileName); in deconvoluteResults()
505 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove((outputFileName+".temp")… in deconvoluteResults()
556 util.mothurRemove(outputFileName); in deconvoluteResults()
570 … { in3.close(); out3.close(); util.mothurRemove(outputFileName); util.mothurRemove(accnosFileName)… in deconvoluteResults()
583 util.mothurRemove(trimFileName); in deconvoluteResults()
747 util.appendFiles(thisoutputFileName, outputFName); util.mothurRemove(thisoutputFileName); in driverGroups()
748 util.appendFiles(thisaccnosFileName, accnos); util.mothurRemove(thisaccnosFileName); in driverGroups()
749 …if (trim) { util.appendFiles(thistrimFastaFileName, fasta); util.mothurRemove(thistrimFastaFileNam… in driverGroups()
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H A Dreversecommand.cpp136 …if (m->getControl_pressed()) { inFASTA.close(); outFASTA.close(); util.mothurRemove(fastaReverse… in execute()
167 …if (m->getControl_pressed()) { inQual.close(); outQual.close(); util.mothurRemove(qualReverseFil… in execute()
177 …if (m->getControl_pressed()) { util.mothurRemove(qualReverseFileName); util.mothurRemove(fastaRev… in execute()
H A Ddistancecommand.cpp193 util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); in DistanceCommand()
200 util.mothurRemove(outputFile); in DistanceCommand()
252 util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); in execute()
266 util.mothurRemove(outputFile); in execute()
270 util.mothurRemove(outputFile); in execute()
277 if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFile); return 0; } in execute()
291 util.mothurRemove(tempcolumn); in execute()
295 util.mothurRemove(outputFile); in execute()
737 util.mothurRemove(filename+extension); in createProcesses()
841 util.mothurRemove(column); in sanityCheck()
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H A Ddeconvolutecommand.cpp199 …if (m->getControl_pressed()) { in.close(); outFasta.close(); util.mothurRemove(outFastaFile); retu… in execute()
279 if (m->getControl_pressed()) { util.mothurRemove(outFastaFile); return 0; } in execute()
290 …tTypes.clear(); util.mothurRemove(outFastaFile); outNames.close(); for (int j = 0; j < outputNames… in execute()
312 …) { outputTypes.clear(); util.mothurRemove(outFastaFile); for (int j = 0; j < outputNames.size(); … in execute()
H A Dchimeraperseuscommand.cpp419 util.mothurRemove(countlist); in execute()
434 util.mothurRemove(countlist); in execute()
446 …rol_pressed()) { for (int j = 0; j < outputNames.size(); j++) { util.mothurRemove(outputNames[j])… in execute()
456 …trol_pressed()) { for (int j = 0; j < outputNames.size(); j++) { util.mothurRemove(outputNames[j])… in execute()
652 …driverParams->chimeraFileName, params->chimeraFileName); params->util.mothurRemove(driverParams->c… in driverGroups()
653 …s(driverParams->accnosFileName, params->accnosFileName); params->util.mothurRemove(driverParams->a… in driverGroups()
782 util.mothurRemove((outputFName+extension)); in createProcessesGroups()
785 util.mothurRemove((accnos+extension)); in createProcessesGroups()
788 util.mothurRemove((countlisttemp+extension)); in createProcessesGroups()
842 …if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove((outputFileName+".temp")… in deconvoluteResults()
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H A Dsplitgroupscommand.cpp262 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
356 params->util.mothurRemove(uniqueFasta); in driverRunNameGroup()
361 params->util.mothurRemove(uniqueList); in driverRunNameGroup()
370 params->util.mothurRemove(files[2]+".accnos"); in driverRunNameGroup()
371 params->util.mothurRemove(uniqueName); in driverRunNameGroup()
373 … for (int i = 0; i < params->outputNames.size(); i++) { params->util.mothurRemove(params->outputN… in driverRunNameGroup()
436 … for (int i = 0; i < params->outputNames.size(); i++) { params->util.mothurRemove(params->outputN… in driverRunCount()
439 if (params->fastafile != "") { params->util.mothurRemove(uniqueFasta); } in driverRunCount()
440 if (params->listfile != "") { params->util.mothurRemove(uniqueList); } in driverRunCount()
561 params->util.mothurRemove(it->second.filename); in driverSplitFlow()
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H A Dmakesharedcommand.cpp558 if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; } in createSharedFromBiom()
568 if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; } in createSharedFromBiom()
579 if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; } in createSharedFromBiom()
612 if (m->getControl_pressed()) { out.close(); util.mothurRemove(filename); return 0; } in createSharedFromBiom()
660 if (m->getControl_pressed()) { util.mothurRemove(filename); return 0; } in createSharedFromBiom()
931 out.close(); if (!pickedGroups) { util.mothurRemove(filename); } in createSharedFromListGroup()
991 if (!pickedGroups) { out.close(); util.mothurRemove(filename); } in createSharedFromListGroup()
1004 if (!pickedGroups) { out.close(); util.mothurRemove(filename); } in createSharedFromListGroup()
1045 if (!pickedGroups) { out.close(); util.mothurRemove(filename); } in createSharedFromListGroup()
1103 if (!pickedGroups) { out.close(); util.mothurRemove(filename); } in createSharedFromListGroup()
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H A Dpairwiseseqscommand.cpp254 util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); in PairwiseSeqsCommand()
259 util.mothurRemove(outputFile); in PairwiseSeqsCommand()
310 util.mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile); in execute()
315 util.mothurRemove(outputFile); in execute()
319 util.mothurRemove(outputFile); in execute()
339 util.mothurRemove(tempcolumn); in execute()
342 util.mothurRemove(outputFile); in execute()
358 … if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFile); return 0; } in execute()
888 util.mothurRemove(filename+extension); in createProcesses()
947 util.mothurRemove(column); in sanityCheck()
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H A Dparsimonycommand.cpp228 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
247 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
284 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
319 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
327 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
381 …for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } outputTypes.cl… in execute()
390 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
H A Dmergecountcommand.cpp104 util.mothurRemove(outputFileName); in execute()
174 if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return 0; } in execute()
179 if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return 0; } in execute()
H A Dpcacommand.cpp172 …rol_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
205 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
227 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
338 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in process()
344 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in process()
H A Dclustercommand.cpp360 …if (m->getControl_pressed()) { for (int j = 0; j < outputNames.size(); j++) { util.mothurRemove(o… in execute()
446 util.mothurRemove(ucVsearchFile); util.mothurRemove(logfile); in runVsearchCluster()
450 util.mothurRemove(vsearchFastafile); delete vParse; in runVsearchCluster()
451 …trol_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in runVsearchCluster()
597 …rabundFile.close(); sabundFile.close(); util.mothurRemove((fileroot+ tag + ".rabund")); util.moth… in runMothurCluster()
598 … listFile.close(); util.mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; in runMothurCluster()
644 …rabundFile.close(); sabundFile.close(); util.mothurRemove((fileroot+ tag + ".rabund")); util.moth… in runMothurCluster()
645 … listFile.close(); util.mothurRemove((fileroot+ tag + ".list")); outputTypes.clear(); return 0; in runMothurCluster()
H A Dgetsharedotucommand.cpp272 …putTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
325 if (m->getControl_pressed()) { outNames.close(); util.mothurRemove(outputFileNames); return 0; } in process()
403 util.mothurRemove(outputFileNames); in process()
488 …putTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in runShared()
520 if (m->getControl_pressed()) { outNames.close(); util.mothurRemove(outputFileNames); return 0; } in process()
569 util.mothurRemove(outputFileNames); in process()
H A Dsummarysharedcommand.cpp333 util.mothurRemove(outputFileName); in execute()
334 if (mult ) { util.mothurRemove(outAllFileName); } in execute()
340 util.mothurRemove(outAllFileName); in execute()
344 …if (m->getControl_pressed()) { if (mult) { util.mothurRemove(outAllFileName); } util.mothurRemov… in execute()
384 …if (m->getControl_pressed()) { util.mothurRemove(outAllFileName); util.mothurRemove(outputFileNa… in execute()
652 util.mothurRemove((sumFileName + extension)); in runCalcs()
653 …if (mult) { util.appendFiles((sumAllFile + extension), sumAllFile); util.mothurRemove((sumAllFile… in runCalcs()
662 util.mothurRemove((sumFileName + extension)); in runCalcs()

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