/dports/biology/mothur/mothur-1.46.1/source/read/ |
H A D | readcluster.cpp | 132 … 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() [all …]
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H A D | splitmatrix.cpp | 105 …); 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()
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/dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
H A D | blastdb.cpp | 118 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() [all …]
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H A D | blastalign.cpp | 42 util.mothurRemove(candidateFileName); // files used to run bl2seq in ~BlastAlignment() 43 util.mothurRemove(templateFileName); in ~BlastAlignment() 44 util.mothurRemove(blastFileName); in ~BlastAlignment()
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/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | shhhseqscommand.cpp | 168 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() [all …]
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H A D | sortseqscommand.cpp | 273 … 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() [all …]
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H A D | chimeravsearchcommand.cpp | 412 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() [all …]
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H A D | mgclustercommand.cpp | 514 …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()
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H A D | clustersplitcommand.cpp | 426 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() [all …]
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H A D | deuniqueseqscommand.cpp | 159 …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()
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H A D | chimerauchimecommand.cpp | 723 …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() [all …]
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H A D | chimeraslayercommand.cpp | 375 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() [all …]
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H A D | reversecommand.cpp | 136 …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()
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H A D | distancecommand.cpp | 193 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() [all …]
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H A D | deconvolutecommand.cpp | 199 …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()
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H A D | chimeraperseuscommand.cpp | 419 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() [all …]
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H A D | splitgroupscommand.cpp | 262 …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() [all …]
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H A D | makesharedcommand.cpp | 558 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() [all …]
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H A D | pairwiseseqscommand.cpp | 254 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() [all …]
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H A D | parsimonycommand.cpp | 228 …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()
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H A D | mergecountcommand.cpp | 104 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()
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H A D | pcacommand.cpp | 172 …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()
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H A D | clustercommand.cpp | 360 …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()
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H A D | getsharedotucommand.cpp | 272 …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()
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H A D | summarysharedcommand.cpp | 333 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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