| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | screenseqscommand.cpp | 367 …rol_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
371 …E]: no sequences were bad, removing " + badAccnosFile + "\n\n"); util.mothurRemove(badAccnosFile);… in execute()
402 util.mothurRemove(strippedAccnos); in execute()
455 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(o… in execute()
536 if (m->getControl_pressed()) { util.mothurRemove(goodSeqFile); return numFastaSeqs; } in runFastaScreening()
648 util.mothurRemove(outSummary+".temp"); in screenAlignReport()
721 util.mothurRemove(outSummary+".temp"); in screenContigs()
807 util.mothurRemove(outSummary+".temp"); in screenSummary()
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| H A D | aligncommand.cpp | 240 …if (m->getControl_pressed()) { util.mothurRemove(accnosFileName); util.mothurRemove(alignFileName)… in execute()
243 … if (util.isBlank(accnosFileName)) { util.mothurRemove(accnosFileName); hasAccnos = false; } in execute()
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| H A D | aligncheckcommand.cpp | 168 if (m->getControl_pressed()) { in.close(); out.close(); util.mothurRemove(outfile); return 0; } in execute()
205 if (m->getControl_pressed()) { util.mothurRemove(outfile); return 0; } in execute()
223 if (m->getControl_pressed()) { util.mothurRemove(outfile); return 0; } in execute()
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| H A D | systemcommand.cpp | 110 util.mothurRemove(redirectFileName); in execute()
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| H A D | mergefilecommand.cpp | 174 util.mothurRemove(outputFileName); in execute()
179 if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return 0; } in execute()
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| H A D | parsefastaqcommand.cpp | 352 if(util.isBlank(ffqnoMatchFile)){ util.mothurRemove(ffqnoMatchFile); } in execute()
356 if(util.isBlank(ffnoMatchFile)){ util.mothurRemove(ffnoMatchFile); } in execute()
361 if(util.isBlank(fqnoMatchFile)){ util.mothurRemove(fqnoMatchFile); } in execute()
367 if(util.isBlank(rfqnoMatchFile)){ util.mothurRemove(rfqnoMatchFile); } in execute()
371 if(util.isBlank(rfnoMatchFile)){ util.mothurRemove(rfnoMatchFile); } in execute()
376 if(util.isBlank(rqnoMatchFile)){ util.mothurRemove(rqnoMatchFile); } in execute()
393 …trol_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
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| H A D | makecontigscommand.cpp | 652 … if (decompressionHelped) { util.mothurRemove(fileInputs[0]); util.mothurRemove(fileInputs[1]); } in processSingleFileOption()
662 if (outQualFile != "") { util.mothurRemove(outQualFile); } in processSingleFileOption()
663 if (outScrapQualFile != "") { util.mothurRemove(outScrapQualFile); } in processSingleFileOption()
1010 … util.appendFiles(outMisMatchFile, compositeMisMatchFile); util.mothurRemove(outMisMatchFile); in processMultipleFileOption()
1011 … util.appendFiles(outFastaFile, compositeFastaFile); util.mothurRemove(outFastaFile); in processMultipleFileOption()
1012 …util.appendFiles(outScrapFastaFile, compositeScrapFastaFile); util.mothurRemove(outScrapFastaFile); in processMultipleFileOption()
1017 util.mothurRemove(outQualFile); util.mothurRemove(outScrapQualFile); in processMultipleFileOption()
1021 …if (!makeQualFile) { util.mothurRemove(compositeQualFile); util.mothurRemove(compositeScrapQualFil… in processMultipleFileOption()
2124 …gparams->bundle->util.mothurRemove(theseFileInputs[0]); gparams->bundle->util.mothurRemove(theseFi… in driverContigsGroups()
2125 … if (theseQIInputs[0] != "NONE") { gparams->bundle->util.mothurRemove(theseQIInputs[0]); } in driverContigsGroups()
[all …]
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| H A D | phylotypecommand.cpp | 210 for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } in execute()
295 for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } in execute()
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| H A D | getlineagecommand.cpp | 250 }else { util.mothurRemove(accnosFileName); } in execute()
258 } else { util.mothurRemove(accnosFileName); } in execute()
262 …putTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
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| H A D | mergegroupscommand.cpp | 222 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
507 … if (m->getControl_pressed()) { out.close(); util.mothurRemove(accnosFile); return 0; } in processCountFile()
528 util.mothurRemove(accnosFile); in processCountFile()
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| H A D | getdistscommand.cpp | 140 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
319 util.mothurRemove(outputFileName+".temp"); in readPhylip()
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| H A D | removedistscommand.cpp | 141 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
322 util.mothurRemove(outputFileName+".temp"); in readPhylip()
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| H A D | libshuffcommand.cpp | 192 …_pressed()) { delete groupMap; delete matrix; outGroups.close(); util.mothurRemove(newGroupFile); … in execute()
208 …if (m->getControl_pressed()) { delete groupMap; delete matrix; util.mothurRemove(newGroupFile); re… in execute()
278 …putTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
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| H A D | removelineagecommand.cpp | 258 …}else{ m->mothurOut("\n*** No contaminants to remove ***\n"); util.mothurRemove(accnosFileName); } in execute()
265 … }else{ m->mothurOut("\n*** No contaminants to remove ***\n"); util.mothurRemove(accnosFileName); } in execute()
268 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
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| H A D | clusterfragmentscommand.cpp | 231 …if (m->getControl_pressed()) { util.mothurRemove(newFastaFile); util.mothurRemove(newNamesFile); r… in execute()
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| H A D | seqsummarycommand.cpp | 181 if (m->getControl_pressed()) { util.mothurRemove(outputFile); return 0; } in execute()
241 if (m->getControl_pressed()) { util.mothurRemove(outputFile); return 0; } in execute()
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| H A D | mergetaxsummarycommand.cpp | 140 util.mothurRemove(outputFileName); in execute()
220 if (m->getControl_pressed()) { util.mothurRemove(outputFileName); return 0; } in execute()
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| H A D | makefastqcommand.cpp | 153 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
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| H A D | removerarecommand.cpp | 209 …if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(ou… in execute()
350 …{ delete groupMap; outGroup.close(); util.mothurRemove(outputGroupFileName); } out.close(); util.… in processList()
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| H A D | chimerabellerophoncommand.cpp | 149 …rol_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i])… in execute()
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| /dports/biology/mothur/mothur-1.46.1/source/classifier/ |
| H A D | bayesian.cpp | 70 …f (m->getControl_pressed()) { util.mothurRemove(phyloTreeName); util.mothurRemove(probFileName);… in Bayesian()
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| H A D | taxonomyequalizer.cpp | 64 if (m->getControl_pressed()) { util.mothurRemove(equalizedFile); } in TaxEqualizer()
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| /dports/biology/mothur/mothur-1.46.1/source/chimera/ |
| H A D | bellerophon.cpp | 411 if (m->getControl_pressed()) { outTemp.close(); util.mothurRemove(file); return 0; } in writePrefs()
444 if (m->getControl_pressed()) { inTemp.close(); util.mothurRemove(file); return 0; } in readPrefs()
454 util.mothurRemove(file); in readPrefs()
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| /dports/biology/mothur/mothur-1.46.1/TestMothur/ |
| H A D | distcdataset.cpp | 53 util.mothurRemove(accnosfile); in getFiles()
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| /dports/biology/mothur/mothur-1.46.1/source/ |
| H A D | mothur.cpp | 123 if (!createLogFile) { util.mothurRemove(newlogFileName); } in main()
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