| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | blastdb.cpp | 42 bool ableToOpen = util.openInputFile(formatdbCommand, in, "no error"); in.close(); in BlastDB() local
43 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requi… in BlastDB()
49 ableToOpen = util.openInputFile(blastCommand, in2, "no error"); in2.close(); in BlastDB()
50 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires… in BlastDB()
56 ableToOpen = util.openInputFile(megablastCommand, in3, "no error"); in3.close(); in BlastDB()
57 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur req… in BlastDB()
88 bool ableToOpen = util.openInputFile(formatdbCommand, in, "no error"); in.close(); in BlastDB() local
89 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requ… in BlastDB()
95 ableToOpen = util.openInputFile(blastCommand, in2, "no error"); in2.close(); in BlastDB()
96 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires… in BlastDB()
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | mergetaxsummarycommand.cpp | 81 bool ableToOpen; in MergeTaxSummaryCommand() local
83 ableToOpen = util.openInputFile(fileNames[i], in, "noerror"); in MergeTaxSummaryCommand()
87 if (!ableToOpen) { in MergeTaxSummaryCommand()
92 ableToOpen = util.openInputFile(tryPath, in2, "noerror"); in MergeTaxSummaryCommand()
99 if (!ableToOpen) { in MergeTaxSummaryCommand()
104 ableToOpen = util.openInputFile(tryPath, in2, "noerror"); in MergeTaxSummaryCommand()
112 if (!ableToOpen) { in MergeTaxSummaryCommand()
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| H A D | mergesfffilecommand.cpp | 117 … bool ableToOpen = util.checkLocations(filenames[i], current->getLocations()); in MergeSfffilesCommand() local
119 if (!ableToOpen) { in MergeSfffilesCommand()
338 bool ableToOpen = util.checkLocations(filename, current->getLocations()); in readFile() local
340 if (!ableToOpen) { //can't find it in readFile()
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| H A D | srainfocommand.cpp | 124 bool ableToOpen = util.openInputFile(fasterQLocation, in, "no error"); in.close(); in SRAInfoCommand() local
125 if(!ableToOpen) { in SRAInfoCommand()
159 bool ableToOpen = util.openInputFile(prefetchLocation, in, "no error"); in.close(); in SRAInfoCommand() local
160 if(!ableToOpen) { in SRAInfoCommand()
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| H A D | chimeraccodecommand.cpp | 109 bool ableToOpen = util.openInputFile(maskfile, in); in ChimeraCcodeCommand() local
110 if (!ableToOpen) { abort = true; } in ChimeraCcodeCommand()
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| H A D | sffmultiplecommand.cpp | 254 bool ableToOpen = util.checkLocations(lookupFileName, current->getLocations()); in SffMultipleCommand() local
255 if (!ableToOpen) { abort=true; } in SffMultipleCommand()
269 bool ableToOpen = util.openInputFile(tryPath, in2, "noerror"); in SffMultipleCommand() local
273 if (!ableToOpen) { m->mothurOut("Unable to open " + lookupFileName + ".\n"); abort=true; } in SffMultipleCommand()
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| H A D | chimeraslayercommand.cpp | 268 bool ableToOpen = util.openInputFile(formatdbCommand, in, "no error"); in.close(); in ChimeraSlayerCommand() local
269 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requi… in ChimeraSlayerCommand()
275 ableToOpen = util.openInputFile(blastCommand, in2, "no error"); in2.close(); in ChimeraSlayerCommand()
276 …if(!ableToOpen) { m->mothurOut("[ERROR]: " + blastCommand + " file does not exist. mothur requires… in ChimeraSlayerCommand()
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| H A D | shhhercommand.cpp | 136 bool ableToOpen = util.checkLocations(fName, current->getLocations()); in ShhherCommand() local
137 if (ableToOpen) { in ShhherCommand()
165 bool ableToOpen = util.checkLocations(lookupFileName, current->getLocations()); in ShhherCommand() local
166 if (ableToOpen) { in ShhherCommand()
175 bool ableToOpen = util.checkLocations(lookupFileName, current->getLocations()); in ShhherCommand() local
176 if (ableToOpen) { in ShhherCommand()
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| H A D | clustercommand.cpp | 182 … bool ableToOpen = util.openInputFile(vsearchLocation, in, "no error"); in.close(); in ClusterCommand() local
183 if(!ableToOpen) { in ClusterCommand()
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| H A D | chimeravsearchcommand.cpp | 224 bool ableToOpen = util.openInputFile(vsearchLocation, in, "no error"); in.close(); in ChimeraVsearchCommand() local
225 if(!ableToOpen) { in ChimeraVsearchCommand()
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| H A D | clustersplitcommand.cpp | 291 … bool ableToOpen = util.openInputFile(vsearchLocation, in, "no error"); in.close(); in ClusterSplitCommand() local
292 if(!ableToOpen) { in ClusterSplitCommand()
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| /dports/biology/mothur/mothur-1.46.1/source/ |
| H A D | validparameter.cpp | 285 bool ableToOpen = false; in validFile() local
296 …cations(filename, current->getLocations())) { container[parameter] = filename; ableToOpen = true; } in validFile()
300 if ((it->first == "phylip") && (ableToOpen)) { in validFile()
312 if (ableToOpen) { in validFile()
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| H A D | utils.cpp | 596 bool ableToOpen; in checkLocations() local
602 if (!ableToOpen) { in checkLocations()
612 if (!ableToOpen) { in checkLocations()
623 if (!ableToOpen) { in checkLocations()
633 if (!ableToOpen) { in checkLocations()
641 if (!ableToOpen) { in checkLocations()
667 bool ableToOpen; in checkLocations() local
673 if (!ableToOpen) { in checkLocations()
682 if (!ableToOpen) { in checkLocations()
692 if (!ableToOpen) { in checkLocations()
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