Searched refs:biomfile (Results 1 – 10 of 10) sorted by relevance
/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | biominfocommand.cpp | 122 biomfile = validParameter.validFile(parameters, "biom"); in BiomInfoCommand() 123 if (biomfile == "not open") { biomfile = ""; abort = true; } in BiomInfoCommand() 124 …else if (biomfile == "not found") { biomfile = ""; m->mothurOut("[ERROR]: You must provide a biom … in BiomInfoCommand() 125 else { current->setBiomFile(biomfile); } in BiomInfoCommand() 150 if (util.isHDF5(biomfile)) { format = "hdf5"; } in BiomInfoCommand() 187 if (format == "hdf5") { biom = new BiomHDF5(biomfile, label); } in execute() 188 else { biom = new BiomSimple(biomfile, label); } in execute() 191 string filename = biomfile; in execute() 193 fileroot = outputdir + util.getRootName(util.getSimpleName(biomfile)); in execute()
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H A D | renamefilecommand.cpp | 210 biomfile = validParameter.validFile(parameters, "biom"); in RenameFileCommand() 211 …if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine… in RenameFileCommand() 212 else if (biomfile == "not found") { biomfile = ""; } in RenameFileCommand() 213 if (biomfile != "") { numFiles++; } in RenameFileCommand() 362 if (biomfile != "") { in execute() 363 newName = getNewName(biomfile, "biom"); in execute() 364 renameOrCopy(biomfile, newName); in execute()
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H A D | makesharedcommand.cpp | 106 biomfile = validParameter.validFile(parameters, "biom"); in SharedCommand() 107 if (biomfile == "not open") { biomfile = ""; abort = true; } in SharedCommand() 108 else if (biomfile == "not found") { biomfile = ""; } in SharedCommand() 109 else { current->setBiomFile(biomfile); } in SharedCommand() 160 biomfile = current->getBiomFile(); in SharedCommand() 161 …if (biomfile != "") { m->mothurOut("Using " + biomfile + " as input file for the biom parameter.\… in SharedCommand() 211 …if ((listfile == "") && (biomfile == "") && (countfile != "")) { //building a shared file from a c… in SharedCommand() 229 else if (biomfile != "") { createSharedFromBiom(); } in execute() 473 string filename = biomfile; in createSharedFromBiom() 493 util.openInputFile(biomfile, in); in createSharedFromBiom() [all …]
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H A D | setcurrentcommand.cpp | 236 biomfile = validParameter.validFile(parameters, "biom"); in SetCurrentCommand() 237 …if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine… in SetCurrentCommand() 238 else if (biomfile == "not found") { biomfile = ""; } in SetCurrentCommand() 239 if (biomfile != "") { current->setBiomFile(biomfile); } in SetCurrentCommand()
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H A D | setcurrentcommand.h | 42 … rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summa… variable
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H A D | biominfocommand.h | 50 string fileroot, biomfile, label, basis, output, format; variable
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H A D | renamefilecommand.h | 39 … rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summa…
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H A D | makesharedcommand.h | 70 string fileroot, listfile, groupfile, biomfile, ordergroupfile, countfile, sharedfile; variable
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/dports/biology/mothur/mothur-1.46.1/source/ |
H A D | currentfile.cpp | 85 … if (biomfile != "") { m->mothurOut("biom=" + biomfile, out); m->mothurOutEndLine(out); } in printCurrentFiles() 118 if (biomfile != "") { m->mothurOut("biom=" + biomfile); m->mothurOutEndLine(); } in printCurrentFiles() 162 if (biomfile != "") { return true; } in hasCurrentFiles() 207 biomfile = ""; in clearCurrentFiles()
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H A D | currentfile.h | 54 …etBiomFile() { lock_guard<std::mutex> guard(currentProtector); return biomfile; } in getBiomFile() 61 …void setBiomFile(string f) { lock_guard<std::mutex> guard(currentProtector); biomfile = util.get… in setBiomFile() 141 … rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, filefile, testFi… variable 201 biomfile = ""; in CurrentFile()
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