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Searched refs:biomfile (Results 1 – 10 of 10) sorted by relevance

/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dbiominfocommand.cpp122 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()
H A Drenamefilecommand.cpp210 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()
H A Dmakesharedcommand.cpp106 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 …]
H A Dsetcurrentcommand.cpp236 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()
H A Dsetcurrentcommand.h42 … rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summa… variable
H A Dbiominfocommand.h50 string fileroot, biomfile, label, basis, output, format; variable
H A Drenamefilecommand.h39 … rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summa…
H A Dmakesharedcommand.h70 string fileroot, listfile, groupfile, biomfile, ordergroupfile, countfile, sharedfile; variable
/dports/biology/mothur/mothur-1.46.1/source/
H A Dcurrentfile.cpp85 … 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()
H A Dcurrentfile.h54 …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()