X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removelineagecommand.cpp;h=9fec2496068950b4863448fe500b17cbc957670a;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=5f5435f8679a9b65bb4799dae9dff30555818d3c;hpb=f06fdb807822f8e06db003ed809c87250905cfc8;p=mothur.git diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp index 5f5435f..9fec249 100644 --- a/removelineagecommand.cpp +++ b/removelineagecommand.cpp @@ -169,16 +169,19 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { //check for required parameters fastafile = validParameter.validFile(parameters, "fasta", true); - if (fastafile == "not open") { abort = true; } + if (fastafile == "not open") { fastafile = ""; abort = true; } else if (fastafile == "not found") { fastafile = ""; } + else { m->setFastaFile(fastafile); } namefile = validParameter.validFile(parameters, "name", true); - if (namefile == "not open") { abort = true; } + if (namefile == "not open") { namefile = ""; abort = true; } else if (namefile == "not found") { namefile = ""; } + else { m->setNameFile(namefile); } groupfile = validParameter.validFile(parameters, "group", true); if (groupfile == "not open") { abort = true; } else if (groupfile == "not found") { groupfile = ""; } + else { m->setGroupFile(groupfile); } alignfile = validParameter.validFile(parameters, "alignreport", true); if (alignfile == "not open") { abort = true; } @@ -187,14 +190,15 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { listfile = validParameter.validFile(parameters, "list", true); if (listfile == "not open") { abort = true; } else if (listfile == "not found") { listfile = ""; } + else { m->setListFile(listfile); } taxfile = validParameter.validFile(parameters, "taxonomy", true); - if (taxfile == "not open") { abort = true; } + if (taxfile == "not open") { taxfile = ""; abort = true; } else if (taxfile == "not found") { taxfile = m->getTaxonomyFile(); if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); } else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; } - } + }else { m->setTaxonomyFile(taxfile); } string usedDups = "true"; string temp = validParameter.validFile(parameters, "dups", false); @@ -216,7 +220,12 @@ RemoveLineageCommand::RemoveLineageCommand(string option) { if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; } if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; } - + + if ((namefile == "") && ((fastafile != "") || (taxfile != ""))){ + vector files; files.push_back(fastafile); files.push_back(taxfile); + parser.getNameFile(files); + } + } } @@ -243,7 +252,7 @@ int RemoveLineageCommand::execute(){ if (listfile != "") { readList(); } - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } if (outputNames.size() != 0) { m->mothurOutEndLine(); @@ -305,7 +314,7 @@ int RemoveLineageCommand::readFasta(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } Sequence currSeq(in); name = currSeq.getName(); @@ -359,7 +368,7 @@ int RemoveLineageCommand::readList(){ //for each bin for (int i = 0; i < list.getNumBins(); i++) { - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list.get(i); @@ -422,7 +431,7 @@ int RemoveLineageCommand::readName(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> firstCol; in >> secondCol; @@ -500,7 +509,7 @@ int RemoveLineageCommand::readGroup(){ bool wroteSomething = false; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> group; //read from second column @@ -551,14 +560,15 @@ int RemoveLineageCommand::readTax(){ if (hasConPos != string::npos) { taxonsHasConfidence[i] = true; searchTaxons[i] = getTaxons(listOfTaxons[i]); - noConfidenceTaxons[i] = removeConfidences(listOfTaxons[i]); + noConfidenceTaxons[i] = listOfTaxons[i]; + m->removeConfidences(noConfidenceTaxons[i]); } } while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column in >> tax; //read from second column @@ -573,7 +583,8 @@ int RemoveLineageCommand::readTax(){ int hasConfidences = tax.find_first_of('('); if (hasConfidences != string::npos) { - newtax = removeConfidences(tax); + newtax = tax; + m->removeConfidences(newtax); } int pos = newtax.find(noConfidenceTaxons[j]); @@ -605,7 +616,8 @@ int RemoveLineageCommand::readTax(){ string noNewTax = tax; int hasConfidences = tax.find_first_of('('); if (hasConfidences != string::npos) { - noNewTax = removeConfidences(tax); + noNewTax = tax; + m->removeConfidences(noNewTax); } int pos = noNewTax.find(noConfidenceTaxons[j]); @@ -722,29 +734,6 @@ vector< map > RemoveLineageCommand::getTaxons(string tax) { exit(1); } } -/**************************************************************************************************/ -string RemoveLineageCommand::removeConfidences(string tax) { - try { - - string taxon = ""; - int taxLength = tax.length(); - for(int i=0;ierrorOut(e, "RemoveLineageCommand", "removeConfidences"); - exit(1); - } -} //********************************************************************************************************************** //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name int RemoveLineageCommand::readAlign(){ @@ -770,7 +759,7 @@ int RemoveLineageCommand::readAlign(){ out << endl; while(!in.eof()){ - if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; } in >> name; //read from first column