X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.cpp;h=923ca72eccbd2f88bad0b36b0c15fba58f1b829c;hb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;hp=c320fa4d8854f003486bc71c8e6b0806ec7ae0e3;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git diff --git a/removerarecommand.cpp b/removerarecommand.cpp index c320fa4..923ca72 100644 --- a/removerarecommand.cpp +++ b/removerarecommand.cpp @@ -58,6 +58,31 @@ string RemoveRareCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string RemoveRareCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "rabund") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "sabund") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "shared") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "group") { outputFileName = "pick" + m->getExtension(inputName); } + else if (type == "list") { outputFileName = "pick" + m->getExtension(inputName); } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "RemoveRareCommand", "getOutputFileNameTag"); + exit(1); + } +} + //********************************************************************************************************************** RemoveRareCommand::RemoveRareCommand(){ try { @@ -220,7 +245,7 @@ RemoveRareCommand::RemoveRareCommand(string option) { string temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; } - else { convert(temp, nseqs); } + else { m->mothurConvert(temp, nseqs); } temp = validParameter.validFile(parameters, "bygroup", false); if (temp == "not found") { temp = "f"; } byGroup = m->isTrue(temp); @@ -251,7 +276,7 @@ int RemoveRareCommand::execute(){ if (listfile != "") { processList(); } if (sharedfile != "") { processShared(); } - 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(); @@ -301,9 +326,8 @@ int RemoveRareCommand::processList(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(listfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile); - string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile); - + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + getOutputFileNameTag("list", listfile); + string outputGroupFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile); ofstream out, outGroup; m->openOutputFile(outputFileName, out); @@ -353,7 +377,8 @@ int RemoveRareCommand::processList(){ if (groupfile != "") { groupMap = new GroupMap(groupfile); groupMap->readMap(); SharedUtil util; - util.setGroups(Groups, groupMap->namesOfGroups); + vector namesGroups = groupMap->getNamesOfGroups(); + util.setGroups(Groups, namesGroups); m->openOutputFile(outputGroupFileName, outGroup); } @@ -365,7 +390,7 @@ int RemoveRareCommand::processList(){ //for each bin for (int i = 0; i < list->getNumBins(); i++) { - if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); remove(outputGroupFileName.c_str()); } out.close(); remove(outputFileName.c_str()); return 0; } + if (m->control_pressed) { if (groupfile != "") { delete groupMap; outGroup.close(); m->mothurRemove(outputGroupFileName); } out.close(); m->mothurRemove(outputFileName); return 0; } //parse out names that are in accnos file string binnames = list->get(i); @@ -422,7 +447,7 @@ int RemoveRareCommand::processSabund(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + getOutputFileNameTag("sabund", sabundfile); outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName); ofstream out; @@ -521,7 +546,7 @@ int RemoveRareCommand::processRabund(){ try { string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + getOutputFileNameTag("rabund", rabundfile); outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName); ofstream out; @@ -624,11 +649,11 @@ int RemoveRareCommand::processRabund(){ //********************************************************************************************************************** int RemoveRareCommand::processShared(){ try { - m->Groups = Groups; + m->setGroups(Groups); string thisOutputDir = outputDir; if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); } - string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "pick" + m->getExtension(sharedfile); + string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile); outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName); ofstream out;