X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=binsequencecommand.cpp;h=bf14d6b07b3b6ae64c20d3072abb3c3603a9e42c;hb=3247d888e7aafc4a65ec9062a94dfd166c2c5b1d;hp=1601f32873ed6c8eefe41608ceda199a6fa5b5f5;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp index 1601f32..bf14d6b 100644 --- a/binsequencecommand.cpp +++ b/binsequencecommand.cpp @@ -9,6 +9,55 @@ #include "binsequencecommand.h" +//********************************************************************************************************************** +vector BinSeqCommand::getValidParameters(){ + try { + string AlignArray[] = {"fasta","label","name", "group","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector BinSeqCommand::getRequiredParameters(){ + try { + string AlignArray[] = {"fasta"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector BinSeqCommand::getRequiredFiles(){ + try { + string AlignArray[] = {"list"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** +BinSeqCommand::BinSeqCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "BinSeqCommand", "BinSeqCommand"); + exit(1); + } +} //********************************************************************************************************************** BinSeqCommand::BinSeqCommand(string option) { try { @@ -36,10 +85,14 @@ BinSeqCommand::BinSeqCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["fasta"] = tempOutNames; + //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; - outputDir += hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it + outputDir += m->hasPath(globaldata->getListFile()); //if user entered a file with a path then preserve it } @@ -58,7 +111,7 @@ BinSeqCommand::BinSeqCommand(string option) { it = parameters.find("fasta"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["fasta"] = inputDir + it->second; } } @@ -66,7 +119,7 @@ BinSeqCommand::BinSeqCommand(string option) { it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } @@ -74,7 +127,7 @@ BinSeqCommand::BinSeqCommand(string option) { it = parameters.find("group"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["group"] = inputDir + it->second; } } @@ -92,7 +145,7 @@ BinSeqCommand::BinSeqCommand(string option) { label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } @@ -111,7 +164,7 @@ BinSeqCommand::BinSeqCommand(string option) { else if (groupfile == "not found") { groupfile = ""; } if (abort == false) { -// openInputFile(fastafile, in); +// m->openInputFile(fastafile, in); fasta = new FastaMap(); if (groupfile != "") { groupMap = new GroupMap(groupfile); @@ -181,7 +234,6 @@ int BinSeqCommand::execute(){ readNamesFile(); } - //read list file read = new ReadOTUFile(globaldata->getListFile()); read->read(&*globaldata); @@ -199,6 +251,8 @@ int BinSeqCommand::execute(){ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + if(allLines == 1 || labels.count(list->getLabel()) == 1){ error = process(list); @@ -208,7 +262,7 @@ int BinSeqCommand::execute(){ userLabels.erase(list->getLabel()); } - if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = list->getLabel(); delete list; @@ -230,7 +284,8 @@ int BinSeqCommand::execute(){ list = input->getListVector(); } - + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; @@ -255,6 +310,8 @@ int BinSeqCommand::execute(){ delete list; } + if(m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } + m->mothurOutEndLine(); m->mothurOut("Output File Names: "); m->mothurOutEndLine(); for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); } @@ -273,7 +330,7 @@ int BinSeqCommand::execute(){ void BinSeqCommand::readNamesFile() { try { vector dupNames; - openInputFile(namesfile, inNames); + m->openInputFile(namesfile, inNames); string name, names, sequence; @@ -284,7 +341,7 @@ void BinSeqCommand::readNamesFile() { dupNames.clear(); //parse names into vector - splitAtComma(names, dupNames); + m->splitAtComma(names, dupNames); //store names in fasta map sequence = fasta->getSequence(name); @@ -292,7 +349,7 @@ void BinSeqCommand::readNamesFile() { fasta->push_back(dupNames[i], sequence); } - gobble(inNames); + m->gobble(inNames); } inNames.close(); @@ -308,11 +365,11 @@ int BinSeqCommand::process(ListVector* list) { try { string binnames, name, sequence; - string outputFileName = outputDir + getRootName(getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta"; - openOutputFile(outputFileName, out); + string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->getListFile())) + list->getLabel() + ".fasta"; + m->openOutputFile(outputFileName, out); //save to output list of output file names - outputNames.push_back(outputFileName); + outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName); m->mothurOut(list->getLabel()); m->mothurOutEndLine();