X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterfragmentscommand.cpp;h=4a338419af8900f8b7ebd693225a7e9f4d193481;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=ad1bd81b4a9d4554751cfbbc5eb836e107e7b53d;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp index ad1bd81..4a33841 100644 --- a/clusterfragmentscommand.cpp +++ b/clusterfragmentscommand.cpp @@ -66,6 +66,28 @@ string ClusterFragmentsCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string ClusterFragmentsCommand::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 == "fasta") { outputFileName = "fragclust.fasta"; } + else if (type == "name") { outputFileName = "fragclust.names"; } + 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, "ClusterFragmentsCommand", "getOutputFileNameTag"); + exit(1); + } +} + //********************************************************************************************************************** ClusterFragmentsCommand::ClusterFragmentsCommand(){ try { @@ -147,7 +169,7 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { // ...at some point should added some additional type checking... namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not found") { namefile = ""; } - else if (namefile == "not open") { abort = true; } + else if (namefile == "not open") { namefile = ""; abort = true; } else { readNameFile(); m->setNameFile(namefile); } string temp; @@ -157,6 +179,11 @@ ClusterFragmentsCommand::ClusterFragmentsCommand(string option) { temp = validParameter.validFile(parameters, "percent", false); if (temp == "not found"){ temp = "0"; } m->mothurConvert(temp, percent); + if (namefile == "") { + vector files; files.push_back(fastafile); + parser.getNameFile(files); + } + } } @@ -225,8 +252,8 @@ int ClusterFragmentsCommand::execute(){ string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile)); - string newFastaFile = fileroot + "fragclust.fasta"; - string newNamesFile = fileroot + "fragclust.names"; + string newFastaFile = fileroot + getOutputFileNameTag("fasta"); + string newNamesFile = fileroot + getOutputFileNameTag("name"); if (m->control_pressed) { return 0; }