X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=corraxescommand.cpp;h=72fa03b75edc196aafcaaa4b6ade6f95d1106d48;hp=a1c3a3d6cd9e6849fb5f86be42a1d46bcd9bc138;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=5d77fd07180d1fb8561ff1962e6d7429caf8555e diff --git a/corraxescommand.cpp b/corraxescommand.cpp index a1c3a3d..72fa03b 100644 --- a/corraxescommand.cpp +++ b/corraxescommand.cpp @@ -14,16 +14,16 @@ //********************************************************************************************************************** vector CorrAxesCommand::setParameters(){ try { - CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes); - CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared); - CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund); - CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata); - CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes); - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); - CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); - CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","corraxes",false,true,true); parameters.push_back(paxes); + CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(prelabund); + CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false); parameters.push_back(pmetadata); + CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pnumaxes); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); + CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups); + CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -55,13 +55,29 @@ string CorrAxesCommand::getHelpString(){ exit(1); } } +//********************************************************************************************************************** +string CorrAxesCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "corraxes") { pattern = "[filename],[tag],corr.axes"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CorrAxesCommand", "getOutputPattern"); + exit(1); + } +} + //********************************************************************************************************************** CorrAxesCommand::CorrAxesCommand(){ try { abort = true; calledHelp = true; setParameters(); vector tempOutNames; - outputTypes["corr.axes"] = tempOutNames; + outputTypes["corraxes"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand"); @@ -92,7 +108,7 @@ CorrAxesCommand::CorrAxesCommand(string option) { } vector tempOutNames; - outputTypes["corr.axes"] = tempOutNames; + outputTypes["corraxes"] = tempOutNames; //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -265,9 +281,11 @@ int CorrAxesCommand::execute(){ /*************************************************************************************/ // calc the r values // /************************************************************************************/ - - string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes"; - outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName)); + variables["[tag]"] = method; + string outputFileName = getOutputFileName("corraxes", variables); + outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName); ofstream out; m->openOutputFile(outputFileName, out); out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint); @@ -321,7 +339,7 @@ int CorrAxesCommand::calcPearson(map >& axes, ofstream& ou //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentSharedBinLabels[i]; } else { out << metadataLabels[i]; } //find the averages this otu - Y @@ -456,7 +474,7 @@ int CorrAxesCommand::calcSpearman(map >& axes, ofstream& o //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentSharedBinLabels[i]; } else { out << metadataLabels[i]; } //find the ranks of this otu - Y @@ -609,7 +627,7 @@ int CorrAxesCommand::calcKendall(map >& axes, ofstream& ou //for each otu for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) { - if (metadatafile == "") { out << i+1; } + if (metadatafile == "") { out << m->currentSharedBinLabels[i]; } else { out << metadataLabels[i]; } //find the ranks of this otu - Y @@ -816,7 +834,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector& thisloo for (int h = 0; h < diff; h++) { binLabel += "0"; } } binLabel += sbinNumber; - if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; } + if (i < m->currentSharedBinLabels.size()) { binLabel = m->currentSharedBinLabels[i]; } newBinLabels.push_back(binLabel); } @@ -825,7 +843,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector& thisloo for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; } thislookup = newLookup; - m->currentBinLabels = newBinLabels; + m->currentSharedBinLabels = newBinLabels; return 0; @@ -905,16 +923,11 @@ int CorrAxesCommand::getMetadata(){ m->openInputFile(metadatafile, in); string headerLine = m->getline(in); m->gobble(in); - istringstream iss (headerLine,istringstream::in); - - //read the first label, because it refers to the groups - string columnLabel; - iss >> columnLabel; m->gobble(iss); + vector pieces = m->splitWhiteSpace(headerLine); //save names of columns you are reading - while (!iss.eof()) { - iss >> columnLabel; m->gobble(iss); - metadataLabels.push_back(columnLabel); + for (int i = 1; i < pieces.size(); i++) { + metadataLabels.push_back(pieces[i]); } int count = metadataLabels.size();