X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;h=2043a128bd94bc755cb7ef10f5a8b8d9bdb5a6be;hb=bd27c2b0612942815b7417c79f7ee41f669a2a34;hp=3cd844a36d5a5c253786b4eb29745388b042d2d4;hpb=943d3038553f82378567d3b651969146716e5862;p=mothur.git diff --git a/pcoacommand.cpp b/pcoacommand.cpp index 3cd844a..2043a12 100644 --- a/pcoacommand.cpp +++ b/pcoacommand.cpp @@ -11,51 +11,69 @@ #include "pcoacommand.h" #include "readphylipvector.h" + //********************************************************************************************************************** -vector PCOACommand::getValidParameters(){ +vector PCOACommand::setParameters(){ try { - string Array[] = {"phylip", "metric","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip); + CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric); + 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); } return myArray; } catch(exception& e) { - m->errorOut(e, "PCOACommand", "getValidParameters"); + m->errorOut(e, "PCOACommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -PCOACommand::PCOACommand(){ +string PCOACommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["pcoa"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; + string helpString = ""; + helpString += "The pcoa command parameters are phylip and metric"; + helpString += "The phylip parameter allows you to enter your distance file."; + helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"; + helpString += "Example pcoa(phylip=yourDistanceFile).\n"; + helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "PCOACommand", "PCOACommand"); + m->errorOut(e, "PCOACommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector PCOACommand::getRequiredParameters(){ - try { - string Array[] = {"phylip"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "getRequiredParameters"); - exit(1); - } +string PCOACommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "pcoa") { pattern = "[filename],pcoa.axes"; } + else if (type == "loadings") { pattern = "[filename],pcoa.loadings"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "PCOACommand", "getOutputPattern"); + exit(1); + } } + + //********************************************************************************************************************** -vector PCOACommand::getRequiredFiles(){ +PCOACommand::PCOACommand(){ try { - vector myArray; - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["pcoa"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "PCOACommand", "getRequiredFiles"); + m->errorOut(e, "PCOACommand", "PCOACommand"); exit(1); } } @@ -67,11 +85,10 @@ PCOACommand::PCOACommand(string option) { //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"phylip","metric","outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser. getParameters(); @@ -105,8 +122,14 @@ PCOACommand::PCOACommand(string option) { //required parameters phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } - else if (phylipfile == "not found") { phylipfile = ""; abort = true; } - else { filename = phylipfile; } + else if (phylipfile == "not found") { + //if there is a current phylip file, use it + phylipfile = m->getPhylipFile(); + if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; } + }else { m->setPhylipFile(phylipfile); } + + filename = phylipfile; //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"){ @@ -114,9 +137,6 @@ PCOACommand::PCOACommand(string option) { outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it } - //error checking on files - if (phylipfile == "") { m->mothurOut("You must provide a distance file before running the pcoa command."); m->mothurOutEndLine(); abort = true; } - string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; } metric = m->isTrue(temp); } @@ -128,23 +148,6 @@ PCOACommand::PCOACommand(string option) { } } //********************************************************************************************************************** -void PCOACommand::help(){ - try { - - m->mothurOut("The pcoa command parameters are phylip and metric"); m->mothurOutEndLine(); - m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine(); - m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine(); - m->mothurOut("Example pcoa(phylip=yourDistanceFile).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** -PCOACommand::~PCOACommand(){} -//********************************************************************************************************************** int PCOACommand::execute(){ try { @@ -171,7 +174,7 @@ int PCOACommand::execute(){ vector > G = D; //vector > copy_G; - m->mothurOut("\nProcessing...\n\n"); + m->mothurOut("\nProcessing...\n"); for(int count=0;count<2;count++){ linearCalc.recenter(offset, D, G); if (m->control_pressed) { return 0; } @@ -185,7 +188,7 @@ int PCOACommand::execute(){ output(fbase, names, G, d); - 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 (metric) { @@ -193,13 +196,13 @@ int PCOACommand::execute(){ vector< vector > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file - 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; } double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine(); - 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; } } } @@ -242,17 +245,23 @@ void PCOACommand::output(string fnameRoot, vector name_list, vector variables; + variables["[filename]"] = fnameRoot; + string pcoaDataFile = getOutputFileName("pcoa",variables); + m->openOutputFile(pcoaDataFile, pcaData); pcaData.setf(ios::fixed, ios::floatfield); pcaData.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa.axes"); - outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes"); + outputNames.push_back(pcoaDataFile); + outputTypes["pcoa"].push_back(pcoaDataFile); - ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc); + ofstream pcaLoadings; + string loadingsFile = getOutputFileName("loadings",variables); + m->openOutputFile(loadingsFile, pcaLoadings); pcaLoadings.setf(ios::fixed, ios::floatfield); pcaLoadings.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa.loadings"); - outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings"); + outputNames.push_back(loadingsFile); + outputTypes["loadings"].push_back(loadingsFile); pcaLoadings << "axis\tloading\n"; for(int i=0;i