X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;fp=pcacommand.cpp;h=a91143bbd87c28deedc6edc03af4ffbea95f37de;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=23c066b7beff9dd0d6c1da089221a07e510411ae;hpb=36a867cbd85d9c276d3c8d13f25a150bbbe2466b;p=mothur.git diff --git a/pcacommand.cpp b/pcacommand.cpp index 23c066b..a91143b 100644 --- a/pcacommand.cpp +++ b/pcacommand.cpp @@ -11,50 +11,54 @@ #include "inputdata.h" //********************************************************************************************************************** -vector PCACommand::getValidParameters(){ +vector PCACommand::setParameters(){ try { - string Array[] = {"label", "groups","metric","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared); + CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund); + CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups); + CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric); + CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + 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, "PCACommand", "getValidParameters"); + m->errorOut(e, "PCACommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -PCACommand::PCACommand(){ +string PCACommand::getHelpString(){ try { - abort = true; calledHelp = true; - vector tempOutNames; - outputTypes["pca"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; + string helpString = ""; + helpString += "The pca command parameters are shared, relabund, label, groups and metric. shared or relabund is required unless you have a valid current file."; + helpString += "The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n"; + helpString += "The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n"; + helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"; + helpString += "Example pca(groups=yourGroups).\n"; + helpString += "Example pca(groups=A-B-C).\n"; + helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"; + return helpString; } catch(exception& e) { - m->errorOut(e, "PCACommand", "PCACommand"); + m->errorOut(e, "PCACommand", "getHelpString"); exit(1); } } //********************************************************************************************************************** -vector PCACommand::getRequiredParameters(){ - try { - vector myArray; - return myArray; - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector PCACommand::getRequiredFiles(){ +PCACommand::PCACommand(){ try { - string Array[] = {"shared","relabund","or"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; + abort = true; calledHelp = true; + setParameters(); + vector tempOutNames; + outputTypes["pca"] = tempOutNames; + outputTypes["loadings"] = tempOutNames; } catch(exception& e) { - m->errorOut(e, "PCACommand", "getRequiredFiles"); + m->errorOut(e, "PCACommand", "PCACommand"); exit(1); } } @@ -64,15 +68,11 @@ PCACommand::PCACommand(string option) { try { abort = false; calledHelp = false; - globaldata = GlobalData::getInstance(); - //allow user to run help if(option == "help") { help(); abort = true; calledHelp = true; } else { - //valid paramters for this command - string Array[] = {"label","groups","metric","outputdir", "inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser. getParameters(); @@ -84,22 +84,62 @@ PCACommand::PCACommand(string option) { for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } - //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); if (inputDir == "not found"){ inputDir = ""; } - + //initialize outputTypes vector tempOutNames; outputTypes["pca"] = tempOutNames; outputTypes["loadings"] = tempOutNames; - //make sure the user has already run the read.otu command - if ((globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) { - m->mothurOut("You must read a list and a group, shared or relabund file before you can use the pca command."); m->mothurOutEndLine(); abort = true; + //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); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("shared"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["shared"] = inputDir + it->second; } + } + + it = parameters.find("relabund"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["relabund"] = inputDir + it->second; } + } } - if (globaldata->getSharedFile() != "") { mode = "shared"; inputFile = globaldata->getSharedFile(); } - if (globaldata->getRelAbundFile() != "") { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); } + //check for required parameters + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else if (sharedfile == "not found") { sharedfile = ""; } + else { mode = "sharedfile"; inputFile = sharedfile; } + + relabundfile = validParameter.validFile(parameters, "relabund", true); + if (relabundfile == "not open") { relabundfile = ""; abort = true; } + else if (relabundfile == "not found") { relabundfile = ""; } + else { mode = "relabund"; inputFile = relabundfile; } + + if ((sharedfile == "") && (relabundfile == "")) { + //is there are current file available for any of these? + //give priority to shared, then list, then rabund, then sabund + //if there is a current shared file, use it + sharedfile = m->getSharedFile(); + if (sharedfile != "") { inputFile = sharedfile; mode = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { + relabundfile = m->getRelAbundFile(); + if (relabundfile != "") { inputFile = relabundfile; mode = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); } + else { + m->mothurOut("No valid current files. You must provide a relabund or shared file."); m->mothurOutEndLine(); + abort = true; + } + } + } + //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 = ""; @@ -110,13 +150,13 @@ PCACommand::PCACommand(string option) { metric = m->isTrue(temp); label = validParameter.validFile(parameters, "label", false); - if (label == "not found") { label = ""; labels = globaldata->labels; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } } + if (label == "not found") { label = ""; if(labels.size() == 0) { m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } } else { m->splitAtDash(label, labels); } groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { m->splitAtDash(groups, Groups); } - globaldata->Groups = Groups; + m->Groups = Groups; } @@ -127,25 +167,6 @@ PCACommand::PCACommand(string option) { } } //********************************************************************************************************************** -void PCACommand::help(){ - try { - m->mothurOut("The pca command can only be run after a successful read.otu command of a shared or relabund file."); m->mothurOutEndLine(); - m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine(); - m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n"); - m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n"); - m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine(); - m->mothurOut("Example pca(groups=yourGroups).\n"); - m->mothurOut("Example pca(groups=A-B-C).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "PCACommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** -PCACommand::~PCACommand(){} -//********************************************************************************************************************** int PCACommand::execute(){ try { @@ -344,7 +365,7 @@ int PCACommand::process(vector& lookupFloat){ string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile)); string outputFileName = fbase + lookupFloat[0]->getLabel(); - output(outputFileName, globaldata->Groups, G, d); + output(outputFileName, m->Groups, G, d); if (metric) {