X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;fp=pcoacommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=02e165e978dc071ba19808139060866d7e41388c;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git diff --git a/pcoacommand.cpp b/pcoacommand.cpp deleted file mode 100644 index 02e165e..0000000 --- a/pcoacommand.cpp +++ /dev/null @@ -1,270 +0,0 @@ - -/* - * pcacommand.cpp - * Mothur - * - * Created by westcott on 1/4/10. - * Copyright 2010 Schloss Lab. All rights reserved. - * - */ - -#include "pcoacommand.h" -#include "readphylipvector.h" - - -//********************************************************************************************************************** -vector PCOACommand::setParameters(){ - try { - CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,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", "setParameters"); - exit(1); - } -} -//********************************************************************************************************************** -string PCOACommand::getHelpString(){ - try { - 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", "getHelpString"); - exit(1); - } -} - - -//********************************************************************************************************************** -PCOACommand::PCOACommand(){ - try { - abort = true; calledHelp = true; - setParameters(); - vector tempOutNames; - outputTypes["pcoa"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "PCOACommand"); - exit(1); - } -} -//********************************************************************************************************************** - -PCOACommand::PCOACommand(string option) { - try { - abort = false; calledHelp = false; - - //allow user to run help - if(option == "help") { help(); abort = true; calledHelp = true; } - else if(option == "citation") { citation(); abort = true; calledHelp = true;} - - else { - vector myArray = setParameters(); - - OptionParser parser(option); - map parameters = parser. getParameters(); - - ValidParameters validParameter; - map::iterator it; - - //check to make sure all parameters are valid for command - 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 = ""; } - else { - string path; - it = parameters.find("phylip"); - //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["phylip"] = inputDir + it->second; } - } - } - - //initialize outputTypes - vector tempOutNames; - outputTypes["pcoa"] = tempOutNames; - outputTypes["loadings"] = tempOutNames; - - //required parameters - phylipfile = validParameter.validFile(parameters, "phylip", true); - if (phylipfile == "not open") { abort = true; } - 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"){ - outputDir = ""; - outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it - } - - string temp = validParameter.validFile(parameters, "metric", false); if (temp == "not found"){ temp = "T"; } - metric = m->isTrue(temp); - } - - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "PCOACommand"); - exit(1); - } -} -//********************************************************************************************************************** -int PCOACommand::execute(){ - try { - - if (abort == true) { if (calledHelp) { return 0; } return 2; } - - cout.setf(ios::fixed, ios::floatfield); - cout.setf(ios::showpoint); - cerr.setf(ios::fixed, ios::floatfield); - cerr.setf(ios::showpoint); - - vector names; - vector > D; - - fbase = outputDir + m->getRootName(m->getSimpleName(filename)); - - ReadPhylipVector readFile(filename); - names = readFile.read(D); - - if (m->control_pressed) { return 0; } - - double offset = 0.0000; - vector d; - vector e; - vector > G = D; - //vector > copy_G; - - m->mothurOut("\nProcessing...\n"); - - for(int count=0;count<2;count++){ - linearCalc.recenter(offset, D, G); if (m->control_pressed) { return 0; } - linearCalc.tred2(G, d, e); if (m->control_pressed) { return 0; } - linearCalc.qtli(d, e, G); if (m->control_pressed) { return 0; } - offset = d[d.size()-1]; - if(offset > 0.0) break; - } - - if (m->control_pressed) { return 0; } - - output(fbase, names, G, d); - - if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; } - - if (metric) { - - for (int i = 1; i < 4; i++) { - - vector< vector > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file - - 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++) { m->mothurRemove(outputNames[i]); } 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(); } - m->mothurOutEndLine(); - - return 0; - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "execute"); - exit(1); - } -} -/*********************************************************************************************************************************/ - -void PCOACommand::get_comment(istream& f, char begin, char end){ - try { - char d=f.get(); - while(d != end){ d = f.get(); } - d = f.peek(); - } - catch(exception& e) { - m->errorOut(e, "PCOACommand", "get_comment"); - exit(1); - } -} -/*********************************************************************************************************************************/ - -void PCOACommand::output(string fnameRoot, vector name_list, vector >& G, vector d) { - try { - int rank = name_list.size(); - double dsum = 0.0000; - for(int i=0;i= 0) { G[i][j] *= pow(d[j],0.5); } - else { G[i][j] = 0.00000; } - } - } - - ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc); - pcaData.setf(ios::fixed, ios::floatfield); - pcaData.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa.axes"); - outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes"); - - ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc); - pcaLoadings.setf(ios::fixed, ios::floatfield); - pcaLoadings.setf(ios::showpoint); - outputNames.push_back(fnameRoot+"pcoa.loadings"); - outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings"); - - pcaLoadings << "axis\tloading\n"; - for(int i=0;ierrorOut(e, "PCOACommand", "output"); - exit(1); - } -} - -/*********************************************************************************************************************************/ -