--- /dev/null
+
+/*
+ * pcacommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 1/4/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "pcoacommand.h"
+#include "readphylipvector.h"
+
+
+//**********************************************************************************************************************
+vector<string> 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<string> 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<string> 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<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser. getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::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<string> 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<string> names;
+ vector<vector<double> > 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<double> d;
+ vector<double> e;
+ vector<vector<double> > G = D;
+ //vector<vector<double> > 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<double> > 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<string> name_list, vector<vector<double> >& G, vector<double> d) {
+ try {
+ int rank = name_list.size();
+ double dsum = 0.0000;
+ for(int i=0;i<rank;i++){
+ dsum += d[i];
+ for(int j=0;j<rank;j++){
+ if(d[j] >= 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;i<rank;i++){
+ pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
+ }
+
+ pcaData << "group";
+ for(int i=0;i<rank;i++){
+ pcaData << '\t' << "axis" << i+1;
+ }
+ pcaData << endl;
+
+ for(int i=0;i<rank;i++){
+ pcaData << name_list[i] << '\t';
+ for(int j=0;j<rank;j++){
+ pcaData << G[i][j] << '\t';
+ }
+ pcaData << endl;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCOACommand", "output");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************************************************/
+
projects / mothur.git / blobdiff