+++ /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);
- }
-}
-
-/*********************************************************************************************************************************/
-
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