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/*
* 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","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["pcoa"] = tempOutNames;
outputTypes["loadings"] = tempOutNames;
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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "getHelpString");
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->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
PCOACommand::PCOACommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string, string> parameters = parser. getParameters();
ValidParameters validParameter;
phylipfile = validParameter.validFile(parameters, "phylip");
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") {
//if there is a current phylip file, use it
phylipfile = current->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter.\n"); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required.\n"); abort = true; }
}else { current->setPhylipFile(phylipfile); }
filename = phylipfile;
if (outputdir == ""){ outputdir += util.hasPath(phylipfile); }
string temp = validParameter.valid(parameters, "metric"); if (temp == "not found"){ temp = "T"; }
metric = util.isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "PCOACommand");
exit(1);
}
}
//**********************************************************************************************************************
int PCOACommand::execute(){
try {
if (abort) { 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 + util.getRootName(util.getSimpleName(filename));
ReadPhylipVector readFile(filename);
names = readFile.read(D);
if (m->getControl_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->getControl_pressed()) { return 0; }
linearCalc.tred2(G, d, e); if (m->getControl_pressed()) { return 0; }
linearCalc.qtli(d, e, G); if (m->getControl_pressed()) { return 0; }
offset = d[d.size()-1];
if(offset > 0.0) break;
}
if (m->getControl_pressed()) { return 0; }
output(fbase, names, G, d);
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.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->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.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->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
}
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } 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;
map<string, string> variables;
variables["[filename]"] = fnameRoot;
string pcoaDataFile = getOutputFileName("pcoa",variables);
util.openOutputFile(pcoaDataFile, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
outputNames.push_back(pcoaDataFile);
outputTypes["pcoa"].push_back(pcoaDataFile);
ofstream pcaLoadings;
string loadingsFile = getOutputFileName("loadings",variables);
util.openOutputFile(loadingsFile, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
outputNames.push_back(loadingsFile);
outputTypes["loadings"].push_back(loadingsFile);
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];
for(int j=0;j<rank;j++){
pcaData << '\t' << G[i][j];
}
pcaData << endl;
}
}
catch(exception& e) {
m->errorOut(e, "PCOACommand", "output");
exit(1);
}
}
/*********************************************************************************************************************************/
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