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);

}

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);

}

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);

}

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);

}

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);

}

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);

}

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);

}