/*
 *  pcacommand.cpp
 *  mothur
 *
 *  Created by westcott on 1/7/11.
 *  Copyright 2011 Schloss Lab. All rights reserved.
 *
 */

#include "pcacommand.h"
#include "inputdata.h"

//**********************************************************************************************************************
vector<string> PCACommand::setParameters(){	
	try {
		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared);	
		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(prelabund);
		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
		CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
		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["pca"] = 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, "PCACommand", "setParameters");
		exit(1);
	}
}
//**********************************************************************************************************************
string PCACommand::getHelpString(){	
	try {
		string helpString = "";
		helpString += "The pca command parameters are shared, relabund, label, groups and metric.  shared or relabund is required unless you have a valid current file."; 
		helpString += "The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n";
		helpString += "The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n";
		helpString += "The metric parameter allows you to indicate if would like the pearson correlation coefficient calculated. Default=True";
		helpString += "Example pca(groups=yourGroups).\n";
		helpString += "Example pca(groups=A-B-C).\n";
		
		return helpString;
	}
	catch(exception& e) {
		m->errorOut(e, "PCACommand", "getHelpString");
		exit(1);
	}
}
//**********************************************************************************************************************
string PCACommand::getOutputPattern(string type) {
    try {
        string pattern = "";
        
        if (type == "pca") {  pattern = "[filename],[distance],pca.axes"; } 
        else if (type == "loadings") {  pattern = "[filename],[distance],pca.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, "PCACommand", "getOutputPattern");
        exit(1);
    }
}
//**********************************************************************************************************************
PCACommand::PCACommand(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;
			sharedfile = validParameter.validFile(parameters, "shared");
			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
			else if (sharedfile == "not found") { sharedfile = ""; }
			else {  mode = "sharedfile"; inputFile = sharedfile; current->setSharedFile(sharedfile); }
			
			relabundfile = validParameter.validFile(parameters, "relabund");
			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
			else if (relabundfile == "not found") { relabundfile = ""; }
			else {  mode = "relabund"; inputFile = relabundfile; current->setRelAbundFile(relabundfile); }
			
			
			if ((sharedfile == "") && (relabundfile == "")) { 
				//is there are current file available for any of these?
				//give priority to shared, then list, then rabund, then sabund
				//if there is a current shared file, use it
				sharedfile = current->getSharedFile(); 
				if (sharedfile != "") { inputFile = sharedfile; mode = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.\n");  }
				else { 
					relabundfile = current->getRelAbundFile(); 
					if (relabundfile != "") { inputFile = relabundfile; mode = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter.\n");  }
					else { 
						m->mothurOut("No valid current files. You must provide a relabund or shared file.\n");  
						abort = true;
					}
				}
			}
				
			if (outputdir == ""){	 outputdir += util.hasPath(inputFile); }
						
			string temp = validParameter.valid(parameters, "metric");	if (temp == "not found"){	temp = "T";				}
			metric = util.isTrue(temp); 
			
			label = validParameter.valid(parameters, "label");			
			if (label == "not found") { label = ""; if(labels.size() == 0) {  m->mothurOut("You did not provide a label, I will use the first label in your inputfile.\n");  } }
			else { util.splitAtDash(label, labels); }
			
			groups = validParameter.valid(parameters, "groups");			
			if (groups == "not found") { groups = "";  }
			else { util.splitAtDash(groups, Groups); if (Groups.size() != 0) { if (Groups[0]== "all") { Groups.clear(); } }	}
					
			
		}
		
	}
	catch(exception& e) {
		m->errorOut(e, "PCACommand", "PCACommand");
		exit(1);
	}
}
//**********************************************************************************************************************
int PCACommand::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);
		
		//get first line of shared file
		vector< vector<double> > matrix;
		InputData* input;
		if (mode == "sharedfile")			{  
			input = new InputData(inputFile, "sharedfile", Groups);
		}else if (mode == "relabund")	{ 
			input = new InputData(inputFile, "relabund", Groups);
		}else {  m->mothurOut("[ERROR]: filetype not recognized.\n");   return 0; }
		
		SharedRAbundFloatVectors* lookupFloat = input->getSharedRAbundFloatVectors();
		string lastLabel = lookupFloat->getLabel();
        Groups = lookupFloat->getNamesGroups();
			
		set<string> processedLabels;
		set<string> userLabels = labels;
		
		//if the user gave no labels, then use the first one read
		if (labels.size() == 0) { 
			label = lastLabel;  
			
			process(lookupFloat);
		}
		
		//as long as you are not at the end of the file or done wih the lines you want
		while((lookupFloat != nullptr) && (userLabels.size() != 0)) {
			
            if (m->getControl_pressed()) {  for (int i = 0; i < outputNames.size(); i++) {	util.mothurRemove(outputNames[i]);  } delete input; delete lookupFloat; return 0;  }
			
			if(labels.count(lookupFloat->getLabel()) == 1){
				processedLabels.insert(lookupFloat->getLabel());
				userLabels.erase(lookupFloat->getLabel());
				
				process(lookupFloat);
			}
			
			if ((util.anyLabelsToProcess(lookupFloat->getLabel(), userLabels, "") ) && (processedLabels.count(lastLabel) != 1)) {
				string saveLabel = lookupFloat->getLabel();
				
				delete lookupFloat;
				lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
				
				process(lookupFloat);
				
				processedLabels.insert(lookupFloat->getLabel());
				userLabels.erase(lookupFloat->getLabel());
				
				//restore real lastlabel to save below
				lookupFloat->setLabels(saveLabel);
			}
			
			lastLabel = lookupFloat->getLabel();
			
			//get next line to process
			//prevent memory leak
			delete lookupFloat;
			lookupFloat = input->getSharedRAbundFloatVectors();
		}
		
		
		if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) {	util.mothurRemove(outputNames[i]);  } delete input; delete lookupFloat;  return 0;  }
		
		//output error messages about any remaining user labels
		bool needToRun = false;
		for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
			m->mothurOut("Your file does not include the label " + *it); 
            if (processedLabels.count(lastLabel) != 1)  { m->mothurOut(". I will use " + lastLabel + ".\n"); needToRun = true;  }
			else                                        { m->mothurOut(". Please refer to " + lastLabel + ".\n");               }
		}
		
		//run last label if you need to
		if (needToRun )  {
			delete lookupFloat;
			lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
			
			process(lookupFloat);
			
			delete lookupFloat;
		}	
		
		delete input;
		
		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, "PCACommand", "execute");
		exit(1);
	}
}

/**********************************************************************************************************************
vector< vector<double> > PCACommand::createMatrix(vector<SharedRAbundFloatVector*> lookupFloat){
	try {
		vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
		
		//fill matrix with shared files relative abundances
		for (int i = 0; i < lookupFloat.size(); i++) {
			for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
				matrix[i].push_back(lookupFloat[i]->getAbundance(j));
			}
		}
		
		vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
		for (int i = 0; i < transposeMatrix.size(); i++) {
			for (int j = 0; j < matrix.size(); j++) {
				transposeMatrix[i].push_back(matrix[j][i]);
			}
		}
		
		matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
		
		return matrix;
	}
	catch(exception& e) {
		m->errorOut(e, "PCACommand", "createMatrix");	
		exit(1);
	}
}*/
//**********************************************************************************************************************

int PCACommand::process(SharedRAbundFloatVectors*& lookupFloat){
	try {
		m->mothurOut("\nProcessing " + lookupFloat->getLabel()); m->mothurOutEndLine();
	
		int numOTUs = lookupFloat->getNumBins();
		int numSamples = lookupFloat->getNumGroups();
		
		vector< vector<double> > matrix(numSamples);
		vector<double> colMeans(numOTUs);
		
		//fill matrix with shared relative abundances, re-center
        vector<SharedRAbundFloatVector*> data = lookupFloat->getSharedRAbundFloatVectors();
		for (int i = 0; i < numSamples; i++) {
			matrix[i].resize(numOTUs, 0);
			
			for (int j = 0; j < numOTUs; j++) {
				matrix[i][j] = data[i]->get(j);
				colMeans[j] += matrix[i][j];
			}
            delete data[i];
		}
        data.clear();

		for(int j=0;j<numOTUs;j++){
			colMeans[j] = colMeans[j] / (double)numSamples;
		}
		
		vector<vector<double> > centered = matrix;
		for(int i=0;i<numSamples;i++){
			for(int j=0;j<numOTUs;j++){
				centered[i][j] = centered[i][j] - colMeans[j];				
			}
		}

		
		vector< vector<double> > transpose(numOTUs);
		for (int i = 0; i < numOTUs; i++) {
			transpose[i].resize(numSamples, 0);
			
			for (int j = 0; j < numSamples; j++) {
				transpose[i][j] = centered[j][i];
			}
		}

		vector<vector<double> > crossProduct = linearCalc.matrix_mult(transpose, centered);	
		
		vector<double> d;
		vector<double> e;

		linearCalc.tred2(crossProduct, d, e);		if (m->getControl_pressed()) { return 0; }
		linearCalc.qtli(d, e, crossProduct);		if (m->getControl_pressed()) { return 0; }
		
		vector<vector<double> > X = linearCalc.matrix_mult(centered, crossProduct);
		
		if (m->getControl_pressed()) { return 0; }
		
		string fbase = outputdir + util.getRootName(util.getSimpleName(inputFile));
		//string outputFileName = fbase + lookupFloat[0]->getLabel();
		output(fbase, lookupFloat->getLabel(), Groups, X, d);
		
		if (metric) {   
			
			vector<vector<double> > observedEuclideanDistance = linearCalc.getObservedEuclideanDistance(centered);
			
			for (int i = 1; i < 4; i++) {
				
				vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file
				
				if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) {	util.mothurRemove(outputNames[i]);  } return 0; }

				double corr = linearCalc.calcPearson(PCAEuclidDists, observedEuclideanDistance);
								
				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; }
			}
		}
		
		return 0;
	}
	catch(exception& e) {
		m->errorOut(e, "PCACommand", "process");	
		exit(1);
	}
}
/*********************************************************************************************************************************/

void PCACommand::output(string fbase, string label, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
	try {

		int numEigenValues = d.size();
		double dsum = 0.0000;
		for(int i=0;i<numEigenValues;i++){
			dsum += d[i];
		}
		
		ofstream pcaData;
        map<string, string> variables; 
        variables["[filename]"] = fbase;
        variables["[distance]"] = label;
        string pcaFileName = getOutputFileName("pca",variables);
        util.openOutputFile(pcaFileName, pcaData);
		pcaData.setf(ios::fixed, ios::floatfield);
		pcaData.setf(ios::showpoint);	
		outputNames.push_back(pcaFileName);
		outputTypes["pca"].push_back(pcaFileName);
		
		ofstream pcaLoadings;
        string loadingsFilename = getOutputFileName("loadings",variables);
         util.openOutputFile(loadingsFilename, pcaLoadings);
		pcaLoadings.setf(ios::fixed, ios::floatfield);
		pcaLoadings.setf(ios::showpoint);
		outputNames.push_back(loadingsFilename);
		outputTypes["loadings"].push_back(loadingsFilename);	
		
		pcaLoadings << "axis\tloading\n";
		for(int i=0;i<numEigenValues;i++){
			pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
		}
		
		pcaData << "group";
		for(int i=0;i<numEigenValues;i++){
			pcaData << '\t' << "axis" << i+1;
		}
		pcaData << endl;
		
		for(int i=0;i<name_list.size();i++){
			pcaData << name_list[i];
			for(int j=0;j<numEigenValues;j++){  pcaData << '\t' << G[i][j];  }
			pcaData << endl;
		}
	}
	catch(exception& e) {
		m->errorOut(e, "PCACommand", "output");
		exit(1);
	}
}
/*********************************************************************************************************************************/