X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;fp=pcacommand.cpp;h=0000000000000000000000000000000000000000;hb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;hp=ee0a5462de87049f6b026546492203be630ea8d7;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
deleted file mode 100644
index ee0a546..0000000
--- a/pcacommand.cpp
+++ /dev/null
@@ -1,607 +0,0 @@
-
-/*
- *  pcacommand.cpp
- *  Mothur
- *
- *  Created by westcott on 1/4/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "pcacommand.h"
-
-//**********************************************************************************************************************
-vector<string> PCACommand::getValidParameters(){	
-	try {
-		string Array[] =  {"phylip", "outputdir","inputdir"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "getValidParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-PCACommand::PCACommand(){	
-	try {
-		abort = true;
-		//initialize outputTypes
-		vector<string> tempOutNames;
-		outputTypes["pcoa"] = tempOutNames;
-		outputTypes["loadings"] = tempOutNames;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "PCACommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredParameters(){	
-	try {
-		string Array[] =  {"phylip"};
-		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "getRequiredParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> PCACommand::getRequiredFiles(){	
-	try {
-		vector<string> myArray;
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "getRequiredFiles");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-PCACommand::PCACommand(string option)  {
-	try {
-		abort = false;
-		
-		//allow user to run help
-		if(option == "help") { help(); abort = true; }
-		
-		else {
-			//valid paramters for this command
-			string Array[] =  {"phylip","outputdir", "inputdir"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-			
-			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") { phylipfile = ""; abort = true; }	
-			else {	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	
-			}
-			
-			//error checking on files	
-			if (phylipfile == "")	{ m->mothurOut("You must provide a distance file before running the pca command."); m->mothurOutEndLine(); abort = true; }		
-		}
-
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "PCACommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-void PCACommand::help(){
-	try {
-	
-		m->mothurOut("The pca command..."); m->mothurOutEndLine();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "help");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-PCACommand::~PCACommand(){}
-//**********************************************************************************************************************
-int PCACommand::execute(){
-	try {
-	
-		if (abort == true) { return 0; }
-		
-		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));
-		
-		read(filename, names, 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;
-		//int rank = D.size();
-		
-		m->mothurOut("\nProcessing...\n");
-		
-		for(int count=0;count<2;count++){
-			recenter(offset, D, G);		if (m->control_pressed) { return 0; }
-			tred2(G, d, e);				if (m->control_pressed) { return 0; }
-			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++) {	remove(outputNames[i].c_str());  } 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, "PCACommand", "execute");
-		exit(1);
-	}
-}
-/*********************************************************************************************************************************/
-
-inline double SIGN(const double a, const double b)
-{
-    return b>=0 ? (a>=0 ? a:-a) : (a>=0 ? -a:a);
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::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, "PCACommand", "get_comment");
-		exit(1);
-	}
-}	
-
-/*********************************************************************************************************************************/
-
-int PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
-	try {
-		//     int count1=0;
-		//     int count2=0;
-		
-		int rank;
-		f >> rank;
-		
-		name_list.resize(rank);
-		d.resize(rank);
-		if(square_m == 1){
-			for(int i=0;i<rank;i++)
-				d[i].resize(rank);
-			for(int i=0;i<rank;i++) {
-				f >> name_list[i];
-				//			cout << i << "\t" << name_list[i] << endl;
-				for(int j=0;j<rank;j++) {
-					if (m->control_pressed) { return 0; }
-					
-					f >> d[i][j];
-					if (d[i][j] == -0.0000)
-						d[i][j] = 0.0000;
-				}
-			}
-		}
-		else if(square_m == 2){
-			for(int i=0;i<rank;i++){
-				d[i].resize(rank);
-			}
-			d[0][0] = 0.0000;
-			f >> name_list[0];
-			for(int i=1;i<rank;i++){
-				f >> name_list[i];
-				d[i][i]=0.0000;
-				for(int j=0;j<i;j++){
-					if (m->control_pressed) { return 0; }
-					f >> d[i][j];
-					if (d[i][j] == -0.0000)
-						d[i][j] = 0.0000;
-					d[j][i]=d[i][j];
-				}
-			}
-		}
-		
-		return 0;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "read_phylip");
-		exit(1);
-	}
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
-	try {
-		ifstream f;
-		m->openInputFile(fname, f);
-			
-		//check whether matrix is square
-		char d;
-		int q = 1;
-		int numSeqs;
-		string name;
-		
-		f >> numSeqs >> name; 
-		
-		while((d=f.get()) != EOF){
-			
-			//is d a number meaning its square
-			if(isalnum(d)){ 
-				q = 1; 
-				break; 
-			}
-			
-			//is d a line return meaning its lower triangle
-			if(d == '\n'){
-				q = 2;
-				break;
-			}
-		}
-		f.close();
-		
-		//reopen to get back to beginning
-		m->openInputFile(fname, f);			
-		read_phylip(f, q, names, D);
-	}
-		catch(exception& e) {
-		m->errorOut(e, "PCACommand", "read");
-		exit(1);
-	}
-}
-
-/*********************************************************************************************************************************/
-
-double PCACommand::pythag(double a, double b)	{	return(pow(a*a+b*b,0.5));	}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::matrix_mult(vector<vector<double> > first, vector<vector<double> > second, vector<vector<double> >& product){
-	try {
-		int first_rows = first.size();
-		int first_cols = first[0].size();
-		int second_cols = second[0].size();
-		
-		product.resize(first_rows);
-		for(int i=0;i<first_rows;i++){
-			product[i].resize(second_cols);
-		}
-		
-		for(int i=0;i<first_rows;i++){
-			for(int j=0;j<second_cols;j++){
-				product[i][j] = 0.0;
-				for(int k=0;k<first_cols;k++){
-					product[i][j] += first[i][k] * second[k][j];
-				}
-			}
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "matrix_mult");
-		exit(1);
-	}
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){
-	try {
-		int rank = D.size();
-		
-		vector<vector<double> > A(rank);
-		vector<vector<double> > C(rank);
-		for(int i=0;i<rank;i++){
-			A[i].resize(rank);
-			C[i].resize(rank);
-		}
-		
-		double scale = -1.0000 / (double) rank;
-		
-		for(int i=0;i<rank;i++){
-			A[i][i] = 0.0000;
-			C[i][i] = 1.0000 + scale;
-			for(int j=i+1;j<rank;j++){
-				A[i][j] = A[j][i] = -0.5 * D[i][j] * D[i][j] + offset;
-				C[i][j] = C[j][i] = scale;
-			}
-		}
-		
-		matrix_mult(C,A,A);
-		matrix_mult(A,C,G);
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "recenter");
-		exit(1);
-	}
-
-}
-
-/*********************************************************************************************************************************/
-
-//  This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479
-
-void PCACommand::tred2(vector<vector<double> >& a, vector<double>& d, vector<double>& e){
-	try {
-		double scale, hh, h, g, f;
-		
-		int n = a.size();
-		
-		d.resize(n);
-		e.resize(n);
-		
-		for(int i=n-1;i>0;i--){
-			int l=i-1;
-			h = scale = 0.0000;
-			if(l>0){
-				for(int k=0;k<l+1;k++){
-					scale += fabs(a[i][k]);
-				}
-				if(scale == 0.0){
-					e[i] = a[i][l];
-				}
-				else{
-					for(int k=0;k<l+1;k++){
-						a[i][k] /= scale;
-						h += a[i][k] * a[i][k];
-					}
-					f = a[i][l];
-					g = (f >= 0.0 ? -sqrt(h) : sqrt(h));
-					e[i] = scale * g;
-					h -= f * g;
-					a[i][l] = f - g;
-					f = 0.0;
-					for(int j=0;j<l+1;j++){
-						a[j][i] = a[i][j] / h;
-						g = 0.0;
-						for(int k=0;k<j+1;k++){
-							g += a[j][k] * a[i][k];
-						}
-						for(int k=j+1;k<l+1;k++){
-							g += a[k][j] * a[i][k];
-						}
-						e[j] = g / h;
-						f += e[j] * a[i][j];
-					}
-					hh = f / (h + h);
-					for(int j=0;j<l+1;j++){
-						f = a[i][j];
-						e[j] = g = e[j] - hh * f;
-						for(int k=0;k<j+1;k++){
-							a[j][k] -= (f * e[k] + g * a[i][k]);
-						}
-					}
-				}
-			}
-			else{
-				e[i] = a[i][l];
-			}
-			
-			d[i] = h;
-		}
-		
-		d[0] = 0.0000;
-		e[0] = 0.0000;
-		
-		for(int i=0;i<n;i++){
-			int l = i;
-			if(d[i] != 0.0){
-				for(int j=0;j<l;j++){
-					g = 0.0000;
-					for(int k=0;k<l;k++){
-						g += a[i][k] * a[k][j];
-					}
-					for(int k=0;k<l;k++){
-						a[k][j] -= g * a[k][i];
-					}
-				}
-			}
-			d[i] = a[i][i];
-			a[i][i] = 1.0000;
-			for(int j=0;j<l;j++){
-				a[j][i] = a[i][j] = 0.0;
-			}
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "tred2");
-		exit(1);
-	}
-
-}
-
-/*********************************************************************************************************************************/
-
-//  This function is taken from Numerical Recipes in C++ by Press et al., 2nd edition, pg. 479
-
-void PCACommand::qtli(vector<double>& d, vector<double>& e, vector<vector<double> >& z) {
-	try {
-		int m, i, iter;
-		double s, r, p, g, f, dd, c, b;
-		
-		int n = d.size();
-		for(int i=1;i<=n;i++){
-			e[i-1] = e[i];
-		}
-		e[n-1] = 0.0000;
-		
-		for(int l=0;l<n;l++){
-			iter = 0;
-			do {
-				for(m=l;m<n-1;m++){
-					dd = fabs(d[m]) + fabs(d[m+1]);
-					if(fabs(e[m])+dd == dd) break;
-				}
-				if(m != l){
-					if(iter++ == 30) cerr << "Too many iterations in tqli\n";
-					g = (d[l+1]-d[l]) / (2.0 * e[l]);
-					r = pythag(g, 1.0);
-					g = d[m] - d[l] + e[l] / (g + SIGN(r,g));
-					s = c = 1.0;
-					p = 0.0000;
-					for(i=m-1;i>=l;i--){
-						f = s * e[i];
-						b = c * e[i];
-						e[i+1] = (r=pythag(f,g));
-						if(r==0.0){
-							d[i+1] -= p;
-							e[m] = 0.0000;
-							break;
-						}
-						s = f / r;
-						c = g / r;
-						g = d[i+1] - p;
-						r = (d[i] - g) * s + 2.0 * c * b;
-						d[i+1] = g + ( p = s * r);
-						g = c * r - b;
-						for(int k=0;k<n;k++){
-							f = z[k][i+1];
-							z[k][i+1] = s * z[k][i] + c * f;
-							z[k][i] = c * z[k][i] - s * f;
-						}
-					}
-					if(r == 0.00 && i >= l) continue;
-					d[l] -= p;
-					e[l] = g;
-					e[m] = 0.0;
-				}
-			} while (m != l);
-		}
-		
-		int k;
-		for(int i=0;i<n;i++){
-			p=d[k=i];
-			for(int j=i;j<n;j++){
-				if(d[j] >= p){
-					p=d[k=j];
-				}
-			}
-			if(k!=i){
-				d[k]=d[i];
-				d[i]=p;
-				for(int j=0;j<n;j++){
-					p=z[j][i];
-					z[j][i] = z[j][k];
-					z[j][k] = p;
-				}
-			}
-		}
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCACommand", "qtli");
-		exit(1);
-	}
-}
-
-/*********************************************************************************************************************************/
-
-void PCACommand::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").c_str(), ios::trunc);
-		pcaData.setf(ios::fixed, ios::floatfield);
-		pcaData.setf(ios::showpoint);	
-		outputNames.push_back(fnameRoot+"pcoa");
-		outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
-		
-		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, "PCACommand", "output");
-		exit(1);
-	}
-}
-
-/*********************************************************************************************************************************/
-