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A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
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+++ /dev/null
-
-/*
- * 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);
- }
-}
-
-/*********************************************************************************************************************************/
-
+++ /dev/null
-#ifndef PCACOMMAND_H
-#define PCACOMMAND_H
-
-/*
- * pcacommand.h
- * Mothur
- *
- * Created by westcott on 1/4/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-
-
-/*****************************************************************/
-class PCACommand : public Command {
-
-public:
- PCACommand(string);
- PCACommand();
- ~PCACommand();
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
-
-private:
-
- bool abort;
- string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
- float cutoff, precision;
- vector<string> outputNames;
- map<string, vector<string> > outputTypes;
-
- void get_comment(istream&, char, char);
- int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
- void read(string, vector<string>&, vector<vector<double> >&);
- double pythag(double, double);
- void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
- void recenter(double, vector<vector<double> >, vector<vector<double> >&);
- void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
- void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
- void output(string, vector<string>, vector<vector<double> >, vector<double>);
-
-};
-
-/*****************************************************************/
-
-#endif
-
--- /dev/null
+
+/*
+ * 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);
+ }
+}
+
+/*********************************************************************************************************************************/
+
--- /dev/null
+#ifndef PCACOMMAND_H
+#define PCACOMMAND_H
+
+/*
+ * pcacommand.h
+ * Mothur
+ *
+ * Created by westcott on 1/4/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+
+
+/*****************************************************************/
+class PCACommand : public Command {
+
+public:
+ PCACommand(string);
+ PCACommand();
+ ~PCACommand();
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
+ int execute();
+ void help();
+
+private:
+
+ bool abort;
+ string phylipfile, columnfile, namefile, format, filename, fbase, outputDir;
+ float cutoff, precision;
+ vector<string> outputNames;
+ map<string, vector<string> > outputTypes;
+
+ void get_comment(istream&, char, char);
+ int read_phylip(istream&, int, vector<string>&, vector<vector<double> >&);
+ void read(string, vector<string>&, vector<vector<double> >&);
+ double pythag(double, double);
+ void matrix_mult(vector<vector<double> >, vector<vector<double> >, vector<vector<double> >&);
+ void recenter(double, vector<vector<double> >, vector<vector<double> >&);
+ void tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
+ void qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
+ void output(string, vector<string>, vector<vector<double> >, vector<double>);
+
+};
+
+/*****************************************************************/
+
+#endif
+
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