X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;h=3cd844a36d5a5c253786b4eb29745388b042d2d4;hb=943d3038553f82378567d3b651969146716e5862;hp=fbcb7e08779d14f28277d8b5e8d0a8ce3b088174;hpb=e6c4a7223199d800d496356604eb34dfe273673d;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index fbcb7e0..3cd844a 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -26,8 +26,7 @@ vector<string> PCOACommand::getValidParameters(){
 //**********************************************************************************************************************
 PCOACommand::PCOACommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["pcoa"] = tempOutNames;
 		outputTypes["loadings"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> PCOACommand::getRequiredFiles(){
 
 PCOACommand::PCOACommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -149,7 +148,7 @@ PCOACommand::~PCOACommand(){}
 int PCOACommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		cout.setf(ios::fixed, ios::floatfield);
 		cout.setf(ios::showpoint);
@@ -170,12 +169,12 @@ int PCOACommand::execute(){
 		vector<double> d;
 		vector<double> e;
 		vector<vector<double> > G = D;
-		vector<vector<double> > copy_G;
+		//vector<vector<double> > copy_G;
 				
 		m->mothurOut("\nProcessing...\n\n");
 		
 		for(int count=0;count<2;count++){
-			recenter(offset, D, G);					if (m->control_pressed) { return 0; }
+			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];
@@ -198,7 +197,7 @@ int PCOACommand::execute(){
 				
 				double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 				
-				m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
+				m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 				
 				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
 			}
@@ -231,40 +230,6 @@ void PCOACommand::get_comment(istream& f, char begin, char end){
 }	
 /*********************************************************************************************************************************/
 
-void PCOACommand::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;
-			}
-		}
-		
-		A = linearCalc.matrix_mult(C,A);
-		G = linearCalc.matrix_mult(A,C);
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PCOACommand", "recenter");
-		exit(1);
-	}
-
-}
-
-/*********************************************************************************************************************************/
-
 void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
 	try {
 		int rank = name_list.size();