X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcacommand.cpp;h=27e448bdfa1060a91c701c25fe301907e3529ec7;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=e273e5fe7079ffab790ccf5498e69675a0fafeef;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/pcacommand.cpp b/pcacommand.cpp
index e273e5f..27e448b 100644
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -117,12 +117,12 @@ PCACommand::PCACommand(string option)  {
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  mode = "sharedfile"; inputFile = sharedfile; }
+			else {  mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			relabundfile = validParameter.validFile(parameters, "relabund", true);
 			if (relabundfile == "not open") { relabundfile = ""; abort = true; }	
 			else if (relabundfile == "not found") { relabundfile = ""; }
-			else {  mode = "relabund"; inputFile = relabundfile; }
+			else {  mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
 			
 			
 			if ((sharedfile == "") && (relabundfile == "")) { 
@@ -157,7 +157,7 @@ PCACommand::PCACommand(string option)  {
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = "";  }
 			else { m->splitAtDash(groups, Groups);	}			
-			m->Groups = Groups;			
+			m->setGroups(Groups);			
 			
 		}
 		
@@ -203,7 +203,7 @@ int PCACommand::execute(){
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
 			
-			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
+			if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
 			
 			if(labels.count(lookupFloat[0]->getLabel()) == 1){
 				processedLabels.insert(lookupFloat[0]->getLabel());
@@ -236,7 +236,7 @@ int PCACommand::execute(){
 		}
 		
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
 		
 		//output error messages about any remaining user labels
 		set<string>::iterator it;
@@ -264,7 +264,7 @@ int PCACommand::execute(){
 		for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {	delete lookupFloat[i];	} } lookupFloat.clear();
 		delete input;
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+		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();
@@ -319,7 +319,6 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 		vector< vector<double> > matrix(numSamples);
 		vector<double> colMeans(numOTUs);
 		
-				
 		//fill matrix with shared relative abundances, re-center
 		for (int i = 0; i < lookupFloat.size(); i++) {
 			matrix[i].resize(numOTUs, 0);
@@ -366,7 +365,7 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 		
 		string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
 		string outputFileName = fbase + lookupFloat[0]->getLabel();
-		output(outputFileName, m->Groups, X, d);
+		output(outputFileName, m->getGroups(), X, d);
 		
 		if (metric) {   
 			
@@ -376,13 +375,13 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 				
 				vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file
 				
-				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } return 0; }
+				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 
 				double corr = linearCalc.calcPearson(PCAEuclidDists, observedEuclideanDistance);
 								
 				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; }
+				if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } return 0; }
 			}
 		}
 		
@@ -427,7 +426,7 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
 		}
 		pcaData << endl;
 		
-		for(int i=0;i<numEigenValues;i++){
+		for(int i=0;i<name_list.size();i++){
 			pcaData << name_list[i] << '\t';
 			for(int j=0;j<numEigenValues;j++){
 				pcaData << G[i][j] << '\t';