X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;h=02e165e978dc071ba19808139060866d7e41388c;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=6ebf6536e70042941fe4d4ec401f7035949da66c;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 6ebf653..02e165e 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -37,7 +37,7 @@ string PCOACommand::getHelpString(){
 		helpString += "The phylip parameter allows you to enter your distance file.";
 		helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"; 
 		helpString += "Example pcoa(phylip=yourDistanceFile).\n";
-		helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+		helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -69,6 +69,7 @@ PCOACommand::PCOACommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -110,7 +111,7 @@ PCOACommand::PCOACommand(string option)  {
 				phylipfile = m->getPhylipFile(); 
 				if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 			
 			filename = phylipfile;  
 			
@@ -157,7 +158,7 @@ int PCOACommand::execute(){
 		vector<vector<double> > G = D;
 		//vector<vector<double> > copy_G;
 				
-		m->mothurOut("\nProcessing...\n\n");
+		m->mothurOut("\nProcessing...\n");
 		
 		for(int count=0;count<2;count++){
 			linearCalc.recenter(offset, D, G);		if (m->control_pressed) { return 0; }
@@ -171,7 +172,7 @@ int PCOACommand::execute(){
 		
 		output(fbase, names, G, d);
 		
-		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; }
 		
 		if (metric) {   
 			
@@ -179,13 +180,13 @@ int PCOACommand::execute(){
 							
 				vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa 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(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
 				
 				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; }
 			}
 		}