X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pcoacommand.cpp;h=2043a128bd94bc755cb7ef10f5a8b8d9bdb5a6be;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=6ebf6536e70042941fe4d4ec401f7035949da66c;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 6ebf653..2043a12 100644
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -15,10 +15,10 @@
 //**********************************************************************************************************************
 vector<string> PCOACommand::setParameters(){	
 	try {
-		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-		CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+		CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -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) {
@@ -45,6 +45,22 @@ string PCOACommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string PCOACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "pcoa") {  pattern = "[filename],pcoa.axes"; } 
+        else if (type == "loadings") {  pattern = "[filename],pcoa.loadings"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PCOACommand", "getOutputPattern");
+        exit(1);
+    }
+}
 
 
 //**********************************************************************************************************************
@@ -69,6 +85,7 @@ 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 +127,7 @@ 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 +174,7 @@ 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 +188,7 @@ 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 +196,13 @@ 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; }
 			}
 		}
 		
@@ -228,17 +245,23 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
 			}
 		}
 		
-		ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+		ofstream pcaData;
+        map<string, string> variables; 
+        variables["[filename]"] = fnameRoot;
+        string pcoaDataFile = getOutputFileName("pcoa",variables);
+        m->openOutputFile(pcoaDataFile, pcaData);
 		pcaData.setf(ios::fixed, ios::floatfield);
 		pcaData.setf(ios::showpoint);	
-		outputNames.push_back(fnameRoot+"pcoa.axes");
-		outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
+		outputNames.push_back(pcoaDataFile);
+		outputTypes["pcoa"].push_back(pcoaDataFile);
 		
-		ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+		ofstream pcaLoadings;
+        string loadingsFile = getOutputFileName("loadings",variables);
+        m->openOutputFile(loadingsFile, pcaLoadings);
 		pcaLoadings.setf(ios::fixed, ios::floatfield);
 		pcaLoadings.setf(ios::showpoint);
-		outputNames.push_back(fnameRoot+"pcoa.loadings");
-		outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");	
+		outputNames.push_back(loadingsFile);
+		outputTypes["loadings"].push_back(loadingsFile);	
 		
 		pcaLoadings << "axis\tloading\n";
 		for(int i=0;i<rank;i++){