X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pcoacommand.cpp;h=2043a128bd94bc755cb7ef10f5a8b8d9bdb5a6be;hp=02e165e978dc071ba19808139060866d7e41388c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 02e165e..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);		}
@@ -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);
+    }
+}
 
 
 //**********************************************************************************************************************
@@ -229,17 +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++){