X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=otuhierarchycommand.cpp;h=e32e0b6c339c5b80108a3e874ce9c990ef5a2376;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=edfdaea6a1a5c02b1a8b0c96b10768be4770b1a5;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index edfdaea..e32e0b6 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -46,7 +46,26 @@ string OtuHierarchyCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "otuheirarchy") {  outputFileName =  "otu.hierarchy"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "OtuHierarchyCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){	
 	try {
@@ -67,6 +86,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(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();
@@ -109,6 +129,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
 					abort = true;
 				}
 			}else if (listFile == "not open") { abort = true; }	
+			else { m->setListFile(listFile); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -178,13 +199,13 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + "." + getOutputFileNameTag("otuheirarchy");
 		m->openOutputFile(outputFileName, out);
 		
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
 		for (int i = 0; i < lists[1].getNumBins(); i++) {
 		
-			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
 			
 			string names = lists[1].get(i);
 			
@@ -217,7 +238,7 @@ int OtuHierarchyCommand::execute(){
 		
 		out.close();
 		
-		if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Name: "); m->mothurOutEndLine();