X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=38d3bdf929f4ffc110f76ab0a55b12d66ef4ad08;hb=6ede3bf5c0a9eedb23f24577a97da81ab3e1f7df;hp=f402f2a8ab15a1808a461d376818d97d98c5c5c7;hpb=a626c629e4d4840cd2ce04d98055dcfef1f8593a;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index f402f2a..38d3bdf 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -53,7 +53,28 @@ string PhylotypeCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string PhylotypeCommand::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 == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            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, "PhylotypeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 PhylotypeCommand::PhylotypeCommand(){	
 	try {
@@ -198,13 +219,13 @@ int PhylotypeCommand::execute(){
 		string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
 		
 		ofstream outList;
-		string outputListFile = fileroot + "tx.list";
+		string outputListFile = fileroot + "tx." + getOutputFileNameTag("list");
 		m->openOutputFile(outputListFile, outList);
 		ofstream outSabund;
-		string outputSabundFile = fileroot + "tx.sabund";
+		string outputSabundFile = fileroot + "tx." + getOutputFileNameTag("sabund");
 		m->openOutputFile(outputSabundFile, outSabund);
 		ofstream outRabund;
-		string outputRabundFile = fileroot + "tx.rabund";
+		string outputRabundFile = fileroot + "tx." + getOutputFileNameTag("rabund");
 		m->openOutputFile(outputRabundFile, outRabund);
 		
 		outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
@@ -232,6 +253,7 @@ int PhylotypeCommand::execute(){
 				
 				ListVector list;
 				list.setLabel(level);
+                
 				//go through nodes and build listvector 
 				for (itCurrent = currentNodes.begin(); itCurrent != currentNodes.end(); itCurrent++) {
 			
@@ -244,6 +266,7 @@ int PhylotypeCommand::execute(){
 					//make the names compatable with listvector
 					string name = "";
 					for (int i = 0; i < names.size(); i++) {  
+                        
                         if (names[i] != "unknown") {
                             if (namefile != "") {	
                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
@@ -255,9 +278,8 @@ int PhylotypeCommand::execute(){
                         }
 					}
 					name = name.substr(0, name.length()-1);  //rip off extra ','
-					
 					//add bin to list vector
-					list.push_back(name);
+					if (name != "") { list.push_back(name); } //caused by unknown
 				}	
 				
 				//print listvector