X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotypecommand.cpp;h=eddddfa0534f547cfa1802b75211f1c6c9950f65;hb=9b53f130ac9af5e95444ce2e817fce25ed19ff03;hp=2d2db08a40ea5e1aa8712902dcd419ddb1ad757a;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index 2d2db08..eddddfa 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);
@@ -251,11 +272,14 @@ int PhylotypeCommand::execute(){
                                 map<string, string>::iterator itNames = namemap.find(names[i]);  //make sure this name is in namefile
                                 
                                 if (itNames != namemap.end()) {  name += namemap[names[i]] + ",";   } //you found it in namefile
-                                else { m->mothurOut(names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); exit(1);  }
+                                else { m->mothurOut("[ERROR]: " + names[i] + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
                                 
                             }else{   name += names[i] + ",";	}
                         }
 					}
+                    
+                    if (m->control_pressed) { break; }
+                    
 					name = name.substr(0, name.length()-1);  //rip off extra ','
 					//add bin to list vector
 					if (name != "") { list.push_back(name); } //caused by unknown