X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getcoremicrobiomecommand.cpp;h=63af3abb3a595cff133a2caac91dea1aa1e420c1;hb=49d2b7459c5027557564b21e9487dadafbbbdc96;hp=97e2c7a47d47003b20e6eacd2a42d25a4ad7f9e4;hpb=f816b683e586575bfe3479760a8afd5ab08e8573;p=mothur.git

diff --git a/getcoremicrobiomecommand.cpp b/getcoremicrobiomecommand.cpp
index 97e2c7a..63af3ab 100644
--- a/getcoremicrobiomecommand.cpp
+++ b/getcoremicrobiomecommand.cpp
@@ -6,7 +6,7 @@
 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
 //
 
-#include "GetCoreMicroBiomeCommand.h"
+#include "getcoremicrobiomecommand.h"
 
 
 //**********************************************************************************************************************
@@ -51,13 +51,34 @@ string GetCoreMicroBiomeCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string GetCoreMicroBiomeCommand::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 == "coremicrobiome") {  outputFileName =  "core.microbiome"; }
+            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, "GetCoreMicroBiomeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+
 //**********************************************************************************************************************
 GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(){	
 	try {
 		abort = true; calledHelp = true;
 		setParameters();
         vector<string> tempOutNames;
-		outputTypes["coremicrobiom"] = tempOutNames; 
+		outputTypes["coremicrobiome"] = tempOutNames; 
 	}
 	catch(exception& e) {
 		m->errorOut(e, "GetCoreMicroBiomeCommand", "GetCoreMicroBiomeCommand");
@@ -111,7 +132,9 @@ GetCoreMicroBiomeCommand::GetCoreMicroBiomeCommand(string option)  {
 				}
             }
            
-        
+            vector<string> tempOutNames;
+            outputTypes["coremicrobiome"] = tempOutNames; 
+
 			//check for parameters
             sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { abort = true; }
@@ -285,8 +308,8 @@ int GetCoreMicroBiomeCommand::execute(){
 int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& lookup){
 	try {
         
-        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiom";
-        outputNames.push_back(outputFileName);  outputTypes["coremicrobiom"].push_back(outputFileName);
+        string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + getOutputFileNameTag("coremicrobiome");
+        outputNames.push_back(outputFileName);  outputTypes["coremicrobiome"].push_back(outputFileName);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
         
@@ -370,8 +393,8 @@ int GetCoreMicroBiomeCommand::createTable(vector<SharedRAbundFloatVector*>& look
         if (m->control_pressed) { return 0; }
         
         if ((samples != -1) || (abund != -1))  {
-            string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomlist";
-            outputNames.push_back(outputFileName2);  outputTypes["coremicrobiom"].push_back(outputFileName2);
+            string outputFileName2 = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + lookup[0]->getLabel() + ".core.microbiomelist";
+            outputNames.push_back(outputFileName2);  outputTypes["coremicrobiome"].push_back(outputFileName2);
             ofstream out2;
             m->openOutputFile(outputFileName2, out2);