X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=indicatorcommand.cpp;h=f98620b2ee0bd4cc70bc10d1db908d8de40de995;hb=078d7227da8dda9ae8620822fa32d51ec2706fc3;hp=97f480e749b7042a07a39d0f48890ff137d49dd0;hpb=d2390ede25cc211f95f99e377d5654bad7e6950e;p=mothur.git

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index 97f480e..f98620b 100644
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -57,7 +57,27 @@ string IndicatorCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string IndicatorCommand::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 == "tree")       {   outputFileName =  "indicator.tre";   }
+            else if (type == "summary")    {   outputFileName =  "indicator.summary";   }
+            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, "IndicatorCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 IndicatorCommand::IndicatorCommand(){	
 	try {
@@ -240,7 +260,6 @@ int IndicatorCommand::execute(){
 			util.setGroups(Groups, nameGroups);
 			designMap->setNamesOfGroups(nameGroups);
 			
-			//loop through the Groups and fill Globaldata's Groups with the design file info
 			vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
 			m->setGroups(namesSeqs);
 		}
@@ -386,7 +405,7 @@ int IndicatorCommand::GetIndicatorSpecies(){
 	try {
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
 		outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 		
 		ofstream out;
@@ -501,7 +520,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(inputFileName);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("summary");
 		outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 		
 		ofstream out;
@@ -521,7 +540,7 @@ int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
 		
 		string treeOutputDir = outputDir;
 		if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
-		string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+		string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
 		
 		
 		//create a map from tree node index to names of descendants, save time later to know which sharedRabund you need