working on mgcluster count file change

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 47f55311cc6037a7dca827338d51ab903027fc40..8019def31cad9acc54c1308171bf796e949890a1 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -54,6 +54,28 @@ string ClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string ClusterCommand::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, "ClusterCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 ClusterCommand::ClusterCommand(){      
        try {
                abort = true; calledHelp = true; 
@@ -183,7 +205,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "T"; }
                        hard = m->isTrue(temp);
@@ -193,7 +215,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
-                       convert(temp, cutoff); 
+                       m->mothurConvert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));  
                        
                        method = validParameter.validFile(parameters, "method", false);
@@ -287,13 +309,17 @@ int ClusterCommand::execute(){
                if (outputDir == "") { outputDir += m->hasPath(distfile); }
                fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
                
-               m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
-               m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
-               m->openOutputFile(fileroot+ tag + ".list",              listFile);
+        string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+        string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        
+               m->openOutputFile(sabundFileName,       sabundFile);
+               m->openOutputFile(rabundFileName,       rabundFile);
+               m->openOutputFile(listFileName, listFile);
                
-               outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
-               outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-               outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+               outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+               outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+               outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
                
                
                time_t estart = time(NULL);