added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / hclustercommand.cpp

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index b2af0349c9b341a635ad9eb341a3a5e35198f90e..cf35cd9d6fa4c2a8fe1349b63399eb60007a4217 100644 (file)
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -52,6 +52,28 @@ string HClusterCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string HClusterCommand::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, "HClusterCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 HClusterCommand::HClusterCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -182,14 +204,14 @@ HClusterCommand::HClusterCommand(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);
                        
                        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);
@@ -219,13 +241,17 @@ HClusterCommand::HClusterCommand(string option)  {
                                else if (method == "weighted")  { tag = "wn";  }
                                else                                                    { tag = "an";  }
                        
-                               m->openOutputFile(fileroot+ tag + ".sabund",    sabundFile);
-                               m->openOutputFile(fileroot+ tag + ".rabund",    rabundFile);
-                               m->openOutputFile(fileroot+ tag + ".list",              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");
+                               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(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+                outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+                outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
                        }
                }
        }