added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 50e1bfa7e590d6e2fa47b4c184700b440cdb9621..f124b6002ee2c247db14716b4be81cb9ec10d8f2 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -52,6 +52,27 @@ string ParsimonyCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string ParsimonyCommand::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 == "parsimony") {  outputFileName =  "parsimony"; }
+            else if (type == "psummary") {  outputFileName =  "psummary"; }
+            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, "ParsimonyCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 ParsimonyCommand::ParsimonyCommand(){  
@@ -204,11 +225,11 @@ int ParsimonyCommand::execute() {
             delete reader;
        
                        if(outputDir == "") { outputDir += m->hasPath(treefile); }
-                       output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  ".parsimony", itersString);
-                       outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
-                       outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  +  ".parsimony");
+                       output = new ColumnFile(outputDir + m->getSimpleName(treefile)  +  "." + getOutputFileNameTag("parsimony"), itersString);
+                       outputNames.push_back(outputDir + m->getSimpleName(treefile)  +  "." + getOutputFileNameTag("parsimony"));
+                       outputTypes["parsimony"].push_back(outputDir + m->getSimpleName(treefile)  + "." + getOutputFileNameTag("parsimony"));
                                
-                       sumFile = outputDir + m->getSimpleName(treefile) + ".psummary";
+                       sumFile = outputDir + m->getSimpleName(treefile) + "." + getOutputFileNameTag("psummary");
                        m->openOutputFile(sumFile, outSum);
                        outputNames.push_back(sumFile);
                        outputTypes["psummary"].push_back(sumFile);