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

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index 29e2ef0ba39ba4fbe73bf88949bf7a4756d50578..9d68cb5debbbc65472577c4861391bb8ffbde3bc 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -61,7 +61,28 @@ string PhyloDiversityCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string PhyloDiversityCommand::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 == "phylodiv") {  outputFileName =  "phylodiv"; }
+            else if (type == "rarefy") {  outputFileName =  "phylodiv.rarefaction"; }
+            else if (type == "summary") {  outputFileName =  "phylodiv.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, "PhyloDiversityCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 PhyloDiversityCommand::PhyloDiversityCommand(){        
@@ -237,9 +258,9 @@ int PhyloDiversityCommand::execute(){
                        if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) {       m->mothurRemove(outputNames[j]);        } return 0; }
                        
                        ofstream outSum, outRare, outCollect;
-                       string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + ".phylodiv.summary";
-                       string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + ".phylodiv.rarefaction";
-                       string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + ".phylodiv";
+                       string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + "." + getOutputFileNameTag("summary");
+                       string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + "." + getOutputFileNameTag("rarefy");
+                       string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile))  + toString(i+1) + "." + getOutputFileNameTag("phylodiv");
                        
                        if (summary)    { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile);             outputTypes["summary"].push_back(outSumFile);                   }
                        if (rarefy)             { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile);  outputTypes["rarefy"].push_back(outRareFile);                   }