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

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 6792f19f219ad99f0bb13d0eec3b84ae20e67c88..50fbd32c3bcfa39e6b3b9c1014338eceeb7d8a8d 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -64,12 +64,34 @@ string SummarySharedCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string SummarySharedCommand::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 == "summary")            {   outputFileName =  "shared.summary";   }
+            if (type == "phylip")            {   outputFileName =  "dist";   }
+            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, "SummarySharedCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 SummarySharedCommand::SummarySharedCommand(){  
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
                outputTypes["summary"] = tempOutNames;
+        outputTypes["phylip"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
@@ -104,6 +126,7 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["summary"] = tempOutNames;
+            outputTypes["phylip"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -294,7 +317,7 @@ int SummarySharedCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream outputFileHandle, outAll;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "shared.summary";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
                
                //if the users entered no valid calculators don't execute command
                if (sumCalculators.size() == 0) { return 0; }
@@ -325,7 +348,7 @@ int SummarySharedCommand::execute(){
                outputFileHandle.close();
                
                //create file and put column headers for multiple groups file
-               string outAllFileName = ((m->getRootName(sharedfile)) + "sharedmultiple.summary");
+               string outAllFileName = ((m->getRootName(sharedfile)) + "multiple." + getOutputFileNameTag("summary"));
                if (mult == true) {
                        m->openOutputFile(outAllFileName, outAll);
                        outputNames.push_back(outAllFileName);
@@ -763,7 +786,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                             matrix[column][row] = dist;
                         }
                         
-                        string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".dist";
+                        string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + "." + getOutputFileNameTag("phylip");
                         outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                         ofstream outDist;
                         m->openOutputFile(distFileName, outDist);
@@ -856,7 +879,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                     stdmatrix[column][row] = stdDist;
                 }
                 
-                string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".ave.dist";
+                string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".ave." + getOutputFileNameTag("phylip");;
                 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                 ofstream outAve;
                 m->openOutputFile(distFileName, outAve);
@@ -866,7 +889,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
                 
                 outAve.close();
                 
-                distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".std.dist";
+                distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + sumCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".std." + getOutputFileNameTag("phylip");
                 outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
                 ofstream outSTD;
                 m->openOutputFile(distFileName, outSTD);