added sets to amova and homova commands. added oligos to make.contigs. added metadat...

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index a0e6ed5d9bfe95b0fa6724aa05c8a06c4350762e..b5b01e7f97166ed80143d349b9ae8c340d53e654 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "metastatscommand.h"
-#include "metastats.h"
 #include "sharedutilities.h"
 
 
@@ -61,6 +60,27 @@ string MetaStatsCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string MetaStatsCommand::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 == "metastats")        {   outputFileName = "metastats";       }
+            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, "MetaStatsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){  
        try {
@@ -450,7 +470,7 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                        string setB = namesOfGroupCombos[c][1];
                
                        //get filename
-                       string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+                       string outputFileName = outputDir +  m->getRootName(m->getSimpleName(sharedfile)) + thisLookUp[0]->getLabel() + "." + setA + "-" + setB + "." + getOutputFileNameTag("metastats");
                        outputNames.push_back(outputFileName); outputTypes["metastats"].push_back(outputFileName);
                        //int nameLength = outputFileName.length();
                        //char * output = new char[nameLength];
@@ -483,12 +503,13 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); m->mothurOutEndLine(); 
                                outputNames.pop_back();
                        }else {
+                
                                //fill data
                                for (int j = 0; j < thisLookUp[0]->getNumBins(); j++) {
                                        //data[j] = new double[subset.size()];
                                        data2[j].resize(subset.size(), 0.0);
+                   
                                        for (int i = 0; i < subset.size(); i++) {
-                                               //data[j][i] = (subset[i]->getAbundance(j));
                                                data2[j][i] = (subset[i]->getAbundance(j));
                                        }
                                }
@@ -500,7 +521,6 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                MothurMetastats mothurMeta(threshold, iters);
                                mothurMeta.runMetastats(outputFileName , data2, setACount);
                                m->mothurOutEndLine();
-                               
                                m->mothurOutEndLine(); 
                        }