X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=metastatscommand.cpp;h=b5b01e7f97166ed80143d349b9ae8c340d53e654;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=e23224bf20e9977e842bc78e765cd95e018a1666;hpb=6b2ac07f3e9ee57594d2358a3a25f9f700bd7362;p=mothur.git

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index e23224b..b5b01e7 100644
--- 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 {
@@ -232,21 +252,19 @@ int MetaStatsCommand::execute(){
 		//only 1 combo
 		if (numGroups == 2) { processors = 1; }
 		else if (numGroups < 2)	{ m->mothurOut("Not enough sets, I need at least 2 valid sets. Unable to complete command."); m->mothurOutEndLine(); m->control_pressed = true; }
-		
-//		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-			if(processors != 1){
-				int numPairs = namesOfGroupCombos.size();
-				int numPairsPerProcessor = numPairs / processors;
+
+        if(processors != 1){
+            int numPairs = namesOfGroupCombos.size();
+            int numPairsPerProcessor = numPairs / processors;
 			
-				for (int i = 0; i < processors; i++) {
-					int startPos = i * numPairsPerProcessor;
-					if(i == processors - 1){
-						numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
-					}
-					lines.push_back(linePair(startPos, numPairsPerProcessor));
-				}
-			}
-//		#endif
+            for (int i = 0; i < processors; i++) {
+                int startPos = i * numPairsPerProcessor;
+                if(i == processors - 1){
+                    numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
+                }
+                lines.push_back(linePair(startPos, numPairsPerProcessor));
+            }
+        }
 		
 		//as long as you are not at the end of the file or done wih the lines you want
 		while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -345,7 +363,7 @@ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
 				}else{
 					int process = 1;
 					vector<int> processIDS;
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 					//loop through and create all the processes you want
 					while (process != processors) {
 						int pid = fork();
@@ -452,7 +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];
@@ -485,12 +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));
 					}
 				}
@@ -502,7 +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(); 
 			}