trim.seqs fix

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index f0496b2f1f49198b813247e4d10297504e426ae1..e13e37c92c3103a3aabd1a4a6a7c68db443592ef 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -26,7 +26,7 @@ vector<string> MetaStatsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){  
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["metastats"] = tempOutNames;
        }
@@ -64,12 +64,12 @@ vector<string> MetaStatsCommand::getRequiredFiles(){
 MetaStatsCommand::MetaStatsCommand(string option) {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -205,7 +205,7 @@ MetaStatsCommand::~MetaStatsCommand(){}
 int MetaStatsCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                designMap = new GroupMap(designfile);
                designMap->readDesignMap();
@@ -346,7 +346,6 @@ int MetaStatsCommand::execute(){
 
 int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
        try {
-               if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
                
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
@@ -365,7 +364,11 @@ int MetaStatsCommand::process(vector<SharedRAbundVector*>& thisLookUp){
                                                }else if (pid == 0){
                                                        driver(lines[process].start, lines[process].num, thisLookUp);
                                                        exit(0);
-                                               }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                                               }else { 
+                                                       m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                                                       for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                                                       exit(0);
+                                               }
                                        }
                                        
                                        //do my part
@@ -441,7 +444,6 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
                                }
                                
                                m->mothurOut("Comparing " + setA + " and " + setB + "..."); m->mothurOutEndLine(); 
-                               
                                metastat_main(output, thisLookUp[0]->getNumBins(), subset.size(), threshold, iters, data, setACount);
                                
                                m->mothurOutEndLine(); 
@@ -462,45 +464,3 @@ int MetaStatsCommand::driver(int start, int num, vector<SharedRAbundVector*>& th
        }
 }
 //**********************************************************************************************************************
-int MetaStatsCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
-       try {
-               
-               vector<SharedRAbundVector*> newLookup;
-               for (int i = 0; i < thislookup.size(); i++) {
-                       SharedRAbundVector* temp = new SharedRAbundVector();
-                       temp->setLabel(thislookup[i]->getLabel());
-                       temp->setGroup(thislookup[i]->getGroup());
-                       newLookup.push_back(temp);
-               }
-               
-               //for each bin
-               for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
-                       if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
-               
-                       //look at each sharedRabund and make sure they are not all zero
-                       bool allZero = true;
-                       for (int j = 0; j < thislookup.size(); j++) {
-                               if (thislookup[j]->getAbundance(i) != 0) { allZero = false;  break;  }
-                       }
-                       
-                       //if they are not all zero add this bin
-                       if (!allZero) {
-                               for (int j = 0; j < thislookup.size(); j++) {
-                                       newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
-                               }
-                       }
-               }
-
-               for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
-
-               thislookup = newLookup;
-               
-               return 0;
- 
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MetaStatsCommand", "eliminateZeroOTUS");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************