pca command

[mothur.git] / metastatscommand.cpp

diff --git a/metastatscommand.cpp b/metastatscommand.cpp
index 08c94ba3261c47c33d13368d9fbd84718cb5f3a2..81715e0abe84b485b96eb9997120dbe127dd6a5e 100644 (file)
--- a/metastatscommand.cpp
+++ b/metastatscommand.cpp
@@ -26,6 +26,7 @@ vector<string> MetaStatsCommand::getValidParameters(){
 //**********************************************************************************************************************
 MetaStatsCommand::MetaStatsCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["metastats"] = tempOutNames;
@@ -118,7 +119,7 @@ MetaStatsCommand::MetaStatsCommand(string option) {
                        
                        //make sure the user has already run the read.otu command
                        if ((globaldata->getSharedFile() == "")) {
-                                m->mothurOut("You must read a list and a group, or a shared file before you can use the normalize.shared command."); m->mothurOutEndLine(); abort = true; 
+                                m->mothurOut("You must read a list and a group, or a shared file before you can use the metastats command."); m->mothurOutEndLine(); abort = true; 
                        }
 
                        //check for optional parameter and set defaults
@@ -346,7 +347,6 @@ 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 +365,11 @@ 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 +445,6 @@ 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 +465,3 @@ 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);
-       }
-}
-//**********************************************************************************************************************