added checks for ^C to quit command instead of program

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index f03152bcfa84047813da249e0fedb3673139861c..213fd49588bbf8a9278bc04c14d474bd11ccb278 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -49,6 +49,7 @@ SharedCommand::SharedCommand(string o) : outputDir(o) {
                //clears file before we start to write to it below
                for (int i=0; i<groups.size(); i++) {
                        remove((fileroot + groups[i] + ".rabund").c_str());
+                       outputNames.push_back((fileroot + groups[i] + ".rabund"));
                }
 
        }
@@ -76,6 +77,14 @@ int SharedCommand::execute(){
                string lastLabel = SharedList->getLabel();
                vector<SharedRAbundVector*> lookup; 
                
+               if (m->control_pressed) { 
+                       delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL; 
+                       for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+                       out.close(); remove(filename.c_str()); 
+                       for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                       return 1; 
+               }
+                               
                if ((globaldata->Groups.size() == 0) && (SharedList->getNumSeqs() != groupMap->getNumSeqs())) {  //if the user has not specified any groups and their files don't match exit with error
                        m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); 
                        
@@ -88,6 +97,8 @@ int SharedCommand::execute(){
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
                                delete it3->second;
                        }
+                       delete input;
+                       globaldata->ginput = NULL;
                        delete SharedList;
                        globaldata->gSharedList = NULL;
                        
@@ -121,14 +132,30 @@ int SharedCommand::execute(){
                set<string> userLabels = globaldata->labels;    
        
                while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+                       if (m->control_pressed) { 
+                               delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL; 
+                               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+                               out.close(); remove(filename.c_str()); 
+                               for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                               return 1; 
+                       }
                
                        if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
-                       
+                                       
                                        lookup = SharedList->getSharedRAbundVector();
+                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                        if (pickedGroups) { //check for otus with no seqs in them
                                                eliminateZeroOTUS(lookup);
                                        }
-                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                                       
+                                       if (m->control_pressed) { 
+                                               delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL; 
+                                               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                                               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+                                               out.close(); remove(filename.c_str()); 
+                                               for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                                               return 1; 
+                                       }
                                        
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -144,10 +171,20 @@ int SharedCommand::execute(){
                                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                                        lookup = SharedList->getSharedRAbundVector();
+                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                                        if (pickedGroups) { //check for otus with no seqs in them
                                                eliminateZeroOTUS(lookup);
                                        }
-                                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                                       
+                                       
+                                       if (m->control_pressed) { 
+                                               delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL; 
+                                               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                                               for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
+                                               out.close(); remove(filename.c_str()); 
+                                               for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                                               return 1; 
+                                       }
                                        
                                        printSharedData(lookup); //prints info to the .shared file
                                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -181,10 +218,18 @@ int SharedCommand::execute(){
                        SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
                                        
                        lookup = SharedList->getSharedRAbundVector();
+                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
                        if (pickedGroups) { //check for otus with no seqs in them
                                eliminateZeroOTUS(lookup);
                        }
-                       m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+                       
+                       if (m->control_pressed) { 
+                                       delete input;  globaldata->ginput = NULL; 
+                                       for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
+                                       out.close(); remove(filename.c_str()); 
+                                       for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                                       return 1; 
+                       }
                        
                        printSharedData(lookup); //prints info to the .shared file
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
@@ -205,7 +250,19 @@ int SharedCommand::execute(){
                globaldata->setListFile("");
                globaldata->setGroupFile("");
                globaldata->setSharedFile(filename);
-
+               
+               if (m->control_pressed) { 
+                               delete input;  globaldata->ginput = NULL; 
+                               remove(filename.c_str()); 
+                               for (int i=0; i<groups.size(); i++) {  remove((fileroot + groups[i] + ".rabund").c_str());              }
+                               return 1; 
+               }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+               for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
+               m->mothurOut(filename); m->mothurOutEndLine();
+               m->mothurOutEndLine();
                
                return 0;
        }
@@ -237,7 +294,7 @@ void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
        }
 }
 //**********************************************************************************************************************
-void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+int SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
        try {
                
                vector<SharedRAbundVector*> newLookup;
@@ -250,6 +307,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
                
                //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;
@@ -268,7 +326,8 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
        
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                thislookup = newLookup;
-       
+               
+               return 0;
  
        }
        catch(exception& e) {
@@ -277,7 +336,7 @@ void SharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
        }
 }
 //**********************************************************************************************************************
-void SharedCommand::createMisMatchFile() {
+int SharedCommand::createMisMatchFile() {
        try {
                ofstream outMisMatch;
                string outputMisMatchName = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
@@ -294,6 +353,7 @@ void SharedCommand::createMisMatchFile() {
                        
                        //go through list and if group returns "not found" output it
                        for (int i = 0; i < SharedList->getNumBins(); i++) {
+                               if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
                        
                                string names = SharedList->get(i); 
                                
@@ -332,6 +392,8 @@ void SharedCommand::createMisMatchFile() {
                        
                        //go through listfile and get names
                        for (int i = 0; i < SharedList->getNumBins(); i++) {
+                               if (m->control_pressed) {  return 0; } 
+
                                
                                string names = SharedList->get(i); 
                
@@ -362,6 +424,7 @@ void SharedCommand::createMisMatchFile() {
                        
                        //loop through names in seqNames and if they aren't in namesIn list output them
                        for (int i = 0; i < seqNames.size(); i++) {
+                               if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
                                
                                itMatch = namesInList.find(seqNames[i]);
                                
@@ -372,7 +435,8 @@ void SharedCommand::createMisMatchFile() {
                        }               
                        outMisMatch.close();
                }
- 
+               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "SharedCommand", "createMisMatchFile");