added checks for ^C to quit command instead of program

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 2e553d96db111a7a0828af855eb7251081014131..7f8755645ce6664c5a299073e0ae1cbc6e875025 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -168,6 +168,8 @@ int GetSharedOTUCommand::execute(){
                int error = groupMap->readMap();
                if (error == 1) { delete groupMap; return 0; }
                
+               if (m->control_pressed) { delete groupMap; return 0; }
+               
                globaldata->gGroupmap = groupMap;
                
                if (Groups.size() == 0) {
@@ -189,6 +191,8 @@ int GetSharedOTUCommand::execute(){
                        openInputFile(fastafile, inFasta);
                        
                        while(!inFasta.eof()) {
+                               if (m->control_pressed) { inFasta.close(); delete groupMap; return 0; }
+                               
                                Sequence seq(inFasta); gobble(inFasta);
                                if (seq.getName() != "") {  seqs.push_back(seq);   }
                        }
@@ -208,6 +212,12 @@ int GetSharedOTUCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((!in.eof()) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
+                       if (m->control_pressed) { 
+                               if (lastlist != NULL) {         delete lastlist;        }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  
+                               delete groupMap; return 0;
+                       }
+                       
                        list = new ListVector(in);
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){                       
@@ -267,6 +277,7 @@ int GetSharedOTUCommand::execute(){
                
                if (lastlist != NULL) {         delete lastlist;        }
                
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); }  delete groupMap; return 0; } 
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -283,7 +294,7 @@ int GetSharedOTUCommand::execute(){
        }
 }
 /***********************************************************/
-void GetSharedOTUCommand::process(ListVector* shared) {
+int GetSharedOTUCommand::process(ListVector* shared) {
        try {
                
                map<string, string> fastaMap;
@@ -304,6 +315,7 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                                
                //go through each bin, find out if shared
                for (int i = 0; i < shared->getNumBins(); i++) {
+                       if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
                        
                        bool uniqueOTU = true;
                        
@@ -405,6 +417,8 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        outputNames.push_back(outputFileFasta);
                        
                        for (int k = 0; k < seqs.size(); k++) {
+                               if (m->control_pressed) { outFasta.close(); return 0; }
+                       
                                //if this is a sequence we want, output it
                                it = fastaMap.find(seqs[k].getName());
                                if (it != fastaMap.end()) {
@@ -421,7 +435,8 @@ void GetSharedOTUCommand::process(ListVector* shared) {
                        
                        outFasta.close();
                }
-
+               
+               return 0;
                
        }
        catch(exception& e) {