added checks for ^C to quit command instead of program

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 86d6d50ed4295da62d957868386036d838a222be..69ce031a50c37caed255347378979e3b94d37b62 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -318,6 +318,8 @@ int ChimeraSeqsCommand::execute(){
                if (method == "bellerophon") {//run bellerophon separately since you need to read entire fastafile to run it
                        chimera->getChimeras();
                        
+                       if (m->control_pressed) { delete chimera;       return 0;       }
+                       
                        ofstream out;
                        openOutputFile(outputFileName, out);
                        
@@ -328,6 +330,8 @@ int ChimeraSeqsCommand::execute(){
                        out.close();
                        out2.close(); 
                        
+                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); delete chimera;       return 0;       }
+                       
                        //delete accnos file if its blank 
                        if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                        
@@ -343,6 +347,8 @@ int ChimeraSeqsCommand::execute(){
                //reads template
                chimera->setTemplateFile(templatefile);
                
+               if (m->control_pressed) { delete chimera;       return 0;       }
+               
                if  (method != "chimeracheck") {   
                        if (chimera->getUnaligned()) { 
                                m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine(); 
@@ -354,6 +360,8 @@ int ChimeraSeqsCommand::execute(){
                //some methods need to do prep work before processing the chimeras
                chimera->doPrep(); 
                
+               if (m->control_pressed) { delete chimera;       return 0;       }
+               
                templateSeqsLength = chimera->getLength();
                
                ofstream outHeader;
@@ -376,6 +384,15 @@ int ChimeraSeqsCommand::execute(){
                                
                                driver(lines[0], outputFileName, fastafile, accnosFileName);
                                
+                               if (m->control_pressed) { 
+                                       remove(outputFileName.c_str()); 
+                                       remove(tempHeader.c_str()); 
+                                       remove(accnosFileName.c_str());
+                                       for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+                                       delete chimera;
+                                       return 0;
+                               }
+                               
                                //delete accnos file if its blank 
                                if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                                                                
@@ -435,6 +452,14 @@ int ChimeraSeqsCommand::execute(){
                                                remove(nonBlankAccnosFiles[h].c_str());
                                        }
                                }else{ hasAccnos = false;  }
+                               
+                               if (m->control_pressed) { 
+                                       remove(outputFileName.c_str()); 
+                                       remove(accnosFileName.c_str());
+                                       for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+                                       delete chimera;
+                                       return 0;
+                               }
 
                        }
 
@@ -447,6 +472,15 @@ int ChimeraSeqsCommand::execute(){
                        
                        driver(lines[0], outputFileName, fastafile, accnosFileName);
                        
+                       if (m->control_pressed) { 
+                                       remove(outputFileName.c_str()); 
+                                       remove(tempHeader.c_str()); 
+                                       remove(accnosFileName.c_str());
+                                       for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
+                                       delete chimera;
+                                       return 0;
+                       }
+                       
                        //delete accnos file if its blank 
                        if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                #endif
@@ -471,7 +505,7 @@ int ChimeraSeqsCommand::execute(){
                if (hasAccnos) {  m->mothurOut(accnosFileName); m->mothurOutEndLine();  }
                m->mothurOutEndLine();
 
-
+               for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                
                m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
                
@@ -499,6 +533,8 @@ int ChimeraSeqsCommand::driver(linePair* line, string outputFName, string filena
                
                for(int i=0;i<line->numSeqs;i++){
                
+                       if (m->control_pressed) {       return 1;       }
+               
                        Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
                                
                        if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
@@ -508,6 +544,8 @@ int ChimeraSeqsCommand::driver(linePair* line, string outputFName, string filena
                                }else{
                                        //find chimeras
                                        chimera->getChimeras(candidateSeq);
+                                       
+                                       if (m->control_pressed) {       delete candidateSeq; return 1;  }
                
                                        //print results
                                        chimera->print(out, out2);
@@ -525,7 +563,7 @@ int ChimeraSeqsCommand::driver(linePair* line, string outputFName, string filena
                out2.close();
                inFASTA.close();
                                
-               return 1;
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraSeqsCommand", "driver");
@@ -535,7 +573,7 @@ int ChimeraSeqsCommand::driver(linePair* line, string outputFName, string filena
 
 /**************************************************************************************************/
 
-void ChimeraSeqsCommand::createProcesses(string outputFileName, string filename, string accnos) {
+int ChimeraSeqsCommand::createProcesses(string outputFileName, string filename, string accnos) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 0;
@@ -559,6 +597,8 @@ void ChimeraSeqsCommand::createProcesses(string outputFileName, string filename,
                        int temp = processIDS[i];
                        wait(&temp);
                }
+               
+               return 0;
 #endif         
        }
        catch(exception& e) {