added checks for ^C to quit command instead of program

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 94cba4a10e344f5e27593a4723adb662cb9ab458..257587fa048ac3b494fa4f0ed4481f2cd505e513 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -213,6 +213,8 @@ int AlignCommand::execute(){
                vector<string> outputNames;
                
                for (int s = 0; s < candidateFileNames.size(); s++) {
+                       if (m->control_pressed) { return 0; }
+                       
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
                        if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
@@ -234,8 +236,9 @@ int AlignCommand::execute(){
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
                                
-                               int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-                               if (exitCommand == 0) { 
+                               driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                               
+                               if (m->control_pressed) { 
                                        remove(accnosFileName.c_str()); 
                                        remove(alignFileName.c_str()); 
                                        remove(reportFileName.c_str()); 
@@ -280,7 +283,7 @@ int AlignCommand::execute(){
                                        lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                                }
                                
-                               int exitCommand = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
+                               createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
                                
                                rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
                                rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
@@ -317,7 +320,7 @@ int AlignCommand::execute(){
                                        m->mothurOutEndLine();
                                }else{ hasAccnos = false;  }
                                
-                               if (exitCommand == 0) { 
+                               if (m->control_pressed) { 
                                        remove(accnosFileName.c_str()); 
                                        remove(alignFileName.c_str()); 
                                        remove(reportFileName.c_str()); 
@@ -332,8 +335,9 @@ int AlignCommand::execute(){
                        
                        lines.push_back(new linePair(0, numFastaSeqs));
                        
-                       int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
-                       if (exitCommand == 0) { 
+                       driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                       
+                       if (m->control_pressed) { 
                                remove(accnosFileName.c_str()); 
                                remove(alignFileName.c_str()); 
                                remove(reportFileName.c_str()); 
@@ -494,7 +498,7 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 0;
-               int exitCommand;
+               int exitCommand = 1;
                //              processIDS.resize(0);
                
                //loop through and create all the processes you want