adding mothurout.h and .cpp to repo

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 3b4b6c93e232a25bab87a855c6955d177926e823..94cba4a10e344f5e27593a4723adb662cb9ab458 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -234,7 +234,13 @@ int AlignCommand::execute(){
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
                                
-                               driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                               int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                               if (exitCommand == 0) { 
+                                       remove(accnosFileName.c_str()); 
+                                       remove(alignFileName.c_str()); 
+                                       remove(reportFileName.c_str()); 
+                                       return 0; 
+                               }
                                
                                //delete accnos file if its blank else report to user
                                if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
@@ -274,7 +280,7 @@ int AlignCommand::execute(){
                                        lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                                }
                                
-                               createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]); 
+                               int exitCommand = 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());
@@ -310,6 +316,13 @@ int AlignCommand::execute(){
                                        }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
                                        m->mothurOutEndLine();
                                }else{ hasAccnos = false;  }
+                               
+                               if (exitCommand == 0) { 
+                                       remove(accnosFileName.c_str()); 
+                                       remove(alignFileName.c_str()); 
+                                       remove(reportFileName.c_str()); 
+                                       return 0; 
+                               }
                        }
 #else
                        ifstream inFASTA;
@@ -319,7 +332,13 @@ int AlignCommand::execute(){
                        
                        lines.push_back(new linePair(0, numFastaSeqs));
                        
-                       driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                       int exitCommand = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
+                       if (exitCommand == 0) { 
+                               remove(accnosFileName.c_str()); 
+                               remove(alignFileName.c_str()); 
+                               remove(reportFileName.c_str()); 
+                               return 0; 
+                       }
                        
                        //delete accnos file if its blank else report to user
                        if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
@@ -374,7 +393,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
                inFASTA.seekg(line->start);
                
                for(int i=0;i<line->numSeqs;i++){
-               
+                       
+                       if (m->control_pressed) {  return 0; }
+                       
                        Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
@@ -469,10 +490,11 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName,
 
 /**************************************************************************************************/
 
-void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
+int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 0;
+               int exitCommand;
                //              processIDS.resize(0);
                
                //loop through and create all the processes you want
@@ -483,7 +505,7 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName,
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
+                               exitCommand = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
                                exit(0);
                        }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
                }
@@ -493,6 +515,8 @@ void AlignCommand::createProcesses(string alignFileName, string reportFileName,
                        int temp = processIDS[i];
                        wait(&temp);
                }
+               
+               return exitCommand;
 #endif         
        }
        catch(exception& e) {