more changes to error.seqs command and quality scores classses

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 8a229e3cade2cff57569e16b0e4b682d8dd0be65..39408427d87d439d6cdf8e637dd656df5049becd 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -64,6 +64,7 @@ vector<string> AlignCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -554,7 +555,8 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        if (m->control_pressed) {  return 0; }
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
-                       
+                       report.setCandidate(candidateSeq);
+
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
@@ -617,7 +619,6 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                                        accnosFile << candidateSeq->getName() << wasBetter << endl;
                                }
                                
-                               report.setCandidate(candidateSeq);
                                report.setTemplate(templateSeq);
                                report.setSearchParameters(search, searchScore);
                                report.setAlignmentParameters(align, alignment);
@@ -705,7 +706,8 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                        istringstream iss (tempBuf,istringstream::in);
 
                        Sequence* candidateSeq = new Sequence(iss);  
-       
+                       report.setCandidate(candidateSeq);
+
                        int origNumBases = candidateSeq->getNumBases();
                        string originalUnaligned = candidateSeq->getUnaligned();
                        int numBasesNeeded = origNumBases * threshold;
@@ -776,7 +778,6 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
                                        MPIWroteAccnos = true;
                                }
                                
-                               report.setCandidate(candidateSeq);
                                report.setTemplate(templateSeq);
                                report.setSearchParameters(search, searchScore);
                                report.setAlignmentParameters(align, alignment);
@@ -849,7 +850,11 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                                out.close();
                                
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
                //force parent to wait until all the processes are done