X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=b6a2c0bcd46b7bfeaf48ad548dea6dec5ca3a823;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=63a117d5064cc8178051017173bacdfd80cb6b3a;hpb=f09bacac01a842a74c1c1b69070852cc969ff506;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 63a117d..b6a2c0b 100644
--- 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;
@@ -153,15 +154,17 @@ AlignCommand::AlignCommand(string option)  {
 	
 					int ableToOpen;
 					ifstream in;
-
 					ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
-				
+					in.close();	
+					
 					//if you can't open it, try default location
 					if (ableToOpen == 1) {
 						if (m->getDefaultPath() != "") { //default path is set
 							string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 							m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							candidateFileNames[i] = tryPath;
 						}
 					}
@@ -171,12 +174,14 @@ AlignCommand::AlignCommand(string option)  {
 						if (m->getOutputDir() != "") { //default path is set
 							string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 							m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							candidateFileNames[i] = tryPath;
 						}
 					}
 					
-					in.close();					
+									
 
 					if (ableToOpen == 1) { 
 						m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
@@ -305,7 +310,7 @@ int AlignCommand::execute(){
 			int start = time(NULL);
 		
 #ifdef USE_MPI	
-				int pid, end, numSeqsPerProcessor; 
+				int pid, numSeqsPerProcessor; 
 				int tag = 2001;
 				vector<unsigned long int> MPIPos;
 				MPIWroteAccnos = false;
@@ -550,7 +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;
@@ -613,7 +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);
@@ -701,7 +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;
@@ -750,6 +756,7 @@ int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& align
 							delete nast;
 							nast = nast2;
 							needToDeleteCopy = true;
+							wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 						}else{  
 							wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 							delete nast2;
@@ -771,7 +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);
@@ -844,7 +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