X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=aligncommand.cpp;h=8a229e3cade2cff57569e16b0e4b682d8dd0be65;hb=df41d90a9611eab75d0516e2654ed8580f8df24c;hp=b4af28a2990a44d69527d4c5cb7e5984d8b73033;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/aligncommand.cpp b/aligncommand.cpp
index b4af28a..8a229e3 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -153,15 +153,17 @@ 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 +173,14 @@ 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(); 
@@ -562,10 +566,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 								
 				Sequence temp = templateDB->findClosestSequence(candidateSeq);
 				Sequence* templateSeq = &temp;
-				
+			
 				float searchScore = templateDB->getSearchScore();
 								
 				Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
+		
 				Sequence* copy;
 				
 				Nast* nast2;
@@ -580,6 +585,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
 					string wasBetter =  "";
 					//if the user wants you to try the reverse
 					if (flip) {
+				
 						//get reverse compliment
 						copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 						copy->reverseComplement();
@@ -748,6 +754,7 @@ 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;