testing 1.14.0

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index b4af28a2990a44d69527d4c5cb7e5984d8b73033..8a229e3cade2cff57569e16b0e4b682d8dd0be65 100644 (file)
--- 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;