working on chimeras

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index 7782d1eac5354261c6727e240a33ae2d89984224..708a85472dc53fecec1f022ce86512a82d620c30 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -218,6 +218,7 @@ int AlignCommand::execute(){
                        string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
                        string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
                        string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
+                       bool hasAccnos = true;
                        
                        int numFastaSeqs = 0;
                        for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
@@ -307,7 +308,7 @@ int AlignCommand::execute(){
                                                mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well."); 
                                        }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
                                        mothurOutEndLine();
-                               }
+                               }else{ hasAccnos = false;  }
                        }
 #else
                        ifstream inFASTA;
@@ -320,7 +321,7 @@ int AlignCommand::execute(){
                        driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
                        
                        //delete accnos file if its blank else report to user
-                       if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  }
+                       if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
                        else { 
                                mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
                                if (!flip) {
@@ -331,7 +332,10 @@ int AlignCommand::execute(){
                        
 #endif
                        
-                       
+                       mothurOut("Output File Names: " + alignFileName + ", " + reportFileName);
+                       if (hasAccnos)  {       mothurOut(", " + accnosFileName + ".");         }
+                       else                    {       mothurOut(".");                                                         }
+                       mothurOutEndLine();
                        
                        mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
                        mothurOutEndLine();