fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index e2b1dc197eb8d3399156a3ca752bff5da267101f..5a3027229bb8e91bdacfa25dea566a5273ca9d9d 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -74,7 +74,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                if (temp.getName() != "") {
                                        templateSequences.push_back(temp);
                                        //save longest base
-                                       if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+                                       if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
                                }
                        }
                        
@@ -94,11 +94,10 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        if (temp.getName() != "") {
                                templateSequences.push_back(temp);
                                //save longest base
-                               if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length()+1; }
+                               if (temp.getUnaligned().length() >= longest)  { longest = (temp.getUnaligned().length()+1); }
                        }
                }
                fastaFile.close();
-               
        #endif
        
                numSeqs = templateSequences.size();