changed tags on temp blast db to include template name

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index e2b1dc197eb8d3399156a3ca752bff5da267101f..6909f47b1235c72b67ae409907af97346dfa8007 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();
@@ -130,7 +129,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        #endif
                }
                else if(method == "suffix")             {       search = new SuffixDB(numSeqs);                                                         }
-               else if(method == "blast")              {       search = new BlastDB(gapOpen, gapExtend, match, misMatch);      }
+               else if(method == "blast")              {       search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);   }
                else {
                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
                        m->mothurOutEndLine();