fixed bugs in venn and aligner

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
index 5fc9b676f128dd0a1d6999918b4fcb42357c407e..534747ac9208df062efc2bf2149430ff417d4a72 100644 (file)
--- a/database.cpp
+++ b/database.cpp
@@ -15,7 +15,8 @@
 
 Database::Database(string fastaFileName){              //      This assumes that the template database is in fasta format, may 
                                                                                                //      need to alter this in the future?
-
+       longest = 0;
+       
        ifstream fastaFile;
        openInputFile(fastaFileName, fastaFile);
        
@@ -43,6 +44,13 @@ Database::Database(string fastaFileName){            //      This assumes that the template dat
                        }
                }
                templateSequences[i] = Sequence(seqName, aligned);
+               
+               //necessary because Sequence constructor by default sets whatever it reads to unaligned
+               //the setUnaligned function remove gap char.
+               templateSequences[i].setUnaligned(templateSequences[i].getUnaligned());
+               
+               if (templateSequences[i].getUnaligned().length() > longest)  { longest = templateSequences[i].getUnaligned().length(); }
+               
                fastaFile.putback(letter);
        }
        
@@ -64,4 +72,10 @@ Database::~Database(){
 
 float Database::getSearchScore()       {       return searchScore;             }       //      we're assuming that the search is already done
 
+
 /**************************************************************************************************/
+
+int Database::getLongestBase() {       return longest+1;               }       
+
+/**************************************************************************************************/
+