fixed bug with aligner in database class, worked on chimeras

[mothur.git] / database.cpp

diff --git a/database.cpp b/database.cpp
index 534747ac9208df062efc2bf2149430ff417d4a72..9784ef93035bbf896eb3ec2c7090cbda7a426227 100644 (file)
--- a/database.cpp
+++ b/database.cpp
@@ -24,12 +24,12 @@ Database::Database(string fastaFileName){           //      This assumes that the template dat
        mothurOut("Reading in the " + fastaFileName + " template sequences...\t");      cout.flush();
 
        //all of this is elsewhere already!
-       numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>');   //      count the number of
-       fastaFile.seekg(0);                                                                                                                                             //      sequences
+       //numSeqs=count(istreambuf_iterator<char>(fastaFile),istreambuf_iterator<char>(), '>'); //      count the number of
+       //fastaFile.seekg(0);                                                                                                                                           //      sequences
        
-       templateSequences.resize(numSeqs);
+       //templateSequences.resize(numSeqs);
        
-       string seqName, sequence;
+       /*string seqName, sequence;
        for(int i=0;i<numSeqs;i++){
                fastaFile >> seqName;
                seqName = seqName.substr(1);
@@ -52,8 +52,21 @@ Database::Database(string fastaFileName){            //      This assumes that the template dat
                if (templateSequences[i].getUnaligned().length() > longest)  { longest = templateSequences[i].getUnaligned().length(); }
                
                fastaFile.putback(letter);
+       }*/
+       
+       while (!fastaFile.eof()) {
+               Sequence temp(fastaFile);
+               
+               templateSequences.push_back(temp);
+               
+               //save longest base
+               if (temp.getUnaligned().length() > longest)  { longest = temp.getUnaligned().length(); }
+               
+               gobble(fastaFile);
        }
        
+       numSeqs = templateSequences.size();
+       
        fastaFile.close();
        //all of this is elsewhere already!