chimeracode

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 50a0401b2cb8780765ba56a3ba2c025380c4e212..b139f3eb7a47bcc86f0920bdc0fc22bad368816a 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -50,7 +50,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
                
-               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -b 1 -m 8 -W 28 -v " + toString(n);
+               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -v " + toString(n) + " -b " + toString(n);;
                blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
                system(blastCommand.c_str());
                
@@ -82,9 +82,9 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
 }
 /**************************************************************************************************/
 //assumes you have added all the template sequences using the addSequence function and run generateDB.
-map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
+vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
        try{
-               map<int, float> topMatches;
+               vector<int> topMatches;
                
                ofstream queryFile;
                openOutputFile(queryFileName, queryFile);
@@ -96,7 +96,7 @@ map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
                //      wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
                //      long.  With this setting, it seems comparable in speed to the suffix tree approach.
        
-               string blastCommand = path + "blast/bin/blastall -p blastn -d " + dbFileName + " -m 8 -W 28 -b " + toString(n) + " -v " + toString(n);
+               string blastCommand = path + "blast/bin/megablast -e 1e-10 -d " + dbFileName + " -m 8 -b " + toString(n) + " -v " + toString(n); //-W 28 -p blastn
                blastCommand += (" -i " + queryFileName + " -o " + blastFileName);
                system(blastCommand.c_str());
                
@@ -106,22 +106,18 @@ map<int, float> BlastDB::findClosest(Sequence* seq, int n) {
                string dummy;
                int templateAccession;
                gobble(m8FileHandle);
-//string name = seq->getName();
-//ofstream out;
-//openOutputFileAppend(name, out);     
+               
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
-//out << dummy << '\t' <<  templateAccession   << '\t' << searchScore << endl;
+                       
                        //get rest of junk in line
-                       while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); 
-                       //out << c; 
-                       if (c == 10 || c == 13){        break;  }       } 
+                       while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
                        gobble(m8FileHandle);
-                       topMatches[templateAccession] = searchScore;
+                       topMatches.push_back(templateAccession);
                }
                m8FileHandle.close();
-//out.close();         
+               
                return topMatches;
        }
        catch(exception& e) {