changes while setting up test files

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 979d507c23d61b4537d62a1a4736721624616fb2..6cfa3c685767457e6b9e9e10400ca1806929574c 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -17,7 +17,6 @@
 BlastDB::BlastDB(float gO, float gE, float m, float mM) : Database(), 
 gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
        
-       globaldata = GlobalData::getInstance();
        count = 0;
 
        int randNumber = rand();
@@ -30,7 +29,6 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
 
 BlastDB::BlastDB() : Database() {
        try {
-               globaldata = GlobalData::getInstance();
                count = 0;
 
                int randNumber = rand();
@@ -140,6 +138,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
+                       //cout << templateAccession << '\t' << searchScore << endl;
                        
                        //get rest of junk in line
                        while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
@@ -151,7 +150,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                m8FileHandle.close();
                remove((queryFileName+seq->getName()).c_str());
                remove((blastFileName+seq->getName()).c_str());
-//cout << "\n\n" ;             
+//cout << "\n" ;               
                return topMatches;
        }
        catch(exception& e) {
@@ -184,7 +183,7 @@ void BlastDB::generateDB() {
        
                //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
                
-               path = globaldata->argv;
+               path = m->argv;
                path = path.substr(0, (path.find_last_of('m')));
        
                string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability