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();
BlastDB::BlastDB() : Database() {
try {
- globaldata = GlobalData::getInstance();
count = 0;
int randNumber = rand();
m8FileHandle.close();
remove((queryFileName+seq->getName()).c_str());
remove((blastFileName+seq->getName()).c_str());
-//cout << "\n\n" ;
+//cout << "\n" ;
return topMatches;
}
catch(exception& e) {
//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