//**************************************************************************************************/
-BlastAlignment::BlastAlignment(float go, float ge, float m, float mm) :
- match(m), // This is the score to award for two nucleotides matching (match >= 0)
+BlastAlignment::BlastAlignment(float go, float ge, float ma, float mm) :
+ match(ma), // This is the score to award for two nucleotides matching (match >= 0)
mismatch(mm) // This is the penalty to assess for a mismatch (mismatch <= 0)
{
- globaldata = GlobalData::getInstance();
- path = globaldata->argv;
+ path = m->argv;
path = path.substr(0, (path.find_last_of('m')));
gapOpen = abs(go); // This is the penalty to assess for opening a gap (gapOpen >= 0)
//**************************************************************************************************/
BlastAlignment::~BlastAlignment(){ // The desctructor should clean up by removing the temporary
- remove(candidateFileName.c_str()); // files used to run bl2seq
- remove(templateFileName.c_str());
- remove(blastFileName.c_str());
+ m->mothurRemove(candidateFileName); // files used to run bl2seq
+ m->mothurRemove(templateFileName);
+ m->mothurRemove(blastFileName);
}
//**************************************************************************************************/
// to the pairwise entry in the Sequence class for the
// candidate and template Sequence objects
ifstream blastFile;
- openInputFile(blastFileName, blastFile);
+ m->openInputFile(blastFileName, blastFile);
seqAaln = "";
seqBaln = "";