//**************************************************************************************************/
-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 = "";
string candidateName, templateName;
- while(d=blastFile.get() != '='){}
+ while((d=blastFile.get()) != '='){}
blastFile >> candidateName; // Get the candidate sequence name from flatfile
- while(d=blastFile.get() != '('){}
+ while((d=blastFile.get()) != '('){}
blastFile >> candidateLength; // Get the candidate sequence length from flatfile
- while(d=blastFile.get()){
+ while((d=blastFile.get())){
if(d == '>'){
blastFile >> templateName; // Get the template sequence name from flatfile
break;
pairwiseLength = 0;
// string dummy;
-// while(dummy != "query:"){ cout << dummy << endl;blastFile >> dummy; }
+// while(dummy != "query:"){ m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy; }
// blastFile >> seqBend;
-// cout << seqBend << endl;
+// m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
// for(int i=0;i<seqBend;i++){
// seqAaln += 'Z';
// seqBaln += 'X';
}
}
- while(d=blastFile.get() != '='){}
+ while((d=blastFile.get()) != '='){}
blastFile >> templateLength; // Get the template sequence length from flatfile
- while(d=blastFile.get() != 'Q'){} // Suck up everything else until we get to the start of the alignment
+ while((d=blastFile.get()) != 'Q'){} // Suck up everything else until we get to the start of the alignment
int queryStart, sbjctStart, queryEnd, sbjctEnd;
string queryLabel, sbjctLabel, query, sbjct;
while(queryLabel == "Query:"){
blastFile >> queryStart >> query >> queryEnd;
- while(d=blastFile.get() != 'S'){};
+ while((d=blastFile.get()) != 'S'){};
blastFile >> sbjctLabel >> sbjctStart >> sbjct >> sbjctEnd;