// 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 = "";
pairwiseLength = 0;
// string dummy;
-// while(dummy != "query:"){ mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy; }
+// while(dummy != "query:"){ m->mothurOut(dummy, ""); m->mothurOutEndLine(); blastFile >> dummy; }
// blastFile >> seqBend;
-// mothurOut(toString(seqBend), ""); mothurOutEndLine();
+// m->mothurOut(toString(seqBend), ""); m->mothurOutEndLine();
// for(int i=0;i<seqBend;i++){
// seqAaln += 'Z';
// seqBaln += 'X';