X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=blastalign.cpp;h=bb7192ad498c405fc476ae722db2478fa1b407ab;hp=624210f5f977ac505a32119e574561ec7e92dcc2;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=28d65de5f06f5b033109a3b8bbb6d3c4060914d3

diff --git a/blastalign.cpp b/blastalign.cpp
index 624210f..bb7192a 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -18,12 +18,11 @@
 
 //**************************************************************************************************/
 
-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)
@@ -38,9 +37,9 @@ BlastAlignment::BlastAlignment(float go, float ge, float m, float mm) :
 //**************************************************************************************************/
 
 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);
 }
 
 //**************************************************************************************************/
@@ -72,7 +71,7 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 															//	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 = "";
@@ -102,9 +101,9 @@ void BlastAlignment::setPairwiseSeqs(){	//	This method call assigns the blast ge
 			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';