changing command name classify.shared to classifyrf.shared

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index 04c7716de2958ec69353a53c0d737f8ae9cfe9dd..bb7192ad498c405fc476ae722db2478fa1b407ab 100644 (file)
--- 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 = "";