added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index 624210f5f977ac505a32119e574561ec7e92dcc2..9af31dfa3e65e130d0bc347600aa28405f94b7f4 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)
@@ -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';