fixed metastats, added resize to cluster.classic, added code to kill children if...

[mothur.git] / blastalign.cpp

diff --git a/blastalign.cpp b/blastalign.cpp
index 624210f5f977ac505a32119e574561ec7e92dcc2..5e7fb61aa77e7c34ca7367393766b1a5455c9213 100644 (file)
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -72,7 +72,7 @@ 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 +102,9 @@ 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';