created mothurOut class to handle logfiles

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index 396a6b4b91c4496b80dfc3009cdda4a0f34b12e6..17db069cdedb8a019d980c32fc4b6e7767fab27b 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -92,7 +92,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosestSequences");
+               m->errorOut(e, "BlastDB", "findClosestSequences");
                exit(1);
        }
 
@@ -139,7 +139,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                return topMatches;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "findClosest");
+               m->errorOut(e, "BlastDB", "findClosest");
                exit(1);
        }
 }
@@ -158,7 +158,7 @@ void BlastDB::addSequence(Sequence seq) {
                count++;
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "addSequence");
+               m->errorOut(e, "BlastDB", "addSequence");
                exit(1);
        }
 }
@@ -166,7 +166,7 @@ void BlastDB::addSequence(Sequence seq) {
 void BlastDB::generateDB() {
        try {
        
-               //mothurOut("Generating the temporary BLAST database...\t");    cout.flush();
+               //m->mothurOut("Generating the temporary BLAST database...\t"); cout.flush();
                
                path = globaldata->argv;
                path = path.substr(0, (path.find_last_of('m')));
@@ -174,10 +174,10 @@ void BlastDB::generateDB() {
                string formatdbCommand = path + "blast/bin/formatdb -p F -o T -i " + dbFileName;        //      format the database, -o option gives us the ability
                system(formatdbCommand.c_str());                                                                //      to get the right sequence names, i think. -p F
                                                                                                                                        //      option tells formatdb that seqs are DNA, not prot
-               //mothurOut("DONE."); mothurOutEndLine();       mothurOutEndLine(); cout.flush();
+               //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine(); cout.flush();
        }
        catch(exception& e) {
-               errorOut(e, "BlastDB", "generateDB");
+               m->errorOut(e, "BlastDB", "generateDB");
                exit(1);
        }
 }