created mothurOut class to handle logfiles

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 6ca8c2945bb4600e6c7f518b1d7c4dfa1a529225..f8651079c8da037e6aeb119d494a350ae410597a 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -99,11 +99,11 @@ void ChimeraSlayer::doPrep() {
                //run filter on template
                for (int i = 0; i < templateSeqs.size(); i++) {  runFilter(templateSeqs[i]);  }
                
-               mothurOutEndLine(); mothurOut("It took " + toString(time(NULL) - start) + " secs to filter.");  mothurOutEndLine();
+               m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to filter.");    m->mothurOutEndLine();
 
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "doprep");
+               m->errorOut(e, "ChimeraSlayer", "doprep");
                exit(1);
        }
 }
@@ -111,9 +111,9 @@ void ChimeraSlayer::doPrep() {
 ChimeraSlayer::~ChimeraSlayer() {      delete decalc;  if (searchMethod == "kmer") {  delete databaseRight;  delete databaseLeft;  }    }
 //***************************************************************************************************************
 void ChimeraSlayer::printHeader(ostream& out) {
-       mothurOutEndLine();
-       mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
-       mothurOutEndLine();
+       m->mothurOutEndLine();
+       m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
+       m->mothurOutEndLine();
        
        out << "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 }
@@ -129,7 +129,7 @@ void ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                        
                        if (chimeraFlag == "yes") {     
                                if ((chimeraResults[0].bsa >= minBS) || (chimeraResults[0].bsb >= minBS)) {
-                                       mothurOut(querySeq->getName() + "\tyes"); mothurOutEndLine();
+                                       m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
                                        outAcc << querySeq->getName() << endl;
                                }
                        }
@@ -140,7 +140,7 @@ void ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "print");
+               m->errorOut(e, "ChimeraSlayer", "print");
                exit(1);
        }
 }
@@ -247,7 +247,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                return 0;
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "getChimeras");
+               m->errorOut(e, "ChimeraSlayer", "getChimeras");
                exit(1);
        }
 }
@@ -282,7 +282,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
 
        }
        catch(exception& e) {
-               errorOut(e, "ChimeraSlayer", "printBlock");
+               m->errorOut(e, "ChimeraSlayer", "printBlock");
                exit(1);
        }
 }