created mothurOut class to handle logfiles

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index 598e301648978ab642274edb69ffa41bbea6f205..8d0662f9c404cb05d4cfed74596a33284d5235d9 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -12,6 +12,7 @@
 /************************************************************/
 
  GroupMap::GroupMap(string filename) {
+       m = MothurOut::getInstance();
        groupFileName = filename;
        openInputFile(filename, fileHandle);
        index = 0;
@@ -33,7 +34,7 @@ int GroupMap::readMap() {
                        
                        it = groupmap.find(seqName);
                        
-                       if (it != groupmap.end()) { error = 1; mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); mothurOutEndLine();  }
+                       if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine();  }
                        else {
                                groupmap[seqName] = seqGroup;   //store data in map
                                seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
@@ -89,7 +90,7 @@ bool GroupMap::isValidGroup(string groupname) {
                return false;
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "isValidGroup");
+               m->errorOut(e, "GroupMap", "isValidGroup");
                exit(1);
        }
 }
@@ -107,7 +108,7 @@ int GroupMap::getNumSeqs(string group) {
                
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "getNumSeqs");
+               m->errorOut(e, "GroupMap", "getNumSeqs");
                exit(1);
        }
 }
@@ -125,7 +126,7 @@ vector<string> GroupMap::getNamesSeqs(){
                return names;
        }
        catch(exception& e) {
-               errorOut(e, "GroupMap", "getNamesSeqs");
+               m->errorOut(e, "GroupMap", "getNamesSeqs");
                exit(1);
        }
 }