moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / groupmap.cpp

diff --git a/groupmap.cpp b/groupmap.cpp
index d57646e3e3dad937d3ca0fa81b26f402cfa1ad4d..47fbc36ee55ec4e2ff3fd9b934621eeef9a79a64 100644 (file)
--- a/groupmap.cpp
+++ b/groupmap.cpp
@@ -14,7 +14,7 @@
  GroupMap::GroupMap(string filename) {
        m = MothurOut::getInstance();
        groupFileName = filename;
-       openInputFile(filename, fileHandle);
+       m->openInputFile(filename, fileHandle);
        index = 0;
 }
 
@@ -27,7 +27,7 @@ int GroupMap::readMap() {
                int error = 0;
 
                while(fileHandle){
-                       fileHandle >> seqName;  gobble(fileHandle);             //read from first column
+                       fileHandle >> seqName;  m->gobble(fileHandle);          //read from first column
                        fileHandle >> seqGroup;                 //read from second column
                        
                        if (m->control_pressed) {  fileHandle.close();  return 1; }
@@ -41,7 +41,7 @@ int GroupMap::readMap() {
                                groupmap[seqName] = seqGroup;   //store data in map
                                seqsPerGroup[seqGroup]++;  //increment number of seqs in that group
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                fileHandle.close();
                return error;