/************************************************************/
GroupMap::GroupMap(string filename) {
+ m = MothurOut::getInstance();
groupFileName = filename;
openInputFile(filename, fileHandle);
index = 0;
int GroupMap::readMap() {
string seqName, seqGroup;
int error = 0;
-
+
while(fileHandle){
- fileHandle >> seqName; //read from first column
+ fileHandle >> seqName; gobble(fileHandle); //read from first column
fileHandle >> seqGroup; //read from second column
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
setNamesOfGroups(seqGroup);
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
return false;
}
catch(exception& e) {
- errorOut(e, "GroupMap", "isValidGroup");
+ m->errorOut(e, "GroupMap", "isValidGroup");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "GroupMap", "getNumSeqs");
+ m->errorOut(e, "GroupMap", "getNumSeqs");
exit(1);
}
}
return names;
}
catch(exception& e) {
- errorOut(e, "GroupMap", "getNamesSeqs");
+ m->errorOut(e, "GroupMap", "getNamesSeqs");
exit(1);
}
}