string GlobalData::getGroupFile() { return groupfile; }
string GlobalData::getOrderFile() { return orderfile; }
string GlobalData::getTreeFile() { return treefile; }
-string GlobalData::getSharedFile() { return sharedfile; }
-//string GlobalData::getFastaFile() { return fastafile; }
+string GlobalData::getSharedFile() { return sharedfile; }
string GlobalData::getFormat() { return format; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
-//void GlobalData::setFastaFile(string file) { fastafile = file; inputFileName = file; }
void GlobalData::setTreeFile(string file) { treefile = file; inputFileName = file; }
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file; }
void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file; }
/******************************************************/
GlobalData::GlobalData() {
+ m = MothurOut::getInstance();
//option definitions should go here...
clear();
gListVector = NULL;
gMatrix = NULL;
gTreemap = NULL;
gSequenceDB = NULL;
+ nameMap = NULL;
}
/*******************************************************/
// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
+ format = "";
}
if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+
+ if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
gTree.clear();
labels.clear(); Groups.clear();
allLines = 1;
runParse = true;
+ names.clear();
}
catch(exception& e) {
- errorOut(e, "GlobalData", "newRead");
+ m->errorOut(e, "GlobalData", "newRead");
exit(1);
}
}
if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;}
if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; }
if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;}
+ if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
}
catch(exception& e) {
- errorOut(e, "GlobalData", "~GlobalData");
+ m->errorOut(e, "GlobalData", "~GlobalData");
exit(1);
}
}