string GlobalData::getNameFile() { return namefile; }
string GlobalData::getGroupFile() { return groupfile; }
string GlobalData::getOrderFile() { return orderfile; }
+string GlobalData::getOrderGroupFile() { return ordergroup; }
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; }
void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setOrderFile(string file) { orderfile = file; }
+void GlobalData::setOrderGroupFile(string file) { ordergroup = file; }
void GlobalData::setFormat(string Format) { format = Format; }
/******************************************************/
GlobalData::GlobalData() {
+ m = MothurOut::getInstance();
//option definitions should go here...
clear();
gListVector = NULL;
gMatrix = NULL;
gTreemap = NULL;
gSequenceDB = NULL;
+ nameMap = NULL;
}
/*******************************************************/
namefile = ""; //do we need this?
groupfile = ""; //do we need this?
orderfile = "";
+ ordergroup = "";
// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
+ format = "";
}
//free memory
if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; }
+
if (gListVector != NULL) { delete gListVector; gListVector = NULL;}
+
if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; }
+
if (ginput != NULL) { delete ginput; ginput = NULL;}
+
if (gorder != NULL) { delete gorder; gorder = NULL; }
+
if (glist != NULL) { delete glist; glist = NULL;}
+
if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; }
+
if (sabund != NULL) { delete sabund; sabund = NULL;}
+
if (rabund != NULL) { delete rabund; rabund = NULL; }
+
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; }
+
gTree.clear();
Treenames.clear();
- labels.clear(); lines.clear(); Groups.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);
}
}