-
+/*
#include "globaldata.hpp"
#include "sharedlistvector.h"
#include "inputdata.h"
/*******************************************************/
-/******************************************************/
+/******************************************************
GlobalData* GlobalData::getInstance() {
if( _uniqueInstance == 0) {
_uniqueInstance = new GlobalData();
}
/*******************************************************/
-/******************************************************/
+/******************************************************
// These functions give you the option parameters of the commands
string GlobalData::getPhylipFile() { return phylipfile; }
string GlobalData::getColumnFile() { return columnfile; }
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::getRelAbundFile() { return relAbundfile; }
string GlobalData::getFormat() { return format; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file; }
void GlobalData::setGroupFile(string file) { groupfile = file; }
void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; }
+void GlobalData::setRelAbundFile(string file) { relAbundfile = 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;
gTreemap = NULL;
gSequenceDB = NULL;
nameMap = NULL;
+ saveNextLabel = "";
}
/*******************************************************/
-/******************************************************/
+/******************************************************
void GlobalData::clear() {
//option definitions should go here...
phylipfile = ""; //do we need this?
namefile = ""; //do we need this?
groupfile = ""; //do we need this?
orderfile = "";
+ ordergroup = "";
// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
+ relAbundfile = "";
+ format = "";
+ saveNextLabel = "";
}
/*******************************************************/
-/******************************************************/
+/******************************************************
void GlobalData::newRead() {
try{
//remove old file names
labels.clear(); Groups.clear();
allLines = 1;
runParse = true;
+ names.clear();
}
catch(exception& e) {
- errorOut(e, "GlobalData", "newRead");
+ m->errorOut(e, "GlobalData", "newRead");
exit(1);
}
}
//******************************************************/
-/******************************************************/
+/*****************************************************
GlobalData::~GlobalData() {
_uniqueInstance = 0;
try {
if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
}
catch(exception& e) {
- errorOut(e, "GlobalData", "~GlobalData");
+ m->errorOut(e, "GlobalData", "~GlobalData");
exit(1);
}
}