+
+
#include "globaldata.hpp"
-#include "tree.h"
-#include "sparsematrix.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
/*******************************************************/
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::getRelAbundFile() { return relAbundfile; }
string GlobalData::getFormat() { return format; }
-string GlobalData::getCandidateFile() { return candidatefile; }
-
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::setCandidateFile(string file) { candidatefile = file; }
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file; }
void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file; }
void GlobalData::setPhylipFile(string file) { phylipfile = 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;
gSparseMatrix = NULL;
+ ginput = NULL;
+ gorder = NULL;
+ glist = NULL;
+ gSharedList = NULL;
+ sabund = NULL;
+ rabund = NULL;
+ gGroupmap = NULL;
+ gMatrix = NULL;
+ gTreemap = NULL;
+ gSequenceDB = NULL;
+ nameMap = NULL;
+ saveNextLabel = "";
}
/*******************************************************/
/******************************************************/
void GlobalData::clear() {
//option definitions should go here...
- phylipfile = "";
- columnfile = "";
+ phylipfile = ""; //do we need this?
+ columnfile = ""; //do we need this?
listfile = "";
rabundfile = "";
sabundfile = "";
- namefile = "";
- groupfile = "";
+ namefile = ""; //do we need this?
+ groupfile = ""; //do we need this?
orderfile = "";
- fastafile = "";
+ ordergroup = "";
+// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
- candidatefile = "";
+ relAbundfile = "";
+ format = "";
+ saveNextLabel = "";
}
+
+
/*******************************************************/
/******************************************************/
void GlobalData::newRead() {
- try{
+ try{
+ //remove old file names
clear();
- gGroupmap = NULL;
- gListVector = NULL;
- gSparseMatrix = NULL;
+
+ //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) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GlobalData", "newRead");
exit(1);
}
}
/******************************************************/
GlobalData::~GlobalData() {
_uniqueInstance = 0;
- if(gListVector != NULL) { delete gListVector; }
- if(gSparseMatrix != NULL) { delete gSparseMatrix; }
- if(gorder != NULL) { delete gorder; }
+ try {
+ 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; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GlobalData", "~GlobalData");
+ exit(1);
+ }
}
/*******************************************************/
projects / mothur.git / blobdiff