From cd10743907df223b7dd5b3a3deb20fde758b8ed7 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Thu, 19 Mar 2009 17:04:49 +0000
Subject: [PATCH] fixed memory leak of groupmap in reads
---
errorchecking.cpp | 4 ++--
fullmatrix.cpp | 4 ++--
libshuffcommand.cpp | 5 +++++
parselistcommand.cpp | 1 +
progress.cpp | 4 ++--
readdistcommand.cpp | 1 +
readmatrix.cpp | 6 +++---
readotucommand.cpp | 2 ++
8 files changed, 18 insertions(+), 9 deletions(-)
diff --git a/errorchecking.cpp b/errorchecking.cpp
index 5f587a9..9a08462 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -171,8 +171,8 @@ bool ErrorCheck::checkInput(string input) {
errorFree = false;
}
- if ((commandName == "libshuff") && (globaldata->gMatrix == NULL)) {
- cout << "You must read in a matrix before you use the libshuff command. " << endl; return false;
+ if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
+ cout << "You must read in a matrix and groupfile before you use the libshuff command. " << endl; return false;
}
if (commandName == "parsimony") {
diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 8eb4813..f4acd78 100644
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -75,7 +75,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
try {
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
+ reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
int count = 0;
@@ -114,7 +114,7 @@ void FullMatrix::readSquareMatrix(ifstream& filehandle) {
void FullMatrix::readLTMatrix(ifstream& filehandle) {
try {
Progress* reading;
- reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
+ reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
int count = 0;
float distance;
diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 2ed7ee5..9ab9108 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -72,6 +72,8 @@ int LibShuffCommand::execute(){
try {
//deltaValues[0] = scores for the difference between AA and AB.
//cValues[0][0][0] = AA at distance 0.0, cValues[0][0][1] = AB at distance 0.0, cValues[0][0][2] = AC at distance 0.0, cValues[0][1][0] = BA at distance 0.0, cValues[0][1][1] = BB...
+ Progress* reading;
+ reading = new Progress("Comparing to random:", iters);
sumDelta.resize(numComp-numGroups, 0.0);
@@ -153,6 +155,7 @@ int LibShuffCommand::execute(){
}
//cout << "iter " << m << endl;
//clear out old Values
+ reading->update(m);
cValues.clear();
//cout << "random sum delta for iter " << m << endl;
@@ -163,6 +166,8 @@ int LibShuffCommand::execute(){
}
+ reading->finish();
+ delete reading;
/**********************************************************/
//find the signifigance of the user matrix' sumdelta values
diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index d9925ad..73fb565 100644
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -135,6 +135,7 @@ int ParseListCommand::execute(){
}
//set groupmap for .shared commands
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
globaldata->gGroupmap = groupMap;
return 0;
diff --git a/progress.cpp b/progress.cpp
index eec8f09..9f3327f 100644
--- a/progress.cpp
+++ b/progress.cpp
@@ -20,7 +20,7 @@ const char marker = '|';
Progress::Progress(string job, int end){
try {
- cout << "*******************#****#****#****#****#****#****#****#****#****#****#\n";
+ cout << "********************#****#****#****#****#****#****#****#****#****#****#\n";
cout << job << marker;
cout.flush();
@@ -72,7 +72,7 @@ void Progress::finish(){
cout << endl;
- cout << "**********************************************************************\n";
+ cout << "***********************************************************************\n";
cout.flush();
}
catch(exception& e) {
diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index a9d7721..6d38f4e 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -21,6 +21,7 @@ ReadDistCommand::ReadDistCommand(){
else if (format == "matrix") {
groupMap = new GroupMap(globaldata->getGroupFile());
groupMap->readMap();
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
globaldata->gGroupmap = groupMap;
}
diff --git a/readmatrix.cpp b/readmatrix.cpp
index 2d98124..9a98d5c 100644
--- a/readmatrix.cpp
+++ b/readmatrix.cpp
@@ -69,7 +69,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
if(square == 0){
- reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
int index = 0;
@@ -111,7 +111,7 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
}
else{
- reading = new Progress("Reading matrix: ", nseqs * nseqs);
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
int index = nseqs;
@@ -202,7 +202,7 @@ void ReadColumnMatrix::read(NameAssignment* nameMap){
list = new ListVector(nameMap->getListVector());
- Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
+ Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
int lt = 1;
int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
diff --git a/readotucommand.cpp b/readotucommand.cpp
index eeb8cd6..2a0d33f 100644
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -43,6 +43,8 @@ int ReadOtuCommand::execute(){
read->read(&*globaldata);
if (globaldata->getFormat() == "shared") {
groupMap->readMap();
+
+ if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; }
globaldata->gGroupmap = groupMap;
shared = new SharedCommand();
--
2.39.5