From: westcott <westcott>
Date: Thu, 18 Jun 2009 16:05:46 +0000 (+0000)
Subject: fixed some bugs
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=02909d6cae9963ba00dc746969a370fa8ca934fc;p=mothur.git
fixed some bugs
---
diff --git a/aligncommand.cpp b/aligncommand.cpp
index ccfd9bb..064189b 100644
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -104,9 +104,13 @@ AlignCommand::AlignCommand(string option){
//**********************************************************************************************************************
-AlignCommand::~AlignCommand(){
- delete templateDB;
- delete alignment;
+AlignCommand::~AlignCommand(){
+
+ if (abort == false) {
+ for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ delete templateDB;
+ delete alignment;
+ }
}
//**********************************************************************************************************************
@@ -178,6 +182,7 @@ int AlignCommand::execute(){
lines.push_back(new linePair(0, numFastaSeqs));
driver(lines[0], alignFileName, reportFileName);
+
}
else{
vector<int> positions;
@@ -216,6 +221,7 @@ int AlignCommand::execute(){
appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
}
+
}
#else
ifstream inFASTA;
@@ -262,7 +268,9 @@ int AlignCommand::driver(linePair* line, string alignFName, string reportFName){
Sequence* candidateSeq = new Sequence(inFASTA);
report.setCandidate(candidateSeq);
- Sequence* templateSeq = templateDB->findClosestSequence(candidateSeq);
+ Sequence temp = templateDB->findClosestSequence(candidateSeq);
+ Sequence* templateSeq = &temp;
+
report.setTemplate(templateSeq);
report.setSearchParameters(search, templateDB->getSearchScore());
diff --git a/alignment.cpp b/alignment.cpp
index 95e9dc2..d64d8b2 100644
--- a/alignment.cpp
+++ b/alignment.cpp
@@ -87,6 +87,23 @@ void Alignment::traceBack(){ // This traceback routine is used by the dynamic
seqBend = seqB.length() - seqBend - 1;
}
+/**************************************************************************************************/
+
+Alignment::~Alignment(){
+ try {
+ for (int i = 0; i < alignment.size(); i++) {
+ for (int j = (alignment[i].size()-1); j >= 0; j--) { alignment[i].pop_back(); }
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Alignment class Function ~Alignment. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Alignment class function ~Alignment. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/**************************************************************************************************/
diff --git a/alignment.hpp b/alignment.hpp
index c033d62..215e4b3 100644
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -23,6 +23,7 @@ class Alignment {
public:
Alignment(int);
Alignment();
+ virtual ~Alignment();
virtual void align(string, string) = 0;
// float getAlignmentScore();
diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index abe000f..1627b42 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -44,11 +44,6 @@ BinSeqCommand::BinSeqCommand(string option){
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not found") { cout << "fasta is a required parameter for the bin.seqs command." << endl; abort = true; }
else if (fastafile == "not open") { abort = true; }
- else {
- openInputFile(fastafile, in);
- fasta = new FastaMap();
- }
-
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
@@ -82,10 +77,14 @@ BinSeqCommand::BinSeqCommand(string option){
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
- else {
- //read in group map info.
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+
+ if (abort == false) {
+ openInputFile(fastafile, in);
+ fasta = new FastaMap();
+ if (groupfile != "") {
+ groupMap = new GroupMap(groupfile);
+ groupMap->readMap();
+ }
}
}
@@ -130,17 +129,12 @@ void BinSeqCommand::help(){
BinSeqCommand::~BinSeqCommand(){
//made new in execute
if (abort == false) {
- delete input;
+ delete input; globaldata->ginput = NULL;
delete read;
- delete list;
- }
-
- //made new in constructor
- delete fasta;
- if (groupfile != "") {
- delete groupMap;
+ globaldata->gListVector = NULL;
+ delete fasta;
+ if (groupfile != "") { delete groupMap; globaldata->gGroupmap = NULL; }
}
-
}
//**********************************************************************************************************************
@@ -155,6 +149,8 @@ int BinSeqCommand::execute(){
//read fastafile
fasta->readFastaFile(in);
+ in.close();
+
//set format to list so input can get listvector
// globaldata->setFormat("list");
diff --git a/blastalign.cpp b/blastalign.cpp
index e4d5e8a..cb6abf9 100644
--- a/blastalign.cpp
+++ b/blastalign.cpp
@@ -154,6 +154,7 @@ void BlastAlignment::setPairwiseSeqs(){ // This method call assigns the blast ge
seqAaln += 'Z'; // again need ot pad the sequences so that they extend to the length
seqBaln += 'X'; // of the template sequence
}
+ blastFile.close();
}
//**************************************************************************************************/
diff --git a/blastdb.cpp b/blastdb.cpp
index 6f4ebcc..e442fa2 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -32,7 +32,7 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
for(int i=0;i<numSeqs;i++){ // generating a fasta file with unaligned template
unalignedFastaFile << '>' << i << endl; // sequences, which will be input to formatdb
- unalignedFastaFile << templateSequences[i]->getUnaligned() << endl;
+ unalignedFastaFile << templateSequences[i].getUnaligned() << endl;
}
unalignedFastaFile.close();
@@ -43,10 +43,10 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
// option tells formatdb that seqs are DNA, not prot
cout << "DONE." << endl << endl; cout.flush();
- emptySequence = new Sequence();
- emptySequence->setName("no_match");
- emptySequence->setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
- emptySequence->setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+ emptySequence = Sequence();
+ emptySequence.setName("no_match");
+ emptySequence.setUnaligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
+ emptySequence.setAligned("XXXXXXXXXXXXXXXXXXXXXXXXXXXXX");
}
@@ -54,6 +54,10 @@ gapOpen(gO), gapExtend(gE), match(m), misMatch(mM) {
/**************************************************************************************************/
BlastDB::~BlastDB(){
+ //for (int i = 0; i < templateSequences.size(); i++) { delete templateSequences[i]; }
+ //templateSequences.clear();
+ //delete emptySequence;
+
remove(queryFileName.c_str()); // let's clean stuff up and remove the temp files
remove(dbFileName.c_str()); // let's clean stuff up and remove the temp files
remove(blastFileName.c_str()); // let's clean stuff up and remove the temp files
@@ -61,7 +65,7 @@ BlastDB::~BlastDB(){
/**************************************************************************************************/
-Sequence* BlastDB::findClosestSequence(Sequence* candidate){
+Sequence BlastDB::findClosestSequence(Sequence* candidate){
ofstream queryFile;
openOutputFile(queryFileName, queryFile);
@@ -93,6 +97,7 @@ Sequence* BlastDB::findClosestSequence(Sequence* candidate){
searchScore = 0.00;
return emptySequence;
}
+ m8FileHandle.close();
}
/**************************************************************************************************/
diff --git a/blastdb.hpp b/blastdb.hpp
index dfb2a2c..f0f17f9 100644
--- a/blastdb.hpp
+++ b/blastdb.hpp
@@ -18,7 +18,7 @@ class BlastDB : public Database {
public:
BlastDB(string, float, float, float, float);
~BlastDB();
- Sequence* findClosestSequence(Sequence*);
+ Sequence findClosestSequence(Sequence*);
private:
string dbFileName;
@@ -30,7 +30,7 @@ private:
float gapExtend;
float match;
float misMatch;
- Sequence* emptySequence;
+ Sequence emptySequence;
GlobalData* globaldata;
};
diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp
index 5e7c0c6..a94954a 100644
--- a/bootstrapsharedcommand.cpp
+++ b/bootstrapsharedcommand.cpp
@@ -179,9 +179,10 @@ void BootSharedCommand::help(){
BootSharedCommand::~BootSharedCommand(){
//made new in execute
if (abort == false) {
- delete input;
+ delete input; globaldata->ginput = NULL;
delete read;
delete util;
+ globaldata->gorder = NULL;
}
}
diff --git a/calculator.h b/calculator.h
index 8b21f70..5dc0812 100644
--- a/calculator.h
+++ b/calculator.h
@@ -21,6 +21,7 @@ class Calculator {
public:
Calculator(){};
+ virtual ~Calculator(){};
Calculator(string n, int c, bool m) : name(n), cols(c), multiple(m) {};
virtual EstOutput getValues(SAbundVector*) = 0;
virtual EstOutput getValues(vector<SharedRAbundVector*>) = 0;
diff --git a/clustercommand.cpp b/clustercommand.cpp
index 4db95b4..eeba407 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -120,8 +120,10 @@ void ClusterCommand::help(){
//**********************************************************************************************************************
ClusterCommand::~ClusterCommand(){
- delete cluster;
- delete rabund;
+ if (abort == false) {
+ delete cluster;
+ delete rabund;
+ }
}
//**********************************************************************************************************************
@@ -177,6 +179,10 @@ int ClusterCommand::execute(){
globaldata->setNameFile("");
globaldata->setFormat("list");
+ sabundFile.close();
+ rabundFile.close();
+ listFile.close();
+
return 0;
}
catch(exception& e) {
diff --git a/collectcommand.cpp b/collectcommand.cpp
index 2dd843f..c65080f 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -195,11 +195,13 @@ void CollectCommand::help(){
//**********************************************************************************************************************
CollectCommand::~CollectCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ //delete order;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->gorder = NULL;
+ }
}
//**********************************************************************************************************************
@@ -252,7 +254,7 @@ int CollectCommand::execute(){
userLabels.erase(lastOrder->getLabel());
}
- if (count != 1) { delete lastOrder; }
+ if (count != 1) { delete lastOrder; }
lastOrder = order;
order = (input->getOrderVector());
count++;
diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 6127c2d..86d5ffc 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -117,7 +117,7 @@ CollectSharedCommand::CollectSharedCommand(string option){
if (abort == false) {
string fileNameRoot = getRootName(globaldata->inputFileName);
-// format = globaldata->getFormat();
+ format = globaldata->getFormat();
int i;
validCalculator = new ValidCalculators();
@@ -214,12 +214,13 @@ void CollectSharedCommand::help(){
//**********************************************************************************************************************
CollectSharedCommand::~CollectSharedCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
- delete util;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete util;
+ delete validCalculator;
+ globaldata->gorder = NULL;
+ }
}
//**********************************************************************************************************************
diff --git a/command.hpp b/command.hpp
index 27355dd..1dd5e87 100644
--- a/command.hpp
+++ b/command.hpp
@@ -18,9 +18,11 @@
#include "validparameter.h"
class Command {
+
public:
virtual int execute() = 0;
virtual void help() = 0;
+ virtual ~Command() { }
};
#endif
diff --git a/database.cpp b/database.cpp
index f849146..852e2d2 100644
--- a/database.cpp
+++ b/database.cpp
@@ -41,7 +41,7 @@ Database::Database(string fastaFileName){ // This assumes that the template dat
aligned += letter;
}
}
- templateSequences[i] = new Sequence(seqName, aligned);
+ templateSequences[i] = Sequence(seqName, aligned);
fastaFile.putback(letter);
}
@@ -51,6 +51,24 @@ Database::Database(string fastaFileName){ // This assumes that the template dat
cout << "DONE." << endl; cout.flush();
}
+/**************************************************************************************************/
+
+Database::~Database(){
+ try {
+
+ //for (int i = 0; i < templateSequences.size(); i++) { delete templateSequences[i]; }
+ templateSequences.clear();
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the Database class Function ~Database. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the Database class function ~Database. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/**************************************************************************************************/
diff --git a/database.hpp b/database.hpp
index 2fced3f..02cad03 100644
--- a/database.hpp
+++ b/database.hpp
@@ -20,12 +20,13 @@ class Sequence;
class Database {
public:
Database(string);
- virtual Sequence* findClosestSequence(Sequence*) = 0;
+ virtual ~Database();
+ virtual Sequence findClosestSequence(Sequence*) = 0;
virtual float getSearchScore();
protected:
int numSeqs;
float searchScore;
- vector<Sequence*> templateSequences;
+ vector<Sequence> templateSequences;
};
#endif
diff --git a/datavector.hpp b/datavector.hpp
index 692332f..b3c7c90 100644
--- a/datavector.hpp
+++ b/datavector.hpp
@@ -23,7 +23,7 @@ public:
DataVector(string l) : label(l) {};
DataVector(const DataVector& dv) : label(dv.label){};//, maxRank(dv.maxRank), numBins(dv.numBins), numSeqs(dv.numSeqs) {};
DataVector(ifstream&);
- ~DataVector(){};
+ virtual ~DataVector(){};
// virtual int getNumBins() { return numBins; }
// virtual int getNumSeqs() { return numSeqs; }
diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 3ec5f73..2fe7a25 100644
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -96,6 +96,7 @@ int DeconvoluteCommand::execute() {
fastamap->printNamesFile(out);
fastamap->printCondensedFasta(outFasta);
+ in.close();
out.close();
outFasta.close();
diff --git a/display.h b/display.h
index 0207bbf..ee827e5 100644
--- a/display.h
+++ b/display.h
@@ -18,6 +18,7 @@ public:
virtual void reset() = 0;
virtual void close() = 0;
virtual bool isCalcMultiple() = 0;
+ virtual ~Display() {}
private:
diff --git a/dist.h b/dist.h
index 4200bf9..6e42ae3 100644
--- a/dist.h
+++ b/dist.h
@@ -18,6 +18,7 @@ class Dist {
public:
Dist(){dist = 0;}
+ virtual ~Dist() {}
virtual void calcDist(Sequence, Sequence) = 0;
double getDist() { return dist; }
protected:
diff --git a/distancecommand.cpp b/distancecommand.cpp
index 065c14a..0c9d011 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -47,6 +47,7 @@ DistanceCommand::DistanceCommand(string option){
ifstream inFASTA;
openInputFile(fastafile, inFASTA);
alignDB = SequenceDB(inFASTA);
+ inFASTA.close();
}
//check for optional parameter and set defaults
@@ -195,7 +196,7 @@ int DistanceCommand::execute(){
}
}
#else
- ifstream inFASTA
+ ifstream inFASTA;
driver(0, numSeqs, outputFile, cutoff);
#endif
diff --git a/distancedb.cpp b/distancedb.cpp
index 3cb739d..25c95c7 100644
--- a/distancedb.cpp
+++ b/distancedb.cpp
@@ -40,7 +40,7 @@ DistanceDB::DistanceDB(string fastaFileName, string distanceFileName) : Database
/**************************************************************************************************/
-Sequence* DistanceDB::findClosestSequence(Sequence* candidateSeq){
+Sequence DistanceDB::findClosestSequence(Sequence* candidateSeq){
hit simAccession = mostSimSequenceVector[searchIndex];
// string candidateSeqName, closestMatchSeqName, junk;
diff --git a/distancedb.hpp b/distancedb.hpp
index 9c13faf..8da1d10 100644
--- a/distancedb.hpp
+++ b/distancedb.hpp
@@ -17,7 +17,7 @@ class DistanceDB : public Database {
public:
DistanceDB(string, string);
- Sequence* findClosestSequence(Sequence*);
+ Sequence findClosestSequence(Sequence*);
private:
diff --git a/engine.cpp b/engine.cpp
index 03422e2..a2d5250 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -47,8 +47,8 @@ bool InteractEngine::getInput(){
//bool errorFree;
//ErrorCheck* errorCheckor = new ErrorCheck();
- cout << "mothur v.1.3.0" << endl;
- cout << "Last updated: 5/29/2009" << endl << endl;
+ cout << "mothur v.1.4.0" << endl;
+ cout << "Last updated: 6/21/2009" << endl << endl;
cout << "by" << endl;
cout << "Patrick D. Schloss" << endl << endl;
cout << "Department of Microbiology" << endl;
@@ -147,7 +147,7 @@ bool BatchEngine::getInput(){
int quitCommandCalled = 0;
while(quitCommandCalled == 0){
-
+
if (inputBatchFile.eof()) { input = "quit()"; }
else { getline(inputBatchFile, input); }
@@ -175,6 +175,8 @@ bool BatchEngine::getInput(){
}
gobble(inputBatchFile);
}
+
+ inputBatchFile.close();
return 1;
}
catch(exception& e) {
@@ -280,12 +282,14 @@ string ScriptEngine::getNextCommand(string& commandString) {
commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
}else { commandString = ""; } //you have reached the last command.
- //get rid of any extra spaces in between commands
- //string space = " ";
-
- //while(commandString.at(0) == ' ')
- //commandString = commandString.substr(1, commandString.length());
-
+ //get rid of spaces in between commands if any
+ if (commandString.length() > 0) {
+ while (commandString[0] == ' ') {
+ commandString = commandString.substr(1,commandString.length());
+ if (commandString.length() == 0) { break; }
+ }
+ }
+
return nextcommand;
}
catch(exception& e) {
diff --git a/fileoutput.h b/fileoutput.h
index 7dfb0c0..a047a20 100644
--- a/fileoutput.h
+++ b/fileoutput.h
@@ -9,7 +9,7 @@ class FileOutput {
public:
FileOutput(){};
- ~FileOutput(){};
+ virtual ~FileOutput(){};
virtual void initFile(string) = 0;
virtual void initFile(string, vector<string>) = 0;
diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 95d51f3..c38bfcb 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -104,6 +104,8 @@ void FilterSeqsCommand::doHard() {
openInputFile(hard, fileHandle);
fileHandle >> filter;
+
+ fileHandle.close();
}
diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index ea6ef17..4fa8413 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -115,6 +115,7 @@ int GetgroupCommand::execute(){
if (in.eof() != true) { in >> nextLabel; }
}
+ in.close();
out.close();
return 0;
}
diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index e0c1720..40c656b 100644
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -84,6 +84,8 @@ int GetlabelCommand::execute(){
in >> label;
count++;
}
+
+ in.close();
return 0;
}
diff --git a/getlinecommand.cpp b/getlinecommand.cpp
index 6802978..800f9d8 100644
--- a/getlinecommand.cpp
+++ b/getlinecommand.cpp
@@ -84,6 +84,8 @@ int GetlineCommand::execute(){
in >> label;
count++;
}
+
+ in.close();
return 0;
}
diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 35e6924..65c1806 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -156,11 +156,13 @@ void GetOTURepCommand::help(){
//**********************************************************************************************************************
GetOTURepCommand::~GetOTURepCommand(){
- delete input;
- delete read;
- delete fasta;
- if (groupfile != "") {
- delete groupMap;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete fasta;
+ if (groupfile != "") {
+ delete groupMap; globaldata->gGroupmap = NULL;
+ }
}
}
@@ -177,8 +179,10 @@ int GetOTURepCommand::execute(){
//read fastafile
fasta->readFastaFile(in);
+ in.close();
+
//set format to list so input can get listvector
-// globaldata->setFormat("list");
+ globaldata->setFormat("list");
//if user gave a namesfile then use it
if (namesfile != "") {
diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index c978bb1..0dfaa63 100644
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -108,6 +108,7 @@ void GetRAbundCommand::help(){
//**********************************************************************************************************************
GetRAbundCommand::~GetRAbundCommand(){
+ if (abort == false) { globaldata->gListVector = NULL; }
}
//**********************************************************************************************************************
diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 6670980..1e10736 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -186,7 +186,7 @@ int GetSAbundCommand::execute(){
sabund->print(out);
delete sabund;
}
- delete lastOrder;
+ delete lastOrder; globaldata->gorder = NULL;
out.close();
return 0;
diff --git a/globaldata.cpp b/globaldata.cpp
index fe3c11b..0d728a1 100644
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -1,6 +1,9 @@
#include "globaldata.hpp"
+#include "sharedlistvector.h"
+#include "inputdata.h"
+#include "fullmatrix.h"
/*******************************************************/
@@ -50,6 +53,16 @@ GlobalData::GlobalData() {
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;
}
/*******************************************************/
@@ -74,11 +87,24 @@ void GlobalData::clear() {
/******************************************************/
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;}
+
gTree.clear();
Treenames.clear();
labels.clear(); lines.clear(); Groups.clear();
@@ -100,9 +126,28 @@ void GlobalData::newRead() {
/******************************************************/
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;}
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function ~GlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the GlobalData class function ~GlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
}
/*******************************************************/
diff --git a/globaldata.hpp b/globaldata.hpp
index 6515521..6f66cbe 100644
--- a/globaldata.hpp
+++ b/globaldata.hpp
@@ -9,6 +9,8 @@
#include "listvector.hpp"
#include "tree.h"
#include "sparsematrix.hpp"
+#include "sequencedb.h"
+
class ListVector;
class SharedListVector;
diff --git a/gotohoverlap.hpp b/gotohoverlap.hpp
index bf3c636..85176ef 100644
--- a/gotohoverlap.hpp
+++ b/gotohoverlap.hpp
@@ -30,6 +30,7 @@ class GotohOverlap : public Alignment {
public:
GotohOverlap(float, float, float, float, int);
void align(string, string);
+ ~GotohOverlap() {}
private:
float gapOpen;
diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index d4e893b..7a729c6 100644
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -128,9 +128,10 @@ void HeatMapCommand::help(){
//**********************************************************************************************************************
HeatMapCommand::~HeatMapCommand(){
-
- delete read;
- delete heatmap;
+ if (abort == false) {
+ delete read;
+ delete heatmap;
+ }
}
//**********************************************************************************************************************
@@ -272,11 +273,11 @@ int HeatMapCommand::execute(){
heatmap->getPic(lastRAbund);
}
- delete lastRAbund;
+ delete lastRAbund; globaldata->rabund = NULL;
}
- delete input;
+ delete input; globaldata->ginput = NULL;
return 0;
}
catch(exception& e) {
diff --git a/heatmapsimcommand.cpp b/heatmapsimcommand.cpp
index 3b0d798..f332994 100644
--- a/heatmapsimcommand.cpp
+++ b/heatmapsimcommand.cpp
@@ -171,10 +171,12 @@ void HeatMapSimCommand::help(){
//**********************************************************************************************************************
HeatMapSimCommand::~HeatMapSimCommand(){
- delete input;
- delete read;
- delete heatmap;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete heatmap;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
diff --git a/inputdata.cpp b/inputdata.cpp
index b237bb4..b4373c9 100644
--- a/inputdata.cpp
+++ b/inputdata.cpp
@@ -72,7 +72,7 @@ ListVector* InputData::getListVector(){
return list;
}
else{
- return 0;
+ return NULL;
}
}
catch(exception& e) {
@@ -98,7 +98,7 @@ SharedListVector* InputData::getSharedListVector(){
return SharedList;
}
else{
- return 0;
+ return NULL;
}
}
catch(exception& e) {
@@ -124,7 +124,7 @@ SharedOrderVector* InputData::getSharedOrderVector(){
return SharedOrder;
}else{
- return 0;
+ return NULL;
}
}
catch(exception& e) {
@@ -170,7 +170,7 @@ OrderVector* InputData::getOrderVector(){
return output;
}
else{
- return 0;
+ return NULL;
}
}
catch(exception& e) {
@@ -246,7 +246,7 @@ SAbundVector* InputData::getSAbundVector(){
return sabund;
}
else{
- return 0;
+ return NULL;
}
}
catch(exception& e) {
diff --git a/kmerdb.cpp b/kmerdb.cpp
index 572acda..40cc1f6 100644
--- a/kmerdb.cpp
+++ b/kmerdb.cpp
@@ -50,10 +50,17 @@ KmerDB::KmerDB(string fastaFileName, int kSize) : Database(fastaFileName), kmerS
cout << "DONE." << endl << endl; cout.flush();
}
+/**************************************************************************************************/
+
+KmerDB::~KmerDB(){
+
+ //for (int i = 0; i < templateSequences.size(); i++) { delete templateSequences[i]; }
+ // templateSequences.clear();
+}
/**************************************************************************************************/
-Sequence* KmerDB::findClosestSequence(Sequence* candidateSeq){
+Sequence KmerDB::findClosestSequence(Sequence* candidateSeq){
Kmer kmer(kmerSize);
@@ -94,7 +101,7 @@ void KmerDB::generateKmerDB(string kmerDBName){
for(int i=0;i<numSeqs;i++){ // for all of the template sequences...
- string seq = templateSequences[i]->getUnaligned(); // ...take the unaligned sequence...
+ string seq = templateSequences[i].getUnaligned(); // ...take the unaligned sequence...
int numKmers = seq.length() - kmerSize + 1;
vector<int> seenBefore(maxKmer+1,0);
diff --git a/kmerdb.hpp b/kmerdb.hpp
index eb10061..5019858 100644
--- a/kmerdb.hpp
+++ b/kmerdb.hpp
@@ -25,7 +25,8 @@ class KmerDB : public Database {
public:
KmerDB(string, int);
- Sequence* findClosestSequence(Sequence*);
+ ~KmerDB();
+ Sequence findClosestSequence(Sequence*);
private:
void generateKmerDB(string);
diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 75e6137..fd41391 100644
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -256,7 +256,7 @@ void LibShuffCommand::printCoverageFile() {
}
outCov << endl;
}
-
+ outCov.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printCoverageFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -305,7 +305,7 @@ void LibShuffCommand::printSummaryFile() {
}
}
-
+ outSum.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the LibShuffCommand class Function printSummaryFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index e848647..4ae8e24 100644
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -170,9 +170,11 @@ void MatrixOutputCommand::help(){
//**********************************************************************************************************************
MatrixOutputCommand::~MatrixOutputCommand(){
- delete input;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 3342c48..497d535 100644
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -88,6 +88,8 @@ int MergeFileCommand::execute(){
inputFile.close();
}
+
+ outputFile.close();
return 0;
}
catch(exception& e) {
diff --git a/observable.h b/observable.h
index 457a176..05e537a 100644
--- a/observable.h
+++ b/observable.h
@@ -13,6 +13,7 @@ public:
virtual void registerDisplay(Display*) = 0;
virtual void removeDisplay(Display*) = 0;
virtual void notifyDisplays() = 0;
+ virtual ~Observable() {}
};
/***********************************************************************/
diff --git a/parselistcommand.cpp b/parselistcommand.cpp
index 332074d..c12bd47 100644
--- a/parselistcommand.cpp
+++ b/parselistcommand.cpp
@@ -184,9 +184,11 @@ int ParseListCommand::execute(){
//**********************************************************************************************************************
ParseListCommand::~ParseListCommand(){
- delete list;
- delete input;
- delete read;
+
+ globaldata->gSharedList = NULL;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+
}
//**********************************************************************************************************************
void ParseListCommand::process(SharedListVector* thisList) {
diff --git a/rarefactcommand.cpp b/rarefactcommand.cpp
index 6bf42fc..8820328 100644
--- a/rarefactcommand.cpp
+++ b/rarefactcommand.cpp
@@ -171,11 +171,12 @@ void RareFactCommand::help(){
//**********************************************************************************************************************
RareFactCommand::~RareFactCommand(){
- delete order;
- delete input;
- delete rCurve;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ globaldata->gorder = NULL;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index fdc9678..6461b3b 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -154,10 +154,11 @@ void RareFactSharedCommand::help(){
//**********************************************************************************************************************
RareFactSharedCommand::~RareFactSharedCommand(){
- delete input;
- delete rCurve;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
diff --git a/readcolumn.cpp b/readcolumn.cpp
index 1d29208..59c3bd5 100644
--- a/readcolumn.cpp
+++ b/readcolumn.cpp
@@ -153,8 +153,8 @@ void ReadColumnMatrix::read(NameAssignment* nameMap){
/***********************************************************************/
ReadColumnMatrix::~ReadColumnMatrix(){
- delete D;
- delete list;
+ //delete D;
+ //delete list;
}
diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index b03f12e..392d12b 100644
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -53,8 +53,8 @@ ReadDistCommand::ReadDistCommand(string option){
else if (groupfile == "not found") { groupfile = ""; }
else {
globaldata->setGroupFile(groupfile);
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
+ //groupMap = new GroupMap(groupfile);
+ //groupMap->readMap();
}
namefile = validParameter.validFile(parameters, "name", true);
@@ -150,8 +150,9 @@ void ReadDistCommand::help(){
//**********************************************************************************************************************
ReadDistCommand::~ReadDistCommand(){
- delete read;
- delete nameMap;
+ if (abort == false) {
+ if (format != "matrix") { delete read; delete nameMap; }
+ }
}
//**********************************************************************************************************************
@@ -164,16 +165,20 @@ int ReadDistCommand::execute(){
ifstream in;
openInputFile(distFileName, in);
matrix = new FullMatrix(in); //reads the matrix file
+ in.close();
//memory leak prevention
- //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; }
+ if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix; }
globaldata->gMatrix = matrix; //save matrix for coverage commands
}else {
read->read(nameMap);
//to prevent memory leak
- if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
+
+ if (globaldata->gListVector != NULL) { delete globaldata->gListVector; }
globaldata->gListVector = read->getListVector();
+
if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix; }
globaldata->gSparseMatrix = read->getMatrix();
+
}
return 0;
}
diff --git a/readmatrix.hpp b/readmatrix.hpp
index 66480e7..d8f9bd1 100644
--- a/readmatrix.hpp
+++ b/readmatrix.hpp
@@ -22,6 +22,7 @@ class ReadMatrix {
public:
ReadMatrix(){ D = new SparseMatrix(); }
+ virtual ~ReadMatrix() {}
virtual void read(NameAssignment*){};
virtual void read(GlobalData* globaldata){};
void setCutoff(float c) { cutoff = c; }
diff --git a/readotu.cpp b/readotu.cpp
index 286a2be..b97c902 100644
--- a/readotu.cpp
+++ b/readotu.cpp
@@ -13,7 +13,7 @@
ReadOTUFile::ReadOTUFile(string pf): philFile(pf){
- openInputFile(philFile, fileHandle);
+ //openInputFile(philFile, fileHandle);
}
/***********************************************************************/
diff --git a/readotu.h b/readotu.h
index e318af4..b259733 100644
--- a/readotu.h
+++ b/readotu.h
@@ -27,7 +27,7 @@ public:
~ReadOTUFile();
void read(GlobalData* globaldata);
private:
- ifstream fileHandle;
+ //ifstream fileHandle;
string philFile;
InputData* input;
InputData* inputSabund;
diff --git a/readphylip.cpp b/readphylip.cpp
index bc39b52..a1063e9 100644
--- a/readphylip.cpp
+++ b/readphylip.cpp
@@ -180,6 +180,6 @@ void ReadPhylipMatrix::read(NameAssignment* nameMap){
/***********************************************************************/
ReadPhylipMatrix::~ReadPhylipMatrix(){
- delete D;
- delete list;
+ // delete D;
+ // delete list;
}
diff --git a/readtree.cpp b/readtree.cpp
index d3790df..670c6e0 100644
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -177,6 +177,8 @@ int ReadNewickTree::read() {
}
if (error != 0) { readOk = error; }
+
+ filehandle.close();
return readOk;
}
catch(exception& e) {
diff --git a/readtree.h b/readtree.h
index c8e866a..0cdf8b1 100644
--- a/readtree.h
+++ b/readtree.h
@@ -23,7 +23,7 @@ class Tree;
class ReadTree {
public:
ReadTree();
- ~ReadTree() {};
+ virtual ~ReadTree() {};
virtual int read() = 0;
int readSpecialChar(istream&, char, string);
diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 88e34ff..d301b13 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -33,14 +33,13 @@ ReadTreeCommand::ReadTreeCommand(string option){
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- globaldata->runParse = true;
globaldata->newRead();
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (treefile == "not open") { abort = true; }
else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true; }
-// else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
+ else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 1c70a2b..ca1d616 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -160,6 +160,9 @@ int ScreenSeqsCommand::execute(){
if(groupfile != "") { screenGroupFile(badSeqNames); }
if(alignreport != "") { screenAlignReport(badSeqNames); }
+ goodSeqOut.close();
+ badSeqOut.close();
+ inFASTA.close();
return 0;
}
catch(exception& e) {
diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 24ef1d1..3259931 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -139,6 +139,7 @@ int SeqSummaryCommand::execute(){
cout << "Maximum:\t" << startPosition[ptile100] << '\t' << endPosition[ptile100] << '\t' << seqLength[ptile100] << '\t' << ambigBases[ptile100] << '\t' << longHomoPolymer[ptile100] << endl;
cout << "# of Seqs:\t" << numSeqs << endl;
+ outSummary.close();
return 0;
}
catch(exception& e) {
diff --git a/shen.cpp b/shen.cpp
index 152a138..3d1c277 100644
--- a/shen.cpp
+++ b/shen.cpp
@@ -27,7 +27,9 @@ EstOutput Shen::getValues(SAbundVector* rank){
double f0 = ace[0]-rank->getNumBins();
data[0] = f0 * (1 - pow(1 - f1/n/f0, m));
-
+
+ delete calc;
+
return data;
}
catch(exception& e) {
diff --git a/suffixdb.cpp b/suffixdb.cpp
index 15f7753..5e6fd10 100644
--- a/suffixdb.cpp
+++ b/suffixdb.cpp
@@ -35,7 +35,7 @@ SuffixDB::SuffixDB(string fastaFileName) : Database(fastaFileName) {
/**************************************************************************************************/
-Sequence* SuffixDB::findClosestSequence(Sequence* candidateSeq){
+Sequence SuffixDB::findClosestSequence(Sequence* candidateSeq){
int minValue = 2000;
int closestSequenceNo = 0;
@@ -52,3 +52,11 @@ Sequence* SuffixDB::findClosestSequence(Sequence* candidateSeq){
}
/**************************************************************************************************/
+
+SuffixDB::~SuffixDB(){
+
+ for (int i = (suffixForest.size()-1); i >= 0; i--) { suffixForest.pop_back(); }
+ // templateSequences.clear();
+
+}
+/**************************************************************************************************/
diff --git a/suffixdb.hpp b/suffixdb.hpp
index 15114cf..f211aa7 100644
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -27,7 +27,8 @@ class SuffixDB : public Database {
public:
SuffixDB(string);
- Sequence* findClosestSequence(Sequence*);
+ ~SuffixDB();
+ Sequence findClosestSequence(Sequence*);
private:
vector<SuffixTree> suffixForest;
diff --git a/suffixnodes.hpp b/suffixnodes.hpp
index 82d4be9..63918fa 100644
--- a/suffixnodes.hpp
+++ b/suffixnodes.hpp
@@ -24,6 +24,7 @@ class SuffixNode {
public:
SuffixNode(int, int, int);
+ virtual ~SuffixNode() {}
virtual void print(string, int) = 0;
virtual void setChildren(char, int);
virtual int getNumChildren();
@@ -49,6 +50,7 @@ class SuffixLeaf : public SuffixNode { // most of the methods are already set in
public:
SuffixLeaf(int, int, int); // we just need to define a constructor and
+ ~SuffixLeaf() {}
void print(string, int); // print method
};
@@ -58,6 +60,7 @@ class SuffixBranch : public SuffixNode {
public:
SuffixBranch(int, int, int);
+ ~SuffixBranch() {}
void print(string, int); // need a special method for printing the node because there are children
void eraseChild(char); // need a special method for erasing the children
void setChildren(char, int); // need a special method for setting children
diff --git a/suffixtree.cpp b/suffixtree.cpp
index 492460d..0dbe2c0 100644
--- a/suffixtree.cpp
+++ b/suffixtree.cpp
@@ -41,16 +41,17 @@ SuffixTree::SuffixTree(){}
SuffixTree::~SuffixTree(){
for(int i=0;i<nodeVector.size();i++){ delete nodeVector[i]; }
+ nodeVector.clear();
}
//********************************************************************************************************************
-void SuffixTree::loadSequence(Sequence* seq){
+void SuffixTree::loadSequence(Sequence seq){
nodeCounter = 0; // initially there are 0 nodes in the tree
activeStartPosition = 0;
activeEndPosition = -1;
- seqName = seq->getName();
- sequence = seq->convert2ints();
+ seqName = seq.getName();
+ sequence = seq.convert2ints();
sequence += '5'; // this essentially concatenates a '$' to the end of the sequence to
int seqLength = sequence.length(); // make it a cononical suffix tree
diff --git a/suffixtree.hpp b/suffixtree.hpp
index 28b6fd1..b85cee9 100644
--- a/suffixtree.hpp
+++ b/suffixtree.hpp
@@ -38,7 +38,7 @@ public:
~SuffixTree();
// SuffixTree(string, string);
- void loadSequence(Sequence*);
+ void loadSequence(Sequence);
string getSeqName();
void print();
int countSuffixes(string, int&);
diff --git a/summarycommand.cpp b/summarycommand.cpp
index fa6d11a..ee4ba9f 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -194,10 +194,12 @@ void SummaryCommand::help(){
//**********************************************************************************************************************
SummaryCommand::~SummaryCommand(){
- delete sabund;
- delete input;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->sabund = NULL;
+ }
}
//**********************************************************************************************************************
@@ -272,7 +274,7 @@ int SummaryCommand::execute(){
outputFileHandle << endl;
}
- if (count != 1) { delete lastSAbund; }
+ if (count != 1) { delete lastSAbund; }
lastSAbund = sabund;
sabund = input->getSAbundVector();
@@ -304,6 +306,8 @@ int SummaryCommand::execute(){
outputFileHandle << endl;
}
+ outputFileHandle.close();
+
delete lastSAbund;
return 0;
}
diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 7c1275f..4006b2d 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -204,8 +204,10 @@ void SummarySharedCommand::help(){
//**********************************************************************************************************************
SummarySharedCommand::~SummarySharedCommand(){
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
@@ -335,7 +337,7 @@ int SummarySharedCommand::execute(){
for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
- delete input;
+ delete input; globaldata->ginput = NULL;
return 0;
}
diff --git a/tree.cpp b/tree.cpp
index c078f4f..ee17e6f 100644
--- a/tree.cpp
+++ b/tree.cpp
@@ -668,7 +668,7 @@ void Tree::parseTreeFile() {
if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
}
}
-
+ filehandle.close();
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the Tree class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
diff --git a/treecalculator.h b/treecalculator.h
index 16663bf..35d061c 100644
--- a/treecalculator.h
+++ b/treecalculator.h
@@ -24,7 +24,7 @@ class TreeCalculator {
public:
TreeCalculator(){};
TreeCalculator(string n) : name(n) {};
- ~TreeCalculator(){};
+ virtual ~TreeCalculator(){};
virtual EstOutput getValues(Tree*) = 0;
virtual EstOutput getValues(Tree*, string, string) = 0;
diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 0f106c4..88b1b46 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -205,11 +205,13 @@ void TreeGroupCommand::help(){
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
- delete input;
- if (format == "sharedfile") {delete read;}
- else { delete readMatrix; delete matrix; delete list; }
- delete tmap;
- delete validCalculator;
+ if (abort == false) {
+
+ if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL;}
+ else { delete readMatrix; delete matrix; delete list; }
+ delete tmap;
+ delete validCalculator;
+ }
}
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index e616b74..1989365 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -179,6 +179,7 @@ int TrimSeqsCommand::execute(){
if(qThreshold != 0) { success = stripQualThreshold(currSeq, qFile); }
else if(qAverage != 0) { success = cullQualAverage(currSeq, qFile); }
if(!success) { trashCode += 'q'; }
+ qFile.close();
}
if(barcodes.size() != 0){
success = stripBarcode(currSeq, group);
@@ -308,6 +309,8 @@ void TrimSeqsCommand::getOligos(vector<ofstream*>& outFASTAVec){
}
}
+ inOligos.close();
+
numFPrimers = forPrimer.size();
numRPrimers = revPrimer.size();
}
diff --git a/venncommand.cpp b/venncommand.cpp
index 70c136b..343461a 100644
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -181,10 +181,13 @@ void VennCommand::help(){
//**********************************************************************************************************************
VennCommand::~VennCommand(){
- delete input;
- delete read;
- delete venn;
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete venn;
+ globaldata->sabund = NULL;
+ }
+
}
//**********************************************************************************************************************
@@ -342,6 +345,7 @@ int VennCommand::execute(){
delete lastSAbund;
}
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
return 0;
}
catch(exception& e) {