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file.h
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file.h
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/* ================================================================= *
* file.h : Header file with supporting class definitions *
* *
* pal-MEM: An efficient (MUMmer-like) tool to retrieve reads *
* containing Maximum Exact Matches using hashing based *
* algorithm *
* Developer: Victoria Carr *
* *
* Modified program from E-MEM *
* https://github.com/lucian-ilie/E-MEM *
* Developer: Nilesh Khiste *
* *
* This program is free software: you can redistribute it and/or *
* modify it under the terms of the GNU General Public License as *
* published by the Free Software Foundation, either version 3 of *
* the License, or (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public *
* License along with this program. *
* *
* This file is subject to the terms and conditions defined in the *
* file 'LICENSE', which is part of this source code package. *
* ================================================================= */
using namespace std;
#define CHARS2BITS(x) (2*(x)) //convert char position to bit position
#define DATATYPE_WIDTH 64 // number of bits
#define RANDOM_SEQ_SIZE 10
#define NUM_TMP_FILES 24
class commonData {
public:
static int32_t minMemLen;
static int32_t maxMemLen;
static int32_t d;
static int32_t numThreads;
static int32_t kmerSize;
static char nucmer_path[256];
static int32_t lenBuffer;
};
int32_t commonData::minMemLen=48; // 2 bit representation
int32_t commonData::maxMemLen=200;
int32_t commonData::lenBuffer=46;
int32_t commonData::d=1;
int32_t commonData::numThreads=1;
int32_t commonData::kmerSize=30; //2 bit representation
char commonData::nucmer_path[256]={'\0'};\
class seqData {
public:
uint64_t start;
uint64_t end;
std::string seq;
std::string header;
int keep=1;
int pair_file_no;
seqData()
{
start=0;
end=0;
};
bool operator ()(const seqData &obj1, const seqData &obj2)
{
return (obj2.start>obj1.end?true:false);
}
};
class posData {
public:
uint64_t L1Bound;
uint64_t R1Bound;
uint64_t L2Bound;
uint64_t R2Bound;
uint64_t palLength;
std::string seq;
posData() {}
bool operator () (const posData &obj1, const posData &obj2)
{
if (obj1.L1Bound < obj2.L1Bound) {
return true;
} else if (obj1.L1Bound > obj2.L1Bound) {
return false;
} else {
if (obj1.L2Bound < obj2.L2Bound)
return true;
else
return false;
}
}
};
class mapObject {
public:
uint64_t left;
uint64_t right;
mapObject() {
left=0;
right=0;
}
mapObject(uint64_t x, uint64_t y) {
left=x;
right=y;
}
bool operator()(const uint64_t &x, const mapObject &y)
{
return x < y.left;
}
};
class seqFileReadInfo {
fstream file1, file2;
int numSeqFiles;
uint64_t size;
string strTmp, strName;
uint64_t binReadSize;
uint64_t binReadsLocation;
uint64_t currPos;
uint64_t numSequences;
string& randomStr()
{
static string str("NNNNNNNNNN");
return str;
}
void processTmpString(uint64_t &sz, uint64_t &blockNCount)
{
string line = strTmp;
strTmp.clear();
totalBases=0;
binReadsLocation=0;
processInput(line, sz, blockNCount);
}
/*
* Function converts a character sequence into an array of integers.
* Input: character string
* Output: array of integers, total number of bases
*/
void processInput(string &str, uint64_t &sz, uint64_t &blockNCount)
{
int chooseLetter=0;
/* Processing the sequences by encoding the base pairs into 2 bits. */
for ( std::string::iterator it=str.begin(); it!=str.end(); ++it){
if (totalBases == sz){
strTmp += *it;
continue;
}else if (totalBases >= size) {
strTmp += *it;
}
switch(*it)
{
case 'A':
case 'a':
binReads[binReadsLocation] <<= 2; // shift left by 2 bits
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
break;
case 'C':
case 'c':
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 1;
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
break;
case 'G':
case 'g':
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 2;
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
break;
case 'T':
case 't':
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 3;
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
break;
default:
if(!blockNCount)
blockNCount=totalBases+1;
chooseLetter = rand() % 4;
if (chooseLetter == 0)
binReads[binReadsLocation] <<= 2;
else if (chooseLetter == 1)
{
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 1;
}
else if (chooseLetter == 2)
{
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 2;
}
else
{
binReads[binReadsLocation] <<= 2;
binReads[binReadsLocation] |= 3;
}
}
totalBases++;
if ((totalBases%32)==0){
binReadsLocation++;
}
}
}
public:
uint64_t *binReads;
uint64_t totalBases;
std::vector <mapObject> blockOfNs;
seqFileReadInfo() {
size=0;
currPos=0;
binReadSize=0;
binReadsLocation=0;
numSequences=0;
totalBases=0;
numSeqFiles=0;
}
void setFiles(vector<string> &filenames)
{
numSeqFiles=filenames.size();
if (numSeqFiles >= 1){
file1.open(filenames[0], ios::in);
if(!file1.is_open()) {
cout << "ERROR: unable to open " << filenames[0] << " file" << endl;
exit( EXIT_FAILURE );
}
if (numSeqFiles == 2){
file2.open(filenames[1], ios::in);
if(!file2.is_open()) {
cout << "ERROR: unable to open " << filenames[1] << " file" << endl;
exit( EXIT_FAILURE );
}
}
}
}
void setNumSequences(uint64_t numSeq) {
numSequences = numSeq;
}
void setSize(uint64_t sizeSet) {
size = sizeSet;
}
uint64_t &getNumSequences() {
return numSequences;
}
uint64_t &getSize() {
return size;
}
void openFile(string s, fstream &file){
file.open(s, ios::in);
if(!file.is_open()) {
cout << "ERROR: unable to open "<< s << " file" << endl;
exit( EXIT_FAILURE );
}
}
void setReverseFile() {
char buffer[256];
memset(buffer,0,256);
sprintf(buffer, "%s/revComp", commonData::nucmer_path);
if (numSeqFiles >= 1){
file1.close();
if (numSeqFiles == 2){
file2.close();
}
}
openFile(buffer, file1);
numSeqFiles = 1;
}
void closeFile() {
if (numSeqFiles >= 1){
file1.close();
if (numSeqFiles == 2){
file2.close();
}
}
}
void destroy() {
currPos=0;
binReadSize=0;
binReadsLocation=0;
totalBases=0;
strName.clear();
strTmp.clear();
clearMapForNs();
delete [] binReads;
}
void clearFileFlag()
{
if (numSeqFiles >= 1){
file1.clear();
file1.seekg(0, ios::beg);
if (numSeqFiles == 2){
file2.clear();
file2.seekg(0, ios::beg);
}
}
}
uint64_t allocBinArray(int split)
{
if (split)
size = size/commonData::d;
binReadSize = floor((size+numSequences*RANDOM_SEQ_SIZE+commonData::d)/32+4);
binReads = new uint64_t[binReadSize+1];
memset(binReads, 0, sizeof(uint64_t)*(binReadSize+1));
if (numSequences)
blockOfNs.reserve(numSequences+10);
return size;
}
void clearMapForNs()
{
blockOfNs.clear();
}
void clearTmpString()
{
strTmp.clear();
strName.clear();
clearMapForNs();
}
void getKmerLeftnRightBoundForNs(uint64_t &currKmerPos, mapObject &bounds)
{
uint64_t right=0;
/*
* Since we do all computation with bits, all our
* positions are even. Here I return 1 (odd position),
* an indication of no Ns towards left
*/
if (!blockOfNs.size()){
bounds.left=0x1;
bounds.right=CHARS2BITS(totalBases-1);
return;
}
vector<mapObject>::iterator it;
it=upper_bound(blockOfNs.begin(), blockOfNs.end(), currKmerPos, mapObject());
/* No N block beyond this point */
if (it == blockOfNs.end())
right = CHARS2BITS(totalBases-1);
else
right = (*it).left-2;
/* This function never gets a position which is N */
if (!currKmerPos || it==blockOfNs.begin()){
bounds.left=0x1;
bounds.right=right;
return;
}
--it;
bounds.left=(*it).right+2;
bounds.right=right;
return;
}
bool checkKmerForNs(uint64_t &currKmerPos, vector<mapObject>::iterator &it)
{
if (!blockOfNs.size())
return false;
while(it != blockOfNs.end())
{
if ((*it).left>currKmerPos)
break;
else
++it;
}
/* No N block beyond this point */
if (it == blockOfNs.end()){
--it;
/* Current position within N block */
if (((*it).left <=currKmerPos) && (currKmerPos <= (*it).right)){
++it;
return true;
}else{
++it;
return false;
}
}
if ((*it).left > (currKmerPos+commonData::kmerSize-2)){
if (it != blockOfNs.begin()){
--it;
if ((*it).right < currKmerPos){
++it;
return false;
}else {
++it;
return true;
}
}else
return false;
}else {
return true;
}
}
void setCurrPos() {
currPos+=size;;
}
uint64_t getCurrPos() {
return currPos;
}
void resetCurrPos() {
currPos=0;
}
bool readChunks()
{
string line;
uint64_t blockNCount=0;
int minSize = commonData::minMemLen/2-1;
uint64_t sz=size+minSize;
/* Process anything remaining from the last iteration */
processTmpString(sz, blockNCount);
if (numSeqFiles >= 1){
while(getline( file1, line ).good()){
if(line[0] == '>' || (totalBases == sz)){
if( !strName.empty()){
if(line[0] != '>') {
processInput(line, sz, blockNCount);
}else {
processInput(randomStr(), sz, blockNCount);
}
if (totalBases == sz) {
if ((totalBases%32)!=0)
{
uint64_t offset = CHARS2BITS(totalBases)%DATATYPE_WIDTH;
binReads[binReadsLocation] <<= (DATATYPE_WIDTH-offset);
binReadsLocation++;
binReads[binReadsLocation]=0;
}
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
return true;
}
}
if( !line.empty() ){
strName = line.substr(1);
}
} else if( !strName.empty() ){
processInput(line, sz, blockNCount);
}
}
if (numSeqFiles == 2) {
while(getline( file2, line ).good()){
if(line[0] == '>' || (totalBases == sz)){
if( !strName.empty()){
if(line[0] != '>') {
processInput(line, sz, blockNCount);
}else {
processInput(randomStr(), sz, blockNCount);
}
if (totalBases == sz) {
if ((totalBases%32)!=0)
{
uint64_t offset = CHARS2BITS(totalBases)%DATATYPE_WIDTH;
binReads[binReadsLocation] <<= (DATATYPE_WIDTH-offset);
binReadsLocation++;
binReads[binReadsLocation]=0;
}
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
return true;
}
}
if( !line.empty() ){
strName = line.substr(1);
}
} else if( !strName.empty() ){
processInput(line, sz, blockNCount);
}
}
}
}
if( !strName.empty() ){
if ((totalBases%32)!=0)
{
uint64_t offset = CHARS2BITS(totalBases)%DATATYPE_WIDTH;
binReads[binReadsLocation] <<= (DATATYPE_WIDTH-offset);
binReadsLocation++;
binReads[binReadsLocation]=0;
}
if (blockNCount){
blockOfNs.push_back(mapObject(CHARS2BITS(blockNCount-1), CHARS2BITS(totalBases-1)));
blockNCount=0;
}
if (!strTmp.size())
strName.clear();
return true;
}
return false;
}
void flipCharacter(char &in, char &out)
{
switch(in)
{
case 'A':
case 'a':
out='T';
break;
case 'C':
case 'c':
out='G';
break;
case 'G':
case 'g':
out='C';
break;
case 'T':
case 't':
out='A';
break;
default:
out=in;
}
}
void flipNswap(string &content)
{
string::iterator itBeg = content.begin();
string::iterator itEnd = --content.end();
char beg=0, end=0;
uint64_t d=0;
while ((d=distance(itBeg,itEnd)))
{
flipCharacter(*itBeg, end);
flipCharacter(*itEnd, beg);
(*itEnd)=end;
(*itBeg)=beg;
++itBeg;
--itEnd;
if(d==1)
break;
}
if (!d)
flipCharacter(*itEnd, *itEnd);
}
void writeReverseComplementString(string &name, string &content, fstream &file)
{
file << ">" << name << "\n";
flipNswap(content);
file << content ;
}
void generateSeqPos(vector<seqData> &vecSeqInfo) {
seqData s;
uint64_t i=0,j=0;
string line;
clearFileFlag();
if (numSeqFiles >= 1){
while(getline(file1, line).good() ){
if(line[0] == '>'){
if(!strName.empty()) {
s.start=CHARS2BITS(j);
s.end=CHARS2BITS(i-1);
s.pair_file_no=1;
s.seq.assign(strtok(const_cast<char *>(strName.c_str())," \t\n"));
vecSeqInfo.push_back(s);
s.seq.clear();
i+=RANDOM_SEQ_SIZE;
j=i;
strName.clear();
}
if(!line.empty())
strName=line.substr(1);
} else if( !strName.empty() ) {
i+=line.length();
}
}
if (numSeqFiles == 2){
while(getline(file2, line).good() ){
if(line[0] == '>'){
if(!strName.empty()) {
s.start=CHARS2BITS(j);
s.end=CHARS2BITS(i-1);
s.pair_file_no=2;
s.seq.assign(strtok(const_cast<char *>(strName.c_str())," \t\n"));
vecSeqInfo.push_back(s);
s.seq.clear();
i+=RANDOM_SEQ_SIZE;
j=i;
strName.clear();
}
if(!line.empty())
strName=line.substr(1);
} else if( !strName.empty() ) {
i+=line.length();
}
}
}
}
if( !strName.empty() ) {
i+=line.length();
s.start=CHARS2BITS(j);
s.end=CHARS2BITS(i-1);
s.seq.assign(strtok(const_cast<char *>(strName.c_str())," \t\n"));
vecSeqInfo.push_back(s);
s.seq.clear();
strName.clear();
}
}
void generateRevComplement() {
string line,content;
fstream revFile;
char buffer[256];
memset(buffer,0,256);
sprintf(buffer, "%s/revComp", commonData::nucmer_path);
revFile.open(buffer, ios::out);
if (!revFile.is_open())
{
cout << "ERROR: unable to open temporary reverse complement file" << endl;
exit( EXIT_FAILURE );
}
clearFileFlag();
if (numSeqFiles >= 1){
while(getline( file1, line ).good()){
size += (line.length()+1);
if(line[0] == '>'){
if(!strName.empty()) {
numSequences++;
size += RANDOM_SEQ_SIZE;
writeReverseComplementString(strName, content, revFile);
content.clear();
strName.clear();
}
if(!line.empty())
strName=line.substr(1);
} else if( !strName.empty() ) {
content += "\n";
content += line;
}
}
// Catches the last sequence line
if( !strName.empty() ) {
size += (line.length()+1);
content += "\n";
content += line;
numSequences++;
writeReverseComplementString(strName, content, revFile);
content.clear();
strName.clear();
}
if (numSeqFiles == 2){
while(getline( file2, line ).good()){
size += (line.length()+1);
if(line[0] == '>'){
if(!strName.empty()) {
numSequences++;
size += RANDOM_SEQ_SIZE;
writeReverseComplementString(strName, content, revFile);
content.clear();
strName.clear();
}
if(!line.empty())
strName=line.substr(1);
} else if( !strName.empty() ) {
content += "\n";
content += line;
}
}
// Catches the last sequence line
if( !strName.empty() ) {
size += (line.length()+1);
content += "\n";
content += line;
numSequences++;
writeReverseComplementString(strName, content, revFile);
content.clear();
strName.clear();
}
}
}
revFile.close();
}
void convertToNucl(uint64_t bin, string &sequence) {
if (bin == 0) {
sequence += 'A';
} else if (bin == 1) {
sequence += 'C';
} else if (bin == 2) {
sequence += 'G';
} else if (bin == 3) {
sequence += 'T';
}
}
void getFlankingSeq(string &sequence, uint64_t start, uint64_t end) {
uint64_t currBin;
uint32_t offset;
for (uint64_t pos = (start / 2); pos != (end / 2); ++pos) {
currBin = binReads[(pos * 2) / DATATYPE_WIDTH];
offset = (pos * 2) % DATATYPE_WIDTH;
currBin &= global_mask_right[(DATATYPE_WIDTH - offset) / 2 - 1];
currBin >>= ((DATATYPE_WIDTH - 2) - offset);
convertToNucl(currBin, sequence);
}
}
};
class outFileReadInfo {
fstream outFile;
public:
void writeString(string &content, fstream &file)
{
file << content << "\n";
}
void writeFiles(vector<seqData> &vecSeqInfo, vector<string> &filenames, string nonIRFilename, string IRFilename) {
seqData s;
uint64_t lineNum = 0;
string line;
uint64_t totalNumLines=vecSeqInfo.size();
if (filenames.size() >= 1) {
fstream palFile1;
fstream outFile1;
string IRFilename1;
string nonIRFilename1;
if (filenames.size() == 1) {
IRFilename1 = IRFilename + "_IR.fasta";
nonIRFilename1 = nonIRFilename + "_paired_to_IR.fasta";
} else {
IRFilename1 = IRFilename + "_IR_1.fasta";
nonIRFilename1 = nonIRFilename + "_paired_to_IR_1.fasta";
}
palFile1.open(IRFilename1, ios::out);
if(!palFile1.is_open()) {
cout << "ERROR: unable to open " << IRFilename1 << " file" << endl;
exit( EXIT_FAILURE );
}
outFile1.open(nonIRFilename1, ios::out);
if(!outFile1.is_open()) {
cout << "ERROR: unable to open " << nonIRFilename1 << " file" << endl;
exit( EXIT_FAILURE );
}
fstream file1;
file1.open(filenames[0], ios::in);
while (getline(file1, line).good()) {
if (line[0] == '>') {
if (!vecSeqInfo[totalNumLines/2 + lineNum].keep) {
line = strtok(const_cast<char *>(line.c_str()), " \t\n");
writeString(line, outFile1);
}
if (!vecSeqInfo[lineNum].keep)
writeString(vecSeqInfo[lineNum].header, palFile1);
} else {
if (!vecSeqInfo[totalNumLines/2 + lineNum].keep)
writeString(line, outFile1);
if (!vecSeqInfo[lineNum].keep)
writeString(line, palFile1);
++lineNum;
}
}
file1.close();
palFile1.close();
outFile1.close();
if (filenames.size() == 2) {
fstream palFile2;
fstream outFile2;
string IRFilename2 = IRFilename + "_IR_2.fasta";
string nonIRFilename2 = nonIRFilename + "_paired_to_IR_2.fasta";
palFile2.open(IRFilename2, ios::out);
if(!palFile2.is_open()) {
cout << "ERROR: unable to open " << IRFilename2 << " file" << endl;
exit( EXIT_FAILURE );
}
outFile2.open(nonIRFilename2, ios::out);
if(!outFile2.is_open()) {
cout << "ERROR: unable to open " << nonIRFilename2 << " file" << endl;
exit( EXIT_FAILURE );
}
fstream file2;
file2.open(filenames[1], ios::in);
while (getline(file2, line).good()) {
if (line[0] == '>') {
if (!vecSeqInfo[lineNum - totalNumLines/2].keep) {
line = strtok(const_cast<char *>(line.c_str()), " \t\n");
writeString(line, outFile2);
}
if (!vecSeqInfo[lineNum].keep)
writeString(vecSeqInfo[lineNum].header, palFile2);
} else {
if (!vecSeqInfo[lineNum - totalNumLines/2].keep)
writeString(line, outFile2);
if (!vecSeqInfo[lineNum].keep)
writeString(line, palFile2);
++lineNum;
}
}
file2.close();
palFile2.close();
outFile2.close();
}
}
}
};
class SeqPos {
public:
uint64_t lR;
uint64_t rR;
uint64_t lQ;
uint64_t rQ;
SeqPos() {
}
SeqPos(uint64_t lr, uint64_t rr, uint64_t lq, uint64_t rq)
{
lR=lr;
rR=rr;
lQ=lq;
rQ=rq;
}
};
class MemExt {
public:
uint64_t lR;
uint64_t rR;
uint64_t lQ;
uint64_t rQ;
MemExt() {
}
MemExt(uint64_t lr, uint64_t rr, uint64_t lq, uint64_t rq)
{
lR=lr;
rR=rr;
lQ=lq;
rQ=rq;
}
bool operator () (const MemExt &obj1, const MemExt &obj2)
{
if (obj1.lQ<obj2.lQ)
return true;
else if (obj1.lQ>obj2.lQ)
return false;
else{
if (obj1.lR<obj2.lR)
return true;
else
return false;
}
}
};
class tmpFilesInfo {
fstream *TmpFiles;
fstream tabFile;
vector <MemExt> MemExtVec;
uint64_t numMemsInFile;
bool checkMEMExt(uint64_t &lr, uint64_t &rr, uint64_t &lq, uint64_t &rq, seqFileReadInfo &QueryFile, seqFileReadInfo &RefFile) {
if ((!lq && QueryFile.getCurrPos()) || rq == CHARS2BITS(QueryFile.totalBases-1)) {
return true;
}else if((!lr && RefFile.getCurrPos()) || rr == CHARS2BITS(RefFile.totalBases-1)) {
return true;
}
return false;
}
void writeToFile(uint64_t lQ, uint64_t rQ, uint64_t lR, uint64_t rR) {
MemExt m;
m.lQ=lQ;
m.lR=lR;
m.rQ=rQ;
m.rR=rR;
TmpFiles[m.lQ/numMemsInFile].write((char *)&m, sizeof(MemExt));
}
void writeToVector(uint64_t lQ, uint64_t rQ, uint64_t lR, uint64_t rR) {
MemExt m;
m.lQ=lQ;
m.lR=lR;
m.rQ=rQ;
m.rR=rR;
MemExtVec.emplace_back(m);
}
public:
tmpFilesInfo(int numFiles) {
TmpFiles = new fstream[numFiles];
}
~tmpFilesInfo() {
delete [] TmpFiles;
}
void setNumMemsInFile(uint64_t size, uint64_t &numSequences) {
numMemsInFile = ((2*(size*commonData::d+numSequences*RANDOM_SEQ_SIZE+commonData::d))/NUM_TMP_FILES);
}
static bool compare_reference (const MemExt &obj1, const MemExt &obj2)
{
if (obj1.lR<obj2.lR)
return true;
else if (obj1.lR>obj2.lR)
return false;
else{
if (obj1.lQ<obj2.lQ)
return true;
else
return false;
}
}
static bool sortReverse (const MemExt &obj1, const MemExt &obj2)
{
if (obj1.lQ + obj1.lR > obj2.lQ + obj2.lR)
return true;
else if (obj1.lQ + obj1.lR < obj2.lQ + obj2.lR)
return false;
else{
if (obj1.rQ + obj1.rR > obj2.rQ + obj2.rR)
return true;
else
return false;
}
}
static bool myUnique(const MemExt &obj1, const MemExt &obj2)
{
if((obj1.lQ==obj2.lQ) && (obj1.rQ==obj2.rQ) && (obj1.rR==obj2.rR) && (obj1.lR==obj2.lR))
return true;
else