Access Object attributes in C++ [closed] - c++

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I am relatively new to C++ programming and I have done a code which is not performing as expected.
The code is a bit long [pasted at end for reference] but I will just point to my concern in the code:
I define an object of a class inside a while loop:
...
objVec[obj_i] = new ChipSeqRegion(refID, strand, midPoint, start, end, posArray, frac_posArray, negArray, frac_negArray);
//testing
cout<<"printing object number: "<<obj_i<<endl;
objVec[obj_i]->PrintID();
cout<<"printing frac pos array: "<<endl;
objVec[obj_i]->PrintFracPosArray();
obj_i++;
}
objVec[0]->PrintID();
cout<<endl;
objVec[0]->PrintFracPosArray();
cout<<endl;
objVec[1]->PrintID();
objVec[1]->PrintFracPosArray();
cout<<endl;
objVec[2]->PrintID();
objVec[2]->PrintFracPosArray();
}
In the above code fragment PrintID and PrintFracPosArray are just procedures[members of same class] to print contents of the variables/Arrays.
Now, If I try to print the object attributes refID and posArray inside the loop then all printed values come out different and as assigned and expected.
But outside the loop the printID attribute prints values uniquely [as expected] but posArray attributes just repeat the value last assigned in the loop.
I want to access all values uniquely outside the loop which is my concern.
I am sure this might be from a scope conflict or the way the variables are getting passed.
Any help will be great !!!
Thanks in advance.
A quick look on detailed code below can clarify any questions:
Detailed Code:[Apologies for bad presentation]
#include <iostream>
#include <string>
#include <fstream>
#include <cstring>
#include <sstream>
#include <cstdlib>
#include <vector>
#include <iomanip>
#include <cmath>
#include "api/BamReader.h"
#include "api/BamWriter.h"
#include "api/BamAlignment.h"
#include "api/BamAux.h"
using namespace std;
using namespace BamTools;
BamReader reader;
BamAlignment al;
int const windowSize = 10;
int halfWindowSize = windowSize/2;
int const N = windowSize + 1;
//determine the gap score
float gap = -2;
//default value for matrix F
double negNum = -100000;
float F[N][N];
int xTraceBack[N][N];
int yTraceBack[N][N];
float maxScore;
int x_coord = 0;
int y_coord = 0;
//collections of arrays from chipSeq data after loading data
class ChipSeqRegion{
private:
int ref_id, mid_p, start_p, end_p;
char genomeStrand;
float* pos_array;
float* frac_positiveArray;
float* neg_array;
float* frac_negativeArray;
float* gap;
public:
ChipSeqRegion (int refID, char strand, int midPoint, int start, int end, float* posArray, float* frac_posArray, float* negArray, float* frac_negArray);
//accessors
int GetRefID(){return ref_id;}
int GetMidPoint(){return mid_p;}
void PrintID();
void PrintFracPosArray();
//destructor
~ChipSeqRegion(){
delete [] pos_array;
delete [] frac_positiveArray;
delete [] neg_array;
delete [] frac_negativeArray;
}
};
ChipSeqRegion::ChipSeqRegion(int refID, char strand, int midPoint, int start, int end, float* posArray, float* frac_posArray, float* negArray, float* frac_negArray){
ref_id = refID;
genomeStrand = strand;
mid_p = midPoint;
start_p = start;
end_p = end;
pos_array = posArray;
frac_positiveArray = frac_posArray;
neg_array = negArray;
frac_negativeArray = frac_negArray;
}
void ChipSeqRegion::PrintID(){
cout<<"ref id is: "<<ref_id<<endl;
}
void ChipSeqRegion::PrintFracPosArray(){
cout<<"this is raw pos data"<<endl;
for (int i = 0; i<windowSize; i++){
cout<<pos_array[i]<<'\t';
}
cout<<"this is frac data"<<endl;
for (int i = 0; i<windowSize; i++){
cout<<frac_positiveArray[i]<<'\t';
}
cout<<endl;
}
class ChipSeqLoader{
public:
void LoadData (string bamFileName, string coordFileName);
void GetRegions();
private:
string nameOfBamFile;
string nameOfCoordFile;
};
void ChipSeqLoader::LoadData(string bamFileName, string coordFileName){
nameOfBamFile = bamFileName;
nameOfCoordFile = coordFileName;
int obj_i = 0;
int objSize = 6;
ChipSeqRegion **objVec = new ChipSeqRegion* [objSize];
//reading coordinates
ifstream CoordFile;
char chrom[5], strand;
string sChr1, sChr2, withmotif, dot;
int start, end, midPoint;
float tag;
CoordFile.open(coordFileName.c_str());
if (CoordFile.is_open()){
while (!CoordFile.eof()){
CoordFile>>chrom;
CoordFile>>withmotif;
CoordFile>>dot;
CoordFile>>start;
CoordFile>>end;
CoordFile>>tag;
CoordFile>>strand;
CoordFile.ignore(200,'\n');
midPoint = (start+end)/2;
ostringstream convert1;
ostringstream convert2;
convert1<<chrom[3];
convert2<<chrom[4];
sChr1 = convert1.str();
sChr2 = convert2.str();
string sChrom;
sChrom = sChr1+sChr2;
int refID;
if (sChr1 =="X\0"){
refID = 19;
}else if (sChr1 == "Y\0"){
refID = 20;
}else{
refID = atoi(sChrom.c_str())-1;
}
int intStrand;
if (strand == '+'){
intStrand = 0;
}else if (strand == '-'){
intStrand = 1;
}
cout<<endl;
cout<<sChrom<<'\t'<<refID<<'\t'<<start<<'\t'<<end<<'\t'<<midPoint<<'\t'
<<strand<<'\t'<<intStrand<<endl;
//get information from the coordinates to return array
BamRegion region(refID, midPoint-600, refID, midPoint+600);
reader.SetRegion(region);
if(!reader.SetRegion(region)){
std::cout<<"could not set region."<<endl;
}
float posArray[windowSize];
float negArray[windowSize];
float frac_posArray[windowSize];
float frac_negArray[windowSize];
for (int index = 0; index < windowSize; index ++){
posArray[index] = 0;
negArray[index] = 0;
}
int posPosition;
int negPosition;
//if reverse strand, calculate and return the end position
//if positive strand, return the position
//put them in separate arrays
while (reader.GetNextAlignment(al)){
if (al.MapQuality>0 && al.IsReverseStrand()== true){
negPosition = al.GetEndPosition();
if (negPosition>=midPoint-halfWindowSize && negPosition <midPoint+halfWindowSize){
negArray[negPosition-midPoint+halfWindowSize]++;
}
}else if (al.MapQuality>0){
posPosition = al.Position;
if (posPosition>=midPoint-halfWindowSize && posPosition <midPoint+halfWindowSize){
posArray[posPosition-midPoint+halfWindowSize]++;
}
}
}
float posMax = 0, negMax = 0, max = 0;
float temp;
for (int i= 0; i<windowSize; i++){
temp = posArray[i];
if (temp>posMax){
posMax = temp;
}
}
for (int i = 0; i<windowSize; i++){
temp = negArray[i];
if (temp>negMax){
negMax = temp;
}
}
if (posMax>=negMax){
max = posMax;
}else{
max = negMax;
}
for (int i = 0; i<windowSize; i++){
frac_posArray[i] = posArray[i]/max;
frac_negArray[i] = negArray[i]/max;
}
objVec[obj_i] = new ChipSeqRegion(refID, strand, midPoint, start, end, posArray, frac_posArray, negArray, frac_negArray);
//testing
cout<<"printing object number: "<<obj_i<<endl;
objVec[obj_i]->PrintID();
cout<<"printing frac pos array: "<<endl;
objVec[obj_i]->PrintFracPosArray();
obj_i++;
}
objVec[0]->PrintID();
cout<<endl;
objVec[0]->PrintFracPosArray();
cout<<endl;
objVec[1]->PrintID();
objVec[1]->PrintFracPosArray();
cout<<endl;
objVec[2]->PrintID();
objVec[2]->PrintFracPosArray();
}
}
int main(int argc, char* argv[]) {
string bamFileName, coordFileName;
if (argc == 3){
bamFileName = argv[1];
coordFileName = argv[2];
}else{
std::cout << "Wrong number of arguments." <<endl;
return 1;
}
if (!reader.Open(bamFileName)){
std::cout<< "Could not open input Bam file." <<endl;
return 1;
}
if (!reader.LocateIndex()){
std::cout<<"Could not locate index file."<<endl;
return 1;
}
ChipSeqLoader loader;
loader.LoadData(bamFileName, coordFileName);
return 0;
}

Answer 1

All your objects point to the same piece of data, namely posArray and frac_posArray which are defined in the loop: if you look at the ChipSeqRegion class constructor, it accepts 2 arrays (with the very same names as the arrays cited above), ie. 2 pointers to sequences of data in memory. These pointers in the constructors are simply copied over in the instance fields:
pos_array = posArray;
frac_positiveArray = frac_posArray;
instead of copying the array contents, as it should probably be:
pos_array = new int[windowSize];
memcpy(pos_array,posArray, sizeof(int)*windowSize); // or use std::copy_n
frac_positiveArray = new int[windowSize];
memcpy(frac_positivearray,frac_posArray, sizeof(int)*windowSize); // or use std::copy_n
You probably will have the same issue with other arrays in the class.