vector of pointers to class object c++

roshyara · 11-27-2011, 01:29 PM

I am trying to read one file

having rows with usually a certain fixed number of columns,
different comments marked with the start letter #, with some blank lines.
Blank lines and comment line should be ignored while reading.
The file may also contain by mistake wrong number of columns which should be corrected first as well.
Each row gives a class object and it should be saved as an element vector of class object.

For this purpose I have written a code. Everything works fine till end but while terminating the program it comes unknown problem.
Could anyone please help me in finding out mistake? I have marked the possible mistake place as c++ comments.
thank you

File to be read:

#myfile.txt
1 snp1 1.1 1
2 snp2 1.2 2
3 snp3 1.2 3
# 1
#2

#3
#test

5 snp5 1.5 5
#test
5 snp5 1.5 5
#2 test
6 snp6 1.5 6
#3test
#test
#1
4 snp4 1.4 4
5 snp5 1.5 5
#
Code to read and save this file:

Code:

#include<iostream>
#include<istream>
#include<string>
#include<fstream>
#include<sstream>
#include<vector>
#include<algorithm>

using namespace std;

struct CSNP{
	friend ostream& operator <<(ostream& out, const CSNP& pCSNP);
	string nchr;
	string  snpName;
	 double cm_pos;
	 int bp;
	static bool three_columns;
	static CSNP* fillUpLocusInfo(const vector<string> lines);
	vector<CSNP*> lociInfo;
	static void readMapFile(const string & fileName, vector<CSNP*>& snpVec);
	CSNP(): nchr(""), snpName(""),  cm_pos(0), bp(0){ }
	~CSNP();	
};
bool CSNP::three_columns =false;
CSNP::~CSNP(){
	for (unsigned int i=0;i<lociInfo.size();++i)
	{
		delete lociInfo[i];
		lociInfo[i]=NULL;
	}
}

void error (const string&  msg){
cerr<<"\n EROOR: " <<msg <<endl;
exit(1);
}
int main (int argc, char** argv){
	if(argv[1]==0)
	error("No file exits. please give argv[1]. ")	;
 CSNP SNP;
SNP.readMapFile(argv[1],SNP.lociInfo);
cout <<"SNP.lociInfo.size(): "<< SNP.lociInfo.size()<<endl;
for (unsigned int i=0; i<SNP.lociInfo.size();++i)
	cout<< *(SNP.lociInfo[i]) << '\n';

SNP.~CSNP();	
return 0;
}
ostream& operator<<(ostream &out, const CSNP &pCSNP)
	  {
	    // This was your display-function. Look up "operator overloading" if you
	    // don't understand what is going on here.
	    return out << "chr No:"<< pCSNP.nchr<< ", SNP ID: "<< pCSNP.snpName
	               << ", cm_pos: " << pCSNP.cm_pos<< " and bp: "<< pCSNP.bp;
	  }

CSNP* CSNP::fillUpLocusInfo(const vector<string> lines){
	CSNP* pCSNP=new CSNP;
	if( !three_columns && lines.size()==3)
		{
		three_columns=true;
		pCSNP->nchr=lines[0];
		pCSNP->snpName=lines[1];
		pCSNP->bp=(long int )atoi(lines[2].c_str());
		}
		else if(!three_columns&& lines.size()==4)
		{
		pCSNP->nchr=lines[0];
		pCSNP->snpName=lines[1];
		pCSNP->cm_pos=atof(lines[2].c_str());
		pCSNP->bp=(long int )atoi(lines[3].c_str());
					
		}
	return pCSNP;	
}	

void CSNP::readMapFile(const string & fileName, vector<CSNP*>& snpVec)
{
	static long int countSNPs=1;
	ifstream in;	in.close(); in.clear();
	ios_base::iostate i= in.rdstate();
	in.open(fileName.c_str(),ios::in);
	if(!in){
	in.setstate(ios_base::failbit);
		in.clear();
	}	
	in>>ws;
	string buffer;
	vector<string> snp;
	while(!in.eof()&& getline(in,buffer, '\n'))
	{
		//getline(in,buffer, '\n');
		if(!buffer.size()|| (buffer.substr(0,1)=="#"))
			continue;
		istringstream line(buffer);
		//vector<string> tokens;
		while(getline(line, buffer, ' '))
			{
				snp.push_back(buffer);
			}
		cout << "snp.size(): "<<snp.size() <<endl;  //for test only
		CSNP* pCSNP;
		pCSNP=CSNP::fillUpLocusInfo(snp);
		cout << *pCSNP<<endl;
		snpVec.push_back(pCSNP);
/* This above line is making problem. If I deactivate this 
above line then it works fine. I think I have problem with either creating vector vector<CSNP*> snpVec or the function 
CSNP::fillUpLocusInfo(const string & lines)
*/
		pCSNP=NULL;
		snp.resize(0);
		++countSNPs;
		
	}
		cout << "i& ios::eofbit()" << (i& ios::eofbit)<<endl;
		cout << "i& ios::failbit()" << (i& ios::failbit)<<endl;
		cout << "i& ios::badbit()" << (i& ios::badbit)<<endl;
		in.clear();
		in.close();
return;}

dwhitney67 · 11-28-2011, 05:57 AM

It is not necessary to manually call the class destructor; this is done automatically when the object falls out of scope, and hence is destroyed. Thus remove this line of code from your main() function:

Code:

...
SNP.~CSNP();
...

roshyara · 11-29-2011, 01:52 AM

I have deleted it but it still crashes. I do not know why. If you could have a look little bit deeply??

dwhitney67 · 11-29-2011, 05:59 AM

Quote:

Originally Posted by roshyara

I have deleted it but it still crashes. I do not know why. If you could have a look little bit deeply??

I do not know why either. I copy/pasted the code you originally posted, removed the offending line I mentioned earlier, and compiled the program. I then created the data (text) file with the information you supplied, and then ran the program. It completed successfully. I then re-ran the program using valgrind, and it also reported that all allocated memory had been freed.

Thus barring the possibility that you changed more of your code than you are admitting to, I find it hard to believe that the code is still causing an anomaly. Perhaps you failed to recompile the code after you made a change??

roshyara · 12-11-2011, 06:02 AM

Quote:

Originally Posted by dwhitney67

I do not know why either. I copy/pasted the code you originally posted, removed the offending line I mentioned earlier, and compiled the program. I then created the data (text) file with the information you supplied, and then ran the program. It completed successfully. I then re-ran the program using valgrind, and it also reported that all allocated memory had been freed.

Thus barring the possibility that you changed more of your code than you are admitting to, I find it hard to believe that the code is still causing an anomaly. Perhaps you failed to recompile the code after you made a change??

thank you so much dwhitney67! It worked well now. Do you think I can use RAII std::tr1::shared_ptr at this case in stead of delete?

ArthurSittler · 12-16-2011, 01:13 AM

I do not see any declaration of snpVec in the code. Am I simply missing it, or does it not exist?
If snpVec were a vector of CSNP*, it would provide push_back() of the CSNP* pCSNP to build a list by appending the new pointer at the end of the list.