GCC compile

[raman]

I am unable to compile a C++ program which I have downloaded from internet.

 

I have no knowledge of c++, but use other languages like perl on linux. So i tried to compile on Linux using gcc, g++, cc etc. however I got two errors:

 

main.cpp: In function ‘int main(int, char**)’:

main.cpp:44: error: ‘atoi’ was not declared in this scope

 

I tried in Turbo C++ compiler also, but that gave 25 errors.

Being unfamiliar with C++, I cannot solve the errors. But can someone compile the program and send them or tell me the options with gcc or the linux compilers so that I may be able to compile this.

 

 

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

using namespace std;

#define AC

bool read_profile(string fname,vector<vector<double> >& profile,string& seq);
//main
int main(int argc, char * argv[])
{
int LG;
vector<double> vec;
int veclen,seqlen;
double sum,ave;
int j,k,lg;
string seqid,seq,fname,fnameout;
vector<vector<double > > oneprofile;

if(argc!=4)
{
cout<<"usage: programm LG PSSM_file¡¡outname"<<endl;
return 0;
}
LG=atoi(argv[1]);
if(LG<=0)
{
cout<<"invalid value of LG "<<LG<<endl;
return 0;
}
fname=argv[2];
fnameout=argv[3];


#ifdef AC
cout<<"calculate AC variables...";
#else
cout<<"calculate ACC variables...";
#endif

#ifndef AC
vector< double > cc;
#endif

vector<double> ave_local;
ave_local.resize(20);

vector<double> ac;
ac.resize(20);


if(!read_profile(fname,oneprofile,seq))
{
cout<<"cannot read profile from "<<fname<<endl;
return 0;
}
seqlen=(int)oneprofile.size();
if(LG>=seqlen)
{
cout<<"too large value of LG (must be less than the length of the sequence)"<<endl;
return 0;
}

#ifdef AC
veclen=LG*20;
vec.resize(veclen);
#else
int index;
veclen=LG*400;
vec.resize(veclen);
cc.resize(380);
int k1,k2;
double ave1,ave2;
#endif

for(k=0;k<20;k++)
ave_local[k]=0;
for(j=0;j<seqlen;j++)
{
for(k=0;k<20;k++)
ave_local[k]+=oneprofile[j][k];
}
for(k=0;k<20;k++)
ave_local[k]/=seqlen;


for(lg=1;lg<=LG;lg++)
{
//calculate AC variable
for(k=0;k<20;k++)
{
ave=ave_local[k];
sum=0;
for(j=0;j<seqlen-lg;j++)
{
sum+=(oneprofile[j][k]-ave)*(oneprofile[j+lg][k]-ave);
}
sum/=(seqlen-lg);
ac[k]=sum;
}
#ifdef AC
for(k=0;k<20;k++)
vec[(lg-1)*20+k]=ac[k];
#else
for(k=0;k<20;k++)
vec[(lg-1)*400+k]=ac[k];
#endif

#ifndef AC
//calculate CC variable
for(k1=0;k1<20;k1++)
for(k2=0;k2<20;k2++)
{
if(k1!=k2)
{
sum=0;

ave1=ave_local[k1];
ave2=ave_local[k2];

sum=0;
for(j=0;j<seqlen-lg;j++)
sum+=(oneprofile[j][k1]-ave1)*(oneprofile[j+lg][k2]-ave2);
sum/=(seqlen-lg);
if(k1>k2)
index=k1*19+k2;
else
index=k1*19+k2-1;
cc[index]=sum;
}
}
for(k=0;k<380;k++)
vec[(lg-1)*400+k+20]=cc[k];
#endif

}
ofstream fileout(fnameout.c_str());
if(!fileout.is_open())
{
cout<<"cannot open file for out, file: "<<fnameout<<endl;
return 0;
}
for(j=0;j<veclen;j++)
fileout<<vec[j]<<endl;

cout<<"done"<<endl;
return 1;
}
bool read_profile(string fname,vector<vector<double> >& profile,string& seq)
{
const int aapsi2rank[20]={0,14,11,2,1,13,3,5,6,7,9,8,10,4,12,15,16,18,19,17};
string filename,line;
ifstream filein;
int j,ni;
char c;
double tempd;
vector<double> one_profile;
one_profile.resize(20);


filein.open(fname.c_str());
if(!filein.is_open())
return false;

profile.clear();
seq.clear();
getline(filein,line);//ignore the first three lines
getline(filein,line);
getline(filein,line);
while(!filein.eof())
{
getline(filein,line);
if(line.empty())//terminate
break;
stringstream ss(line);
ss>>ni>>c;
seq.push_back(c);
for(j=0;j<20;j++)
{
if(ss.eof())
return false;
ss>>tempd;
one_profile[aapsi2rank[j]]=tempd;
}
profile.push_back(one_profile);
}
return true;
}

[pastcow]

Try adding an

 

#include <stdlib.h>

 

up at the top of the code with the rest of the includes

[broseph]

you will need to use g++ to compile C++ programs. GCC is for compiling (among other things) C code.

 

 

Including stdlib.h should fix it.