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//////////////////////////////////////////////////////////////////
// //
// PLINK (c) 2005-2009 Shaun Purcell //
// //
// This file is distributed under the GNU General Public //
// License, Version 2. Please see the file COPYING for more //
// details //
// //
//////////////////////////////////////////////////////////////////
#include <iostream>
#include <string>
#include <vector>
#include "zed.h"
#include "helper.h"
#include "nlist.h"
extern Plink * PP;
ZInput::ZInput(string f, bool cmode)
{
open(f,cmode);
}
ZInput::ZInput()
{
//
}
void ZInput::open(string f, bool cmode)
{
filename = f;
compressed = cmode;
#ifndef WITH_ZLIB
if ( compressed )
{
error("ZLIB support is not currently compiled in");
}
#endif
if ( compressed )
{
zinf.open( filename.c_str() );
if ( ! zinf.is_open() )
error("Problem opening " + filename + "\n");
}
else
{
inf.open( filename.c_str() );
if ( ! inf.is_open() )
error("Problem opening " + filename + "\n");
}
}
string ZInput::readLine()
{
if ( compressed )
{
zinf.getline(buf,MAX_LINE_LENGTH,'\n');
}
else
{
inf.getline(buf,MAX_LINE_LENGTH,'\n');
}
return buf;
// std::cerr << buf
// << "\t(" << inf.rdbuf()->in_avail()
// << " chars left in buffer) ";
}
char ZInput::readChar()
{
char c;
if ( compressed )
{
zinf.get(c);
}
else
{
inf.get(c);
}
return c;
}
vector<string> ZInput::tokenizeLine()
{
string s = readLine();
vector<string> tok;
string buf;
stringstream ss(s);
while (ss >> buf)
tok.push_back(buf);
return tok;
}
void ZInput::close()
{
if ( compressed )
inf.close();
else
zinf.close();
}
bool ZInput::endOfFile()
{
// Check -- eof() doesn't work here -- look up the differences between
// these different file states
if ( compressed )
return zinf.fail() || ( ! zinf.good() ) ;
else
return inf.fail() || ( ! inf.good() ) ;
}
void ZInput::unbuffered()
{
if ( compressed )
zinf.rdbuf()->pubsetbuf(0,0);
}
void ZOutput::open(string f, bool cmode)
{
filename = f;
compressed = cmode;
#ifndef WITH_ZLIB
if ( compressed )
{
PP->printLOG("Warning: ZLIB support not enabled, so writing uncompressed file\n");
compressed = false;
}
#endif
if ( compressed )
{
zoutf.open( filename.c_str() );
if ( ! zoutf.is_open() )
{
error("Problem opening " + filename );
}
}
else
{
outf.open( filename.c_str() );
if ( ! outf.is_open() )
{
error("Problem opening " + filename );
}
}
}
ZOutput::ZOutput(string f, bool cmode)
{
open(f,cmode);
}
ZOutput::ZOutput()
{
//
}
void ZOutput::write(string s)
{
if ( compressed )
zoutf << s;
else
outf << s;
}
void ZOutput::writeLine(string s)
{
if ( compressed )
zoutf << s << endl;
else
outf << s << endl;
}
void ZOutput::close()
{
if ( compressed )
zoutf.close();
else
outf.close();
}
void ZOutput::unbuffered()
{
if ( compressed )
zoutf.rdbuf()->pubsetbuf(0,0);
}
void fileCompress()
{
#ifndef WITH_ZLIB
error("ZLIB support is not compiled in");
#endif
PP->printLOG("Compressing [ " + par::compress_filename + " ]...\n");
ZInput zin( par::compress_filename , false );
ZOutput zout( par::compress_filename+".gz", true );
while ( ! zin.endOfFile() )
{
string line = zin.readLine();
if ( zin.endOfFile() )
break;
zout.writeLine(line);
}
zin.close();
zout.close();
PP->printLOG("Wrote compressed file to [ " + par::compress_filename + ".gz ]\n");
}
void fileUncompress()
{
#ifndef WITH_ZLIB
error("ZLIB support is not compiled in");
#endif
PP->printLOG("Uncompressing [ " + par::compress_filename + " ]...\n");
int s = par::compress_filename.size();
if ( s < 3 || par::compress_filename.substr(s-3,3) != ".gz" )
error("Filename must end if .gz");
ZInput zin( par::compress_filename , true );
ZOutput zout( par::compress_filename.substr(0,s-3), false );
while ( ! zin.endOfFile() )
{
string line = zin.readLine();
if ( zin.endOfFile() )
break;
zout.writeLine(line);
}
zin.close();
zout.close();
PP->printLOG("Wrote uncompressed file to [ "
+ par::compress_filename.substr(0,s-3) + " ]\n");
}
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