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/*******************************************************************************
* $Id: GappedAlignment.cpp,v 1.27 2004/03/01 02:40:08 darling Exp $
* This file is copyright 2002-2007 Aaron Darling and authors listed in the AUTHORS file.
* Please see the file called COPYING for licensing, copying, and modification
* Please see the file called COPYING for licensing details.
* **************
******************************************************************************/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libMems/GappedAlignment.h"
#include <sstream>
#include "libGenome/gnFilter.h"
#include <fstream>
using namespace std;
using namespace genome;
namespace mems {
GappedAlignment::GappedAlignment() :
AbstractGappedAlignment< SparseAbstractMatch<> >()
{}
GappedAlignment::GappedAlignment( uint seq_count, gnSeqI align_length ) :
AbstractGappedAlignment< SparseAbstractMatch<> >( seq_count, align_length )
{
align_matrix.resize(seq_count);
}
void GappedAlignment::SetAlignment( const vector< string >& seq_align ){
align_matrix = seq_align;
if( seq_align.size() > 0 )
SetAlignmentLength(seq_align[0].size());
else
SetAlignmentLength(0);
}
std::ostream& operator<<( std::ostream& os, const GappedAlignment& ga ); //write to source.
std::ostream& operator<<( std::ostream& os, const GappedAlignment& ga ){
os << "GappedAlignmentSeqs: " << ga.SeqCount() << endl;
os << ga.AlignmentLength();
for( uint seqI = 0; seqI < ga.SeqCount(); seqI++ )
os << '\t' << ga.Start( seqI );
os << endl;
for( uint seqI = 0; seqI < ga.SeqCount(); seqI++ ){
os << ga.align_matrix[ seqI ] << endl;
}
return os;
};
std::istream& operator>>( std::istream& is, GappedAlignment& ga ); // read from source
std::istream& operator>>( std::istream& is, GappedAlignment& ga ){
uint seq_count;
string nuffin;
is >> nuffin;
is >> seq_count;
ga = GappedAlignment( seq_count, 0 );
is >> nuffin;
for( uint seqI = 0; seqI < seq_count; seqI++ ){
int64 startI;
is >> startI;
ga.SetStart( seqI, startI );
}
for( uint seqI = 0; seqI < seq_count; seqI++ ){
string seq;
is >> seq;
ga.align_matrix.push_back( seq );
}
if( ga.align_matrix.size() > 0 )
ga.SetAlignmentLength( ga.align_matrix[ 0 ].length() );
return is;
};
}
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