void CBitmaskBuilder::SequenceBuffer( CSeqBuffer * ncbi8na )
{
CProgressIndicator progress( "Listing "+NStr::IntToString( m_wSize )+"-mers of length "+NStr::IntToString( m_wLength )+" for "+m_seqId );
fourplanes::CHashGenerator hgen( m_wLength );
for( const char * seq = ncbi8na->GetBeginPtr(); seq < ncbi8na->GetEndPtr(); ++seq ) {
hgen.AddBaseMask( CNcbi8naBase( seq ) );
// cerr << CIupacnaBase( CNcbi8naBase( seq ) ) << "\t";
if( hgen.GetAmbiguityCount() <= (int)m_maxAmb ) {
for( fourplanes::CHashIterator h( hgen ); h; ++h ) {
Uint8 packed = CBitHacks::PackWord( Uint8(*h), m_pattern2na );
// cerr << hex << DISPLAY( Uint8(*h) ) << DISPLAY( m_pattern2na ) << DISPLAY( packed ) << dec << "\n";
SetBit( packed );
}
} //else cerr << "-\n";
progress.Increment();
}
progress.Summary();
}
/*!
* \brief hyperbolic spin transformation from pa to pb by amt (0,1)
*/
Point hspin(const Pnt& pa, const Pnt& pb, double amt){
return Round::loc( pa.boost( hgen(pa,pb,amt) ) );
//versor * dist * amt * .5) );
}
