sequtil_tables.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: sequtil_tables.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:42:27  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: sequtil_tables.cpp,v 1000.1 2004/06/01 19:42:27 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Mati Shomrat
 *
 * File Description:
 *   Shared utility functions for the various sequtil classes.
 */  

#include <ncbi_pch.hpp>
#include "sequtil_tables.hpp"

BEGIN_NCBI_SCOPE
/////////////////////////////////////////////////////////////////////////////
//
// Conversion Tables

// IUPACna to IUPACna
const Uint1 CIupacnaToIupacna::scm_Table[256] = {
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0x41, 0x42, 0x43, 0x44, 0xff, 0xff, 0x47,
    0x48, 0xff, 0xff, 0x4b, 0xff, 0x4d, 0x4e, 0xff,
    0xff, 0xff, 0x52, 0x53, 0x54, 0x54, 0x56, 0x57,
    0xff, 0x59, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0x41, 0x42, 0x43, 0x44, 0xff, 0xff, 0x47,
    0x48, 0xff, 0xff, 0x4b, 0xff, 0x4d, 0x4e, 0xff,
    0xff, 0xff, 0x52, 0x53, 0x54, 0x54, 0x56, 0x57,
    0xff, 0x59, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff, 0xff
};


// IUPACna to NCBI2na
// A -> 0x0 A
// B -> 0x1 C
// C -> 0x1 C
// D -> 0x2 G
// G -> 0x2 G
// H -> 0x0 A
// K -> 0x2 G
// M -> 0x1 C
// N -> 0x0 A
// R -> 0x2 G
// S -> 0x1 C
// T -> 0x3 T
// V -> 0x0 A
// W -> 0x3 T
// Y -> 0x3 T
// U -> 0x3 T
const Uint1 CIupacnaTo2na::scm_Table[1024] = {
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x00, 0x00, 0x00, 0x00,
    0x40, 0x10, 0x04, 0x01,
    0x40, 0x10, 0x04, 0x01,
    0x80, 0x20, 0x08, 0x02,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0x00, 0x00, 0x00, 0x00,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0xff, 0xff, 0xff, 0xff,
    0x40, 0x10, 0x04, 0x01,
    0x00, 0x00, 0x00, 0x00,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0x40, 0x10, 0x04, 0x01,
    0xc0, 0x30, 0x0c, 0x03,
    0xc0, 0x30, 0x0c, 0x03,
    0x00, 0x00, 0x00, 0x00,
    0xc0, 0x30, 0x0c, 0x03,
    0xff, 0xff, 0xff, 0xff,
    0xc0, 0x30, 0x0c, 0x03,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x00, 0x00, 0x00, 0x00,
    0x40, 0x10, 0x04, 0x01,
    0x40, 0x10, 0x04, 0x01,
    0x80, 0x20, 0x08, 0x02,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0x00, 0x00, 0x00, 0x00,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0xff, 0xff, 0xff, 0xff,
    0x40, 0x10, 0x04, 0x01,
    0x00, 0x00, 0x00, 0x00,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0x80, 0x20, 0x08, 0x02,
    0x40, 0x10, 0x04, 0x01,
    0xc0, 0x30, 0x0c, 0x03,
    0xc0, 0x30, 0x0c, 0x03,
    0x00, 0x00, 0x00, 0x00,
    0xc0, 0x30, 0x0c, 0x03,
    0xff, 0xff, 0xff, 0xff,
    0xc0, 0x30, 0x0c, 0x03,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,
    0xff, 0xff, 0xff, 0xff,