/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
#ifndef NNUMBERFROMBASE3_INCLUDED
#define NNUMBERFROMBASE3_INCLUDED


#define nA 0
#define nC 1
#define nG 2
#define nT 3
#define nNOT_PAD_OR_BASE 4
#define nPAD 5

const int nNumberFromBase3MaxValue = 5;

// anything other than acgt is converted to 4
// e.g., x is 4 so it does not match A, C, G, or T
// replace 0, 1, 2, 3 by nA, nC, nG, nT
// * is 5 (ascii 42)
// n is 4 (ascii 78) so n does not match A, C, G, or T

static int nNumberFromBase3[] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 0 to 9 */    
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 10 to 19 */  
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 20 to 29 */                
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 30 to 39 */
4, 4, 5, 4, 4, 4, 4, 4, 4, 4, /* 40 to 49 */  
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 0, 4, 1, 4, 4, /* 60 to 69 */  
4, 2, 4, 4, 4, 4, 4, 4, 4, 4, /* 70 to 79 */  
4, 4, 4, 4, 3, 4, 4, 4, 4, 4, /* 80 to 89 */  
4, 4, 4, 4, 4, 4, 4, 0, 4, 1, /* 90 to 99 */  
4, 4, 4, 2, 4, 4, 4, 4, 4, 4, /* 100 to 109 */
4, 4, 4, 4, 4, 4, 3, 4, 4, 4, /* 110 to 119 */
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4,                 
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 230 to 239 */
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, /* 240 to 249 */
4, 4, 4, 4, 4, 4, 4 };        /* 250 to 256 */


static char cBaseFromNumber3[] = {
   'a', 'c', 'g', 't', 'n', '*' };



#endif