BGI/BASE/src/2bwt/karlin.h

   1 /*
   2
   3    karlin.h
   4
   5    Copyright (C) 2014 The University of Hong Kong.
   6
   7    This program is free software; you can redistribute it and/or
   8    modify it under the terms of the GNU General Public License
   9    as published by the Free Software Foundation; either version 2
  10    of the License, or (at your option) any later version.
  11
  12    This program is distributed in the hope that it will be useful,
  13    but WITHOUT ANY WARRANTY; without even the implied warranty of
  14    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15    GNU General Public License for more details.
  16
  17    You should have received a copy of the GNU General Public License
  18    along with this program; if not, write to the Free Software
  19    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  20
  21 */
  22
  23 #ifndef _karlin_
  24 #define _karlin_
  25
  26 /*
  27 wss:
  28 The following definitions are added to remove dependency on blast.h
  29 */
  30 #include <stdint.h>
  31 #define int4 int32_t
  32 #define uint4 uint32_t
  33 #define int8 int64_t
  34 #define uint8 uint64_t
  35 #define int2 int16_t
  36 #define uint2 uint16_t
  37
  38 extern double BlastKarlin_lambda;
  39 extern double BlastKarlin_K;
  40 extern double BlastKarlin_H;
  41
  42 void BlastKarlinBlkCalc(double* scoreProbabilities, int4 min, int4 max);
  43
  44 int4 BlastComputeLengthAdjustment(double K,
  45                              double logK,
  46                              double alpha_d_lambda,
  47                              double beta,
  48                              int4 query_length,
  49                              uint4 db_length,
  50                              int4 db_num_seqs,
  51                              int4 *length_adjustment);
  52 #endif
  53