src/swsse2/swstriped.h

   1 /******************************************************************
   2   Copyright 2006 by Michael Farrar.  All rights reserved.
   3   This program may not be sold or incorporated into a commercial product,
   4   in whole or in part, without written consent of Michael Farrar.  For
   5   further information regarding permission for use or reproduction, please
   6   contact: Michael Farrar at farrar.michael@gmail.com.
   7 *******************************************************************/
   8
   9 /*
  10   Written by Michael Farrar, 2006.
  11   Please send bug reports and/or suggestions to farrar.michael@gmail.com.
  12 */
  13
  14 #ifndef INCLUDE_SWSTRIPED_H
  15 #define INCLUDE_SWSTRIPED_H
  16
  17 #include <emmintrin.h>
  18
  19 #include "swsse2.h"
  20 #include "fastalib.h"
  21
  22 SW_DATA *
  23 swStripedInit (unsigned char   *querySeq,
  24                int              queryLength,
  25                signed char     *matrix);
  26
  27
  28 void
  29 swStripedScan (unsigned char   *querySeq,
  30                int              queryLength,
  31                FASTA_LIB       *dbLib,
  32                void            *swData,
  33                SEARCH_OPTIONS  *options,
  34                SCORE_LIST      *scores);
  35
  36
  37 void
  38 swStripedComplete (SW_DATA *pSwData);
  39
  40 int
  41 swStripedWord (unsigned char   *querySeq,
  42                int              queryLength,
  43                unsigned char   *dbSeq,
  44                int              dbLength,
  45                unsigned short   gapOpen,
  46                unsigned short   gapExtend,
  47                __m128i         *queryProf,
  48                __m128i         *pvH1,
  49                __m128i         *pvH2,
  50                __m128i         *pvE);
  51
  52
  53 int
  54 swStripedByte (unsigned char   *querySeq,
  55                int              queryLength,
  56                unsigned char   *dbSeq,
  57                int              dbLength,
  58                unsigned short   gapOpen,
  59                unsigned short   gapExtend,
  60                __m128i         *queryProf,
  61                __m128i         *pvH1,
  62                __m128i         *pvH2,
  63                __m128i         *pvE,
  64                unsigned short   bias);
  65
  66 typedef struct {
  67     __m128i        *pvbQueryProf;
  68     __m128i        *pvsQueryProf;
  69     __m128i        *pvH1;
  70     __m128i        *pvH2;
  71     __m128i        *pvE;
  72     unsigned char  *pData;
  73     unsigned short  bias;
  74 } SwStripedData;
  75
  76
  77
  78 #endif /* INCLUDE_SWSTRIPED_H */