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

   1 /*
   2
   3    BWTLoad.h        BWTLoad - Loading BWT index into memory
   4
   5    Copyright (C) 2006, Wong Chi Kwong.
   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 __BWT_LOAD_H__
  24 #define __BWT_LOAD_H__
  25
  26 #include "BWT.h"
  27 #include "HSP.h"
  28 #include "Socket.h"
  29
  30 // This is the only message send by the resident process to a client
  31 // If bwt == NULL signals an error condition
  32
  33 typedef struct BWTIndexPointer {
  34     BWT *bwt;
  35     SaIndexRange *saIndexRange;
  36     int saIndexRangeNumOfChar;
  37     unsigned int *packedDNA;
  38     Annotation *annotation;
  39     SeqOffset *seqOffset;
  40     int numOfSeq;
  41     Ambiguity *ambiguity;
  42     int numOfAmbiguity;
  43     unsigned long long minSeqLength;
  44 } BWTIndexPointer;
  45
  46 // This is the only message send by a client to the resident process
  47 // If BWTCodeFileName[0] == '\0', the resident process will stop
  48
  49 typedef struct BWTIndexFileName {
  50     char BWTCodeFileName[MAX_FILENAME_LEN+1];
  51     char BWTOccValueFileName[MAX_FILENAME_LEN+1];
  52     char SaValueFileName[MAX_FILENAME_LEN+1];
  53     char SaIndexFileName[MAX_FILENAME_LEN+1];
  54     char PackedDNAFileName[MAX_FILENAME_LEN+1];
  55     char AnnotationFileName[MAX_FILENAME_LEN+1];
  56     char AmbiguityFileName[MAX_FILENAME_LEN+1];
  57 } BWTIndexFileName;
  58
  59 #define BWT_INDEX_SOCKET_TYPE    LOCAL_SOCKET
  60 #define BWT_INDEX_SOCKET_NAME    "BWT_INDEX_SOCKET"
  61
  62 #endif