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comparison clustalomega/clustal-omega-0.2.0/src/squid/gsi64.h @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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-1:000000000000 | 0:ff1768533a07 |
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1 /***************************************************************** | |
2 * @LICENSE@ | |
3 *****************************************************************/ | |
4 | |
5 #ifndef GSI64H_INCLUDED | |
6 #define GSI64H_INCLUDED | |
7 #ifdef USE_GSI64 | |
8 | |
9 /* gsi64.h | |
10 * Database indexing (GSI64 format support) | |
11 * CVS $Id: gsi64.h,v 1.2 2000/12/21 23:42:59 eddy Exp) | |
12 * | |
13 * A GSI64 (generic sequence index, 64 bit hack) file is composed of | |
14 * recnum + nfiles + 1 records. Each record contains | |
15 * three fields; key, file number, and disk offset. | |
16 * Record 0 contains: | |
17 * [ "GSI64" ] [ nfiles ] [ recnum ] | |
18 * Records 1..nfiles map file names to file numbers, and contain: | |
19 * [ filename ] [ file number, 1..nfiles ] [ 0 (unused) ] | |
20 * Records nfiles+1 to recnum+nfiles+1 provide disk offset | |
21 * and file number indices for every key: | |
22 * [ key ] [ file number ] [ offset] | |
23 * | |
24 * Because the file is binary, we take some (but not | |
25 * complete) care to improve portability amongst platforms. | |
26 * This means using network order integers (see ntohl()) | |
27 * and defining types for 16 and 64 bit integers. | |
28 * | |
29 * A short test program that verifies the sizes of these | |
30 * data types would be a good idea... | |
31 * | |
32 * Because we use 64-bit offsets, ftell64(), and fseek64(), | |
33 * we rely on the OS actually providing these. This is | |
34 * a temporary hack for human genome analysis. | |
35 */ | |
36 typedef unsigned long long sqd_uint64; /* 64 bit integer. */ | |
37 | |
38 #define GSI64_KEYSIZE 32 /* keys are 32 bytes long */ | |
39 #define GSI64_RECSIZE 42 /* 32 + 2 + 8 bytes */ | |
40 #define SQD_UINT16_MAX 65535 /* 2^16-1 */ | |
41 #define SQD_UINT64_MAX 18446744073709551615LU /* 2^64-1 */ | |
42 | |
43 struct gsi64_s { | |
44 FILE *gsifp; /* open GSI index file */ | |
45 sqd_uint16 nfiles; /* number of files = 16 bit int */ | |
46 sqd_uint64 recnum; /* number of records = 64 bit int */ | |
47 }; | |
48 typedef struct gsi64_s GSI64FILE; | |
49 | |
50 struct gsi64key_s { | |
51 char key[GSI64_KEYSIZE]; | |
52 sqd_uint16 filenum; | |
53 sqd_uint64 offset; | |
54 }; | |
55 struct gsi64index_s { | |
56 char **filenames; | |
57 int *fmt; | |
58 sqd_uint16 nfiles; | |
59 | |
60 struct gsi64key_s *elems; | |
61 sqd_uint64 nkeys; | |
62 }; | |
63 | |
64 | |
65 | |
66 /* if ntohl() and friends are not available, you | |
67 * can slip replacements in by providing sre_ntohl() | |
68 * functions. (i.e., there is a possible portability problem here.) | |
69 */ | |
70 #if 0 | |
71 #define sre_ntohl(x) ntohl(x); | |
72 #define sre_ntohs(x) ntohs(x); | |
73 #define sre_htonl(x) htonl(x); | |
74 #define sre_htons(x) htons(x); | |
75 #endif | |
76 | |
77 /* from gsi64.c | |
78 */ | |
79 extern GSI64FILE *GSI64Open(char *gsifile); | |
80 extern int GSI64GetRecord(GSI64FILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint64 *f3); | |
81 extern int GSI64GetOffset(GSI64FILE *gsi, char *key, char *sqfile, | |
82 int *fmt, long long *ret_offset); | |
83 extern void GSI64Close(GSI64FILE *gsi); | |
84 extern struct gsi64index_s *GSI64AllocIndex(void); | |
85 extern void GSI64FreeIndex(struct gsi64index_s *g); | |
86 extern void GSI64AddFileToIndex(struct gsi64index_s *g, char *filename, int fmt); | |
87 extern void GSI64AddKeyToIndex(struct gsi64index_s *g, char *key, int filenum, long long offset); | |
88 extern void GSI64SortIndex(struct gsi64index_s *g); | |
89 extern void GSI64WriteIndex(FILE *fp, struct gsi64index_s *g); | |
90 extern void GSI64WriteHeader(FILE *fp, int nfiles, long long nkeys); | |
91 extern int GSI64WriteFileRecord(FILE *fp, char *fname, int idx, int fmt); | |
92 extern int GSI64WriteKeyRecord(FILE *fp, char *key, int fileidx, long long offset); | |
93 | |
94 #endif /* USE_GSI64 */ | |
95 #endif /*GSIH_INCLUDED*/ |