/* $Id: ncbisami.h,v 6.3 2000/07/18 19:29:28 shavirin Exp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * File Name: $RCSfile: ncbisami.h,v $ * * Author: Sergei Shavirin * * Initial Version Creation Date: 02/24/1997 * * $Revision: 6.3 $ * * File Description: * Internal include file for ISAM library * * $Log: ncbisami.h,v $ * Revision 6.3 2000/07/18 19:29:28 shavirin * Added new parameter test_non_unique to suppress check for non-unique * strings ids in the database - default - TRUE. * * Revision 6.2 1999/08/25 20:19:24 shavirin * Added parameter for user options to the internal structure. * * Revision 6.1 1999/02/19 22:01:59 madden * Add NlmMFILEPtr to ISAMData typedef * * Revision 6.0 1997/08/25 18:53:32 madden * Revision changed to 6.0 * * Revision 1.6 1997/05/12 19:55:32 shavirin * Some fixes type-changes to support ISAMCreateDatabase() API * * Revision 1.5 1997/05/07 21:14:18 shavirin * Added definitions for fields array encoding and ISAMCreateDatabase() * function. * * Revision 1.4 1997/05/06 21:36:50 shavirin * Added definitions of functions for Codded Array compression * implementation * * Revision 1.3 1997/05/05 18:17:35 shavirin * Added support for platforms without memory mapping * * Revision 1.2 1997/05/01 17:26:16 shavirin * Added String ISAM index functionality * * Revision 1.1 1997/02/24 21:07:17 shavirin * Initial revision * * * ========================================================================== */ #ifndef _NCBISAMI_H_ #define _NCBISAMI_H_ ncbisami /****************************************************************************/ /* INCLUDES */ /****************************************************************************/ #include /****************************************************************************/ /* INTERNAL FINCTION DEFINITIONS */ /****************************************************************************/ #ifdef __cplusplus extern "C" { #endif #ifdef __cplusplus } #endif /****************************************************************************/ /* DEFINES */ /****************************************************************************/ #define MAX_FILENAME_LEN 256 #define LINE_SIZE_CHUNK 4096 #define BUFF_SIZE_CHUNK 1024 #define UID_NUM_CHUNK 1024 #define ISAM_VERSION 1 #define ISAM_DATA_CHAR '\2' #define ENDS_ISAM_KEY(Ptr) ((*Ptr == NULLB) || (*Ptr == ISAM_DATA_CHAR) || (*Ptr == '\n') || (*Ptr == '\r')) #define Log2(N) (log(N)/log(2.0)) #define CA_TMP_CHUNK 4096 #define FA_Mask 0x7F #define DEFAULT_CA_MAX_OFFSET 10000000 /****************************************************************************/ /* TYPEDEFS */ /****************************************************************************/ typedef struct NISAMKeyData { Uint4 key; Uint4 data; } NISAMKeyData, PNTR NISAMKeyDataPtr; typedef struct ISAMUidField { Uint4 uid; Uint4 field; } ISAMUidField, PNTR ISAMUidFieldPtr; typedef struct ISAMData { Int4 type; /* Type of ISAM index */ CharPtr DBFileName; /* Filename of database file */ CharPtr IndexFileName; /* Filename of ISAM index file */ CharPtr CAName; /* Common filename-directory for CA */ CharPtr CADBExt; /* Extention for CA/FA files */ CharPtr CAOffExt; /* Extention for CA-Offset files */ Int4 CAMaxOffset; /* Offset for switch CA DB/Offset file */ Nlm_MemMapPtr mmp; /* Memory map pointer to index file */ NlmMFILEPtr mfp; /* Memory map pointer to database file for numeric search. */ CharPtr FileStart; /* Pointer to index file if no memmap */ Int4 NumTerms; /* Number of terms in database */ Int4 NumSamples; /* Number of terms in ISAM index */ Int4 PageSize; /* Page size of ISAM index */ FILE *db_fd; /* File pointer of ISAM database */ Boolean initialized; /* Is this structure was initialized for ISAM Search ? */ Uint4Ptr KeySamples; /* Pointer to first sample offset in ISAM index */ NISAMKeyDataPtr KeyDataSamples; /* Pointer to first NISAMKeyData structure in ISAM index (for search with data) */ CharPtr line; /* Temporary buffer to work with strings */ Int4 max_line_size; /* Maximum string length in the database */ Int4 idx_option; /* Options set by upper layer */ Boolean test_non_unique; /* Check if data for String ISAM sorted */ } ISAMData, PNTR ISAMDataPtr; typedef struct ISAMTmpCA { Uint1Ptr buffer; /* Buffer with coded array bytes */ Int4 allocated; /* Memory size allocated for the buffer */ Int4 length; /* Final length of CA buffer */ Int4 num_uids; /* Number of coded uids in CA */ Int4 num_bits; /* Number of bits used for CA compression */ Int4 byte_num; /* Temorary value for into CA buffer */ Int4 bit_num; /* Temporary value for CA buffer */ } ISAMTmpCA, PNTR ISAMTmpCAPtr; static Uint4 PowersOfTwo[] = {01,02,04,010,020,040,0100,0200,0400,01000, 02000,04000,010000,020000,040000,0100000, 0200000,0400000,01000000,02000000, 04000000,010000000,020000000,040000000, 0100000000,0200000000,0400000000, 01000000000,02000000000, 04000000000,010000000000, 020000000000}; static Uint1 OneBit[] = {0x80 , 0x40, 0x20, 0x10, 0x8, 0x4, 0x2, 0x1}; #endif