/* lsqfetch.h * =========================================================================== * * 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: lsqfetch.h * * Author: Jinghui Zhang * * Version Creation Date: 5/25/95 * * $Revision: 6.2 $ * * File Description: Utilities for fetching local sequences * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: lsqfetch.h,v $ * Revision 6.2 2001/03/12 23:19:33 kans * added IndexedFastaLib functions - currently uses genome contig naming conventions * * Revision 6.1 1998/02/06 17:41:39 zjing * make the function CheckDnaResidue external * * Revision 6.0 1997/08/25 18:06:30 madden * Revision changed to 6.0 * * Revision 5.2 1997/07/18 21:26:07 zjing * *** empty log message *** * * Revision 5.1 1997/06/19 18:38:18 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 5.0 1996/05/28 13:23:23 ostell * Set to revision 5.0 * * Revision 4.5 1995/11/02 21:37:55 zjing * . * * Revision 4.4 1995/10/11 19:29:28 zjing * add LIBCALL for find_big_bioseq * * Revision 4.3 1995/08/31 18:55:36 zjing * add include file accentr.h * * Revision 4.2 1995/08/04 17:31:32 kans * JZ added LocalSeqFetchInit, LocalSeqFetchDisable * * Revision 4.1 1995/08/03 20:56:18 kans * paths can now be specified in a regular NCBI config file * * Revision 4.0 1995/07/26 13:49:01 ostell * force revision to 4.0 * * Revision 1.1 1995/05/25 19:50:52 zjing * Initial revision * * * * ========================================================================== */ #ifndef _LSQFETCH_ #define _LSQFETCH_ #ifndef _NCBI_SeqMgr_ #include #endif #ifndef _NCBI_Seqloc_ #include #endif #ifndef _NCBI_Seqset_ #include #endif #ifndef _NCBI_SeqUtil_ #include #endif /* #include */ #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /********************************************************************* * * seqid_to_string(sip, name, use_locus) * print the most important field in Seqid to a string stored in * name. * **********************************************************************/ NLM_EXTERN Boolean seqid_to_string PROTO((SeqIdPtr sip, CharPtr name, Boolean use_locus)); /********************************************************************** * * FastaLibBioseqFetchEnable(libs, now) * Initiate the function for fetch a Bioseq from a Fasta Library * file. libs is a list of library file names. * If now = TRUE, open the library files and set the state to * FASTALIB_OPEN. return TRUE for success. * ***********************************************************************/ NLM_EXTERN Boolean FastaLibBioseqFetchEnable PROTO((ValNodePtr libs, Boolean now)); /********************************************************************** * * FastaLibBioseqFetchEnable(libs, now) * Initiate the function for fetch a Bioseq from a Fasta Library * file. libs is a list of library file names. * If now = TRUE, open the library files and set the state to * FASTALIB_OPEN. return TRUE for success. * ***********************************************************************/ NLM_EXTERN void FastaLibBioseqFetchDisable PROTO((void)); #define BIN_ASN 1 #define TEXT_ASN 2 #define FASTA_FILE 3 #define FASTALIB_ERROR 0 /*can not open fasta lib*/ #define FASTALIB_OPEN 1 /*fasta library is open*/ #define FASTALIB_CLOSE 2 /*fasta libary is closed*/ typedef struct fastalib{ Boolean use_locus; Char file_name[100]; FILE *fp; Uint1 state; Int2 order; struct fastalib PNTR next; }FastaLib, PNTR FastaLibPtr; typedef ValNode SingleBspFile, FAR *SingleBspFilePtr; typedef struct filebsp{ /*structure for opening a bioseq from a file*/ Boolean use_locus; CharPtr path; /*path for the files*/ CharPtr ext; /*extension for files*/ Int2 order; /*the order of the search */ }FileBsp, PNTR FileBspPtr; /********************************************************************* * * FileBioseqFetchEnable(path, ext) * Initiate a BioseqFetch function by either reading an ASN.1 * Seq-entry file or FASTA file. path->choice determines the * type of the file, such as text ASN, binary ASN and FASTA file * ext is the extension that is needed to add to the end of the * sequence name to make the sequence file * *********************************************************************/ NLM_EXTERN Boolean FileBioseqFetchEnable PROTO((ValNodePtr path, ValNodePtr ext)); /********************************************************************** * * FileBioseqFetchDisable() * Remove the proc associated with FileBioseqFetch and free all the * sequence names in userdata * ***********************************************************************/ NLM_EXTERN void FileBioseqFetchDisable PROTO((void)); NLM_EXTERN Boolean LocalSeqFetchInit PROTO((Boolean now)); /********************************************************************* * * BioseqFetchInit() * Initiate BioseqFetch functions from local data and Entrez. * Local data files are stored in a config file. * If non is successful, return FALSE * *********************************************************************/ NLM_EXTERN Boolean BioseqFetchInit PROTO((Boolean now)); /*********************************************************************** * * BioseqFetchDisable(): Remove all the functions associated with * BioseqFetch * **********************************************************************/ NLM_EXTERN void BioseqFetchDisable PROTO((void)); NLM_EXTERN void LocalSeqFetchDisable PROTO((void)); /********************************************************************* * * find_big_bioseq(sep) * return the longest Bioseq found in Seq-entry sep * * **********************************************************************/ NLM_EXTERN BioseqPtr LIBCALL find_big_bioseq PROTO((SeqEntryPtr sep)); /*********************************************************************** * * Check if the sequence is a DNA or protein * ck_len: the length for checking * pnon_DNA: store the number of non-DNA residue * return TRUE if it is a DNA sequence, FALSE for protein * ***********************************************************************/ NLM_EXTERN Boolean CheckDnaResidue PROTO((CharPtr seq_ptr, Int4 ck_len, Int4Ptr pnon_DNA)); /**********************************************************************/ /* indexed FASTA lib functions - currently uses genome contig naming convention */ NLM_EXTERN Boolean IndexedFastaLibFetchEnable (CharPtr path); NLM_EXTERN void IndexedFastaLibFetchDisable (void); NLM_EXTERN void CreateFastaIndex (CharPtr file); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif