/* objsset.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: objsset.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 6.5 $ * * File Description: Object manager interface for module NCBI-Seqset * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: objsset.h,v $ * Revision 6.5 2001/05/14 19:54:20 kans * redefine BioseqseqSet_class_gen_prod_set to 17, now in ASN.1 spec * * Revision 6.4 2001/02/14 23:57:28 kans * added define for BioseqseqSet_class_eco_set * * Revision 6.3 1999/09/27 17:48:38 kans * using GatherIndex structure * * Revision 6.2 1999/09/24 23:09:24 kans * adds EXTRA_OBJMGR_FIELDS to several objects * * Revision 6.1 1998/05/29 20:49:26 kans * added BioseqseqSet_class_gen_prod_set, currently same as _other (255) * * Revision 6.0 1997/08/25 18:50:58 madden * Revision changed to 6.0 * * Revision 4.2 1997/06/19 18:42:09 vakatov * [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization * * Revision 4.1 1996/03/06 20:44:45 ostell * added defines for bioseqset classes * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 3.3 1995/05/15 21:22:00 ostell * added Log line * * * * ========================================================================== */ #ifndef _NCBI_Seqset_ #define _NCBI_Seqset_ #ifndef _ASNTOOL_ #include #endif #ifndef _NCBI_General_ #include #endif #ifndef _NCBI_Seq_ #include #endif #undef NLM_EXTERN #ifdef NLM_IMPORT #define NLM_EXTERN NLM_IMPORT #else #define NLM_EXTERN extern #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * loader * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqSetAsnLoad PROTO((void)); /***************************************************************************** * * internal structures for NCBI-Seqset objects * *****************************************************************************/ /***************************************************************************** * * BioseqSet - a collection of sequences * *****************************************************************************/ typedef struct seqset { ObjectIdPtr id; DbtagPtr coll; Int2 level; /* set to INT2_MIN (ncbilcl.h) for not used */ Uint1 _class; CharPtr release; DatePtr date; ValNodePtr descr; SeqEntryPtr seq_set; SeqAnnotPtr annot; GatherIndex idx; /* internal gather/objmgr tracking fields */ SeqEntryPtr seqentry; /* internal seqentry that points to this bioseqset */ } BioseqSet, PNTR BioseqSetPtr; NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetNew PROTO((void)); NLM_EXTERN Boolean LIBCALL BioseqSetAsnWrite PROTO((BioseqSetPtr bsp, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetFree PROTO((BioseqSetPtr bsp)); NLM_EXTERN Int2 LIBCALL BioseqSetLabel PROTO((BioseqSetPtr bssp, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * defines for BioseqSet._class not-set (0) , nuc-prot (1) , -- nuc acid and coded proteins segset (2) , -- segmented sequence + parts conset (3) , -- constructed sequence + parts parts (4) , -- parts for 2 or 3 gibb (5) , -- geninfo backbone gi (6) , -- geninfo genbank (7) , -- converted genbank pir (8) , -- converted pir pub-set (9) , -- all the seqs from a single publication equiv (10) , -- a set of equivalent maps or seqs swissprot (11) , -- converted SWISSPROT pdb-entry (12) , -- a complete PDB entry mut-set (13) , -- set of mutations pop-set (14) , -- population study phy-set (15) , -- phylogenetic study other (255) } DEFAULT not-set , * ******************************************************************************/ #define BioseqseqSet_class_not_set 0 #define BioseqseqSet_class_nuc_prot 1 #define BioseqseqSet_class_segset 2 #define BioseqseqSet_class_conset 3 #define BioseqseqSet_class_parts 4 #define BioseqseqSet_class_gibb 5 #define BioseqseqSet_class_gi 6 #define BioseqseqSet_class_genbank 7 #define BioseqseqSet_class_pir 8 #define BioseqseqSet_class_pub_set 9 #define BioseqseqSet_class_equiv 10 #define BioseqseqSet_class_swissprot 11 #define BioseqseqSet_class_pdb_entry 12 #define BioseqseqSet_class_mut_set 13 #define BioseqseqSet_class_pop_set 14 #define BioseqseqSet_class_phy_set 15 #define BioseqseqSet_class_eco_set 16 #define BioseqseqSet_class_gen_prod_set 17 #define BioseqseqSet_class_other 255 /***************************************************************************** * * BioseqSetFreeComponents(bsp, parts) * Frees associated data of a BioseqSet * if (parts == FALSE) * Calls SeqEntryFreeComponents() for seq-set * else * Calls SeqEntryFree() * Does not free the BioseqSet itself * Called by BioseqSetFree * Used by SeqMgr for caching out * *****************************************************************************/ NLM_EXTERN BioseqSetPtr LIBCALL BioseqSetFreeComponents PROTO((BioseqSetPtr bsp, Boolean parts)); /***************************************************************************** * * SeqEntry - implemented as an ValNode * choice: * 1 = Bioseq * 2 = Bioseq-set * *****************************************************************************/ NLM_EXTERN SeqEntryPtr LIBCALL SeqEntryNew PROTO((void)); NLM_EXTERN Boolean LIBCALL SeqEntryAsnWrite PROTO((SeqEntryPtr sep, AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqEntryPtr LIBCALL SeqEntryAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); NLM_EXTERN SeqEntryPtr LIBCALL SeqEntryFree PROTO((SeqEntryPtr sep)); NLM_EXTERN Int2 LIBCALL SeqEntryLabel PROTO((SeqEntryPtr sep, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * SeqEntryFreeComponents(sep) * Frees components of elements associated with SeqEntry * used by SeqMgr for caching out * *****************************************************************************/ NLM_EXTERN SeqEntryPtr LIBCALL SeqEntryFreeComponents PROTO((SeqEntryPtr sep)); /***************************************************************************** * * Options for SeqEntryAsnRead() * *****************************************************************************/ NLM_EXTERN SeqEntryPtr LIBCALL SeqEntryAsnGet PROTO((AsnIoPtr aip, AsnTypePtr atp, SeqIdPtr sip, Int2 retcode)); #define SEQENTRY_OPTION_MAX_COMPLEX 1 /* option type to use with OP_NCBIOBJSSET */ /* values for retcode, implemented with AsnIoOptions */ #define SEQENTRY_READ_BIOSEQ 1 /* read only Bioseq identified by sip */ #define SEQENTRY_READ_SEG_SET 2 /* read any seg-set it may be part of */ #define SEQENTRY_READ_NUC_PROT 3 /* read any nuc-prot set it may be in */ #define SEQENTRY_READ_PUB_SET 4 /* read pub-set it may be part of */ typedef struct objsset_option { SeqIdPtr sip; /* seq-id to find */ Int2 retcode; /* type of set/seq to return */ Boolean in_right_set; Uint1 working_on_set; /* 2, if in first set of retcode type */ /* 1, if found Bioseq, but not right set */ /* 0, if Bioseq not yet found */ } Op_objsset, PNTR Op_objssetPtr; #define IS_Bioseq(a) ((a)->choice == 1) #define IS_Bioseq_set(a) ((a)->choice == 2) /***************************************************************************** * * loader for ObjSeqSet and Sequence Codes * *****************************************************************************/ NLM_EXTERN Boolean LIBCALL SeqEntryLoad PROTO((void)); #ifdef __cplusplus } #endif #undef NLM_EXTERN #ifdef NLM_EXPORT #define NLM_EXTERN NLM_EXPORT #else #define NLM_EXTERN #endif #endif