/* objseq.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: objseq.h * * Author: James Ostell * * Version Creation Date: 4/1/91 * * $Revision: 4.2 $ * * File Description: Object manager interface for module NCBI-Seq * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * $Log: objseq.h,v $ * Revision 4.2 1996/07/19 22:16:14 ostell * added comment about delta seq gaps * * Revision 4.1 1996/06/16 04:18:12 ostell * added comment on delta seq-ext * * Revision 4.0 1995/07/26 13:48:06 ostell * force revision to 4.0 * * Revision 3.6 1995/07/22 21:59:13 ostell * added support for ASN.1 spec 4.0 * * Revision 3.5 1995/07/11 18:46:25 ostell * replaced Seqdesc neighbors with dbxref * added reftype to Pubdesc * * Revision 3.4 1995/05/15 21:22:00 ostell * added Log line * * * * ========================================================================== */ #ifndef _NCBI_Seq_ #define _NCBI_Seq_ #ifndef _ASNTOOL_ #include #endif #ifndef _NCBI_General_ #include #endif #ifndef _NCBI_Seqloc_ #include #endif #ifndef _NCBI_Pub_ #include #endif #ifndef _NCBI_Seqalign_ #include #endif #ifndef _NCBI_Pubdesc_ #include /* separated out to avoid typedef order problems */ #endif #ifndef _NCBI_Seqfeat_ #include /* include organism for now */ #endif #ifndef _NCBI_Seqres_ #include #endif #ifndef _NCBI_SeqBlock_ #include #endif #ifndef _NCBI_SeqCode_ #include #endif #ifdef __cplusplus extern "C" { #endif /***************************************************************************** * * loader * *****************************************************************************/ Boolean LIBCALL SeqAsnLoad PROTO((void)); /***************************************************************************** * * internal structures for NCBI-Seq objects * *****************************************************************************/ /***************************************************************************** * * SeqAnnot - Sequence annotations * *****************************************************************************/ /***************************************************************************** * * AnnotId is a choice using an ValNode, most types in data.ptrvalue * except integers, in data.intvalue * choice: * 0 = not set 1 = local Object-id , -- local use 2 = ncbi INTEGER 3 = general Dbtag -- any database * *****************************************************************************/ typedef ValNode AnnotId, PNTR AnnotIdPtr; #define ANNOTID_NOT_SET ( (Uint1)0) #define ANNOTID_LOCAL ( (Uint1)1) #define ANNOTID_NCBI ( (Uint1)2) #define ANNOTID_GENERAL ((Uint1)3) Boolean LIBCALL AnnotIdAsnWrite PROTO((AnnotIdPtr anp, AsnIoPtr aip, AsnTypePtr atp)); AnnotIdPtr LIBCALL AnnotIdAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); AnnotIdPtr LIBCALL AnnotIdFree PROTO((AnnotIdPtr anp)); AnnotIdPtr LIBCALL AnnotIdDup PROTO((AnnotIdPtr oldid)); /***************************************************************************** * * These routines process sets or sequences of AnnotId's * *****************************************************************************/ Boolean LIBCALL AnnotIdSetAsnWrite PROTO((AnnotIdPtr anp, AsnIoPtr aip, AsnTypePtr settype, AsnTypePtr elementtype)); AnnotIdPtr LIBCALL AnnotIdSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr settype, AsnTypePtr elementtype)); AnnotIdPtr LIBCALL AnnotIdSetFree PROTO((AnnotIdPtr anp)); /***************************************************************************** * * AlignDef * used to describe a set of alignments in a SeqAnnot * align_type * ALIGN_TYPE_REF set of pairwise alignments to one "master" sequence * ALIGN_TYPE_ALT set of alternate alignments of the same seqs * ALIGN_TYPE_BLOCKS set of (unordered) aligned blocks * ids SeqIds used in alignments * currently only used for ALIGN_TYPE_REF, where the one SeqId of * the "master" sequence is given (one SeqId) * *****************************************************************************/ typedef struct aligndef { Uint1 align_type; SeqIdPtr ids; } AlignDef, PNTR AlignDefPtr; #define ALIGN_TYPE_REF 1 #define ALIGN_TYPE_ALT 2 #define ALIGN_TYPE_BLOCKS 3 #define ALIGN_TYPE_OTHER 255 AlignDefPtr LIBCALL AlignDefNew PROTO((void)); Boolean LIBCALL AlignDefAsnWrite PROTO((AlignDefPtr adp, AsnIoPtr aip, AsnTypePtr atp)); AlignDefPtr LIBCALL AlignDefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); AlignDefPtr LIBCALL AlignDefFree PROTO((AlignDefPtr adp)); /***************************************************************************** * * AnnotDescr uses an ValNode with choice = 1 = name VisibleString , -- a name for this annotation 2 = title VisibleString , -- a title for this annotation 3 = comment VisibleString , -- a more extensive comment 4 = pub Pubdesc -- a reference to the publication 5 = user UserObject -- user structured data object 6 = create-date Date -- date entry created 7 = update-date Date -- date of last update 8 = src Seq-id -- SeqId of entry this came from 9 = align Align-def -- Align-def pointer types with * use data.intvalue. Other use data.ptrvalue ** uses a chain of ValNodes which use data.intvalue for enumerated type * *****************************************************************************/ #define Annot_descr_name 1 #define Annot_descr_title 2 #define Annot_descr_comment 3 #define Annot_descr_pub 4 #define Annot_descr_user 5 #define Annot_descr_create_date 6 #define Annot_descr_update_date 7 #define Annot_descr_src 8 #define Annot_descr_align 9 typedef ValNode AnnotDescr, PNTR AnnotDescrPtr; Boolean LIBCALL AnnotDescrAsnWrite PROTO((AnnotDescrPtr anp, AsnIoPtr aip, AsnTypePtr atp)); AnnotDescrPtr LIBCALL AnnotDescrAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); AnnotDescrPtr LIBCALL AnnotDescrFree PROTO((AnnotDescrPtr anp)); typedef ValNode AnnotDesc, PNTR AnnotDescPtr; Boolean LIBCALL AnnotDescAsnWrite PROTO((AnnotDescPtr anp, AsnIoPtr aip, AsnTypePtr atp)); AnnotDescPtr LIBCALL AnnotDescAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); AnnotDescPtr LIBCALL AnnotDescFree PROTO((AnnotDescPtr anp)); typedef struct seqannot { AnnotIdPtr id; Uint1 db; CharPtr name; AnnotDescrPtr desc; Uint1 type; /* 1=ftable, 2=align, 3=graph 4=ids 5=locs */ Pointer data; struct seqannot PNTR next; } SeqAnnot, PNTR SeqAnnotPtr; SeqAnnotPtr LIBCALL SeqAnnotNew PROTO((void)); Boolean LIBCALL SeqAnnotAsnWrite PROTO((SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr atp)); SeqAnnotPtr LIBCALL SeqAnnotAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); SeqAnnotPtr LIBCALL SeqAnnotFree PROTO((SeqAnnotPtr sap)); Int2 LIBCALL SeqAnnotLabel PROTO((SeqAnnotPtr sap, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * Sets of SeqAnnots * *****************************************************************************/ Boolean LIBCALL SeqAnnotSetAsnWrite PROTO((SeqAnnotPtr sap, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); SeqAnnotPtr LIBCALL SeqAnnotSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); /***************************************************************************** * * SeqHist * *****************************************************************************/ typedef struct seqhist { SeqAlignPtr assembly; DatePtr replace_date; SeqIdPtr replace_ids; DatePtr replaced_by_date; SeqIdPtr replaced_by_ids; Boolean deleted; DatePtr deleted_date; } SeqHist, PNTR SeqHistPtr; SeqHistPtr LIBCALL SeqHistNew PROTO((void)); Boolean LIBCALL SeqHistAsnWrite PROTO((SeqHistPtr shp, AsnIoPtr aip, AsnTypePtr atp)); SeqHistPtr LIBCALL SeqHistAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); SeqHistPtr LIBCALL SeqHistFree PROTO((SeqHistPtr shp)); /***************************************************************************** * * Delta-seq is just a ValNode where * vnp->choice = 1, vnp->data.ptrvalue = SeqLocPtr * vnp->choice = 2, vnp->data.ptrvalue = SeqLitPtr * * SeqLit is a Seq-literal * *****************************************************************************/ typedef ValNode DeltaSeq, PNTR DeltaSeqPtr; Boolean LIBCALL DeltaSeqAsnWrite PROTO((DeltaSeqPtr dsp, AsnIoPtr aip, AsnTypePtr atp)); DeltaSeqPtr LIBCALL DeltaSeqAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); DeltaSeqPtr LIBCALL DeltaSeqFree PROTO((DeltaSeqPtr dsp)); /*** this read/write/free a linked list of DeltaSeq *******/ Boolean LIBCALL DeltaSeqSetAsnWrite PROTO((DeltaSeqPtr dsp, AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); DeltaSeqPtr LIBCALL DeltaSeqSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr set, AsnTypePtr element)); DeltaSeqPtr LIBCALL DeltaSeqSetFree PROTO((DeltaSeqPtr dsp)); /*** here is the SeqLit *********************************** * if seq_data is NULL and length != 0, represents a gap of known length. * if seq_data is NULL and length = 0, represents a gap of unknown length * if seq_data is NULL and length != 0, and fuzz is type lim, class unk, * then represents a gap of unknown length, but which has been spread * evenly across a whole delta seq to match BioseqPtr->length. See * SpreadGapsInDeltaSeq() for support to do this. Useful when the length * of a partially sequenced clone is know, but not specific gap lengths ***********************************************************/ typedef struct seqlit { Int4 length; IntFuzzPtr fuzz; Uint1 seq_data_type; /* see Bioseq below */ ByteStorePtr seq_data; } SeqLit, PNTR SeqLitPtr; SeqLitPtr LIBCALL SeqLitNew PROTO((void)); Boolean LIBCALL SeqLitAsnWrite PROTO((SeqLitPtr slp, AsnIoPtr aip, AsnTypePtr atp)); SeqLitPtr LIBCALL SeqLitAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); SeqLitPtr LIBCALL SeqLitFree PROTO((SeqLitPtr slp)); /***************************************************************************** * * Bioseq. * Inst is incorporated within Bioseq for efficiency * seq_data_type * 0 = not set * 1 = IUPACna * 2 = IUPACaa * 3 = NCBI2na * 4 = NCBI4na * 5 = NCBI8na * 6 = NCBIpna * 7 = NCBI8aa * 8 = NCBIeaa * 9 = NCBIpaa * 11 = NCBIstdaa * seq_ext_type * 0 = none * 1 = seg-ext * 2 = ref-ext * 3 = map-ext * 4 = delta-ext * *****************************************************************************/ #define Seq_code_iupacna 1 #define Seq_code_iupacaa 2 #define Seq_code_ncbi2na 3 #define Seq_code_ncbi4na 4 #define Seq_code_ncbi8na 5 #define Seq_code_ncbipna 6 #define Seq_code_ncbi8aa 7 #define Seq_code_ncbieaa 8 #define Seq_code_ncbipaa 9 #define Seq_code_iupacaa3 10 #define Seq_code_ncbistdaa 11 #define Seq_repr_virtual 1 #define Seq_repr_raw 2 #define Seq_repr_seg 3 #define Seq_repr_const 4 #define Seq_repr_ref 5 #define Seq_repr_consen 6 #define Seq_repr_map 7 #define Seq_repr_delta 8 #define Seq_repr_other 255 #define Seq_mol_dna 1 #define Seq_mol_rna 2 #define Seq_mol_aa 3 #define Seq_mol_na 4 #define Seq_mol_other 255 #define ISA_na(x) ((x==1)||(x==2)||(x==4)) #define ISA_aa(x) (x == 3) typedef struct bioseq { SeqIdPtr id; /* Seq-ids */ ValNodePtr descr; /* Seq-descr */ Uint1 repr, mol; Int4 length; /* -1 if not set */ IntFuzzPtr fuzz; Uint1 topology, strand, seq_data_type, /* as in Seq_code_type above */ seq_ext_type; ByteStorePtr seq_data; Pointer seq_ext; SeqAnnotPtr annot; SeqHistPtr hist; } Bioseq, PNTR BioseqPtr; BioseqPtr LIBCALL BioseqNew PROTO((void)); Boolean LIBCALL BioseqAsnWrite PROTO((BioseqPtr bsp, AsnIoPtr aip, AsnTypePtr atp)); BioseqPtr LIBCALL BioseqAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); BioseqPtr LIBCALL BioseqFree PROTO((BioseqPtr bsp)); Int2 LIBCALL BioseqLabel PROTO((BioseqPtr bsp, CharPtr buffer, Int2 buflen, Uint1 content)); /***************************************************************************** * * BioseqFreeComponents(bsp) * Frees data associated with the Bioseq. * Does not free SeqIds * Does not free Bioseq itself * Used by SeqMgr for caching out * Called by BioseqFree() * *****************************************************************************/ BioseqPtr LIBCALL BioseqFreeComponents PROTO((BioseqPtr bsp)); Boolean LIBCALL BioseqInstAsnWrite PROTO((BioseqPtr bsp, AsnIoPtr aip, AsnTypePtr orig)); Boolean LIBCALL BioseqInstAsnRead PROTO((BioseqPtr bsp, AsnIoPtr aip, AsnTypePtr orig)); Boolean LIBCALL SeqDataAsnWrite PROTO((ByteStorePtr bsp, Uint1 seqtype, AsnIoPtr aip, AsnTypePtr orig)); ByteStorePtr LIBCALL SeqDataAsnRead PROTO((AsnIoPtr aip, AsnTypePtr orig, Uint1Ptr typeptr)); /***************************************************************************** * * Initialize bioseq and seqcode tables and default numbering * *****************************************************************************/ Boolean LIBCALL BioseqLoad PROTO((void)); /***************************************************************************** * * BioseqAsnRead Options * *****************************************************************************/ typedef struct op_objseq { SeqIdPtr sip; /* seq id to find */ Boolean found_it; /* set to TRUE when BioseqAsnRead matches sip */ Boolean load_by_id; /* if TRUE, load only if sip matches */ } Op_objseq, PNTR Op_objseqPtr; /* types for AsnIoOption OP_NCBIOBJSEQ */ #define BIOSEQ_CHECK_ID 1 /* match Op_objseq.sip */ /***************************************************************************** * * SeqDescr uses an ValNode with choice = 1 = * mol-type GIBB-mol , -- type of molecule 2 = ** modif SET OF GIBB-mod , -- modifiers 3 = * method GIBB-method , -- sequencing method 4 = name VisibleString , -- a name for this sequence 5 = title VisibleString , -- a title for this sequence 6 = org Org-ref , -- if all from one organism 7 = comment VisibleString , -- a more extensive comment 8 = num Numbering , -- a numbering system 9 = maploc Dbtag , -- map location of this sequence 10 = pir PIR-block , -- PIR specific info 11 = genbank GB-block , -- GenBank specific info 12 = pub Pubdesc -- a reference to the publication 13 = region VisibleString -- name for this region of sequence 14 = user UserObject -- user structured data object 15 = sp SP-block -- SWISSPROT specific info <16 = neighbors Entrez-link -- links to sequence neighbors > 16 = dbxref Dbtag -- xref to other databases 17 = embl EMBL-block -- EMBL specific info 18 = create-date Date -- date entry created 19 = update-date Date -- date of last update 20 = prf PRF-block -- PRF specific information 21 = pdb PDB-block -- PDB specific information 22 = het Heterogen -- cofactor, etc associated but not bound 23 = source BioSource 24 = molinfo MolInfo types with * use data.intvalue. Other use data.ptrvalue ** uses a chain of ValNodes which use data.intvalue for enumerated type * *****************************************************************************/ #define Seq_descr_mol_type 1 #define Seq_descr_modif 2 #define Seq_descr_method 3 #define Seq_descr_name 4 #define Seq_descr_title 5 #define Seq_descr_org 6 #define Seq_descr_comment 7 #define Seq_descr_num 8 #define Seq_descr_maploc 9 #define Seq_descr_pir 10 #define Seq_descr_genbank 11 #define Seq_descr_pub 12 #define Seq_descr_region 13 #define Seq_descr_user 14 #define Seq_descr_sp 15 #define Seq_descr_dbxref 16 #define Seq_descr_embl 17 #define Seq_descr_create_date 18 #define Seq_descr_update_date 19 #define Seq_descr_prf 20 #define Seq_descr_pdb 21 #define Seq_descr_het 22 #define Seq_descr_source 23 #define Seq_descr_molinfo 24 typedef ValNode SeqDescr, FAR *SeqDescrPtr; Boolean LIBCALL SeqDescrAsnWrite PROTO((SeqDescrPtr anp, AsnIoPtr aip, AsnTypePtr atp)); SeqDescrPtr LIBCALL SeqDescrAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); SeqDescrPtr LIBCALL SeqDescrFree PROTO((SeqDescrPtr anp)); /*** these replace the SeqDescrEAsnWrite() function and add others */ typedef ValNode SeqDesc, FAR *SeqDescPtr; Boolean LIBCALL SeqDescAsnWrite PROTO((SeqDescPtr anp, AsnIoPtr aip, AsnTypePtr atp)); SeqDescPtr LIBCALL SeqDescAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp)); SeqDescPtr LIBCALL SeqDescFree PROTO((SeqDescPtr anp)); Int2 LIBCALL SeqDescLabel PROTO((SeqDescPtr vnp, CharPtr buffer, Int2 buflen, Boolean content)); /***************************************************************************** * * Pubdesc, Numbering, MolInfo, BioSource types defined in objpubd.h * *****************************************************************************/ #ifdef __cplusplus } #endif #endif