1 /* nucprot.h
2  *
3  * ===========================================================================
4  *
5  *                            PUBLIC DOMAIN NOTICE
6  *               National Center for Biotechnology Information
7  *
8  *  This software/database is a "United States Government Work" under the
9  *  terms of the United States Copyright Act.  It was written as part of
10  *  the author's official duties as a United States Government employee and
11  *  thus cannot be copyrighted.  This software/database is freely available
12  *  to the public for use. The National Library of Medicine and the U.S.
13  *  Government have not placed any restriction on its use or reproduction.
14  *
15  *  Although all reasonable efforts have been taken to ensure the accuracy
16  *  and reliability of the software and data, the NLM and the U.S.
17  *  Government do not and cannot warrant the performance or results that
18  *  may be obtained by using this software or data. The NLM and the U.S.
19  *  Government disclaim all warranties, express or implied, including
20  *  warranties of performance, merchantability or fitness for any particular
21  *  purpose.
22  *
23  *  Please cite the author in any work or product based on this material.
24  *
25  * ===========================================================================
26  *
27  * File Name:  nucprot.h
28  *
29  * Author: Karl Sirotkin, Hsiu-Chuan Chen
30  *
31  * File Description:
32  * -----------------
33  *
34  */
35 
36 #ifndef _NUCPROT_
37 #define _NUCPROT_
38 
39 #define Seq_descr_GIBB_mod_dna          0
40 #define Seq_descr_GIBB_mod_rna          1
41 #define Seq_descr_GIBB_mod_extrachr     2
42 #define Seq_descr_GIBB_mod_plasmid      3
43 #define Seq_descr_GIBB_mod_mito         4
44 #define Seq_descr_GIBB_mod_chlo         5
45 #define Seq_descr_GIBB_mod_kinet        6
46 #define Seq_descr_GIBB_mod_cyane        7
47 #define Seq_descr_GIBB_mod_synth        8
48 #define Seq_descr_GIBB_mod_recomb       9
49 #define Seq_descr_GIBB_mod_partial      10
50 #define Seq_descr_GIBB_mod_complete     11
51 #define Seq_descr_GIBB_mod_mutagen      12
52 #define Seq_descr_GIBB_mod_natmut       13
53 #define Seq_descr_GIBB_mod_transposon   14
54 #define Seq_descr_GIBB_mod_insertion    15
55 #define Seq_descr_GIBB_mod_noleft       16
56 #define Seq_descr_GIBB_mod_noright      17
57 #define Seq_descr_GIBB_mod_macronuclear 18
58 #define Seq_descr_GIBB_mod_proviral     19
59 #define Seq_descr_GIBB_mod_est          20
60 #define Seq_descr_GIBB_mod_sts          21
61 #define Seq_descr_GIBB_mod_gss          22
62 
63 BEGIN_NCBI_SCOPE
64 
65 struct GeneRefFeats
66 {
67     bool valid;
68     TSeqFeatList::iterator first;
69     TSeqFeatList::iterator last;
70 
GeneRefFeatsGeneRefFeats71     GeneRefFeats() :
72         valid(false)
73     {}
74 };
75 
76 void CheckDupDates(TEntryList& seq_entries);
77 void ProcNucProt(ParserPtr pp, TEntryList& seq_entries, GeneRefFeats& gene_refs);
78 void ExtractDescrs(TSeqdescList& descrs_from, TSeqdescList& descrs_to, objects::CSeqdesc::E_Choice choice);
79 
80 END_NCBI_SCOPE
81 #endif
82