[svn-inject] Installing original source of ncbi-tools6 (6.0.2)

1 files changed, 347 insertions, 0 deletions

diff --git a/object/objfdef.h b/object/objfdef.h
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+/*  objfdef.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:  objfdef.h
+*
+* Author:  James Ostell
+*   
+* Version Creation Date: 9/94
+*
+* $Revision: 6.1 $
+*
+* File Description:  Object manager for feature definitions
+*
+* Modifications:  
+* --------------------------------------------------------------------------
+* Date	   Name        Description of modification
+* -------  ----------  -----------------------------------------------------
+*
+*
+* $Log: objfdef.h,v $
+* Revision 6.1  1998/06/29 20:31:28  kans
+* explicit defines for FEATDEF_MAX, SEQFEAT_MAX, and SEQDESCR_MAX Boolean array sizes
+*
+* Revision 6.0  1997/08/25 18:49:41  madden
+* Revision changed to 6.0
+*
+* Revision 4.2  1997/06/19 18:41:06  vakatov
+* [WIN32,MSVC++]  Adopted for the "NCBIOBJ.LIB" DLL'ization
+*
+* Revision 4.1  1996/07/17 15:00:12  ostell
+* added preprotein, mat_peptide_aa, sig_peptide_aa, tran sit_peptide_aa
+*
+ * Revision 4.0  1995/07/26  13:48:06  ostell
+ * force revision to 4.0
+ *
+ * Revision 1.4  1995/05/15  21:22:00  ostell
+ * added Log line
+ *
+*
+*
+* ==========================================================================
+*/
+
+#ifndef _NCBI_FeatDef_
+#define _NCBI_FeatDef_
+
+#ifndef _NCBI_SeqFeat_
+#include <objfeat.h>
+#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 FeatDefAsnLoad PROTO((void));
+
+/*****************************************************************************
+*
+*   FeatDef
+*
+*****************************************************************************/
+typedef struct featdef {
+    CharPtr typelabel,
+        menulabel;
+	Uint1 featdef_key,
+		seqfeat_key,
+		entrygroup,
+		displaygroup,
+		molgroup;
+    struct featdef PNTR next;
+} FeatDef, PNTR FeatDefPtr;
+
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefNew PROTO((void));
+NLM_EXTERN Boolean   LIBCALL FeatDefAsnWrite PROTO((FeatDefPtr fdp, AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefFree PROTO((FeatDefPtr fdp));
+
+NLM_EXTERN Boolean   LIBCALL FeatDefSetAsnWrite PROTO((FeatDefPtr fdp, AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetFree PROTO((FeatDefPtr fdp));
+
+
+/*****************************************************************************
+*
+*   FeatDispGroup
+*
+*****************************************************************************/
+typedef struct featdispgroup {
+	Uint1 groupkey;
+    CharPtr groupname;
+    struct featdispgroup PNTR next;
+} FeatDispGroup, PNTR FeatDispGroupPtr;
+
+NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupNew PROTO((void));
+NLM_EXTERN Boolean   LIBCALL FeatDispGroupAsnWrite PROTO((FeatDispGroupPtr fdp, AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupFree PROTO((FeatDispGroupPtr fdp));
+
+NLM_EXTERN Boolean   LIBCALL FeatDispGroupSetAsnWrite PROTO((FeatDispGroupPtr fdp, AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
+NLM_EXTERN FeatDispGroupPtr LIBCALL FeatDispGroupSetFree PROTO((FeatDispGroupPtr fdp));
+
+
+/*****************************************************************************
+*
+*   Data Loader Function
+*   	Loads default FeatDefSet and FeatDispGroupSet from "featdef.val"
+*       located in /ncbi/data directory
+*       returns head of linked list
+*
+*****************************************************************************/
+
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefSetLoad PROTO((void));
+
+/*****************************************************************************
+*
+*   FindFeatDefType(sfp)
+*   	Finds the featdef_type for a SeqFeat
+*       returns FEATDEF_BAD if can't find it
+*
+*****************************************************************************/
+NLM_EXTERN Uint1 LIBCALL FindFeatDefType PROTO((SeqFeatPtr sfp));
+
+/*****************************************************************************
+*
+*   FeatDefLabel(sfp, buf, buflen, type)
+*   	fills in buf with a content based label
+*   	if longer than buflen, makes the last visible char >
+*   	guarantees a '\0' at the end of the string
+*   
+*   NOTE: buf MUST be (buflen+1) long
+*   
+*   	This function makes nicer labels since it can combine elements
+*   	returns length of string or 0 on failure
+*
+*   	type is OM_LABEL_TYPE_ defined in objmgr.h
+*
+*****************************************************************************/
+NLM_EXTERN Int2 LIBCALL FeatDefLabel PROTO((SeqFeatPtr sfp, CharPtr buf, Int2 buflen, Uint1 labeltype));
+
+/*****************************************************************************
+*
+*   FeatDefTypeLabel(sfp)
+*   	returns a short string with the feature type
+*       returns NULL if can't find one
+*
+*****************************************************************************/
+NLM_EXTERN const char * LIBCALL FeatDefTypeLabel PROTO((SeqFeatPtr sfp));
+
+/*****************************************************************************
+*
+*   DispGroupNum()
+*   	returns number of display groups
+*   	returns 0 on failure
+*       loads featdef.val if not already loaded
+*
+*****************************************************************************/
+NLM_EXTERN Int2 LIBCALL DispGroupNum PROTO((void));
+
+/*****************************************************************************
+*
+*   DispGroupFindNext(curr, groupptr, groupname)
+*     returns display groups in order
+*     start with curr=NULL, then return current in curr until function
+*       returns NULL
+*     loads featdef.val if necessary
+*     groupptr is filled in with the key for the group, used
+*       in FeatDefFindNext() below.
+*     groupname points to the string naming the group
+*
+*****************************************************************************/
+NLM_EXTERN FeatDispGroupPtr LIBCALL DispGroupFindNext PROTO((FeatDispGroupPtr curr, Uint1Ptr groupptr, CharPtr PNTR groupname));
+
+/*****************************************************************************
+*
+*   FeatDefNum()
+*   	returns total number of FeatDef
+*       loads featdef.val if necessary
+*
+*****************************************************************************/
+NLM_EXTERN Int2 LIBCALL FeatDefNum PROTO((void));
+
+
+/*****************************************************************************
+*
+*   FeatDefFindNext(curr, keyptr, menulabel, group, for_display)
+*   	returns next FeatDef within display group
+*       if group == FEATDEF_ANY returns all
+*       start with curr = NULL and return current in curr until function
+*         returns NULL
+*       keyptr is filled in with featdef-key
+*       menulabel is filled in with menulabel
+*       if for_display == TRUE then group must match display group
+*         else group must match entrygroup
+*       loads featdef.val if necessary
+*
+*****************************************************************************/
+NLM_EXTERN FeatDefPtr LIBCALL FeatDefFindNext PROTO((FeatDefPtr curr, Uint1Ptr keyptr, CharPtr PNTR menulabel, Uint1 group, Boolean for_display));
+
+/*****************************************************************************
+*
+*   #defines for FeatDef types
+*
+*****************************************************************************/
+
+#define FEATDEF_BAD  0
+#define FEATDEF_ANY  255
+
+#define FEATDEF_GENE  1
+#define FEATDEF_ORG   2
+#define FEATDEF_CDS   3
+#define FEATDEF_PROT  4
+#define FEATDEF_preRNA 5
+#define FEATDEF_mRNA  6
+#define FEATDEF_tRNA  7
+#define FEATDEF_rRNA  8
+#define FEATDEF_snRNA 9
+#define FEATDEF_scRNA 10
+#define FEATDEF_otherRNA 11
+#define FEATDEF_PUB   12
+#define FEATDEF_SEQ   13
+#define FEATDEF_IMP   14
+#define FEATDEF_allele 15
+#define FEATDEF_attenuator 16
+#define FEATDEF_C_region 17
+#define FEATDEF_CAAT_signal 18
+#define FEATDEF_Imp_CDS 19
+#define FEATDEF_conflict 20
+#define FEATDEF_D_loop 21
+#define FEATDEF_D_segment 22
+#define FEATDEF_enhancer 23
+#define FEATDEF_exon 24
+#define FEATDEF_GC_signal 25
+#define FEATDEF_iDNA 26
+#define FEATDEF_intron 27
+#define FEATDEF_J_segment 28
+#define FEATDEF_LTR 29
+#define FEATDEF_mat_peptide 30
+#define FEATDEF_misc_binding 31
+#define FEATDEF_misc_difference 32
+#define FEATDEF_misc_feature 33
+#define FEATDEF_misc_recomb 34
+#define FEATDEF_misc_RNA 35
+#define FEATDEF_misc_signal 36
+#define FEATDEF_misc_structure 37
+#define FEATDEF_modified_base 38
+#define FEATDEF_mutation 39
+#define FEATDEF_N_region 40
+#define FEATDEF_old_sequence 41
+#define FEATDEF_polyA_signal 42
+#define FEATDEF_polyA_site 43
+#define FEATDEF_precursor_RNA 44
+#define FEATDEF_prim_transcript 45
+#define FEATDEF_primer_bind 46
+#define FEATDEF_promoter 47
+#define FEATDEF_protein_bind 48
+#define FEATDEF_RBS 49
+#define FEATDEF_repeat_region 50
+#define FEATDEF_repeat_unit 51
+#define FEATDEF_rep_origin 52
+#define FEATDEF_S_region 53
+#define FEATDEF_satellite 54
+#define FEATDEF_sig_peptide 55
+#define FEATDEF_source 56
+#define FEATDEF_stem_loop 57
+#define FEATDEF_STS 58
+#define FEATDEF_TATA_signal 59
+#define FEATDEF_terminator 60
+#define FEATDEF_transit_peptide 61
+#define FEATDEF_unsure 62
+#define FEATDEF_V_region 63
+#define FEATDEF_V_segment 64
+#define FEATDEF_variation 65
+#define FEATDEF_virion 66
+#define FEATDEF_3clip 67
+#define FEATDEF_3UTR 68
+#define FEATDEF_5clip 69
+#define FEATDEF_5UTR 70
+#define FEATDEF_10_signal 71
+#define FEATDEF_35_signal 72
+#define FEATDEF_site_ref 73
+#define FEATDEF_REGION 74
+#define FEATDEF_COMMENT 75
+#define FEATDEF_BOND 76
+#define FEATDEF_SITE 77
+#define FEATDEF_RSITE 78
+#define FEATDEF_USER 79
+#define FEATDEF_TXINIT 80
+#define FEATDEF_NUM 81
+#define FEATDEF_PSEC_STR 82
+#define FEATDEF_NON_STD_RESIDUE 83
+#define FEATDEF_HET 84
+#define FEATDEF_BIOSRC 85
+#define FEATDEF_preprotein 86
+#define FEATDEF_mat_peptide_aa 87
+#define FEATDEF_sig_peptide_aa 88
+#define FEATDEF_transit_peptide_aa 89
+
+#define FEATDEF_MAX 90 /* size of array needed for featdef filter parameters */
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#undef NLM_EXTERN
+#ifdef NLM_EXPORT
+#define NLM_EXTERN NLM_EXPORT
+#else
+#define NLM_EXTERN
+#endif
+
+#endif