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/* cdrgn.h
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* 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 do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* 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.
*
* ===========================================================================
*
* File Name: cdrgn.h
*
* Author: Jonathan Kans
*
* Version Creation Date: 1/22/95
*
* $Revision: 6.15 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: cdrgn.h,v $
* Revision 6.15 2010/09/21 12:54:12 bollin
* Fixed bug in update mRNA spans button - needs to use original location to
* find mRNA to update.
*
* Revision 6.14 2009/09/02 15:08:39 bollin
* New RNA editing.
*
* Revision 6.13 2008/01/17 21:18:09 bollin
* Fixes for RNA dialog for ncRNA product/class handling
*
* Revision 6.12 2007/12/21 17:30:27 bollin
* Changes to dialog for selecting ncRNA class and RNA type - allow ncRNA class
* Any if selecting RNA type in a constraint context, test dialog to generate
* error if "other" is the class but no text is specified.
*
* Revision 6.11 2007/11/26 21:16:29 bollin
* Moved CreatencRNAClassDialog proto into cdrgn.h
*
* Revision 6.10 2007/09/21 18:05:23 bollin
* code in place for conversion of old-style misc_RNA, snRNA, scRNA, and snoRNA
* features to new ncRNA features, commented out until changeover.
*
* Revision 6.9 2007/09/10 20:08:51 bollin
* Correction to MatchesRnaType
*
* Revision 6.8 2007/09/10 18:47:11 kans
* prototype for SetRnaSpecificQuals, cast for codon argument to ParseTRnaString
*
* Revision 6.7 2007/09/10 18:33:15 bollin
* Changes for new ncRNA and tmRNA class editor.
*
* Revision 6.6 2007/07/25 13:53:12 bollin
* Removed local copy of TruncateLocation from sequin3.c, made TruncateLocation
* function in desktop/cdrgn.c extern and added prototype to cdrgn.h
*
* Revision 6.5 2003/10/23 16:43:56 kans
* changed operon to import feature
*
* Revision 6.4 2003/10/07 13:52:01 kans
* added gap, operon, oriT features and ecotype, estimated_length and operon qualifiers
*
* Revision 6.3 2000/07/08 20:44:00 vakatov
* Get all "#include" out of the 'extern "C" { }' scope; other cleanup...
*
* ==========================================================================
*/
#ifndef _CDRGN_
#define _CDRGN_
#include <dlogutil.h>
#ifdef __cplusplus
extern "C" {
#endif
#define REGISTER_CDRGN_EDIT ObjMgrProcLoad(OMPROC_EDIT,"Edit CdRgn","CDS",OBJ_SEQFEAT,FEATDEF_CDS,OBJ_SEQFEAT,FEATDEF_CDS,NULL,CdRgnGenFunc,PROC_PRIORITY_DEFAULT)
extern ForM CreateCdRgnForm (Int2 left, Int2 top, CharPtr title,
SeqFeatPtr sfp, SeqEntryPtr sep,
FormActnFunc actproc);
extern Int2 LIBCALLBACK CdRgnGenFunc (Pointer data);
extern void CdRgnFeatFormActnProc (ForM f);
extern void CdRgnTranslateWithFrame (ForM f, Uint1 frame);
extern SeqLocPtr PredictCodingRegion (BioseqPtr nuc, BioseqPtr prot, Int2 genCode);
#define REGISTER_GENE_EDIT ObjMgrProcLoad(OMPROC_EDIT,"Edit Gene","Gene",OBJ_SEQFEAT,FEATDEF_GENE,OBJ_SEQFEAT,FEATDEF_GENE,NULL,GeneGenFunc,PROC_PRIORITY_DEFAULT)
extern ForM CreateGeneForm (Int2 left, Int2 top, CharPtr title,
SeqFeatPtr sfp, SeqEntryPtr sep,
FormActnFunc actproc);
extern Int2 LIBCALLBACK GeneGenFunc (Pointer data);
#define REGISTER_PROT_EDIT(PROCNAME,PROCLABEL,SUBTYPE) ObjMgrProcLoad(OMPROC_EDIT,PROCNAME,PROCLABEL,OBJ_SEQFEAT,SUBTYPE,OBJ_SEQFEAT,SUBTYPE,NULL,ProtGenFunc,PROC_PRIORITY_DEFAULT)
extern ForM CreateProtForm (Int2 left, Int2 top, CharPtr title,
SeqFeatPtr sfp, SeqEntryPtr sep,
FormActnFunc actproc);
extern Int2 LIBCALLBACK ProtGenFunc (Pointer data);
#define REGISTER_RNA_EDIT(PROCNAME,PROCLABEL,SUBTYPE) ObjMgrProcLoad(OMPROC_EDIT,PROCNAME,PROCLABEL,OBJ_SEQFEAT,SUBTYPE,OBJ_SEQFEAT,SUBTYPE,NULL,RnaGenFunc,PROC_PRIORITY_DEFAULT)
extern ForM CreateRnaForm (Int2 left, Int2 top, CharPtr title,
SeqFeatPtr sfp, SeqEntryPtr sep,
Uint2 subtype, FormActnFunc actproc);
extern Int2 LIBCALLBACK RnaGenFunc (Pointer data);
extern void ConvertProductQualToRnaRefName (SeqFeatPtr sfp);
extern SeqLocPtr TruncateLocation (SeqLocPtr head, Int4 len);
/* for searching for RNA values of a certain type */
typedef struct rnatype {
Int4 rna_featdef; /* use FEATDEF_ANY for match any RNA */
CharPtr ncrna_class; /* value to look for in ncrna_class qual */
} RnaTypeData, PNTR RnaTypePtr;
extern RnaTypePtr RnaTypeFree (RnaTypePtr rtp);
extern Boolean MatchesRnaType (SeqFeatPtr sfp, RnaTypePtr rtp);
extern void ApplyRnaTypeToSeqFeat (SeqFeatPtr sfp, RnaTypePtr rtp);
extern void ApplyProductToRNA (SeqFeatPtr sfp, CharPtr product);
extern void AddToComment (SeqFeatPtr sfp, CharPtr comment);
extern DialoG RnaTypeDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
extern DialoG CreatencRNAClassDialog (GrouP h, Boolean is_constraint, Nlm_ChangeNotifyProc change_notify, Pointer change_userdata);
NLM_EXTERN void UpdatemRNAAfterEditing(DialoG d, SeqLocPtr old_slp, SeqLocPtr new_slp);
#ifdef __cplusplus
}
#endif
#endif /* ndef _CDRGN_ */
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