NCBI C Toolkit Cross Reference

   /*   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: 6.14 $
  *
  * File Description: 
  *
  * Modifications:  
  * --------------------------------------------------------------------------
  * $Log: cdrgn.h,v $
  * 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);
 
 #ifdef __cplusplus
 }
 #endif
 
 #endif /* ndef _CDRGN_ */