/* 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 #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_ */