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#ifndef _TOASN3_
#define _TOASN3_
/* $Id: toasn3.h,v 6.14 2009/06/03 20:13:16 kans Exp $
* ===========================================================================
*
* 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.
*
* ===========================================================================
*
* Author:
*
* File Description:
*
*
* ===========================================================================
*/
#include <ncbi.h>
#include <seqport.h>
#ifdef __cplusplus
extern "C" {
#endif
#define INFO_ASNOLD 0
#define INFO_ASNNEW 1
#define ERR_REJECT 2
#define ERR_INPUT 4
typedef struct {
ValNodePtr pept;
ValNodePtr cds;
} SeqFeatArr, PNTR SeqFeatArrPtr;
typedef struct {
CharPtr name;
Uint1 num;
} ORGMOD;
typedef struct {
BioseqSetPtr bioset;
ValNodePtr list;
} PubList, PNTR PubListPtr;
typedef struct {
Boolean first;
ValNodePtr list;
} PubSetList, PNTR PubSetListPtr;
typedef struct qualmap{
CharPtr name;
Boolean same;
} QualMap, PNTR QualMapPtr;
typedef struct bsmap{
BioSourcePtr bsp;
Boolean same;
} BSMap, PNTR BSMapPtr;
typedef struct orgfix {
SeqEntryPtr contains;
Boolean desc; /* descriptor containing org-ref */
SeqFeatPtr sfp; /* or feature containing the org-ref */
SeqFeatPtr imp; /* ImpFeat source */
OrgRefPtr orp;
ValNodePtr modif;
BioSourcePtr bsp;
Int4 index;
struct orgfix PNTR next;
} OrgFix, PNTR OrgFixPtr;
typedef struct molfix {
SeqEntryPtr contains;
Uint1 mol; /* mol_type */
ValNodePtr modif; /* descriptor containing modif */
Uint1 method; /* method */
MolInfoPtr molinfo;
Int4 index;
struct molfix PNTR next;
} MolFix, PNTR MolFixPtr;
typedef struct toasn3 {
OrgFixPtr ofp;
MolFixPtr mfp;
Boolean had_biosource;
Boolean had_molinfo;
} ToAsn3, PNTR ToAsn3Ptr;
Int4 ToAsn4(SeqEntryPtr sep);
Int4 SeqEntryPubsAsn4(SeqEntryPtr sep);
Int4 SeqEntryToAsn3(SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean taxserver, SeqEntryFunc taxfun);
Int4 SeqEntryToAsn3Ex(SeqEntryPtr sep, Boolean strip, Boolean correct, Boolean taxserver, SeqEntryFunc taxfun, SeqEntryFunc taxmerge, Boolean gpipeMode);
Int2 seq_loc_compare( SeqLocPtr a, SeqLocPtr b);
void compare_quals(GBQualPtr PNTR qual1, GBQualPtr PNTR qual2);
Boolean feat_join(SeqFeatPtr f1, SeqFeatPtr f2, SeqFeatPtr head);
void count_join(SeqFeatPtr f1, SeqFeatPtr f2);
void CountSourceFeat(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
void CorrectSourceFeat(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
Boolean CheckLocWhole(BioseqPtr bsp, SeqLocPtr slp);
void FindOrg(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
void CheckQuals(BioSourcePtr bsp, GBQualPtr sfp);
void CheckQualsWithComm(BioSourcePtr bsp, SeqFeatPtr sfp);
MolInfoPtr new_info(MolInfoPtr mfi);
MolInfoPtr ModToMolInfo(MolInfoPtr mfi, Uint1 mod);
void ModToBiosource(BioSourcePtr bsp, Uint1 mod);
void StripOld(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
void CkOrg(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
void MergeBSinDescr(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
Int4 FixNucProtSet(SeqEntryPtr sep);
void CheckBS(SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
Int4 BSComparison(BioSourcePtr one, BioSourcePtr two);
Int4 BSComparisonEx(BioSourcePtr one, BioSourcePtr two, Boolean clone);
Int2 BioSourceToGeneticCode(BioSourcePtr biop);
ValNodePtr GetMultBiosource(SeqEntryPtr sep);
/****************************************************
* Does a SeqEntryExplore, calling ImpFeatToCdregion() on
* each feature table found
*
****************************************************/
void EntryChangeImpFeat(SeqEntryPtr sep);
/****************************************************
* Changes a SeqFeat of type Imp-feat CDS to a real
* CdRegion in place (sfp does not change)
* returns TRUE if the change happened
* returns FALSE if no changes were made
* (so also returns FALSE if not an Imp-feat of type CDS)
*
*****************************************************/
Boolean ImpFeatToCdregion(SeqFeatPtr sfp);
void CdCheck(SeqEntryPtr sep, FILE *fp);
/****************************************************
* Creates source string from BioSource structure
* Compare with GBBlock.source
* deletes GBBlock.source if it's the same as from BioSource
*
*****************************************************/
void EntryChangeGBSource(SeqEntryPtr sep);
/****************************************************
* Finds multiple biosource descriptors on the same chain with
* the same taxonomic name, moves subsource, orgmod, and some
* other blocks, conservatively, deletes second biosource
*
*****************************************************/
void EntryMergeDupBioSources(SeqEntryPtr sep);
/****************************************************
* Checks GBBlock.source, .taxonomy, and .div, removes any empty
* GBBlock descriptors, and returns TRUE if information (other
* than PAT or SYN division) exists in the these fields
*
*****************************************************/
Boolean EntryCheckGBBlock(SeqEntryPtr sep);
void EntryChangeImpFeatToProt(SeqEntryPtr sep);
void CombineBSFeat(SeqEntryPtr sep);
void ChangeReplaceToQual(SeqFeatPtr sfp);
void AddReplaceQual(SeqFeatPtr sfp, CharPtr p);
Boolean SeqEntryMoveDbxrefs (SeqEntryPtr sep);
/* functions moved from Sequin */
void NormalizePeriodsOnInitials (SeqEntryPtr sep);
void MoveRnaGBQualProductToName (SeqEntryPtr sep);
void MoveProtGBQualProductToName (SeqEntryPtr sep);
void MoveCdsGBQualProductToName (SeqEntryPtr sep);
void MoveFeatGBQualsToFields (SeqEntryPtr sep);
void StripTitleFromProtsInNucProts (SeqEntryPtr sep);
void GetRidOfEmptyFeatsDescCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
/* from move_cds (S. Bazhin) */
Uint2 move_cds(SeqEntryPtr sep);
Uint2 move_cds_ex (SeqEntryPtr sep, Boolean doPseudo);
/* more functions moved from Sequin, placed in toporg.c */
extern void CleanUpPseudoProducts (Uint2 entityID, SeqEntryPtr sep);
extern void CleanupGenbankCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
extern void MergeAdjacentAnnotsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
extern void CleanupEmptyFeatCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent);
extern void RemoveBioSourceOnPopSet (SeqEntryPtr sep, OrgRefPtr master);
extern Boolean NoBiosourceOrTaxonId (SeqEntryPtr sep);
extern void ExtendGeneFeatIfOnMRNA (Uint2 entityID, SeqEntryPtr sep);
extern void ConvertFullLenSourceFeatToDesc (SeqEntryPtr sep);
extern void ConvertFullLenPubFeatToDesc (SeqEntryPtr sep);
/* SeriousSeqEntryCleanup combines many of the above cleanups */
extern void SeriousSeqEntryCleanup (SeqEntryPtr sep, SeqEntryFunc taxfun, SeqEntryFunc taxmerge);
/* SeriousSeqEntryCleanupBulk does not clean up pseudo products, instead posting a message */
extern void SeriousSeqEntryCleanupBulk (SeqEntryPtr sep);
/* Genome Pipeline variant that leaves redundant gene xrefs, does not normalize descriptor order */
extern void GpipeSeqEntryCleanup (SeqEntryPtr sep);
#ifdef __cplusplus
}
#endif
#endif
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