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/* valid.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: valid.h
*
* Author: James Ostell
*
* Version Creation Date: 1/1/94
*
* $Revision: 6.54 $
*
* File Description: Sequence editing utilities
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
* ==========================================================================
*/
#ifndef _NCBI_Valid_
#define _NCBI_Valid_
/*****************************************************************************
*
* valid.h
* values for cutoff are
* 0 INFO
* 1 WARN
* 2 ERROR
* 3 FATAL
*
*****************************************************************************/
#ifndef _NCBI_Seqport_
#include <seqport.h>
#endif
#ifndef _GATHER_
#include <gather.h>
#endif
#ifndef _SQNUTILS_
#include <sqnutils.h>
#endif
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
typedef void (*SpellCallBackFunc) (char * str);
typedef int (* SpellCheckFunc) (char *String, SpellCallBackFunc);
/* callback type for finer error reporting */
typedef void (LIBCALLBACK *ValidErrorFunc) (
ErrSev severity,
int errcode,
int subcode,
Uint2 entityID,
Uint2 itemtype,
Uint4 itemID,
CharPtr accession,
CharPtr featureID,
CharPtr message,
CharPtr objtype,
CharPtr label,
CharPtr context,
CharPtr location,
CharPtr product,
Pointer userdata
);
#define SET_DEPTH 20
#define VALIDATE_ALL 0
#define VALIDATE_INST 1
#define VALIDATE_HIST 2
#define VALIDATE_CONTEXT 3
#define VALIDATE_GRAPH 4
#define VALIDATE_SET 5
#define VALIDATE_FEAT 6
#define VALIDATE_DESC 7
typedef struct validstruct {
Int2 cutoff; /* lowest errmsg to show 0=default */
Int4 errors[6];
SeqEntryPtr sep; /* top level SeqEntryPtr */
BioseqSetPtr bssp; /* current bioseqset */
BioseqPtr bsp; /* current bioseq */
SeqFeatPtr sfp; /* current feature */
ValNodePtr descr; /* current descriptor */
Uint4 descrs [SET_DEPTH]; /* bit flags set by descriptor type */
Int2 protcnt, nuccnt, segcnt;
CharPtr errbuf;
Boolean patch_seq; /* repair invalid sequence residues? */
Boolean non_ascii_chars; /* non ascii chars found in read? */
Boolean suppress_no_pubs; /* internal use for no pub anywhere message */
Boolean suppress_no_biosrc; /* internal use for no biosource anywhere message */
SpellCheckFunc spellfunc;
SpellCallBackFunc spellcallback;
GatherContextPtr gcp; /* used for reporting the errors */
/* this section used for checking Bioseqs */
Uint2 bsp_partial_val; /* return from SeqLocPartial on segmented SeqLoc */
Boolean onlyspell; /* only do spell check */
Boolean justwarnonspell; /* severity WARNING instead of ERROR on spell */
Boolean useSeqMgrIndexes; /* new style indexing to speed up validation */
Boolean suppressContext; /* suppress context part of message */
Boolean validateAlignments; /* call alignval test suite */
Boolean farIDsInAlignments; /* fetch to get far IDs in alignments */
Boolean alignFindRemoteBsp; /* do remote fetching in alignment validation */
Boolean doSeqHistAssembly; /* do alignment validation in Seq-hist.assembly */
Boolean alwaysRequireIsoJTA; /* force check for iso_jta */
Boolean farFetchCDSproducts; /* lock CDS->products for CdTransCheck, if necessary */
Boolean farFetchMRNAproducts; /* lock MRNA->products for MrnaTransCheck, if necessary */
Boolean locusTagGeneralMatch; /* expect locus_tag to match Seq-id.general of CDS and mRNA product */
Boolean validateIDSet; /* look for gain or loss of general IDs on sequence update */
Boolean seqSubmitParent; /* flag from tbl2asn to suppress no pub message */
Boolean justShowAccession; /* extremely terse output with accession and error type */
Boolean ignoreExceptions; /* report translation and transcription problems even if exception set */
Boolean validateExons; /* check splice sites on exon features except at ends of overlapping CDS */
Boolean inferenceAccnCheck; /* lookup inference qualifier accession.version reference */
Boolean testLatLonSubregion; /* validate coordinates of states and provinces within a country */
Boolean strictLatLonCountry; /* bodies of water do not relax country vs. lat_lon mismatch */
Boolean rubiscoTest; /* look for ribulose bisphosphate variants */
Boolean indexerVersion; /* special tests for GenBank indexers */
Int2 validationLimit; /* limit validation to major classes in Valid1GatherProc */
/* this section used for finer error reporting callback */
ValidErrorFunc errfunc;
Pointer userdata;
Boolean convertGiToAccn;
/* this section used for internal flags */
TextFsaPtr sourceQualTags; /* for detecting structured qual tags in notes */
TextFsaPtr modifiedBases; /* permitted modified bases in PCR_primer qualifier */
TextFsaPtr sgmlStrings; /* for detecting possible SGML tags in strings */
Boolean is_htg_in_sep; /* record has technique of htgs 0 through htgs 3 */
Boolean is_barcode_sep; /* record has technique barcode */
Boolean is_refseq_in_sep; /* record has seqid of type other (refseq) */
Boolean is_gps_in_sep; /* record has genomic product set */
Boolean is_embl_ddbj_in_sep; /* record has embl or ddbj seqid */
Boolean is_insd_in_sep; /* record has genbank/embl/ddbj or tpg/tpe/tpd seqid */
Boolean only_lcl_gnl_in_sep; /* record has seqid of only local or general */
Boolean has_gnl_prot_sep; /* protein Bioseq has general seqid */
Boolean is_smupd_in_sep; /* record in INSD internal processing */
Boolean feat_loc_has_gi; /* at least one feature has a gi location reference */
Boolean feat_prod_has_gi; /* at least one feature has a gi product reference */
Boolean far_fetch_failure; /* a far location or bioseq with no fetch function */
VoidPtr rrna_array; /* sorted feature index array of rRNA features */
VoidPtr trna_array; /* sorted feature index array of tRNA features */
Int4 numrrna; /* number of rRNA features */
Int4 numtrna; /* number of tRNA features */
} ValidStruct, PNTR ValidStructPtr;
NLM_EXTERN Boolean ValidateSeqEntry PROTO((SeqEntryPtr sep, ValidStructPtr vsp));
NLM_EXTERN void ValidStructClear (ValidStructPtr vsp); /* 0 out a ValidStruct */
NLM_EXTERN ValidStructPtr ValidStructNew (void);
NLM_EXTERN ValidStructPtr ValidStructFree (ValidStructPtr vsp);
NLM_EXTERN void SpellCallBack (char * str);
NLM_EXTERN Boolean IsNuclAcc (CharPtr name);
NLM_EXTERN CharPtr GetValidCategoryName (int errcode);
NLM_EXTERN CharPtr GetValidErrorName (int errcode, int subcode);
NLM_EXTERN CharPtr GetValidExplanation (int errcode, int subcode);
NLM_EXTERN CharPtr PNTR GetValidCountryList (void);
NLM_EXTERN Boolean CountryIsValid (CharPtr name, BoolPtr old_countryP, BoolPtr bad_capP);
NLM_EXTERN CharPtr GetCorrectedCountryCapitalization (CharPtr name);
NLM_EXTERN Boolean LookForECnumberPattern (CharPtr str);
NLM_EXTERN Boolean IsCountryInLatLonList (CharPtr country);
NLM_EXTERN Boolean TestLatLonForCountry (CharPtr country, FloatHi lat, FloatHi lon);
NLM_EXTERN CharPtr GuessCountryForLatLon (FloatHi lat, FloatHi lon);
NLM_EXTERN Boolean StringContainsBodyOfWater (CharPtr str);
NLM_EXTERN Boolean ParseStructuredVoucher (CharPtr subname, CharPtr PNTR inst, CharPtr PNTR id);
NLM_EXTERN Boolean VoucherInstitutionIsValid (CharPtr inst);
/* EC_number finite state machine persists to avoid expensive reload, should free on program exit */
NLM_EXTERN void ECNumberFSAFreeAll (void);
NLM_EXTERN Boolean HasTpaUserObject (BioseqPtr bsp);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
|
