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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: 6.16 $
*
* File Description: Sequence editing utilities
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
* $Log: valid.h,v $
* Revision 6.16 2004/10/04 15:50:22 kans
* added vsp->justShowAccession for extremely terse output
*
* Revision 6.15 2004/09/10 17:52:05 kans
* changed ValidateLimit enum to Int2 defines
*
* Revision 6.14 2004/09/10 15:31:43 kans
* added farFetchMRNAproducts, locusTagGeneralMatch, validationLimit flags to vsp
*
* Revision 6.13 2004/05/06 19:42:22 kans
* new function GetValidCountryList for access to country code list, which is now NULL terminated
*
* Revision 6.12 2003/12/02 15:37:37 kans
* added vsp->seqSubmitParent for use by tbl2asn, which usually has a Seq-submit wrapper that is added on-the-fly and not indexed
*
* Revision 6.11 2003/11/14 18:07:17 kans
* alignment parameters to find remote bsp, do seqhist assembly
*
* Revision 6.10 2003/03/05 18:47:45 ford
* Added prototype for IsNuclAcc().
*
* Revision 6.9 2003/02/18 20:19:29 kans
* added vsp->validateIDSet, initial work on validating update against ID set in database
*
* Revision 6.8 2002/10/28 19:30:34 kans
* added farFetchCDSproducts to vsp
*
* Revision 6.7 2002/07/16 17:13:09 kans
* added sourceQualTags to vsp, ERR_SEQ_DESCR_StructuredSourceNote by finite state machine text search
*
* Revision 6.6 2002/03/12 22:27:00 kans
* added alwaysRequireIsoJTA
*
* Revision 6.5 2000/02/14 15:00:19 kans
* added vsp->farIDsInAlignments for use by alignment validator
*
* Revision 6.4 1999/12/24 01:21:06 kans
* added validateAlignments flag controlling call to ValidateSeqAlignWithinValidator
*
* Revision 6.3 1999/07/22 22:04:36 kans
* added suppressContext flag
*
* Revision 6.2 1999/05/03 20:06:36 kans
* if no pubs or no biosource, report only once, not once per bioseq
*
* Revision 6.1 1998/07/02 17:53:47 kans
* useSeqMgrIndexes field added to ValidStructPtr, validator can use either old (nested gathers) or new (SeqMgr indexing) method
*
* Revision 6.0 1997/08/25 18:08:29 madden
* Revision changed to 6.0
*
* Revision 5.1 1997/06/19 18:39:54 vakatov
* [WIN32,MSVC++] Adopted for the "NCBIOBJ.LIB" DLL'ization
*
* Revision 5.0 1996/05/28 13:23:23 ostell
* Set to revision 5.0
*
* Revision 4.1 1996/01/23 23:10:10 kans
* added onlyspell and justwarnonspell to ValidStructPtr
*
* Revision 4.0 1995/07/26 13:49:01 ostell
* force revision to 4.0
*
* Revision 1.4 1995/06/03 13:45:47 ostell
* changes made in valid to use gather functions and ErrPostItem instead
* of previous custom functions
*
* Revision 1.3 1995/05/15 21:46:05 ostell
* added Log line
*
*
*
* ==========================================================================
*/
#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);
#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 */
Int2 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 */
Int2 validationLimit; /* limit validation to major classes in Valid1GatherProc */
TextFsaPtr sourceQualTags; /* for detecting structured qual tags in notes */
} 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 PNTR GetValidCountryList (void);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif
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