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/* tax3api.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: tax3api.h
*
* Author: Jonathan Kans
*
* Version Creation Date: 7/8/04
*
* $Revision: 1.22 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#ifndef _TAX3API_
#define _TAX3API_
#include <ncbi.h>
#include <asn.h>
#include <objtax3.h>
#include <urlquery.h>
#include <objfeat.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
/* low-level connection functions */
NLM_EXTERN CONN Tax3OpenConnection (
void
);
NLM_EXTERN Taxon3ReplyPtr Tax3WaitForReply (
CONN conn
);
/*
Tax3SynchronousQuery opens connection, sends an
ASN.1 request, and waits for a reply, cleaning
up the connection afterwards.
*/
NLM_EXTERN Taxon3ReplyPtr Tax3SynchronousQuery (
Taxon3RequestPtr t3rq
);
/*
Tax3AsynchronousQuery opens connection, send request,
and queues completion routine using urlquery queueing
mechanism.
Tax3CheckQueue should be called several times a second with
a timer. It calls QUERY_CheckQueue to poll connection,
which calls completion routine when result is available,
cleaning up connection afterwards.
Tax3ReadReply take conns and status parameters from completion
routine and reads Taxon3ReplyPtr.
*/
NLM_EXTERN Boolean Tax3AsynchronousQuery (
Taxon3RequestPtr t3rq,
QUEUE* queue,
QueryResultProc resultproc,
VoidPtr userdata
);
NLM_EXTERN Int4 Tax3CheckQueue (
QUEUE* queue
);
NLM_EXTERN Taxon3ReplyPtr Tax3ReadReply (
CONN conn,
EIO_Status status
);
/* request creation function */
NLM_EXTERN Taxon3RequestPtr CreateTaxon3Request (
Int4 taxid,
CharPtr name,
OrgRefPtr orp
);
NLM_EXTERN Taxon3RequestPtr CreateMultiTaxon3Request (ValNodePtr org_list);
NLM_EXTERN Taxon3RequestPtr CreateJoinRequest (ValNodePtr taxon_list);
NLM_EXTERN OrgRefPtr Taxon3GetOrg (OrgRefPtr orp);
NLM_EXTERN ValNodePtr Taxon3GetOrgRefList (ValNodePtr org_list);
NLM_EXTERN void Tax3MergeSourceDescr (SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent);
NLM_EXTERN Int4 Taxon3GetTaxIdByOrgRef (OrgRefPtr orp);
NLM_EXTERN OrgRefPtr Taxon3GetOrgRefByName (CharPtr orgname);
NLM_EXTERN Int4 Taxon3GetTaxIdByName (CharPtr orgname);
NLM_EXTERN void Taxon3ReplaceOrgInSeqEntry (SeqEntryPtr sep, Boolean keep_syn);
NLM_EXTERN void Taxon3ReplaceOrgInSeqEntryEx (SeqEntryPtr sep, Boolean keep_syn, Boolean replace_unpub);
NLM_EXTERN void Taxon3CheckOrgInSeqEntry (SeqEntryPtr sep, ValNodePtr PNTR not_found, ValNodePtr PNTR bad_match);
NLM_EXTERN void CheckTaxNamesAgainstTaxDatabase (ValNodePtr PNTR discrepancy_list, ValNodePtr sep_list);
typedef enum {
eReturnedOrgFlag_normal = 0x004,
eReturnedOrgFlag_misspelled = 0x008,
eReturnedOrgFlag_ambiguous = 0x010,
eReturnedOrgFlag_unpublished = 0x020,
eReturnedOrgFlag_error = 0x040
} EReturnedOrgFlag;
typedef enum {
eSpecificHostFix_unrecognized = 0,
eSpecificHostFix_spelling,
eSpecificHostFix_capitalization,
eSpecificHostFix_truncation,
eSpecificHostFix_replacement,
eSpecificHostFix_ambiguous
} ESpecificHostFix;
NLM_EXTERN void
Taxon3ValidateSpecificHostsInSeqEntry
(SeqEntryPtr sep,
ValNodePtr PNTR misspelled_list,
ValNodePtr PNTR bad_caps_list,
ValNodePtr PNTR ambiguous_list,
ValNodePtr PNTR unrecognized_list);
typedef struct specifichostfix {
ValNodePtr feat_or_desc;
CharPtr bad_specific_host;
CharPtr old_taxname;
CharPtr new_taxname;
Uint1 fix_type;
} SpecificHostFixData, PNTR SpecificHostFixPtr;
extern ValNodePtr SpecificHostFixListFree (ValNodePtr vnp);
extern Boolean ApplyOneSpecificHostFix (SpecificHostFixPtr s);
/* returns ValNodePtr list of SpecificHostFixPtr */
NLM_EXTERN ValNodePtr Taxon3GetSpecificHostFixesInSeqEntry (SeqEntryPtr sep, Boolean caps, Boolean paren);
NLM_EXTERN ValNodePtr GetOrganismTaxLookupFailuresInSeqEntry (SeqEntryPtr sep);
typedef struct taxfixitem {
Uint1 data_choice;
Pointer data;
OrgRefPtr response_org;
CharPtr taxname;
CharPtr suggested_fix;
CharPtr rank;
} TaxFixItemData, PNTR TaxFixItemPtr;
NLM_EXTERN TaxFixItemPtr TaxFixItemNew (void);
NLM_EXTERN TaxFixItemPtr TaxFixItemCopy (TaxFixItemPtr orig);
NLM_EXTERN TaxFixItemPtr TaxFixItemFree (TaxFixItemPtr t);
NLM_EXTERN ValNodePtr LIBCALLBACK TaxFixItemListFree (ValNodePtr vnp);
NLM_EXTERN ValNodePtr Taxon3GetTaxFixList (ValNodePtr biop_list);
NLM_EXTERN OrgRefPtr GetCommonOrgRefForSeqEntry (SeqEntryPtr sep);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif /* _TAX3API_ */
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