NCBI C Toolkit Cross Reference

   /*   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: 1.19 $
  *
  * 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 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 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 = 3,
   eReturnedOrgFlag_misspelled = 4,
   eReturnedOrgFlag_ambiguous = 5,
   eReturnedOrgFlag_error
 } 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);
 
 
 
 #ifdef __cplusplus
 }
 #endif
 
 #undef NLM_EXTERN
 #ifdef NLM_EXPORT
 #define NLM_EXTERN NLM_EXPORT
 #else
 #define NLM_EXTERN
 #endif
 
 #endif /* _TAX3API_ */