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/* txcommon.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: txcommon.h
*
* Author: Vladimir Soussov
*
* File Description: Common data types & prototypes for taxonomy server/client
*
*
* $Log: txcommon.h,v $
* Revision 1.5 2001/09/18 16:55:38 soussov
* switching to the new ASN
*
* Revision 1.4 1999/12/20 17:05:16 soussov
* taxid4gi added
*
* Revision 1.3 1999/01/28 15:43:11 soussov
* rename the formal argument
*
* Revision 1.2 1998/06/12 15:16:07 soussov
* kill some warnings
*
* Revision 1.1 1998/02/10 20:12:05 soussov
* taxon2 related soft
*
* Revision 1.2 1997/05/12 18:31:44 soussov
* 05/12/97
*
* Revision 1.1.1.1 1997/04/30 21:29:57 soussov
* initial tree for taxon2
*
*
*/
#ifndef TXCOMMON_H_DONE
#define TXCOMMON_H_DONE
#include <ncbi.h>
#define TAX_DIV_TXT 0
#define TAX_DIV_CDE 1
#define TAX_DIV_COM 2
#define TAX_GC_NM 0
#define TAX_GC_ABBREV 1
#define TAX_GC_CDE 2
#define TAX_GC_STARTS 3
#define TAX_NAME_SEARCH 0
#define TAX_RE_SEARCH 1
#define TAX_TOKEN_SEARCH 2
#define INHERIT_DIV 0x1
#define INHERIT_GC 0x2
#define INHERIT_MGC 0x4
#define GB_HIDDEN 0x8
#define TAX_HIDDEN 0x10
#define TAX_REFERENCED 0x20
#define TXC_INH_DIV 0x4000000
#define TXC_INH_GC 0x8000000
#define TXC_INH_MGC 0x10000000
/* the following flags are the same (it is not bug) */
#define TXC_SUFFIX 0x20000000
#define TXC_UPDATED 0x20000000
#define TXC_UNCULTURED 0x20000000
#define TXC_GBHIDE 0x40000000
#define TXC_STHIDE 0x80000000
#define TXCL_DEL_NAME 1
#define TXCL_ADD_NAME 2
#define TXCL_ADD_NODE 3
#define TXCL_UPD_NODE 4
#define TXCL_DEL_NODE 5
#define TXCL_DEL_SUBTREE 6
#define TXCL_MOVE_SUBTREE 7
#define TXCL_MERGE_NODES 8
#define TXCL_MOVE_CHILDREN 9
#define TXCL_CIT_LINK 10
#define TXCL_CIT_UNLINK 11
#define TXCL_CIT_DELETE 12
#define TXCL_SS_ADD 13
#define TXCL_SS_CHECK 14
#define TXCL_SS_DELETE 15
#define WWW_NAME_NOT_FOUND -100
#define WWW_NODE_NOT_FOUND -110
#define WWW_MULT_NODES_BEGIN -200
#define WWW_MULT_NODES_END -210
#define WWW_TREE_BEGIN -300
#define WWW_LEVEL_BEGIN -320
#define WWW_LEVEL_END -330
#define WWW_TREE_END -390
#define WWW_LIN_BEGIN -400
#define WWW_LIN_END -490
#define WWW_INFO_BEGIN -500
#define WWW_INFO_END -590
#define WWW_NAMES_BEGIN -600
#define WWW_NAMES_END -690
#define WWW_DIVISION -1000
#define WWW_RANK -1010
#define WWW_GC -1020
#define WWW_MGC -1030
#define WWW_NUCLEOTIDE -1040
#define WWW_PROTEIN -1050
#define WWW_NO_SEQUENCES -2000
#define WWWTAX_NAME_SEARCH 0x1
#define WWWTAX_REXP_SEARCH 0x2
#define WWWTAX_TOKEN_SEARCH 0x4
#define WWW_SHOW_ALL 0x8
#define WWW_SHOW_NUCLEOTIDE 0x10
#define WWW_SHOW_PROTEIN 0x20
#define WWW_SHOW_SEQ 0x30
typedef struct t_TaxNamePublic {
Int4 tax_id;
CharPtr name_txt;
CharPtr unique_name;
Uint1 class_cde;
Uint1 designator;
} TaxName, PNTR TaxNamePtr;
/* taxonomy node */
typedef struct t_TXC_NodeData {
Int4 tax_id;
Uint4 crt_date;
Uint4 upd_date;
Uint4 nucleotides, proteins;
Int1 rank_id;
Int1 gc_id;
Int1 mgc_id;
Int1 div_id;
Char embl_cde[4];
Uint2 hist;
Uint2 flags;
} TXC_NodeData, PNTR TXC_NodeDataPtr;
typedef struct t_TXC_TreeNode {
Int4 tax_id;
Uint4 flags;
char node_label[2];
} PNTR TXC_TreeNodePtr;
typedef struct t_nameClass {
Int2 priority;
char class_txt[34];
} TaxNameClass, PNTR TaxNameClassPtr;
typedef struct t_rank {
char rank_txt[64];
} TaxRank, PNTR TaxRankPtr;
typedef struct t_division {
char div_cde[4];
char div_txt[64];
} TaxDivision, PNTR TaxDivisionPtr;
typedef struct t_genCode {
char gc_name[128];
} TaxGenCode, PNTR TaxGenCodePtr;
typedef struct t_ssRec {
Int4 r_id;
char sname[120];
char rname[120];
Uint1 stype, rtype;
} TaxSSRec, PNTR TaxSSRecPtr;
CharPtr tax_prntTime(Int4 t);
Int4 tax_getBaseTime(void);
Int4 tax_getTime(void);
Int4 tax_findByName(CharPtr sname, int mode, TaxNamePtr* res_name);
Int4 tax_getIdByName(CharPtr org_name, CharPtr qualif, Int1 q_type);
Int4 tax_getDesignator(CharPtr name);
Int4 tax_uniqueName(CharPtr s_name, Int4 tax_id);
Boolean tax_setDesignator(CharPtr name, Int4 tax_id);
Int4 tax_issueTaxId(void);
Boolean tax_addName(Int4 tax_id, CharPtr name, CharPtr uname, Int2 name_class, Boolean designat);
Int4 tax_getOrgNames(Int4 tax_id, TaxNamePtr* org_names);
CharPtr tax_getTaxName(Int4 tax_id, CharPtr* unique_name);
Boolean tax_delName(Int4 tax_id, CharPtr dname);
Boolean tax_delAllNodeNames(Int4 tax_id);
Boolean tax_addNameClass(Int4 class_cde, CharPtr class_txt, Int4 priority);
CharPtr tax_getNameClass(Int4 class_cde, Int4Ptr priority);
Int4 tax_getClass_cde(CharPtr class_txt);
Boolean tax_dumpNameClasses(void (*dmpFunc)(VoidPtr, Int2, Int2, CharPtr), VoidPtr usrData);
Boolean tax_addRank(Int2 rank_id, CharPtr rank_txt);
CharPtr tax_getRank(Int2 rank_id);
Int2 tax_getRankId(CharPtr rank_txt);
Boolean tax_dumpRanks(void (*dmpFunc)(VoidPtr, Int2, CharPtr), VoidPtr usrData);
Boolean tax_addDivision(Int4 div_id, CharPtr div_cde, CharPtr div_txt);
Boolean tax_getDivision(Int2 div_id, CharPtr* div_cde, CharPtr* div_txt);
Int2 tax_getDivisionId(CharPtr div_cde, CharPtr div_txt);
Boolean tax_dumpDivisions(void (*dmpFunc)(VoidPtr, Int2, CharPtr, CharPtr), VoidPtr usrData);
Boolean tax_addGC(Int2 gc_id, CharPtr gc_name);
CharPtr tax_getGCName(Int2 gc_id);
Int2 tax_getGCId(CharPtr gc_txt);
Boolean tax_dumpGCs(void (*dmpFunc)(VoidPtr, Int2, CharPtr), VoidPtr usrData);
Boolean tax_matchName(CharPtr orgName, CharPtr str, Int4 mode);
Int4 tax_getTaxId4GI(Int4 gi);
#endif
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