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/*===========================================================================
*
* 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: cblast.h
*
* Author: Yanli Wang
*
* Initial Version Creation Date: 6/25/2002
*
* File Description:
* header file for the CBLAST server CGI-bin
*
* Modifications:
* --------------------------------------------------------------------------
* $Log: cblast.h,v $
* Revision 1.6 2002/12/31 21:00:33 ywang
* read environment variables from config file
*
* Revision 1.5 2002/12/12 15:59:45 ywang
* wording improvement
*
*
*
* ==========================================================================
*/
#define MMDBCALL "http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid="
#define ENTREZCALL "http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?db=Protein&form=6&Dopt=g&uid="
#define WRPSBCALL "wrpsb.cgi?DATALIB=oasis_sap&INPUT_TYPE=access&GRAPH=2&FILTER=T&SEQUENCE="
#define MaxEntryPerPage 50
/*---------------------------------------------------------------------------*/
/* static global variables */
/*---------------------------------------------------------------------------*/
static Char URLBase[PATH_MAX];
static Char URLcgi[PATH_MAX];
Char CGIurl[PATH_MAX];
Char MMDBcgi[PATH_MAX];
Char CDDhome[PATH_MAX];
Char CGIName[PATH_MAX];
Char CDSRVurl[PATH_MAX];
static Char ENTREZurl[PATH_MAX];
static Char TAXcgi[PATH_MAX];
static Char MMDBurl[PATH_MAX];
static Char DARTcgi[PATH_MAX];
static Char DATApath[PATH_MAX];
static Char REFpath[PATH_MAX];
static Char DOCSUMurl[PATH_MAX];
static Char MAILto[PATH_MAX];
static Char LOGpath[PATH_MAX];
static Char NRPDB[PATH_MAX];
static Char ODBCINI[PATH_MAX];
static Char DARTUSER[PATH_MAX];
static Char DARTPASS[PATH_MAX];
static Char DARTLIB[PATH_MAX];
static Char LDLIBRARYPATH[PATH_MAX];
static Char SYBASE[PATH_MAX];
static Char BLASTDB[PATH_MAX];
static Char NCBI[PATH_MAX];
static Char MMDBpath[PATH_MAX];
Int4 maxseqlen;
typedef struct cblastscoreinfodata{
float seq_identity;
Int2 length;
FloatHi evalue;
FloatHi bit_score;
Int4 score;
} CblastScoreData, PNTR CblastScoreDataPtr;
typedef struct cblastseqinfodata{
Int4 gi, PDBgi, hsp;
/* gi-blast nr representative gi; PDBgi-gi of pdb sequence; hsp-HSP index */
SeqIdPtr pdbid;
CharPtr doc; /* entrez docsum */
Boolean bRep;
Int2 pagenum;
}CblastSeqInfoData, PNTR CblastSeqInfoDataPtr;
typedef struct blastpdbnb {
ValNodePtr csp; /* vnp->data.ptrvalue is CblastScoreDataPtr */
ValNodePtr csip; /* vnp->data.ptrvalue is CblastSeqInfoDataPtr */
SeqAnnotPtr sap;
Int4 query_length;
CharPtr query_title;
Int2 numpages;
} BlastPDBNb, PNTR BlastPDBNbPtr;
typedef struct pdbidinfo {
SeqIdPtr pdbList;
ValNodePtr PDBgiList;
} PDBIdInfo, PNTR PDBIdInfoPtr;
typedef ValNode NeighborInfo, FAR *NeighborInfoPtr;
typedef struct neighborinfodata {
Int4 gi;
Int4 rank;
SeqIdPtr pdbid;
/* for PdbSeqIdPtr */
CharPtr docsum;
Int4 MMDBid;
CharPtr mol;
Uint1 chain;
Int4 seqlen;
Boolean selected;
Int2 pagenum;
struct neighborinfodata PNTR next;
} NeighborInfoData, PNTR NeighborInfoDataPtr;
typedef struct rankinfo {
CharPtr mol;
char chain;
Int4 rank;
} RankInfo, PNTR RankInfoPtr;
typedef ValNode WWWQuery, FAR *WWWQueryPtr;
typedef struct wwwquerydata {
CharPtr name;
CharPtr value;
} WWWQueryData, PNTR WWWQueryDataPtr;
typedef struct snp_feature_info {
Int4 gi, pos, feature_id;
CharPtr title, descr;
Int4 color, id;
} SnpFeatureInfo, PNTR SnpFeatureInfoPtr;
typedef struct cdnb_info{
CharPtr CdName;
unsigned PssmId;
Int2 iClust, iMaprow, iColor;
Int4 from, to;
Boolean bRep, bFinished;
}CdNbInfo, PNTR CdNbInfoPtr;
typedef struct maprow_info{
Int4 from, to;
Int2 iColor;
CharPtr CdName;
CharPtr cdaln;
unsigned PssmId;
}MapRowInfo, PNTR MapRowInfoPtr;
typedef struct cd_info {
Int4 query_length;
SeqAnnotPtr sap;
Int2 cd_num, maprow_num;
ValNodePtr mapinfo;
/* (MapRowInfoPtr) (mapinfo->data.ptrvalue)->data.ptrvalue */
CdNbInfoPtr *cnip;
}CdInfo, PNTR CdInfoPtr;
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