1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
|
/*===========================================================================
*
* 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;
|