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
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
|
<!-- ============================================
::DATATOOL:: Generated from "seqtable.asn"
::DATATOOL:: by application DATATOOL version 2.4.4
::DATATOOL:: on 01/23/2013 23:05:37
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-SeqTable"
================================================= -->
<!--
$Revision: 386776 $
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 authors in any work or product based on this material.
Authors: Mike DiCuccio, Eugene Vasilchenko
ASN.1 interface to table readers
-->
<!-- Elements used by other modules:
SeqTable-column-info,
SeqTable-column,
Seq-table -->
<!-- Elements referenced from other modules:
Seq-id,
Seq-loc,
Seq-interval FROM NCBI-Seqloc -->
<!-- ============================================ -->
<!ELEMENT SeqTable-column-info (
SeqTable-column-info_title?,
SeqTable-column-info_field-id?,
SeqTable-column-info_field-name?)>
<!-- user friendly column name, can be skipped -->
<!ELEMENT SeqTable-column-info_title (#PCDATA)>
<!--
identification of the column data in the objects described by the table
known column data types
position types
-->
<!ELEMENT SeqTable-column-info_field-id (%INTEGER;)>
<!--
location - location as Seq-loc
location-id - location Seq-id
location-gi - gi
location-from - interval from
location-to - interval to
location-strand - location strand
product - product as Seq-loc
product-id - product Seq-id
product-gi - product gi
product-from - product interval from
product-to - product interval to
product-strand - product strand
id-local - main feature fields
id.local.id
xref-id-local - xref.id.local.id
ext - field-name must be "E.xxx", see below
qual - field-name must be "Q.xxx", see below
dbxref - field-name must be "D.xxx", see below
data-imp-key - various data fields
ext-type - extra fields, see also special values for str below
-->
<!ATTLIST SeqTable-column-info_field-id value (
location |
location-id |
location-gi |
location-from |
location-to |
location-strand |
location-fuzz-from-lim |
location-fuzz-to-lim |
product |
product-id |
product-gi |
product-from |
product-to |
product-strand |
product-fuzz-from-lim |
product-fuzz-to-lim |
id-local |
xref-id-local |
partial |
comment |
title |
ext |
qual |
dbxref |
data-imp-key |
data-region |
data-cdregion-frame |
ext-type |
qual-qual |
qual-val |
dbxref-db |
dbxref-tag
) #IMPLIED >
<!--
any column can be identified by ASN.1 text locator string
with omitted object type.
examples:
"data.gene.locus" for Seq-feat.data.gene.locus
"data.imp.key" for Seq-feat.data.imp.key
"qual.qual"
- Seq-feat.qual is SEQUENCE so several columns are allowed
see also "Q.xxx" special value for shorter qual representation
"ext.type.str"
"ext.data.label.str"
"ext.data.data.int"
see also "E.xxx" special value for shorter ext representation
special values start with capital letter:
"E.xxx" - ext.data.label.str = xxx, ext.data.data = data
- Seq-feat.ext.data is SEQUENCE so several columns are allowed
"Q.xxx" - qual.qual = xxx, qual.val = data
- Seq-feat.qual is SEQUENCE so several columns are allowed
"D.xxx" - dbxref.id = xxx, dbxref.tag = data
- Seq-feat.dbxref is SET so several columns are allowed
-->
<!ELEMENT SeqTable-column-info_field-name (#PCDATA)>
<!ELEMENT CommonString-table (
CommonString-table_strings,
CommonString-table_indexes)>
<!-- set of possible values -->
<!ELEMENT CommonString-table_strings (CommonString-table_strings_E*)>
<!ELEMENT CommonString-table_strings_E (#PCDATA)>
<!-- indexes of values -->
<!ELEMENT CommonString-table_indexes (CommonString-table_indexes_E*)>
<!ELEMENT CommonString-table_indexes_E (%INTEGER;)>
<!ELEMENT CommonBytes-table (
CommonBytes-table_bytes,
CommonBytes-table_indexes)>
<!-- set of possible values -->
<!ELEMENT CommonBytes-table_bytes (CommonBytes-table_bytes_E*)>
<!ELEMENT CommonBytes-table_bytes_E (%OCTETS;)>
<!-- indexes of values -->
<!ELEMENT CommonBytes-table_indexes (CommonBytes-table_indexes_E*)>
<!ELEMENT CommonBytes-table_indexes_E (%INTEGER;)>
<!ELEMENT SeqTable-multi-data (
SeqTable-multi-data_int |
SeqTable-multi-data_real |
SeqTable-multi-data_string |
SeqTable-multi-data_bytes |
SeqTable-multi-data_common-string |
SeqTable-multi-data_common-bytes |
SeqTable-multi-data_bit |
SeqTable-multi-data_loc |
SeqTable-multi-data_id |
SeqTable-multi-data_interval)>
<!-- a set of integers, one per row -->
<!ELEMENT SeqTable-multi-data_int (SeqTable-multi-data_int_E*)>
<!ELEMENT SeqTable-multi-data_int_E (%INTEGER;)>
<!-- a set of reals, one per row -->
<!ELEMENT SeqTable-multi-data_real (SeqTable-multi-data_real_E*)>
<!ELEMENT SeqTable-multi-data_real_E (%REAL;)>
<!-- a set of strings, one per row -->
<!ELEMENT SeqTable-multi-data_string (SeqTable-multi-data_string_E*)>
<!ELEMENT SeqTable-multi-data_string_E (#PCDATA)>
<!-- a set of byte arrays, one per row -->
<!ELEMENT SeqTable-multi-data_bytes (SeqTable-multi-data_bytes_E*)>
<!ELEMENT SeqTable-multi-data_bytes_E (%OCTETS;)>
<!-- a set of string with small set of possible values -->
<!ELEMENT SeqTable-multi-data_common-string (CommonString-table)>
<!-- a set of byte arrays with small set of possible values -->
<!ELEMENT SeqTable-multi-data_common-bytes (CommonBytes-table)>
<!--
a set of bits, one per row
this uses bm::bvector<> as its storage mechanism
-->
<!ELEMENT SeqTable-multi-data_bit (%OCTETS;)>
<!-- a set of locations, one per row -->
<!ELEMENT SeqTable-multi-data_loc (Seq-loc*)>
<!ELEMENT SeqTable-multi-data_id (Seq-id*)>
<!ELEMENT SeqTable-multi-data_interval (Seq-interval*)>
<!ELEMENT SeqTable-single-data (
SeqTable-single-data_int |
SeqTable-single-data_real |
SeqTable-single-data_string |
SeqTable-single-data_bytes |
SeqTable-single-data_bit |
SeqTable-single-data_loc |
SeqTable-single-data_id |
SeqTable-single-data_interval)>
<!-- integer -->
<!ELEMENT SeqTable-single-data_int (%INTEGER;)>
<!-- real -->
<!ELEMENT SeqTable-single-data_real (%REAL;)>
<!-- string -->
<!ELEMENT SeqTable-single-data_string (#PCDATA)>
<!-- byte array -->
<!ELEMENT SeqTable-single-data_bytes (%OCTETS;)>
<!-- bit -->
<!ELEMENT SeqTable-single-data_bit EMPTY>
<!ATTLIST SeqTable-single-data_bit value ( true | false ) #REQUIRED >
<!-- location -->
<!ELEMENT SeqTable-single-data_loc (Seq-loc)>
<!ELEMENT SeqTable-single-data_id (Seq-id)>
<!ELEMENT SeqTable-single-data_interval (Seq-interval)>
<!ELEMENT SeqTable-sparse-index (
SeqTable-sparse-index_indexes |
SeqTable-sparse-index_bit-set)>
<!-- indexes of rows with values -->
<!ELEMENT SeqTable-sparse-index_indexes (SeqTable-sparse-index_indexes_E*)>
<!ELEMENT SeqTable-sparse-index_indexes_E (%INTEGER;)>
<!-- bitset of rows with values -->
<!ELEMENT SeqTable-sparse-index_bit-set (%OCTETS;)>
<!ELEMENT SeqTable-column (
SeqTable-column_header,
SeqTable-column_data?,
SeqTable-column_sparse?,
SeqTable-column_default?,
SeqTable-column_sparse-other?)>
<!--
column description or reference to previously defined info
information about data
-->
<!ELEMENT SeqTable-column_header (SeqTable-column-info)>
<!-- row data -->
<!ELEMENT SeqTable-column_data (SeqTable-multi-data)>
<!-- in case not all rows contain data this field will contain sparse info -->
<!ELEMENT SeqTable-column_sparse (SeqTable-sparse-index)>
<!-- default value for sparse table, or if row data is too short -->
<!ELEMENT SeqTable-column_default (SeqTable-single-data)>
<!-- single value for indexes not listed in sparse table -->
<!ELEMENT SeqTable-column_sparse-other (SeqTable-single-data)>
<!ELEMENT Seq-table (
Seq-table_feat-type,
Seq-table_feat-subtype?,
Seq-table_num-rows,
Seq-table_columns)>
<!-- type of features in this table, equal to Seq-feat.data variant index -->
<!ELEMENT Seq-table_feat-type (%INTEGER;)>
<!-- subtype of features in this table, defined in header SeqFeatData.hpp -->
<!ELEMENT Seq-table_feat-subtype (%INTEGER;)>
<!-- number of rows -->
<!ELEMENT Seq-table_num-rows (%INTEGER;)>
<!-- data in columns -->
<!ELEMENT Seq-table_columns (SeqTable-column*)>
|
