1=head1 NAME
2
3pfamhmmer1db module - part of the Wise2 package
4
5=head1 SYNOPSIS
6
7This module contains the following objects
8
9=over
10
11=item PfamHmmer1DB
12
13=item PfamHmmer1Entry
14
15
16=back
17
18=head1 DESCRIPTION
19
20=head2 Object PfamHmmer1DB
21
22=over
23
24=item en
25
26 Type [PfamHmmer1Entry **] List No documentation
27
28=item dirname
29
30 Type [char *] Scalar  directory name with the models
31
32=item cur
33
34 Type [int] Scalar No documentation
35
36=item def
37
38 Type [RandomModel *] Scalar  default random model
39
40
41
42=back
43
44
45Pfam Hmmer1db is a wrapper around a Pfam Hmmer database.  This is file
46called HMM.s in a directory which has appropiate .HMM and .random
47files
48
49Although this DB will be phased out, it is still around for a while.
50
51This wont be used directly, but rather in a threestatedb model.
52It does not implement a full dynamite style db stream. rather it expects
53threestatedb to prod it in the correct manner.
54
55
56
57
58=head2 Member functions of PfamHmmer1DB
59
60=over
61
62=item hard_link_PfamHmmer1DB
63
64&Wise2::PfamHmmer1DB::hard_link_PfamHmmer1DB(obj)
65
66  Bumps up the reference count of the object
67  Meaning that multiple pointers can 'own' it
68
69
70
71  Argument obj          [UNKN ] Object to be hard linked [PfamHmmer1DB *]
72  Return [UNKN ] Undocumented return value [PfamHmmer1DB *]
73
74
75=item PfamHmmer1DB_alloc_std
76
77&Wise2::PfamHmmer1DB::PfamHmmer1DB_alloc_std(void)
78
79  Equivalent to PfamHmmer1DB_alloc_len(PfamHmmer1DBLISTLENGTH)
80
81
82
83  Return [UNKN ] Undocumented return value [PfamHmmer1DB *]
84
85
86=item en
87
88&Wise2::PfamHmmer1DB::en(obj,i)
89
90  Access members stored in the en list
91  For use principly by API functions
92
93
94
95  Argument obj          [UNKN ] Object holding the list [PfamHmmer1DB *]
96  Argument i            [UNKN ] Position in the list [int]
97  Return [SOFT ] Element of the list [PfamHmmer1Entry *]
98
99
100=item length_en
101
102&Wise2::PfamHmmer1DB::length_en(obj)
103
104  discover the length of the list
105  For use principly by API functions
106
107
108
109  Argument obj          [UNKN ] Object holding the list [PfamHmmer1DB *]
110  Return [UNKN ] length of the list [int]
111
112
113=item flush_en
114
115&Wise2::PfamHmmer1DB::flush_en(obj)
116
117  Frees the list elements, sets length to 0
118  If you want to save some elements, use hard_link_xxx
119  to protect them from being actually destroyed in the free
120
121
122
123  Argument obj          [UNKN ] Object which contains the list  [PfamHmmer1DB *]
124  Return [UNKN ] Undocumented return value [int]
125
126
127=item add_en
128
129&Wise2::PfamHmmer1DB::add_en(obj,add)
130
131  Adds another object to the list. It will expand the list if necessary
132
133
134
135  Argument obj          [UNKN ] Object which contains the list [PfamHmmer1DB *]
136  Argument add          [OWNER] Object to add to the list [PfamHmmer1Entry *]
137  Return [UNKN ] Undocumented return value [boolean]
138
139
140=item set_dirname
141
142&Wise2::PfamHmmer1DB::set_dirname(obj,dirname)
143
144  Replace member variable dirname
145  For use principly by API functions
146
147
148
149  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
150  Argument dirname      [OWNER] New value of the variable [char *]
151  Return [SOFT ] member variable dirname [boolean]
152
153
154=item dirname
155
156&Wise2::PfamHmmer1DB::dirname(obj)
157
158  Access member variable dirname
159  For use principly by API functions
160
161
162
163  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
164  Return [SOFT ] member variable dirname [char *]
165
166
167=item set_cur
168
169&Wise2::PfamHmmer1DB::set_cur(obj,cur)
170
171  Replace member variable cur
172  For use principly by API functions
173
174
175
176  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
177  Argument cur          [OWNER] New value of the variable [int]
178  Return [SOFT ] member variable cur [boolean]
179
180
181=item cur
182
183&Wise2::PfamHmmer1DB::cur(obj)
184
185  Access member variable cur
186  For use principly by API functions
187
188
189
190  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
191  Return [SOFT ] member variable cur [int]
192
193
194=item set_def
195
196&Wise2::PfamHmmer1DB::set_def(obj,def)
197
198  Replace member variable def
199  For use principly by API functions
200
201
202
203  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
204  Argument def          [OWNER] New value of the variable [RandomModel *]
205  Return [SOFT ] member variable def [boolean]
206
207
208=item def
209
210&Wise2::PfamHmmer1DB::def(obj)
211
212  Access member variable def
213  For use principly by API functions
214
215
216
217  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1DB *]
218  Return [SOFT ] member variable def [RandomModel *]
219
220
221=back
222
223=head2 Object PfamHmmer1Entry
224
225=over
226
227=item entryname
228
229 Type [char *] Scalar No documentation
230
231=item is_random
232
233 Type [boolean] Scalar No documentation
234
235=item is_hmmls
236
237 Type [boolean] Scalar No documentation
238
239=item bits_cutoff
240
241 Type [double] Scalar No documentation
242
243
244
245=back
246
247No documentation for PfamHmmer1Entry
248
249=head2 Member functions of PfamHmmer1Entry
250
251=over
252
253=item hard_link_PfamHmmer1Entry
254
255&Wise2::PfamHmmer1Entry::hard_link_PfamHmmer1Entry(obj)
256
257  Bumps up the reference count of the object
258  Meaning that multiple pointers can 'own' it
259
260
261
262  Argument obj          [UNKN ] Object to be hard linked [PfamHmmer1Entry *]
263  Return [UNKN ] Undocumented return value [PfamHmmer1Entry *]
264
265
266=item alloc
267
268&Wise2::PfamHmmer1Entry::alloc(void)
269
270  Allocates structure: assigns defaults if given
271
272
273
274  Return [UNKN ] Undocumented return value [PfamHmmer1Entry *]
275
276
277=item set_entryname
278
279&Wise2::PfamHmmer1Entry::set_entryname(obj,entryname)
280
281  Replace member variable entryname
282  For use principly by API functions
283
284
285
286  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
287  Argument entryname    [OWNER] New value of the variable [char *]
288  Return [SOFT ] member variable entryname [boolean]
289
290
291=item entryname
292
293&Wise2::PfamHmmer1Entry::entryname(obj)
294
295  Access member variable entryname
296  For use principly by API functions
297
298
299
300  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
301  Return [SOFT ] member variable entryname [char *]
302
303
304=item set_is_random
305
306&Wise2::PfamHmmer1Entry::set_is_random(obj,is_random)
307
308  Replace member variable is_random
309  For use principly by API functions
310
311
312
313  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
314  Argument is_random    [OWNER] New value of the variable [boolean]
315  Return [SOFT ] member variable is_random [boolean]
316
317
318=item is_random
319
320&Wise2::PfamHmmer1Entry::is_random(obj)
321
322  Access member variable is_random
323  For use principly by API functions
324
325
326
327  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
328  Return [SOFT ] member variable is_random [boolean]
329
330
331=item set_is_hmmls
332
333&Wise2::PfamHmmer1Entry::set_is_hmmls(obj,is_hmmls)
334
335  Replace member variable is_hmmls
336  For use principly by API functions
337
338
339
340  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
341  Argument is_hmmls     [OWNER] New value of the variable [boolean]
342  Return [SOFT ] member variable is_hmmls [boolean]
343
344
345=item is_hmmls
346
347&Wise2::PfamHmmer1Entry::is_hmmls(obj)
348
349  Access member variable is_hmmls
350  For use principly by API functions
351
352
353
354  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
355  Return [SOFT ] member variable is_hmmls [boolean]
356
357
358=item set_bits_cutoff
359
360&Wise2::PfamHmmer1Entry::set_bits_cutoff(obj,bits_cutoff)
361
362  Replace member variable bits_cutoff
363  For use principly by API functions
364
365
366
367  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
368  Argument bits_cutoff  [OWNER] New value of the variable [double]
369  Return [SOFT ] member variable bits_cutoff [boolean]
370
371
372=item bits_cutoff
373
374&Wise2::PfamHmmer1Entry::bits_cutoff(obj)
375
376  Access member variable bits_cutoff
377  For use principly by API functions
378
379
380
381  Argument obj          [UNKN ] Object holding the variable [PfamHmmer1Entry *]
382  Return [SOFT ] member variable bits_cutoff [double]
383
384
385=back
386
387