Mercurial > repos > yufei-luo > s_mart
comparison commons/core/sql/ITablePathAdaptator.py @ 6:769e306b7933
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author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 # Copyright INRA (Institut National de la Recherche Agronomique) | |
2 # http://www.inra.fr | |
3 # http://urgi.versailles.inra.fr | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 | |
31 | |
32 ## Interface for TablePathAdaptator | |
33 # | |
34 class ITablePathAdaptator (object): | |
35 | |
36 ## Give the data contained in the table as a list of Path instances | |
37 # | |
38 # @return lPaths list of path instances | |
39 # | |
40 def getListOfAllPaths( self ): | |
41 pass | |
42 | |
43 ## Give a list of Path instances having the same identifier | |
44 # | |
45 # @param id integer identifier number | |
46 # @return lPath a list of Path instances | |
47 # | |
48 # @warning old name was getPathList_from_num | |
49 # | |
50 def getPathListFromId( self, id ): | |
51 pass | |
52 | |
53 ## Give a list of Path instances according to the given list of identifier numbers | |
54 # | |
55 # @param lId integer list | |
56 # @return lPath a list of Path instances | |
57 # | |
58 # @warning old name was getPathList_from_numlist | |
59 # | |
60 def getPathListFromIdList( self, lId ): | |
61 pass | |
62 | |
63 ## Give a list of Path instances having the same given query name | |
64 # | |
65 # @param query string name of the query | |
66 # @return lPath a list of Path instances | |
67 # | |
68 # @warning old name was getPathList_from_query | |
69 # | |
70 def getPathListFromQuery( self, query ): | |
71 pass | |
72 | |
73 ## Give a list with all the distinct identifiers corresponding to the query | |
74 # | |
75 # @param query string name of the query | |
76 # @return lId a list of integer | |
77 # | |
78 # @warning old name was getPathList_from_query | |
79 # | |
80 def getIdListFromQuery( self, query ): | |
81 pass | |
82 | |
83 ## Give a list with all the distinct identifiers corresponding to the subject | |
84 # | |
85 # @param subject string name of the subject | |
86 # @return lId a list of integer | |
87 # | |
88 # @warning old name was getPathList_from_subject | |
89 # | |
90 def getIdListFromSubject( self, subject ): | |
91 pass | |
92 | |
93 ## Insert a path instance | |
94 # | |
95 # @param obj a path instance | |
96 # @param delayed boolean indicating if the insert must be delayed | |
97 # | |
98 # @note data are inserted such that the query is always on the direct strand | |
99 # | |
100 # @warning old name was insAPath | |
101 # | |
102 def insert(self, obj, delayed = False): | |
103 pass | |
104 | |
105 ## Insert a list of Path instances | |
106 # | |
107 # @param l a list of Path instances | |
108 # @param delayed boolean | |
109 # | |
110 # @warning old name was insPathList | |
111 # | |
112 def insertList(self, l, delayed = False): | |
113 pass | |
114 | |
115 ## Give a list of the identifier number contained in the table | |
116 # | |
117 # @return l integer list | |
118 # | |
119 # @warning old name was getPath_num | |
120 # | |
121 def getIdList(self): | |
122 pass | |
123 | |
124 ## Give a list of Path instances having the same given subject name | |
125 # | |
126 # @param subject string name of the subject | |
127 # @return lPath a list of Path instances | |
128 # | |
129 # @warning old name was getPath_num | |
130 # | |
131 def getPathListFromSubject( self, subject ): | |
132 pass | |
133 | |
134 ## Give a list of the distinct subject names present in the table | |
135 # | |
136 # @return lDistinctTypeNames string list | |
137 # | |
138 # @warning old name was getListDistinctSubjectName | |
139 # | |
140 def getSubjectList(self): | |
141 pass | |
142 | |
143 ## Give a list of the distinct query names present in the table | |
144 # | |
145 # @return lDistinctQueryNames string list | |
146 # | |
147 # @warning old name was getListDistinctQueryName | |
148 # | |
149 def getQueryList(self): | |
150 pass | |
151 | |
152 ## Give a list of Set instance list from the path contained on a query name | |
153 # | |
154 # @param queryName string query name | |
155 # @return lSet list of set instance | |
156 # | |
157 def getSubjectListFromQuery (self, queryName): | |
158 pass | |
159 | |
160 ## Give a list of Path instances with the given query and subject, both on direct strand | |
161 # | |
162 # @param query string query name | |
163 # @param subject string subject name | |
164 # @return lPaths list of path instances | |
165 # | |
166 # @warning old name was getListPathsWithDirectQueryDirectSubjectPerQuerySubject | |
167 # | |
168 def getPathListWithDirectQueryDirectSubjectFromQuerySubject( self, query, subject ): | |
169 pass | |
170 | |
171 ## Give a list of Path instances with the given query on direct strand and the given subject on reverse strand | |
172 # | |
173 # @param query string query name | |
174 # @param subject string subject name | |
175 # @return lPaths list of path instances | |
176 # | |
177 # @warning old name was getListPathsWithDirectQueryReverseSubjectPerQuerySubject | |
178 # | |
179 def getPathListWithDirectQueryReverseSubjectFromQuerySubject( self, query, subject ): | |
180 pass | |
181 | |
182 ## Give the number of Path instances with the given query name | |
183 # | |
184 # @param query string query name | |
185 # @return pathNb integer the number of Path instances | |
186 # | |
187 # @warning old name was getNbPaths_from_query | |
188 # | |
189 def getNbPathsFromQuery( self, query ): | |
190 pass | |
191 | |
192 ## Give the number of Path instances with the given subject name | |
193 # | |
194 # @param subject string subject name | |
195 # @return pathNb integer the number of Path instances | |
196 # | |
197 # @warning old name was getNbPaths_from_subject | |
198 # | |
199 def getNbPathsFromSubject( self, subject ): | |
200 pass | |
201 | |
202 ## Give the number of distinct path identifiers | |
203 # | |
204 # @return idNb integer the number of Path instances | |
205 # | |
206 # @warning old name was getNbAllPathsnums | |
207 # | |
208 def getNbIds( self ): | |
209 pass | |
210 | |
211 ## Give the number of distinct path identifiers for a given subject | |
212 # | |
213 # subjectName string subject name | |
214 # @return idNb integer the number of Path instances | |
215 # | |
216 # @warning old name was getNbPathsnums_from_subject | |
217 # | |
218 def getNbIdsFromSubject( self, subjectName ): | |
219 pass | |
220 | |
221 ## Give the number of distinct path identifiers for a given query | |
222 # | |
223 # @param queryName string query name | |
224 # @return idNb integer the number of Path instances | |
225 # | |
226 # @warning old name was getNbPathsnums_from_query | |
227 # | |
228 def getNbIdsFromQuery( self, queryName ): | |
229 pass | |
230 | |
231 ## Give a list of Path instances overlapping a given region | |
232 # | |
233 # @param query string query name | |
234 # @param start integer start coordinate | |
235 # @param end integer end coordinate | |
236 # @return lPath list of Path instances | |
237 # | |
238 def getPathListOverlappingQueryCoord( self, query, start, end ): | |
239 pass | |
240 | |
241 ## Give a list of Set instances overlapping a given region | |
242 # | |
243 # @param query string query name | |
244 # @param start integer start coordinate | |
245 # @param end integer end coordinate | |
246 # @return lSet list of Set instances | |
247 # | |
248 # @warning old name was getSetList_from_qcoord | |
249 # | |
250 def getSetListOverlappingQueryCoord(self, query, start, end): | |
251 pass | |
252 | |
253 ## Give a list of Path instances included in a given query region | |
254 # | |
255 # @param query string query name | |
256 # @param start integer start coordinate | |
257 # @param end integer end coordinate | |
258 # @return lPaths list of Path instances | |
259 # | |
260 # @warning old name was getIncludedPathList_from_qcoord | |
261 # | |
262 def getPathListIncludedInQueryCoord( self, query, start, end ): | |
263 pass | |
264 | |
265 ## Give a list of Set instances included in a given region | |
266 # | |
267 # @param query string query name | |
268 # @param start integer start coordinate | |
269 # @param end integer end coordinate | |
270 # @return lSet list of Set instances | |
271 # | |
272 # @warning old name was getInSetList_from_qcoord | |
273 # | |
274 def getSetListIncludedInQueryCoord(self, query, start, end): | |
275 pass | |
276 | |
277 ## Give a a list of Path instances sorted by query coordinates | |
278 # | |
279 # @return lPaths list of Path instances | |
280 # | |
281 # @warning old name was getListOfPathsSortedByQueryCoord | |
282 # | |
283 def getPathListSortedByQueryCoord( self ): | |
284 pass | |
285 | |
286 ## Give a a list of Path instances sorted by query coordinates for a given query | |
287 # | |
288 # @param queryName string query name | |
289 # @return lPaths list of Path instances | |
290 # | |
291 def getPathListSortedByQueryCoordFromQuery( self, queryName ): | |
292 pass | |
293 | |
294 ## Give a list of path instances sorted by increasing E-value | |
295 # | |
296 # queryName string query name | |
297 # @return lPaths list of path instances | |
298 # | |
299 def getPathListSortedByIncreasingEvalueFromQuery( self, queryName ): | |
300 pass | |
301 | |
302 ## Give a cumulative length of all paths (fragments) for a given subject name | |
303 # | |
304 # @param subjectName string subject name | |
305 # @return nb Cumulative length for all path | |
306 # @warning doesn't take into account the overlaps !! | |
307 # @warning old name was getCumulPathLength_from_subject | |
308 # | |
309 def getCumulLengthFromSubject( self, subjectName ): | |
310 pass | |
311 | |
312 ## Give a list of the length of all chains of paths for a given subject name | |
313 # | |
314 # @param subjectName string name of the subject | |
315 # @return lChainLengths list of lengths per chain of paths | |
316 # @warning doesn't take into account the overlaps !! | |
317 # @warning old name was getListChainLength_from_subject | |
318 # | |
319 def getChainLengthListFromSubject( self, subjectName ): | |
320 pass | |
321 | |
322 ## Give a list of identity of all chains of paths for a given subject name | |
323 # | |
324 # @param subjectName string name of the subject | |
325 # @return lChainIdentities list of identities per chain of paths | |
326 # @warning doesn't take into account the overlaps !! | |
327 # @warning old name was getListChainIdentity_from_subject | |
328 # | |
329 def getChainIdentityListFromSubject( self, subjectName ): | |
330 pass | |
331 | |
332 ## Give a list of Path lists sorted by weighted identity. | |
333 # | |
334 # @param qry query name | |
335 # @return lChains list of chains | |
336 # | |
337 def getListOfChainsSortedByAscIdentityFromQuery( self, qry ): | |
338 pass | |
339 | |
340 ## Give a list of the length of all paths for a given subject name | |
341 # | |
342 # @param subjectName string name of the subject | |
343 # @return lPathLengths list of lengths per path | |
344 # @warning doesn't take into account the overlaps !! | |
345 # @warning old name was getListPathLength_from_subject | |
346 # | |
347 def getPathLengthListFromSubject( self, subjectName ): | |
348 pass | |
349 | |
350 ## Give a a list with all distinct identifiers for a given subject sorted in decreasing order according to the length of the chains | |
351 # | |
352 # @return lPathNums a list of paths Id | |
353 # | |
354 # @warning old name was getPathNumListSortedByDecreasingChainLengthFromSubject | |
355 # | |
356 def getIdListSortedByDecreasingChainLengthFromSubject( self, subjectName ): | |
357 pass | |
358 | |
359 ## Give a list of Set instance list from the path contained on a query name | |
360 # | |
361 # @param query string query name | |
362 # @return lSet list of set instance | |
363 # | |
364 # @warning old name was getSetList_from_contig | |
365 # | |
366 def getSetListFromQuery(self, query): | |
367 pass | |
368 | |
369 ## Delete path corresponding to a given identifier number | |
370 # | |
371 # @param id integer identifier number | |
372 # | |
373 # @warning old name was delPath_from_num | |
374 # | |
375 def deleteFromId(self,id): | |
376 pass | |
377 | |
378 ## Delete path corresponding to a given list of identifier number | |
379 # | |
380 # @param lId list of identifier number | |
381 # | |
382 # @warning old name was delPath_from_numlist | |
383 # | |
384 def deleteFromIdList(self,lId): | |
385 pass | |
386 | |
387 ## Join two path by changing id number of id1 and id2 path to the least of id1 and id2 | |
388 # | |
389 # @param id1 integer path number | |
390 # @param id2 integer path number | |
391 # @return newId integer id used to join | |
392 # | |
393 # @warning old name was joinPath | |
394 # | |
395 def joinTwoPaths(self,id1,id2): | |
396 pass | |
397 | |
398 ## Get a new id number | |
399 # | |
400 # @return newId integer new id | |
401 # | |
402 def getNewId(self): | |
403 pass | |
404 | |
405 ## Test if table is empty | |
406 # | |
407 def isEmpty( self ): | |
408 pass | |
409 | |
410 ## Create a 'pathRange' table from a 'path' table. | |
411 # The output table summarizes the information per identifier. | |
412 # The min and max value are taken. | |
413 # The identity is averaged over the fragments. | |
414 # It may overwrite an existing table. | |
415 # | |
416 # @param outTable string name of the output table | |
417 # @return outTable string Table which summarizes the information per identifier | |
418 # | |
419 def path2PathRange( self, outTable="" ): | |
420 pass | |
421 | |
422 ## Return the number of times a given instance is present in the table | |
423 # The identifier is not considered, | |
424 # only coordinates, score, E-value and identity. | |
425 # | |
426 # @return nbOcc integer | |
427 # | |
428 def getNbOccurrences( self, iPath ): | |
429 pass |