Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ncList/NCListCursor.py @ 6:769e306b7933
Change the repository level.
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 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2010 | |
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 import os, os.path, struct | |
32 from commons.core.parsing.GffParser import GffParser | |
33 from SMART.Java.Python.misc.Progress import Progress | |
34 | |
35 | |
36 class Data(object): | |
37 def __init__(self, hIndex, transcript, firstChildLIndex, lastChildLIndex, start, end): | |
38 self.hIndex = hIndex | |
39 self.transcript = transcript | |
40 self.firstChildLIndex = firstChildLIndex | |
41 self.lastChildLIndex = lastChildLIndex | |
42 self.start = start | |
43 self.end = end | |
44 | |
45 class NCListCursor(object): | |
46 | |
47 def __init__(self, cursor = None, ncList = None, lIndex = 0, verbosity = 0): | |
48 self._verbosity = verbosity | |
49 self._mainListData = [] | |
50 if cursor: | |
51 self.copy(cursor) | |
52 else: | |
53 self._ncList = ncList | |
54 self.setLIndex(lIndex) | |
55 | |
56 def setLIndex(self, lIndex): | |
57 self._lIndex = lIndex | |
58 self._start = None | |
59 self._end = None | |
60 self._hIndex = None | |
61 self._gffIndex = None | |
62 self._parentGffIndex = None | |
63 self._parentLIndex = None | |
64 self._parentHIndex = None | |
65 self._parentStart = None | |
66 self._parentEnd = None | |
67 self._transcript = None | |
68 self._firstSiblingLIndex = None | |
69 self._lastSiblingLIndex = None | |
70 self._firstChildLIndex = None | |
71 self._lastChildLIndex = None | |
72 self._mainListIndex = lIndex if lIndex < self._ncList.getSizeFirstList() else None | |
73 | |
74 def precompute(self): | |
75 self._mainListIndex = 0 | |
76 progress = Progress(self._ncList.getSizeFirstList(), "Precomputing data", self._verbosity) | |
77 for i in range(self._ncList.getSizeFirstList()): | |
78 gffIndex, hIndex, parentLIndex, start, end = self._ncList.getLLineElements(i) | |
79 transcript = self._ncList.getIntervalFromAdress(gffIndex) | |
80 firstChildLIndex, nbChildren = self._ncList.getHLineElements(hIndex) | |
81 lastChildLIndex = -1 if firstChildLIndex == -1 else firstChildLIndex + nbChildren-1 | |
82 self._mainListData.append(Data(hIndex, transcript, firstChildLIndex, lastChildLIndex, start, end)) | |
83 progress.inc() | |
84 progress.done() | |
85 | |
86 def _updateFromMainListData(self): | |
87 if not self._mainListData or self._lIndex >= self._ncList.getSizeFirstList(): | |
88 #print "OUT" | |
89 return False | |
90 if self._mainListIndex >= self._ncList.getSizeFirstList(): | |
91 self._hIndex = -1 | |
92 data = self._mainListData[self._mainListIndex] | |
93 self._hIndex = data.hIndex | |
94 self._transcript = data.transcript | |
95 self._firstChildLIndex = data.firstChildLIndex | |
96 self._lastChildLIndex = data.lastChildLIndex | |
97 self._start = data.start | |
98 self._end = data.end | |
99 return True | |
100 | |
101 def getLIndex(self): | |
102 return self._lIndex | |
103 | |
104 def _getCurrentData(self): | |
105 self._gffIndex, self._hIndex, self._parentLIndex, self._start, self._end = self._ncList.getLLineElements(self._lIndex) | |
106 #print "-->", self._lIndex, "-->", self._gffIndex, self._hIndex, self._parentLIndex, self._start, self._end | |
107 if self._end == -1: | |
108 raise Exception("Error") | |
109 | |
110 def _getParentData(self): | |
111 if self._parentLIndex == None: | |
112 self._getCurrentData() | |
113 self._parentGffIndex, self._parentHIndex, greatParentLIndex, self._parentStart, self._parentEnd = self._ncList.getLLineElements(self._parentLIndex) | |
114 | |
115 def _getTranscript(self): | |
116 if self._gffIndex == None: | |
117 self._getCurrentData() | |
118 self._transcript = self._ncList.getIntervalFromAdress(self._gffIndex) | |
119 | |
120 def _getSiblingData(self): | |
121 if self._parentHIndex == None: | |
122 self._getParentData() | |
123 if self._parentHIndex == -1: | |
124 self._firstSiblingLIndex = 0 | |
125 self._lastSiblingLIndex = self._ncList.getSizeFirstList() - 1 | |
126 else: | |
127 self._firstSiblingLIndex, nbSiblings = self._ncList.getHLineElements(self._parentHIndex) | |
128 self._lastSiblingLIndex = -1 if self._firstSiblingLIndex == -1 else self._firstSiblingLIndex + nbSiblings-1 | |
129 | |
130 def _getChildrenData(self): | |
131 if self._hIndex == None: | |
132 self._getCurrentData() | |
133 self._firstChildLIndex, nbChildren = self._ncList.getHLineElements(self._hIndex) | |
134 self._lastChildLIndex = -1 if self._firstChildLIndex == -1 else self._firstChildLIndex + nbChildren-1 | |
135 | |
136 def getGffAddress(self): | |
137 if self._gffIndex == None: | |
138 self._getCurrentData() | |
139 return self._gffIndex | |
140 | |
141 def getStart(self): | |
142 if self._start == None: | |
143 self._getCurrentData() | |
144 return self._start | |
145 | |
146 def getEnd(self): | |
147 if self._end == None: | |
148 self._getCurrentData() | |
149 return self._end | |
150 | |
151 def compare(self, cursor): | |
152 return (self._lIndex == cursor._lIndex) | |
153 | |
154 def getTranscript(self): | |
155 if self.isOut(): | |
156 return None | |
157 if self._transcript == None: | |
158 self._getTranscript() | |
159 return self._transcript | |
160 | |
161 def isFirst(self): | |
162 #print "is last: ", self._lIndex, self._ncList.getSizeFirstList(), self._lastSiblingLIndex | |
163 if self._lIndex < self._ncList.getSizeFirstList() - 1: | |
164 return (self._lIndex == 0) | |
165 if self._firstSiblingLIndex == None: | |
166 self._getSiblingData() | |
167 return (self._lIndex == self._firstSiblingLIndex) | |
168 | |
169 def isLast(self): | |
170 #print "is last: ", self._lIndex, self._ncList.getSizeFirstList(), self._lastSiblingLIndex | |
171 if self._lIndex < self._ncList.getSizeFirstList() - 1: | |
172 return (self._lIndex == self._ncList.getSizeFirstList() - 1) | |
173 if self._lastSiblingLIndex == None: | |
174 self._getSiblingData() | |
175 return (self._lIndex == self._lastSiblingLIndex) | |
176 | |
177 def moveUp(self): | |
178 if self._parentLIndex == None: | |
179 self._getCurrentData() | |
180 self._lIndex = self._parentLIndex | |
181 self._updateFromMainListData() | |
182 self._hIndex = self._parentHIndex | |
183 self._gffIndex = self._parentGffIndex | |
184 self._parentLIndex = None | |
185 self._parentHIndex = None | |
186 self._parentGffIndex = None | |
187 self._transcript = None | |
188 self._firstSiblingLIndex = None | |
189 self._lastSiblingLIndex = None | |
190 self._firstChildLIndex = self._firstChildLIndex | |
191 self._lastChildLIndex = self._lastChildLIndex | |
192 self._start = self._parentStart | |
193 self._end = self._parentEnd | |
194 self._parentStart = None | |
195 self._parentEnd = None | |
196 | |
197 def moveRight(self): | |
198 if self.isOut(): | |
199 return | |
200 #print "IN1", self | |
201 if self._lIndex < self._ncList.getSizeFirstList() - 1 and self._mainListIndex != None: | |
202 self._mainListIndex += 1 | |
203 self._updateFromMainListData() | |
204 #print "IN2", self | |
205 self._lIndex += 1 | |
206 self._hIndex = None | |
207 self._start = None | |
208 self._end = None | |
209 self._transcript = None | |
210 self._gffIndex = None | |
211 self._firstChildLIndex = None | |
212 self._lastChildLIndex = None | |
213 #print "IN3", self | |
214 | |
215 def moveNext(self): | |
216 while not self.isOut() and self.isLast(): | |
217 if self.isTop(): | |
218 self._lIndex = -1 | |
219 return | |
220 self.moveUp() | |
221 #print "F1", self | |
222 self.moveRight() | |
223 #print "F2", self | |
224 | |
225 def moveMiddleSibling(self): | |
226 if self._lIndex < self._ncList.getSizeFirstList() - 1: | |
227 self._mainListIndex = (self._ncList.getSizeFirstList() - 1) / 2 | |
228 self._updateFromMainListData() | |
229 if self._lastSiblingLIndex == None: | |
230 self._getSiblingData() | |
231 self._lIndex = (self._lastSiblingLIndex + self._firstSiblingLIndex) / 2 | |
232 self._hIndex = None | |
233 self._start = None | |
234 self._end = None | |
235 self._gffIndex = None | |
236 self._transcript = None | |
237 self._firstChildLIndex = None | |
238 self._lastChildLIndex = None | |
239 | |
240 def moveSibling(self, lIndex): | |
241 if self._lIndex < self._ncList.getSizeFirstList() - 1: | |
242 self._mainListIndex = lIndex | |
243 self._updateFromMainListData() | |
244 self._lIndex = lIndex | |
245 self._hIndex = None | |
246 self._start = None | |
247 self._end = None | |
248 self._gffIndex = None | |
249 self._transcript = None | |
250 self._firstChildLIndex = None | |
251 self._lastChildLIndex = None | |
252 | |
253 def moveLastSibling(self): | |
254 if self._lIndex < self._ncList.getSizeFirstList() - 1: | |
255 self._mainListIndex = self._ncList.getSizeFirstList() - 1 | |
256 self._updateFromMainListData() | |
257 if self._lastSiblingLIndex == None: | |
258 self._getSiblingData() | |
259 self._lIndex = self._lastSiblingLIndex | |
260 self._hIndex = None | |
261 self._start = None | |
262 self._end = None | |
263 self._gffIndex = None | |
264 self._transcript = None | |
265 self._firstChildLIndex = None | |
266 self._lastChildLIndex = None | |
267 | |
268 def moveDown(self): | |
269 if self._firstChildLIndex == None: | |
270 self._getChildrenData() | |
271 self._parentLIndex = self._lIndex | |
272 self._parentHIndex = self._hIndex | |
273 self._parentGffIndex = self._gffIndex | |
274 self._lIndex = self._firstChildLIndex | |
275 self._lastSiblingLIndex = self._lastChildLIndex | |
276 self._hIndex = None | |
277 self._gffIndex = None | |
278 self._transcript = None | |
279 self._firstChildLIndex = None | |
280 self._lastChildLIndex = None | |
281 self._parentStart = self._start | |
282 self._parentEnd = self._end | |
283 self._start = None | |
284 self._end = None | |
285 | |
286 def isOut(self): | |
287 return (self._lIndex == -1) | |
288 | |
289 def isTop(self): | |
290 if self._parentLIndex == None: | |
291 self._getCurrentData() | |
292 return (self._parentLIndex == -1) | |
293 | |
294 def hasChildren(self): | |
295 if self._hIndex == None: | |
296 self._getCurrentData() | |
297 if self._hIndex == -1: | |
298 return False | |
299 if self._firstChildLIndex == None: | |
300 self._getChildrenData() | |
301 return (self._firstChildLIndex != -1) | |
302 | |
303 def copy(self, cursor): | |
304 self._ncList = cursor._ncList | |
305 self._lIndex = cursor._lIndex | |
306 self._hIndex = cursor._hIndex | |
307 self._gffIndex = cursor._gffIndex | |
308 self._parentLIndex = cursor._parentLIndex | |
309 self._parentHIndex = cursor._parentHIndex | |
310 self._parentGffIndex = cursor._parentGffIndex | |
311 self._transcript = cursor._transcript | |
312 self._firstSiblingLIndex = cursor._firstSiblingLIndex | |
313 self._lastSiblingLIndex = cursor._lastSiblingLIndex | |
314 self._firstChildLIndex = cursor._firstChildLIndex | |
315 self._lastChildLIndex = cursor._lastChildLIndex | |
316 self._mainListData = cursor._mainListData | |
317 self._mainListIndex = cursor._mainListIndex | |
318 self._verbosity = cursor._verbosity | |
319 self._parentStart = cursor._parentStart | |
320 self._parentEnd = cursor._parentEnd | |
321 self._start = cursor._start | |
322 self._end = cursor._end | |
323 | |
324 def __str__(self): | |
325 return "NC-list: %s, Lindex: %s, Hindex: %s, GFFindex: %s, start: %s, end: %s, parent Lindex: %s, parent Hindex: %s, parent GFFindex: %s, transcript: %s, last sibling: %s" % (self._ncList, self._lIndex, self._hIndex, self._gffIndex, self._start, self._end, self._parentLIndex, self._parentHIndex, self._parentGffIndex, self._transcript, self._lastSiblingLIndex) |