Mercurial > repos > urgi-team > teiso

comparison TEisotools-1.1.a/commons/core/coord/SlidingWindow.py @ 13:feef9a0db09d draft

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author urgi-team
date Wed, 20 Jul 2016 09:04:42 -0400
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12:22b0494ec883 13:feef9a0db09d
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 class SlidingWindow(object):
32
33 def __init__( self, length = 1, overlap = 1 ):
34 self._length = length
35 self._overlap = overlap
36 self._start = 1
37 self._end = length
38 self._step = length - overlap
39
40 def slideWindowOnce(self):
41 self._start = self._start + self._step
42 self._end = self._end + self._step
43
44 def getStart(self):
45 return self._start
46
47 def getEnd(self):
48 return self._end
49
50 def setStart(self, start):
51 self._start = start
52
53 def setEnd(self, end):
54 self._end = end
55
56 def getLength(self):
57 return self._length
58
59 def getOverlap(self):
60 return self._overlap
61
62 def getMiddle(self):
63 return self._start + ((self._end - self._start - 1) / 2)
64
65 def setLength(self, length):
66 self._length = length
67
68 def setOverlap(self, overlap):
69 self._overlap = overlap
70
71 def getSlidingMsg(self):
72 return "Window is sliding : %s %s" % (self._start, self._end)
73
74 class SlidingWindowToCountMatchingBases(SlidingWindow):
75
76 def getSetLengthOnWindow( self, iSet ):
77 if self._isSetIncludedInTheWindow(iSet):
78 return iSet.getLength()
79 if self._isWindowIncludedInTheSet(iSet):
80 return self._length
81 elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
82 return self._end - iSet.getMin()+1
83 elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
84 return iSet.getMax() - self._start+1
85
86 def getCoordSetOnWindow( self, iSet ):
87 if self._isSetIncludedInTheWindow(iSet):
88 return iSet.getStart(), iSet.getEnd()
89 if self._isWindowIncludedInTheSet(iSet):
90 return self.getStart(), self.getEnd()
91 elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
92 return iSet.getStart(), self.getEnd()
93 elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
94 return self.getStart(), iSet.getEnd()
95
96 def _isSetIncludedInTheWindow(self, feature):
97 return feature.getMin() >= self._start and feature.getMax() <= self._end
98
99 def _isWindowIncludedInTheSet(self, feature):
100 return self._start >= feature.getMin() and self._end <= feature.getMax()
101
102 def _isSetOverlapTheRightSideOfTheWindow(self, feature):
103 return feature.getMin() <= self._end and feature.getMin() >= self._start
104
105 def _isSetOverlapTheLeftSideOfTheWindow(self, feature):
106 return feature.getMax() <= self._end and feature.getMax() >= self._start