annotate TEisotools-1.1.a/commons/core/coord/SlidingWindow.py @ 15:255c852351c5 draft

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author urgi-team
date Thu, 21 Jul 2016 07:36:44 -0400
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13
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31 class SlidingWindow(object):
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32
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33 def __init__( self, length = 1, overlap = 1 ):
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34 self._length = length
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35 self._overlap = overlap
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36 self._start = 1
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37 self._end = length
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38 self._step = length - overlap
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39
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40 def slideWindowOnce(self):
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41 self._start = self._start + self._step
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42 self._end = self._end + self._step
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43
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44 def getStart(self):
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45 return self._start
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46
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47 def getEnd(self):
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48 return self._end
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49
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50 def setStart(self, start):
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51 self._start = start
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52
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53 def setEnd(self, end):
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54 self._end = end
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55
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56 def getLength(self):
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57 return self._length
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58
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59 def getOverlap(self):
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60 return self._overlap
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61
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62 def getMiddle(self):
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63 return self._start + ((self._end - self._start - 1) / 2)
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64
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65 def setLength(self, length):
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66 self._length = length
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67
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68 def setOverlap(self, overlap):
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69 self._overlap = overlap
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70
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71 def getSlidingMsg(self):
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72 return "Window is sliding : %s %s" % (self._start, self._end)
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73
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74 class SlidingWindowToCountMatchingBases(SlidingWindow):
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75
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76 def getSetLengthOnWindow( self, iSet ):
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77 if self._isSetIncludedInTheWindow(iSet):
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78 return iSet.getLength()
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79 if self._isWindowIncludedInTheSet(iSet):
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80 return self._length
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81 elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
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82 return self._end - iSet.getMin()+1
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83 elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
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84 return iSet.getMax() - self._start+1
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85
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86 def getCoordSetOnWindow( self, iSet ):
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87 if self._isSetIncludedInTheWindow(iSet):
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88 return iSet.getStart(), iSet.getEnd()
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89 if self._isWindowIncludedInTheSet(iSet):
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90 return self.getStart(), self.getEnd()
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91 elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
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92 return iSet.getStart(), self.getEnd()
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93 elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
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94 return self.getStart(), iSet.getEnd()
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95
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96 def _isSetIncludedInTheWindow(self, feature):
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97 return feature.getMin() >= self._start and feature.getMax() <= self._end
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98
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99 def _isWindowIncludedInTheSet(self, feature):
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100 return self._start >= feature.getMin() and self._end <= feature.getMax()
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101
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102 def _isSetOverlapTheRightSideOfTheWindow(self, feature):
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103 return feature.getMin() <= self._end and feature.getMin() >= self._start
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104
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105 def _isSetOverlapTheLeftSideOfTheWindow(self, feature):
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106 return feature.getMax() <= self._end and feature.getMax() >= self._start