Mercurial > repos > urgi-team > teiso

comparison TEisotools-1.0/commons/core/coord/MergedRange.py @ 6:20ec0d14798e draft

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author urgi-team
date Wed, 20 Jul 2016 05:00:24 -0400
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5:4093a2fb58be 6:20ec0d14798e
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 ## Record a region on multiple sequence using Path ID information
32 #
33 class MergedRange(object):
34
35 __slots__ = ("_lId", "_start", "_end")
36
37 ## Constructor
38 #
39 # @param lId list of Path ID
40 # @param start the start coordinate
41 # @param end the end coordinate
42 #
43 def __init__(self, lId = None, start = -1, end = -1):
44 self._lId = lId or []
45 self._start = start
46 self._end = end
47
48 ## Equal operator
49 #
50 # @param o a MergedRange instance
51 #
52 def __eq__(self, o):
53 if type(o) is type(self):
54 return o._lId == self._lId and o._start == self._start and o._end == self._end
55 else:
56 return False
57
58 ## Not equal operator
59 #
60 def __ne__(self, o):
61 return not self.__eq__(o)
62
63 ## Return True if the MergedRange instance overlaps with another MergedRange instance, False otherwise
64 #
65 # @param o a MergedRange instance
66 # @return boolean False or True
67 #
68 def isOverlapping(self, o):
69 if o._start <= self._start and o._end >= self._end:
70 return True
71 if o._start >= self._start and o._start <= self._end or o._end >= self._start and o._end <= self._end:
72 return True
73 return False
74
75 ## Merge coordinates and ID of two Merged Range
76 #
77 # @param o a MergedRange instance
78 #
79 def merge(self, o):
80 self._start = min(self._start, o._start)
81 self._end = max(self._end, o._end)
82 self._lId.extend(o._lId)
83 self._lId.sort()
84
85 ## Set a Merged Range instance using a Match instance
86 #
87 # @param iMatch instance Match instance
88 #
89 def setFromMatch(self, iMatch):
90 self._lId= [iMatch.id]
91 self._start = iMatch.range_query.start
92 self._end = iMatch.range_query.end
93
94 ## Get a Merged Range instance list using a Match instance list
95 #
96 # @param lIMatch list Match instance list
97 # @return lMergedRange list MergedRange instance list
98 #
99 @staticmethod
100 def getMergedRangeListFromMatchList(lIMatch):
101 lMergedRange = []
102 for iMatch in lIMatch:
103 mr = MergedRange()
104 mr.setFromMatch(iMatch)
105 lMergedRange.append(mr)
106 return lMergedRange