Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/MergedRange.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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 ## Constructor
36 #
37 # @param lId list of Path ID
38 # @param start the start coordinate
39 # @param end the end coordinate
40 #
41 def __init__(self, lId = None, start = -1, end = -1):
42 self._lId = lId or []
43 self._start = start
44 self._end = end
45
46 ## Equal operator
47 #
48 # @param o a MergedRange instance
49 #
50 def __eq__(self, o):
51 return o._lId == self._lId and o._start == self._start and o._end == self._end
52
53
54 ## Return True if the MergedRange instance overlaps with another MergedRange instance, False otherwise
55 #
56 # @param o a MergedRange instance
57 # @return boolean False or True
58 #
59 def isOverlapping(self, o):
60 if o._start <= self._start and o._end >= self._end:
61 return True
62 if o._start >= self._start and o._start <= self._end or o._end >= self._start and o._end <= self._end:
63 return True
64 return False
65
66 ## Merge coordinates and ID of two Merged Range
67 #
68 # @param o a MergedRange instance
69 #
70 def merge(self, o):
71 self._start = min(self._start, o._start)
72 self._end = max(self._end, o._end)
73 self._lId.extend(o._lId)
74 self._lId.sort()
75
76 ## Set a Merged Range instance using a Match instance
77 #
78 # @param iMatch instance Match instance
79 #
80 def setFromMatch(self, iMatch):
81 self._lId= [iMatch.id]
82 self._start = iMatch.range_query.start
83 self._end = iMatch.range_query.end
84
85 ## Get a Merged Range instance list using a Match instance list
86 #
87 # @param lIMatch list Match instance list
88 # @return lMergedRange list MergedRange instance list
89 #
90 def getMergedRangeListFromMatchList(lIMatch):
91 lMergedRange = []
92 for iMatch in lIMatch:
93 mr = MergedRange()
94 mr.setFromMatch(iMatch)
95 lMergedRange.append(mr)
96 return lMergedRange
97
98 getMergedRangeListFromMatchList = staticmethod(getMergedRangeListFromMatchList)