Mercurial > repos > urgi-team > teiso

comparison TEisotools-1.0/commons/core/coord/MergedPath.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 import collections
32 from commons.core.coord.Path import Path
33 from commons.core.LoggerFactory import LoggerFactory
34
35 LOG_DEPTH = "repet.commons.core.coord"
36
37 ## Merge Path objects with the same ID in a single object
38 #
39 class MergedPath(object):
40
41 __slots__ = ("_lPaths", "_length", "_ID", "_nbPaths", "_log")
42
43 ## Constructor
44 #
45 def __init__(self, lPaths = None, verbosity = 0):
46 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), verbosity = verbosity)
47 self._lPaths = []
48 self._length = 0
49 self._ID = None
50 self._nbPaths = 0
51
52 if lPaths:
53 for p in lPaths:
54 self.add(p)
55
56 ## repr
57 #
58 def __repr__(self):
59 return self.toString()
60
61 ## Equal operator
62 #
63 def __eq__(self, o):
64 equal = True
65 if type(o) is not type(self):
66 equal = False
67 elif self.getID() != o.getID() or self.getLength() != o.getLength() or self._nbPaths != o._nbPaths:
68 equal = False
69 else:
70 equal = collections.Counter(self.getPathsList()) == collections.Counter(self.getPathsList())
71 return equal
72
73 ## Not equal operator
74 #
75 def __ne__(self, o):
76 return not self.__eq__(o)
77
78 ## Try to add a Path instance to this MergedPath instance
79 #
80 # @param path a Path instance
81 #
82 def add(self, path):
83 if not isinstance(path, Path):
84 msg = "Error when adding to MergedPath : Not a Path"
85 self._log.warning(msg)
86 elif self._ID and self._ID != path.getIdentifier():
87 msg = "Couldn't add Path (%i) to MergedPath (%i) : Different IDs" % (path.getIdentifier(), self._ID)
88 self._log.warning(msg)
89 else:
90 self._ID = path.getIdentifier()
91 self._lPaths.append(path)
92 self._length += path.getAlignInstance().getLengthOnQuery()
93 self._nbPaths = len(self._lPaths)
94
95 ## Get the total length of the Paths in this MergedPath instance
96 #
97 def getLength(self):
98 return self._length
99
100 ## Get the list of Paths objects in this MergedPath instance
101 #
102 def getPathsList(self):
103 return self._lPaths
104
105 ## Get the ID of the Path
106 #
107 def getID(self):
108 return self._ID
109
110 ## Get the number of paths (fragments)
111 #
112 def getNbPaths(self):
113 return self._nbPaths
114
115 ## Get the weighted identity
116 #
117 def getWeightedIdentity(self):
118 res = 0
119 if self._nbPaths > 0:
120 sumIdentity = sum((abs(path.range_query.end - path.range_query.start) + 1) * path.identity for path in self._lPaths)
121 sumSizes = sum(abs(path.range_query.end - path.range_query.start) + 1 for path in self._lPaths)
122 res = sumIdentity / sumSizes
123 res = float("{0:.2f}".format(res)) # Truncate to 2 decimals
124 return res
125
126 ## Return the attributes as a formatted string
127 #
128 def toString(self):
129 string = "Empty MergedPath()"
130 if self._ID:
131 string = "ID: %i" % self._ID
132 string += "\tLength: %i" % self._length
133 string += "\tNbPaths: %i" % self._nbPaths
134 string += "\tPaths:\n"
135 string += "\n".join([p.toString() for p in self._lPaths])
136 return string