diff TEisotools-1.1.a/commons/core/coord/MergedPath.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/coord/MergedPath.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,136 +0,0 @@
-# Copyright INRA (Institut National de la Recherche Agronomique)
-# http://www.inra.fr
-# http://urgi.versailles.inra.fr
-#
-# This software is governed by the CeCILL license under French law and
-# abiding by the rules of distribution of free software.  You can  use, 
-# modify and/ or redistribute the software under the terms of the CeCILL
-# license as circulated by CEA, CNRS and INRIA at the following URL
-# "http://www.cecill.info". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-import collections
-from commons.core.coord.Path import Path
-from commons.core.LoggerFactory import LoggerFactory
-
-LOG_DEPTH = "repet.commons.core.coord"
-
-## Merge Path objects with the same ID in a single object
-#
-class MergedPath(object):
-    
-    __slots__ = ("_lPaths", "_length", "_ID", "_nbPaths", "_log")
-    
-    ## Constructor
-    #
-    def __init__(self, lPaths = None, verbosity = 0):
-        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), verbosity = verbosity)
-        self._lPaths = []
-        self._length = 0
-        self._ID = None
-        self._nbPaths = 0
-        
-        if lPaths:
-            for p in lPaths:
-                self.add(p)
-    
-    ## repr
-    #
-    def __repr__(self):
-        return self.toString()
-    
-    ## Equal operator
-    #
-    def __eq__(self, o):
-        equal = True
-        if type(o) is not type(self):
-            equal = False
-        elif self.getID() != o.getID() or self.getLength() != o.getLength() or self._nbPaths != o._nbPaths:
-            equal = False
-        else:
-            equal = collections.Counter(self.getPathsList()) == collections.Counter(self.getPathsList())
-        return equal
-    
-    ## Not equal operator
-    #
-    def __ne__(self, o):
-        return not self.__eq__(o)
-
-    ## Try to add a Path instance to this MergedPath instance
-    #
-    # @param path a Path instance
-    #
-    def add(self, path):
-        if not isinstance(path, Path):
-            msg = "Error when adding to MergedPath : Not a Path"
-            self._log.warning(msg)
-        elif self._ID and self._ID != path.getIdentifier():
-            msg = "Couldn't add Path (%i) to MergedPath (%i) : Different IDs" % (path.getIdentifier(), self._ID)
-            self._log.warning(msg)
-        else:
-            self._ID = path.getIdentifier() 
-            self._lPaths.append(path)
-            self._length += path.getAlignInstance().getLengthOnQuery()
-            self._nbPaths = len(self._lPaths)
-         
-    ## Get the total length of the Paths in this MergedPath instance
-    #
-    def getLength(self):
-        return self._length
-    
-    ## Get the list of Paths objects in this MergedPath instance
-    # 
-    def getPathsList(self):
-        return self._lPaths
-    
-    ## Get the ID of the Path
-    #
-    def getID(self):
-        return self._ID
-    
-    ## Get the number of paths (fragments)
-    #
-    def getNbPaths(self):
-        return self._nbPaths
-    
-    ## Get the weighted identity
-    #
-    def getWeightedIdentity(self):
-        res = 0
-        if self._nbPaths > 0:
-            sumIdentity = sum((abs(path.range_query.end - path.range_query.start) + 1) * path.identity for path in self._lPaths)
-            sumSizes = sum(abs(path.range_query.end - path.range_query.start) + 1 for path in self._lPaths)
-            res = sumIdentity / sumSizes
-            res = float("{0:.2f}".format(res)) # Truncate to 2 decimals
-        return res
-    
-    ## Return the attributes as a formatted string
-    #
-    def toString(self):
-        string = "Empty MergedPath()"
-        if self._ID:
-            string = "ID: %i" % self._ID
-            string += "\tLength: %i" % self._length
-            string += "\tNbPaths: %i" % self._nbPaths
-            string += "\tPaths:\n"
-            string += "\n".join([p.toString() for p in self._lPaths])
-        return string