diff TEisotools-1.0/commons/core/coord/MergedPath.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/commons/core/coord/MergedPath.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,136 @@
+# 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