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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/commons/core/coord/MergedRange.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,106 @@
+# 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.
+
+## Record a region on multiple sequence using Path ID information
+#
+class MergedRange(object):
+    
+    __slots__ = ("_lId", "_start", "_end")
+
+    ## Constructor
+    #
+    # @param lId list of Path ID
+    # @param start the start coordinate
+    # @param end the end coordinate
+    #
+    def __init__(self, lId = None, start = -1, end = -1):
+        self._lId = lId or []
+        self._start = start
+        self._end = end 
+        
+    ## Equal operator
+    #
+    # @param o a MergedRange instance
+    #        
+    def __eq__(self, o):
+        if type(o) is type(self):
+            return o._lId == self._lId and o._start == self._start and o._end == self._end
+        else:
+            return False
+    
+    ## Not equal operator
+    #
+    def __ne__(self, o):
+        return not self.__eq__(o)
+    
+    ## Return True if the MergedRange instance overlaps with another MergedRange instance, False otherwise 
+    #
+    # @param o a MergedRange instance
+    # @return boolean False or True
+    #
+    def isOverlapping(self, o):
+        if o._start <= self._start and o._end >= self._end:
+            return True
+        if o._start >= self._start and o._start <= self._end or o._end >= self._start and o._end <= self._end:
+            return True
+        return False
+    
+    ## Merge coordinates and ID of two Merged Range     
+    #
+    # @param o a MergedRange instance
+    #
+    def merge(self, o):
+        self._start = min(self._start, o._start)
+        self._end = max(self._end, o._end)   
+        self._lId.extend(o._lId)
+        self._lId.sort()
+        
+    ## Set a Merged Range instance using a Match instance
+    #
+    # @param iMatch instance Match instance 
+    # 
+    def setFromMatch(self, iMatch):
+        self._lId= [iMatch.id]
+        self._start = iMatch.range_query.start
+        self._end = iMatch.range_query.end
+     
+    ## Get a Merged Range instance list using a Match instance list
+    #
+    # @param lIMatch list Match instance list
+    # @return lMergedRange list MergedRange instance list
+    #
+    @staticmethod
+    def getMergedRangeListFromMatchList(lIMatch):
+        lMergedRange = []
+        for iMatch in lIMatch:
+            mr = MergedRange()
+            mr.setFromMatch(iMatch)
+            lMergedRange.append(mr)
+        return lMergedRange