--- a/TEisotools-1.1.a/commons/core/coord/SlidingWindow.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,106 +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.
-
-class SlidingWindow(object):
-        
-    def __init__( self, length = 1, overlap = 1 ):        
-        self._length = length
-        self._overlap = overlap
-        self._start = 1
-        self._end = length
-        self._step = length - overlap
-
-    def slideWindowOnce(self):
-        self._start = self._start + self._step
-        self._end = self._end + self._step
-    
-    def getStart(self):
-        return self._start
-    
-    def getEnd(self):
-        return self._end
-    
-    def setStart(self, start):
-        self._start = start
-    
-    def setEnd(self, end):
-        self._end = end
-    
-    def getLength(self):
-        return self._length
-    
-    def getOverlap(self):
-        return self._overlap
-    
-    def getMiddle(self):
-        return self._start + ((self._end - self._start - 1) / 2)
-    
-    def setLength(self, length):
-        self._length = length
-        
-    def setOverlap(self, overlap):
-        self._overlap = overlap
-    
-    def getSlidingMsg(self):
-        return "Window is sliding : %s %s" % (self._start, self._end)
-
-class SlidingWindowToCountMatchingBases(SlidingWindow):
-    
-    def getSetLengthOnWindow( self, iSet ):
-        if self._isSetIncludedInTheWindow(iSet):
-            return iSet.getLength()
-        if self._isWindowIncludedInTheSet(iSet):
-            return self._length
-        elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
-            return self._end - iSet.getMin()+1
-        elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
-            return iSet.getMax() - self._start+1
-        
-    def getCoordSetOnWindow( self, iSet ):
-        if self._isSetIncludedInTheWindow(iSet):
-            return iSet.getStart(), iSet.getEnd()
-        if self._isWindowIncludedInTheSet(iSet):
-            return self.getStart(), self.getEnd()
-        elif self._isSetOverlapTheRightSideOfTheWindow(iSet):
-            return iSet.getStart(), self.getEnd()
-        elif self._isSetOverlapTheLeftSideOfTheWindow(iSet):
-            return self.getStart(), iSet.getEnd()
-        
-    def _isSetIncludedInTheWindow(self, feature):
-        return feature.getMin() >= self._start and feature.getMax() <= self._end
-    
-    def _isWindowIncludedInTheSet(self, feature):
-        return self._start >= feature.getMin() and self._end <= feature.getMax()
-
-    def _isSetOverlapTheRightSideOfTheWindow(self, feature):
-        return feature.getMin() <= self._end and feature.getMin() >= self._start
-
-    def _isSetOverlapTheLeftSideOfTheWindow(self, feature):
-        return feature.getMax() <= self._end and feature.getMax() >= self._start