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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/commons/core/coord/SlidingWindow.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.
+
+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