# HG changeset patch
# User Nicolas Saunier <nicolas.saunier@polymtl.ca>
# Date 1374782472 14400
# Node ID 6d26dcc7bba05236c0aa14da6779e968c4abac08
# Parent  6e0dedd34920002cec4a39b1f99fa87e6b460ee9
modifications to compute alignment for None indicators

diff -r 6e0dedd34920 -r 6d26dcc7bba0 python/indicators.py
--- a/python/indicators.py	Thu Jul 25 14:21:17 2013 -0400
+++ b/python/indicators.py	Thu Jul 25 16:01:12 2013 -0400
@@ -132,7 +132,6 @@
         else:
             return 1.
         
-
 class SeverityIndicator(TemporalIndicator):
     '''Class for severity indicators 
     field mostSevereIsMax is True 
diff -r 6e0dedd34920 -r 6d26dcc7bba0 python/utils.py
--- a/python/utils.py	Thu Jul 25 14:21:17 2013 -0400
+++ b/python/utils.py	Thu Jul 25 16:01:12 2013 -0400
@@ -219,7 +219,7 @@
         self.aligned = aligned
         self.delta = delta
         self.lengthFunc = lengthFunc
-        self.alignmentShift = 0
+        self.subSequenceIndices = [(0,0)]
 
     def similarities(self, l1, l2, jshift=0):
         from numpy import zeros, int as npint
@@ -273,14 +273,14 @@
                 lcssValues[i] = self.similarityTable.max()
                 similarityTables[i] = self.similarityTable
                 #print self.similarityTable
-            self.alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
-            self.similarityTable = similarityTables[self.alignmentShift]
+            alignmentShift = argMaxDict(lcssValues) # ideally get the medium alignment shift, the one that minimizes distance
+            self.similarityTable = similarityTables[alignmentShift]
         else:
-            self.alignmentShift = 0
+            alignmentShift = 0
             self.similarities(l1, l2)
 
         # threshold values for the useful part of the similarity table are n2-n1-delta and n1-n2-delta
-        self.similarityTable = self.similarityTable[:min(n1, n2+self.alignmentShift+self.delta)+1, :min(n2, n1-self.alignmentShift+self.delta)+1]
+        self.similarityTable = self.similarityTable[:min(n1, n2+alignmentShift+self.delta)+1, :min(n2, n1-alignmentShift+self.delta)+1]
 
         if computeSubSequence:
             self.subSequenceIndices = self.subSequence(self.similarityTable.shape[0]-1, self.similarityTable.shape[1]-1)