Layers are now arranged as a tree data structure.

1 files changed, 17 insertions, 11 deletions

diff --git a/exon_position.py b/exon_position.py
index efe560a..2fd7bed 100644
--- a/exon_position.py
+++ b/exon_position.py
@@ -18,8 +18,9 @@
 import random
 import cairo
 import ka_extensionpoint
-import ka_random
+import model_random
 import model_constraintpool
+import model_locus
 import model_allele
 
 EPSILON = 0.00001
@@ -55,22 +56,25 @@ class Position(model_allele.Allele):
         """Set x_pos, y_pos to random values."""
         cpool = model_constraintpool.ConstraintPool.get_pool()
         constraints = cpool.get(self, POSITION_CONSTRAINT)
-        self.constraint = ka_extensionpoint.create(random.choice(constraints), self.path)
+        self.constraint = ka_extensionpoint.create(random.choice(constraints),
+                                                   self.path)
         self.x_pos, self.y_pos = self.constraint.randomize()
 
     def mutate(self):
         """Make small random changes in position."""
-        if ka_random.is_mutating():
-            if ka_random.is_mutating():
+        if model_random.is_mutating():
+            if model_random.is_mutating():
                 cpool = model_constraintpool.ConstraintPool.get_pool()
                 constraints = cpool.get(self, POSITION_CONSTRAINT)
-                self.constraint = ka_extensionpoint.create(random.choice(constraints), self.path)
-            self.x_pos, self.y_pos = self.constraint.mutate(self.x_pos, self.y_pos)
+                self.constraint = ka_extensionpoint.create(
+                                         random.choice(constraints), self.path)
+            self.x_pos, self.y_pos = self.constraint.mutate(self.x_pos,
+                                                            self.y_pos)
 
-    def shuffle(self):
-        """Exchange x- and y-coordinate."""
-        temp0, temp1 = self.x_pos, self.y_pos
-        self.x_pos, self.y_pos = temp1, temp0 
+    def swap_places(self):
+        """Exchange x- and y-tiles."""
+        self.x_pos, self.y_pos = model_random.swap_parameters(self.x_pos,
+                                                           self.y_pos)
 
     def crossingover(self, other):
         """Returns either a copy of self or a copy of other.
@@ -78,8 +82,9 @@ class Position(model_allele.Allele):
         # check for distinct references, needs to copy content, not references
         post: __return__ is not self
         post: __return__ is not other
+        post: model_locus.unique_check(__return__, self, other) == ''
         """
-        randseq = ka_random.crossing_sequence(1)
+        randseq = model_random.crossing_sequence(1)
         return self.copy() if randseq[0] else other.copy()
 
     def copy(self):
@@ -94,6 +99,7 @@ class Position(model_allele.Allele):
         return new_one
 
     def explain(self):
+        """Returns a string describing details."""
         return u'%4.3f, %4.3f' % (self.x_pos, self.y_pos)
 
     @staticmethod