Layers are now arranged as a tree data structure.

1 files changed, 20 insertions, 11 deletions

diff --git a/ep_sampler_randomwalk.py b/ep_sampler_randomwalk.py
index 5c5e747..ae419f0 100644
--- a/ep_sampler_randomwalk.py
+++ b/ep_sampler_randomwalk.py
@@ -16,7 +16,9 @@
 # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
 import math
-import ka_random
+import ka_debug
+import model_random
+import model_locus
 import model_allele
 import model_constraintpool
 import exon_direction
@@ -39,6 +41,13 @@ class RandomWalkSampler(model_allele.Allele):
         super(RandomWalkSampler, self).__init__(trunk)
         self.direction_steps = [exon_direction.Direction(self.path, 0.0, 0.0)]
 
+    def dot(self):
+        result = ""
+        anchor = ka_debug.dot_id(self) + ' -> '
+        for ref in self.direction_steps:
+            result += ka_debug.dot_ref(anchor, ref)
+        return result
+    
     def __eq__(self, other):
         """Equality based on on number of sections."""
         equal = isinstance(other, RandomWalkSampler) \
@@ -52,7 +61,7 @@ class RandomWalkSampler(model_allele.Allele):
         """Randomizes the walk."""
         cpool = model_constraintpool.ConstraintPool.get_pool()
         sections_constraint = cpool.get(self, SECTIONS_CONSTRAINT)
-        for i in range(ka_random.randint_constrained(sections_constraint)):
+        for dummy in range(model_random.randint_constrained(sections_constraint)):
             direction = exon_direction.Direction(self.path, 0.0, 0.0)
             direction.randomize()
             self.direction_steps.append(direction)
@@ -61,14 +70,13 @@ class RandomWalkSampler(model_allele.Allele):
         """Mutates the random walk."""
         cpool = model_constraintpool.ConstraintPool.get_pool()
         sections_constraint = cpool.get(self, SECTIONS_CONSTRAINT)
-        if ka_random.is_mutating():
-            ka_random.mutate_list(self.direction_steps, sections_constraint,
+        if model_random.is_mutating():
+            model_random.mutate_list(self.direction_steps, sections_constraint,
                                 exon_direction.Direction(self.path, 0.0, 0.0))
 
-    def shuffle(self):
-        """Reorder"""
-        ##!!self.direction_steps.shuffle()
-        pass
+    def swap_places(self):
+        """Reorder steps."""
+        model_random.swap_places(self.direction_steps)
 
     def crossingover(self, other):
         """
@@ -77,10 +85,11 @@ class RandomWalkSampler(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) == ''
         """
         new_one = RandomWalkSampler(self.get_trunk())
-        new_one.direction_steps = ka_random.crossingover(self.direction_steps,
-                                                         other.direction_steps)
+        new_one.direction_steps = model_random.crossingover_list(self.direction_steps,
+                                                              other.direction_steps)
         return new_one
 
     def get_sample_points(self):
@@ -111,5 +120,5 @@ class RandomWalkSampler(model_allele.Allele):
         post: __return__ is not self
         """
         new_one = RandomWalkSampler(self.get_trunk())
-        new_one.direction_steps = ka_random.copy_list(self.direction_steps)
+        new_one.direction_steps = model_random.copy_list(self.direction_steps)
         return new_one