Progress bars for distance matrix and tree building

wolever · Nov 21, 2011 · d2c73e3 · d2c73e3
1 parent b822dcf
commit d2c73e3
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Showing 2 changed files with 18 additions and 0 deletions.
diff --git a/PI/distance.py b/PI/distance.py
@@ -16,6 +16,7 @@
 #
 
 import align, zlib
+import util
 from numpy import *
 
 __all__ = [ "Distance", "Entropic", "PairwiseIdentity", "LocalAlignment" ]
@@ -191,9 +192,14 @@ def _go(self):
         #
         # Compute similarity matrix of SW scores
         #
+        progress = 0
         for i in range(self.N):
             for j in range(self.N):
 
+                if progress % (self.N * self.N / 100) == 0:
+                    util.progress(100, float(progress) / (self.N * self.N) * 100)
+                progress += 1
+
                 if similar[i][j] >= 0:
                     continue
 

diff --git a/PI/phylogeny.py b/PI/phylogeny.py
@@ -19,6 +19,9 @@
 from tree import *
 from pydot import *
 
+
+import util
+
 class Phylogeny:
 
     """Implementation of base phylogenetic class"""
@@ -76,6 +79,14 @@ def _go(self):
         for i in range(n):
             min = 10000
 
+            if n > 100:
+                 if i % (n / 100) == 0:
+                    util.progress(100, float(i) / n * 100)
+            elif n > 10:
+                if i % (n / 10) == 0:
+                    util.progress(100, float(i) / n * 100)
+
+
             for A in Cu:
                 for B in Cu:
                     if A == B:
@@ -108,6 +119,7 @@ def _go(self):
             Cu.remove(C.getRight())
             Cu.add(C)
 
+        util.progress(100, 100)
         self.tree = Cu.pop()
 
         self._cluster(self.tree)