From d2c73e31adb9795660ba5af5c229871c2367628a Mon Sep 17 00:00:00 2001
From: Lothar Braun <braun@net.in.tum.de>
Date: Mon, 21 Nov 2011 17:02:42 +0100
Subject: [PATCH] Progress bars for distance matrix and tree building

---
 PI/distance.py  |  6 ++++++
 PI/phylogeny.py | 12 ++++++++++++
 2 files changed, 18 insertions(+)

diff --git a/PI/distance.py b/PI/distance.py
index 600a630..d7aa2bd 100644
--- 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
index 6847a79..56b9454 100644
--- 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)