From 96f0f45ea87031a4b7ca83826a3d9c882b3ccdbd Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Fri, 8 Oct 2010 13:43:40 -0400
Subject: [PATCH] Finish refactoring of tracks data providers so that they all
 inherit from a single base object, TracksDataProvider.

---
 lib/galaxy/visualization/tracks/data/array_tree.py   |  4 +---
 lib/galaxy/visualization/tracks/data/bam.py          |  9 ++-------
 lib/galaxy/visualization/tracks/data/summary_tree.py | 10 ++++------
 3 files changed, 7 insertions(+), 16 deletions(-)

diff --git a/lib/galaxy/visualization/tracks/data/array_tree.py b/lib/galaxy/visualization/tracks/data/array_tree.py
index a13123dc41d..6b38d41c41d 100644
--- a/lib/galaxy/visualization/tracks/data/array_tree.py
+++ b/lib/galaxy/visualization/tracks/data/array_tree.py
@@ -10,8 +10,6 @@ from math import floor, ceil, log, pow
 from base import TracksDataProvider
 
 class ArrayTreeDataProvider( TracksDataProvider ):
-    def __init__( self, dataset, original_dataset ):
-        self.dataset = dataset
         
     def get_stats( self, chrom ):
         f = open( self.dataset.file_name )
@@ -48,7 +46,7 @@ class ArrayTreeDataProvider( TracksDataProvider ):
         if 'stats' in kwargs:
             return self.get_stats(chrom)
             
-        f = open( self.dataset.file_name )
+        f = open( self.converted_dataset.file_name )
         d = FileArrayTreeDict( f )
         
         # Get the right chromosome
diff --git a/lib/galaxy/visualization/tracks/data/bam.py b/lib/galaxy/visualization/tracks/data/bam.py
index 9278066a736..263f2a5920e 100644
--- a/lib/galaxy/visualization/tracks/data/bam.py
+++ b/lib/galaxy/visualization/tracks/data/bam.py
@@ -16,19 +16,14 @@ MAX_VALS = 5000 # only display first MAX_VALS datapoints
 class BamDataProvider( TracksDataProvider ):
     """
     Provides access to intervals from a sorted indexed BAM file.
-    """
-    def __init__( self, index, original_dataset ):
-        
-        self.index = index
-        self.original_dataset = original_dataset
-        
+    """        
     def get_data( self, chrom, start, end, **kwargs ):
         """
         Fetch intervals in the region 
         """
         start, end = int(start), int(end)
         # Attempt to open the BAM file with index
-        bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.index.file_name )
+        bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.converted_dataset.file_name )
         message = None
         try:
             data = bamfile.fetch(start=start, end=end, reference=chrom)
diff --git a/lib/galaxy/visualization/tracks/data/summary_tree.py b/lib/galaxy/visualization/tracks/data/summary_tree.py
index afd5c0d48a5..a86d82b7f9e 100644
--- a/lib/galaxy/visualization/tracks/data/summary_tree.py
+++ b/lib/galaxy/visualization/tracks/data/summary_tree.py
@@ -6,18 +6,16 @@ import pkg_resources; pkg_resources.require( "bx-python" )
 from galaxy.visualization.tracks.summary import *
 from math import ceil, log
 from galaxy.util.lrucache import LRUCache
+from base import TracksDataProvider
 
 CACHE = LRUCache(20) # Store 20 recently accessed indices for performance
 
-class SummaryTreeDataProvider( object ):
-    def __init__( self, dataset, original_dataset ):
-        self.dataset = dataset
-        
+class SummaryTreeDataProvider( TracksDataProvider ):
     def get_summary( self, chrom, start, end, **kwargs):
-        filename = self.dataset.file_name
+        filename = self.converted_dataset.file_name
         st = CACHE[filename]
         if st is None:
-            st = summary_tree_from_file( self.dataset.file_name )
+            st = summary_tree_from_file( self.converted_dataset.file_name )
             CACHE[filename] = st
             
         # If chrom is not found in blocks, try removing the first three