From ec3eae321a5c1117cafce0248a4313a3af00fc42 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 22 Oct 2012 13:19:09 -0400
Subject: [PATCH] Add chromatin interaction datatype to datatypes.conf, fix bug
 in data chrint data provider, and enable diagonal heat map track.

---
 datatypes_conf.xml.sample                         |  5 +++++
 lib/galaxy/visualization/data_providers/genome.py | 12 ++++++------
 static/scripts/viz/trackster/tracks.js            |  2 +-
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index e96cdb8e81d..4e6bf7d40a0 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -43,6 +43,11 @@
       <display file="ucsc/bigwig.xml" />
       <display file="igb/bigwig.xml" />
     </datatype>
+    <datatype extension="chrint" type="galaxy.datatypes.interval:ChromatinInteractions" display_in_upload="True">
+      <converter file="interval_to_bgzip_converter.xml" target_datatype="bgzip"/>
+      <converter file="interval_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
+      <converter file="interval_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
+    </datatype>
     <!-- MSI added Datatypes -->
     <datatype extension="csv" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="true" /> <!-- FIXME: csv is 'tabular'ized data, but not 'tab-delimited'; the class used here is intended for 'tab-delimited' -->
     <!-- End MSI added Datatypes -->
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index c4fbd449f36..a25164bf42e 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -1444,7 +1444,7 @@ class ChromatinInteractionsDataProvider( GenomeDataProvider ):
         """
         Provides
         """
-        
+
         rval = []
         message = None
         for count, line in enumerate( iterator ):
@@ -1484,15 +1484,15 @@ class ChromatinInteractionsTabixDataProvider( TabixDataProvider, ChromatinIntera
         """
         """
         # Modify start as needed to get earlier interactions with start region.
-        start = max( 0, int( start) - 1000000 )
+        start = max( 0, int( start ) - 1000000 )
         def filter( iter ):
             for line in iter:
                 feature = line.split()
-                s1 = int( feature[1] ), 
-                e1 = int( feature[2] ),
+                s1 = int( feature[1] ) 
+                e1 = int( feature[2] )
                 c = feature[3]
-                s2 = int( feature[4] ),
-                e2 = int( feature[5] ),
+                s2 = int( feature[4] )
+                e2 = int( feature[5] )
                 if ( ( c == chrom ) and ( s1 < end and e1 > start ) and ( s2 < end and e2 > start ) ):
                     yield line
         return filter( TabixDataProvider.get_iterator( self, chrom, start, end ) )
diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js
index 61697240361..427e5ea179a 100644
--- a/static/scripts/viz/trackster/tracks.js
+++ b/static/scripts/viz/trackster/tracks.js
@@ -4156,7 +4156,7 @@ var addable_objects = {
     "FeatureTrack": FeatureTrack,
     "VcfTrack": VcfTrack,
     "ReadTrack": ReadTrack,
-    // "DiagonalHeatmapTrack": DiagonalHeatmapTrack,
+    "DiagonalHeatmapTrack": DiagonalHeatmapTrack,
     "CompositeTrack": CompositeTrack,
     "DrawableGroup": DrawableGroup 
 };