From e4f5b4dcad9059462d8b1bfb35dcbd5515c25f1b Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 9 Sep 2013 16:21:46 +0100
Subject: [PATCH] fix for when FeatureDisplay is not used
---
.../artemis/components/alignment/BamView.java | 20 +++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index c86c72a4e..6b6275c23 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -831,15 +831,19 @@ public class BamView extends JPanel
return 0;
if(offsetLengths == null)
- {
-/* offsetLengths = new Hashtable<String, Integer>(combo.getItemCount());
- int offset = 0;
- for(int i=0; i<combo.getItemCount(); i++)
+ {
+ if(feature_display == null)
{
- String thisSeqName = (String) combo.getItemAt(i);
- offsetLengths.put(thisSeqName, offset);
- offset += seqLengths.get(combo.getItemAt(i));
- }*/
+ offsetLengths = new HashMap<String, Integer>(combo.getItemCount());
+ int offset = 0;
+ for(int i=0; i<combo.getItemCount(); i++)
+ {
+ String thisSeqName = (String) combo.getItemAt(i);
+ offsetLengths.put(thisSeqName, offset);
+ offset += seqLengths.get(combo.getItemAt(i));
+ }
+ return offsetLengths.get(refName);
+ }
final FeatureVector features = feature_display.getEntryGroup().getAllFeatures();
final HashMap<String, Integer> lookup = new HashMap<String, Integer>();
--
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