From deb870cdb1ce8175e1b3ceb4c3ffa7e0f4989a22 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 1 Aug 2011 16:03:29 +0100
Subject: [PATCH] fix for drawing connections between read pairs in inferred
size view when reference sequences are concatenated
---
.../sanger/artemis/components/alignment/BamView.java | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index f65c72654..94ad3da0f 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1130,11 +1130,16 @@ public class BamView extends JPanel
if(samRecord.getAlignmentEnd() < samNextRecord.getAlignmentStart() &&
(samNextRecord.getAlignmentStart()-samRecord.getAlignmentEnd())*pixPerBase > 2.f)
{
- g2.setColor(Color.LIGHT_GRAY);
+ g2.setColor(Color.LIGHT_GRAY);
+ int offset1 = getSequenceOffset(samRecord.getReferenceName());
+ int end1 = samRecord.getAlignmentEnd()+offset1-baseAtStartOfView;
+
+ int offset2 = getSequenceOffset(samNextRecord.getReferenceName());
+ int start2 = samNextRecord.getAlignmentStart()+offset2-baseAtStartOfView;
+
drawTranslucentLine(g2,
- (int)((samRecord.getAlignmentEnd()-getBaseAtStartOfView())*pixPerBase),
- (int)((samNextRecord.getAlignmentStart()-getBaseAtStartOfView())*pixPerBase), ypos);
+ (int)(end1*pixPerBase), (int)(start2*pixPerBase), ypos);
}
if(colourByCoverageColour.isSelected())
--
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