From 453e9b2612436e9a85878b3d2198f2dc2f9efc85 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 1 Jun 2012 15:02:58 +0100
Subject: [PATCH] highlight paired-stack connection link when selected
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 9 +++++++--
1 file changed, 7 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 2215b87a0..0102ed95f 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1569,7 +1569,12 @@ public class BamView extends JPanel
continue;
g2.setStroke(originalStroke);
- g2.setColor(Color.gray);
+
+ if(highlightSAMRecord != null &&
+ highlightSAMRecord.getReadName().equals(pr.sam1.getReadName()))
+ g2.setColor(Color.black);
+ else
+ g2.setColor(Color.gray);
if(pr.sam2 != null)
{
@@ -1590,7 +1595,7 @@ public class BamView extends JPanel
if(pr.sam1.getAlignmentStart() > pr.sam1.getMateAlignmentStart())
{
prStart = pr.sam1.getMateAlignmentStart();
- prEnd = pr.sam1.getAlignmentEnd();
+ prEnd = pr.sam1.getAlignmentStart();
}
else
{
--
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