From e500d6dd705f8e8259d970df0a62744e9302e627 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 7 Mar 2011 16:15:53 +0000
Subject: [PATCH] calculate SNP plot when reading in BAM
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15673 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/alignment/BamView.java | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index d53c57027..8c5a389c5 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -498,6 +498,9 @@ public class BamView extends JPanel
if(isCoverageView(pixPerBase) || isCoverage)
coverageView.addRecord(samRecord);
+ if(isSNPplot)
+ snpPanel.addRecord(samRecord);
+
if(!isCoverageView(pixPerBase))
readsInView.add(samRecord);
}
@@ -639,9 +642,10 @@ public class BamView extends JPanel
coverageView.isRedraw())
{
if(isCoverageView(pixPerBase) || isCoverage)
- {
coverageView.init(this, pixPerBase, start, end);
- }
+
+ if(isSNPplot)
+ snpPanel.init(this, pixPerBase, start, end);
synchronized (this)
{
@@ -2373,6 +2377,8 @@ public class BamView extends JPanel
{
isSNPplot = !isSNPplot;
snpPanel.setVisible(isSNPplot);
+ laststart = -1;
+ lastend = -1;
repaint();
}
});
--
GitLab