From 319794b7d2619c7956439f91f7f01922f2f7b533 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 31 May 2011 13:27:26 +0000
Subject: [PATCH] BamView checks the sequence length matches the BAM header
(SQ) length
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@16186 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 29 +++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index ece8054a7..0f0043735 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1952,6 +1952,35 @@ public class BamView extends JPanel
});
bottomPanel.add(scrollBar, BorderLayout.SOUTH);
}
+ else
+ {
+ if(!concatSequences)
+ {
+ int seqLen = seqLengths.get((String) combo.getSelectedItem());
+ int artemisSeqLen = feature_display.getSequenceLength();
+ if(seqLen != artemisSeqLen)
+ {
+ int newIndex = -1;
+ for(int i=0; i<seqNames.size(); i++)
+ {
+ if(seqLengths.get(seqNames.get(i)) == artemisSeqLen)
+ {
+ // this looks like the correct sequence
+ combo.setSelectedIndex(i);
+ newIndex = i;
+ }
+ }
+
+ JOptionPane.showMessageDialog(null,
+ "The length of the sequence loaded does not match the length of\n"+
+ "the default reference sequence in the BAM ("+seqNames.get(0)+").\n"+
+ (newIndex == -1 ? "" : "The length does match the reference "+
+ seqNames.get(newIndex)+" so this has been\nset as the default."),
+ "Check the reference is correctly selected",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
mainPanel.add(bottomPanel, BorderLayout.SOUTH);
coveragePanel.setPreferredSize(new Dimension(900, 100));
--
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