From cd11337a592060b47eee6aa1a6fc7d22f1e07584 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 4 Aug 2011 09:21:13 +0100
Subject: [PATCH] start on a read list
---
.../artemis/components/alignment/BamView.java | 10 +++++
.../components/alignment/SAMRecordList.java | 42 +++++++++++++++++++
2 files changed, 52 insertions(+)
create mode 100644 uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 96aafd715..f8db207ed 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2363,6 +2363,16 @@ public class BamView extends JPanel
filterFrame.setVisible(true);
}
});
+
+ JMenuItem readList = new JMenuItem("List Reads ...");
+ menu.add(readList);
+ readList.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new SAMRecordList(readsInView);
+ }
+ });
final JMenuItem bamSplitter = new JMenuItem("Clone window");
bamSplitter.addActionListener(new ActionListener()
diff --git a/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java b/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
new file mode 100644
index 000000000..0bd802c34
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/SAMRecordList.java
@@ -0,0 +1,42 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.BorderLayout;
+import java.awt.Graphics;
+import java.util.List;
+
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollBar;
+
+import net.sf.samtools.SAMRecord;
+
+public class SAMRecordList extends JPanel
+{
+ private List<SAMRecord> readsInView;
+ private JScrollBar verticalScroll = new JScrollBar(JScrollBar.VERTICAL);
+
+ public SAMRecordList(List<SAMRecord> readsInView)
+ {
+ this.readsInView = readsInView;
+ JFrame f = new JFrame("Reads");
+ JPanel mainPanel = (JPanel) f.getContentPane();
+ mainPanel.add(verticalScroll, BorderLayout.EAST);
+ mainPanel.add(this, BorderLayout.CENTER);
+ f.pack();
+ f.setVisible(true);
+ }
+
+ protected void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ for(int i=0; i<readsInView.size(); i++)
+ {
+ SAMRecord thisRead = readsInView.get(i);
+ String readStr = thisRead.getReadName()+"\t"+
+ thisRead.getAlignmentStart()+".."+thisRead.getAlignmentEnd()+"\t"+
+ thisRead.getReadLength()+"\t"+
+ thisRead.getMappingQuality();
+ g.drawString(readStr, 10, ((i+12)*12));
+ }
+ }
+}
--
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