diff --git a/uk/ac/sanger/artemis/components/alignment/LookSeqPanel.java b/uk/ac/sanger/artemis/components/alignment/LookSeqPanel.java
new file mode 100644
index 0000000000000000000000000000000000000000..13af786005d1be7b4759b5a1d0c300770abef560
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+++ b/uk/ac/sanger/artemis/components/alignment/LookSeqPanel.java
@@ -0,0 +1,318 @@
+/* LookSeqFrame.java
+ *
+ * created: 2009
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2009 Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.net.MalformedURLException;
+import java.net.URL;
+
+import javax.swing.ButtonGroup;
+import javax.swing.ImageIcon;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFrame;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.JSeparator;
+
+import uk.ac.sanger.artemis.components.DisplayAdjustmentEvent;
+import uk.ac.sanger.artemis.components.DisplayAdjustmentListener;
+import uk.ac.sanger.artemis.components.FeatureDisplay;
+import uk.ac.sanger.artemis.components.SwingWorker;
+
+public class LookSeqPanel extends JPanel
+ implements DisplayAdjustmentListener
+{
+ private static final long serialVersionUID = 1L;
+ /** image icon */
+ private ImageIcon ii;
+ private String urlStr;
+ private String queryStr;
+ private FeatureDisplay feature_display;
+ private int lastStart = -1;
+ private int lastEnd = -1;
+ final JPopupMenu popup = new JPopupMenu("Plot Options");
+
+ public LookSeqPanel()
+ {
+ super();
+ setUpPopupMenu();
+ }
+
+ public LookSeqPanel(URL url)
+ {
+ super();
+ ii = new ImageIcon(url);
+ setUpPopupMenu();
+ }
+
+ /**
+ *
+ * @param urlStr
+ * @param query
+ */
+ public LookSeqPanel(final String urlStr, final String queryStr)
+ {
+ super();
+ setImage(urlStr, queryStr);
+ setUpPopupMenu();
+ }
+
+ private void setUpPopupMenu()
+ {
+ JCheckBoxMenuItem optionCoverage = new JCheckBoxMenuItem("Show coverage", false);
+ optionCoverage.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ queryStr = queryStr.replaceFirst("view=\\w+", "view=coverage");
+ setImage(urlStr, queryStr);
+ revalidate();
+ }
+ });
+ popup.add(optionCoverage);
+
+ JCheckBoxMenuItem optionIndel = new JCheckBoxMenuItem("Show paired reads", true);
+
+ optionIndel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ queryStr = queryStr.replaceFirst("view=\\w+", "view=indel");
+ setImage(urlStr, queryStr);
+ revalidate();
+ }
+ });
+ popup.add(optionIndel);
+
+ ButtonGroup group = new ButtonGroup();
+ group.add(optionCoverage);
+ group.add(optionIndel);
+
+ popup.add(new JSeparator());
+ final JCheckBoxMenuItem perfectIndel =
+ new JCheckBoxMenuItem("Show perfect paired matches", true);
+ perfectIndel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(perfectIndel.isSelected(), "perfect");
+ }
+ });
+ popup.add(perfectIndel);
+
+ final JCheckBoxMenuItem snps =
+ new JCheckBoxMenuItem("Show paired reads with SNPs", true);
+ snps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(snps.isSelected(), "snps");
+ }
+ });
+ popup.add(snps);
+
+ final JCheckBoxMenuItem inversions =
+ new JCheckBoxMenuItem("Show inversions", true);
+ inversions.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(inversions.isSelected(), "inversions");
+ }
+ });
+ popup.add(inversions);
+
+ final JCheckBoxMenuItem single =
+ new JCheckBoxMenuItem("Show single reads", true);
+ single.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(single.isSelected(), "single");
+ }
+ });
+ popup.add(single);
+
+ final JCheckBoxMenuItem inversions_ext =
+ new JCheckBoxMenuItem("Show inversions_ext", true);
+ inversions_ext.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(inversions_ext.isSelected(), "inversions_ext");
+ }
+ });
+ popup.add(inversions_ext);
+
+ final JCheckBoxMenuItem pairlinks =
+ new JCheckBoxMenuItem("Show link pairs", true);
+ pairlinks.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(inversions_ext.isSelected(), "pairlinks");
+ }
+ });
+ popup.add(pairlinks);
+
+ final JCheckBoxMenuItem potsnps =
+ new JCheckBoxMenuItem("Show known SNPs", true);
+ potsnps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(inversions_ext.isSelected(), "potsnps");
+ }
+ });
+ popup.add(potsnps);
+
+ final JCheckBoxMenuItem uniqueness =
+ new JCheckBoxMenuItem("Show uniqueness", true);
+ uniqueness.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setDisplayOption(inversions_ext.isSelected(), "uniqueness");
+ }
+ });
+ popup.add(uniqueness);
+
+ addMouseListener(mouseListener);
+ }
+
+ public void setImage(final String urlStr, final String queryStr)
+ {
+ this.urlStr = urlStr;
+ this.queryStr = queryStr;
+
+
+ try
+ {
+ ii = new ImageIcon(new URL(urlStr+queryStr));
+ setPreferredSize(new Dimension(ii.getIconWidth(),
+ ii.getIconHeight()));
+ }
+ catch (MalformedURLException e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Override the paintComponent
+ */
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ if(ii != null)
+ ii.paintIcon(this,g,0,0);
+ }
+
+
+ public void displayAdjustmentValueChanged(DisplayAdjustmentEvent event)
+ {
+ if(lastStart == event.getStart() && lastEnd == event.getEnd())
+ return;
+
+ lastStart = event.getStart();
+ lastEnd = event.getEnd();
+ queryStr = queryStr.replaceFirst("from=\\d+", "from="+Integer.toString(event.getStart()));
+ queryStr = queryStr.replaceFirst("to=\\d+", "to="+Integer.toString(event.getEnd()));
+
+ if(feature_display != null)
+ {
+ int width = feature_display.getSize().width;
+ queryStr = queryStr.replaceFirst("width=\\d+", "width="+Integer.toString(width));
+ }
+ //System.out.println("displayAdjustmentValueChanged() "+
+ // event.getStart()+".."+event.getEnd());
+ displayImage();
+ }
+
+ private void displayImage()
+ {
+ SwingWorker worker = new SwingWorker()
+ {
+ public Object construct()
+ {
+ setImage(urlStr, queryStr);
+ //System.out.println(queryStr);
+ repaint();
+ return null;
+ }
+ };
+ worker.start();
+ }
+
+ private void setDisplayOption(boolean selected, String option)
+ {
+ if(selected)
+ queryStr = queryStr.replaceFirst("display=", "display=\\|"+option);
+ else
+ queryStr = queryStr.replaceAll("\\|"+option, "");
+
+ setImage(urlStr, queryStr);
+ repaint();
+ revalidate();
+ }
+
+ final MouseListener mouseListener = new MouseAdapter()
+ {
+ /**
+ * Listen for mouse press events.
+ **/
+ public void mousePressed(MouseEvent event)
+ {
+ if(!event.isPopupTrigger())
+ return;
+ popup.show(LookSeqPanel.this, event.getX(), event.getY());
+ }
+ };
+
+ public static void main(String args[])
+ {
+ String urlStr = "http://www.sanger.ac.uk/cgi-bin/teams/team112/lookseq/get_data.pl?";
+ String queryStr = "from=157682&to=479328&chr=MAL1&output=image&width=1024&lane=sample_2a&view=indel&display=|perfect|snps|inversions|pairlinks|potsnps|uniqueness|&debug=0";
+ LookSeqPanel lookseq = new LookSeqPanel(urlStr, queryStr);
+
+ JFrame f = new JFrame();
+ f.getContentPane().add(lookseq);
+ f.pack();
+ f.setVisible(true);
+ }
+
+ public void setFeatureDisplay(FeatureDisplay feature_display)
+ {
+ this.feature_display = feature_display;
+ }
+}
+