diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index e3d731c12e140a9723380872acb004a42483c303..852677712df8da4ff4a69ec89e824971ec7acf55 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.22 2009-03-27 09:03:55 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.23 2009-04-17 11:02:36 tjc Exp $
*/
package uk.ac.sanger.artemis.components.database;
@@ -28,16 +28,24 @@ package uk.ac.sanger.artemis.components.database;
import uk.ac.sanger.artemis.components.*;
import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.Range;
+import javax.swing.Box;
+import javax.swing.JButton;
import javax.swing.JComponent;
import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JTextField;
import javax.swing.JTree;
import javax.swing.JScrollPane;
import javax.swing.JPanel;
@@ -49,8 +57,13 @@ import javax.swing.tree.TreePath;
import org.gmod.schema.organism.Organism;
import org.gmod.schema.organism.OrganismProp;
import org.gmod.schema.sequence.Feature;
+import org.gmod.schema.sequence.FeatureLoc;
import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
@@ -114,11 +127,38 @@ public class DatabaseJPanel extends JPanel
status_line.setBorder(compound);
add(status_line, BorderLayout.SOUTH);
- JLabel title_line = new JLabel("Database List");
+ Box xBox = Box.createHorizontalBox();
+ JLabel title_line = new JLabel("DATABASE");
title_line.setMinimumSize(new Dimension(100, font_height));
- title_line.setPreferredSize(new Dimension(100, font_height));
+ title_line.setPreferredSize(new Dimension(250, font_height));
title_line.setBorder(compound);
- add(title_line, BorderLayout.NORTH);
+ xBox.add(title_line);
+
+ final JTextField openGeneText = new JTextField(6);
+ openGeneText.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ getEntryEditFromDatabase(entry_source, splash_main,
+ openGeneText.getText().trim());
+ }
+ });
+ JButton openBtn = new JButton("Open:");
+ openBtn.setToolTipText("Open Artemis for a chromosome or at a given gene");
+ openBtn.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ getEntryEditFromDatabase(entry_source, splash_main,
+ openGeneText.getText().trim());
+ }
+ });
+ xBox.add(Box.createHorizontalGlue());
+ xBox.add(openBtn);
+ xBox.add(openGeneText);
+
+ add(xBox, BorderLayout.NORTH);
}
/**
@@ -173,7 +213,7 @@ public class DatabaseJPanel extends JPanel
}
catch(NullPointerException npe)
{
- npe.printStackTrace();
+ npe.printStackTrace();
}
}
@@ -190,6 +230,35 @@ public class DatabaseJPanel extends JPanel
final Splash splash_main,
final InputStreamProgressListener stream_progress_listener,
final String entryName)
+ {
+ return show(entry_source,
+ (splash_main == null ? null : splash_main.getCanvas()),
+ (splash_main == null ? null : splash_main.getStatusLabel()),
+ splash_main, stream_progress_listener,
+ entryName, false, false);
+ }
+
+
+ /**
+ * Open an Artemis EntryEdit window
+ * @param entry_source
+ * @param srcComponent
+ * @param status_line
+ * @param splash_main
+ * @param stream_progress_listener
+ * @param entryName e.g. Pfalciparum:Pf3D7_09 or
+ * Pfalciparum:Pf3D7_09:20050..40000
+ * @param isNotSrcFeature true is the entry name may not be a source feature
+ * @return
+ */
+ public static EntryEdit show(final DatabaseEntrySource entry_source,
+ final JComponent srcComponent,
+ final JLabel status_line,
+ final Splash splash_main,
+ final InputStreamProgressListener stream_progress_listener,
+ final String entryName,
+ final boolean isNotSrcFeature,
+ final boolean splitGFFEntry)
{
final String entry[] = entryName.split(":");
String url = (String)entry_source.getLocation();
@@ -221,9 +290,17 @@ public class DatabaseJPanel extends JPanel
Feature f = doc.getFeatureByUniquename(entry[1]);
+ if(isNotSrcFeature && f.getFeatureLocsForFeatureId() != null
+ && f.getFeatureLocsForFeatureId().size() > 0)
+ {
+ Iterator it = f.getFeatureLocsForFeatureId().iterator();
+ f = ((FeatureLoc) it.next()).getFeatureBySrcFeatureId();
+ }
+
return openEntry(Integer.toString(f.getFeatureId()), entry_source,
- splash_main.getCanvas(), splash_main.getStatusLabel(), stream_progress_listener,
- false, splash_main, entry[1], userName, range);
+ srcComponent, status_line,
+ stream_progress_listener,
+ splitGFFEntry, splash_main, f.getUniqueName(), userName, range);
}
/**
@@ -297,7 +374,52 @@ public class DatabaseJPanel extends JPanel
}
/**
- *
+ * Open an Artemis entry given a feature name. If the name is
+ * a feature on the sequence (i.e. not the source feature) the
+ * display will open at that region.
+ * @param entry_source
+ * @param splash_main
+ * @param featureName
+ */
+ private void getEntryEditFromDatabase(final DatabaseEntrySource entry_source,
+ final Splash splash_main,
+ final String featureName)
+ {
+ SwingWorker entryWorker = new SwingWorker()
+ {
+ public Object construct()
+ {
+ Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+ try
+ {
+ DatabaseJPanel.this.setCursor(cbusy);
+ EntryEdit ee = show(entry_source,
+ DatabaseJPanel.this, status_line, splash_main,
+ stream_progress_listener, ":" + featureName,
+ true, splitGFFEntry);
+ goTo(ee, featureName);
+ }
+ catch (NullPointerException npe)
+ {
+ //npe.printStackTrace();
+ JOptionPane.showMessageDialog(DatabaseJPanel.this,
+ featureName + " not found!",
+ "Failed to Open", JOptionPane.WARNING_MESSAGE);
+ logger4j.debug(featureName + " not found!");
+ }
+ finally
+ {
+ DatabaseJPanel.this.setCursor(cdone);
+ }
+ return null;
+ }
+ };
+ entryWorker.start();
+ }
+
+ /**
+ * Open an Artemis entry
* @param srcfeatureId
* @param entry_source
* @param srcComponent
@@ -419,7 +541,6 @@ public class DatabaseJPanel extends JPanel
return null;
}
}
-
return null;
}
@@ -449,4 +570,30 @@ public class DatabaseJPanel extends JPanel
{
this.splitGFFEntry = splitGFFEntry;
}
+
+ /**
+ * Go to a named feature
+ * @param ee
+ * @param geneName
+ */
+ private static void goTo(final EntryEdit ee, final String geneName)
+ {
+ Selection selection = ee.getSelection();
+ selection.clear();
+
+ final StringVector qualifiers_to_search = new StringVector();
+ qualifiers_to_search.add(Options.getOptions().getAllGeneNames());
+
+ FeatureVector features = ee.getEntryGroup().getAllFeatures();
+ for (int i = 0; i < features.size(); i++)
+ {
+ uk.ac.sanger.artemis.Feature thisFeature = features.elementAt(i);
+ if (thisFeature.containsText(geneName, true, false, qualifiers_to_search))
+ {
+ selection.set(thisFeature);
+ break;
+ }
+ }
+ ee.getGotoEventSource().gotoBase(selection.getLowestBaseOfSelection());
+ }
}