diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java
index 2033df0814b49da8488307434b9b6236076750c6..c9e73c343c92bf1f6aeb83237992d9ab253fb2dd 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java
@@ -17,31 +17,38 @@
* 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/genebuilder/ortholog/OrthologPanel.java,v 1.1 2007-03-15 11:39:07 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologPanel.java,v 1.2 2007-03-20 13:48:10 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder.ortholog;
import java.awt.Component;
import java.awt.FlowLayout;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
import javax.swing.Box;
-import javax.swing.JLabel;
+import javax.swing.JButton;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.JTextField;
import uk.ac.sanger.artemis.FeatureChangeEvent;
import uk.ac.sanger.artemis.FeatureChangeListener;
import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.components.genebuilder.JExtendedComboBox;
public class OrthologPanel extends JPanel
implements FeatureChangeListener
{
private static final long serialVersionUID = 1L;
- private QualifierVector orthologQualifiers;
+ private QualifierVector ortho_para_logQualifiers;
public OrthologPanel(final Feature feature)
{
@@ -61,80 +68,160 @@ public class OrthologPanel extends JPanel
return false;
}
- private Component createOrthologQualifiersComponent()
+ private Component createOrthoParaLogQualifiersComponent(final Feature feature)
{
- int nrows = 0;
+ Qualifier orthoQualifier = ortho_para_logQualifiers.getQualifierByName("ortholog");
+ Qualifier paraQualifier = ortho_para_logQualifiers.getQualifierByName("paralog");
- Qualifier idQualifier = orthologQualifiers.getQualifierByName("ID");
+ DocumentEntry entry = (DocumentEntry)feature.getEmblFeature().getEntry();
+ DatabaseDocument doc = (DatabaseDocument)entry.getDocument();
+ final Vector databases = (Vector)doc.getDatabaseNames();
- Box gffBox = Box.createVerticalBox();
- gffBox.add(Box.createVerticalStrut(10));
-
- GridBagLayout grid = new GridBagLayout();
- GridBagConstraints c = new GridBagConstraints();
- c.ipady = 5;
- JPanel gridPanel = new JPanel(grid);
-
-
- if(idQualifier != null)
+ //
+ // ortholog
+ Box xBox = Box.createVerticalBox();
+ JButton addOrthoButton = new JButton("ADD ORTHOLOG");
+ addOrthoButton.addActionListener(new ActionListener()
{
- final String uniquename = (String)idQualifier.getValues().get(0);
- JLabel idField = new JLabel("ID");
-
-
- c.gridx = 0;
- c.gridy = 0;
- c.ipadx = 5;
- c.anchor = GridBagConstraints.EAST;
- gridPanel.add(idField, c);
- c.gridx = 1;
- c.gridy = 0;
- c.ipadx = 0;
- c.anchor = GridBagConstraints.WEST;
- //gridPanel.add(uniquenameTextField, c);
-
+ public void actionPerformed(ActionEvent e)
+ {
+ JExtendedComboBox dbs = new JExtendedComboBox(databases);
+
+ JTextField accession = new JTextField(15);
+
+ Box yBox = Box.createHorizontalBox();
+ yBox.add(dbs);
+ yBox.add(accession);
+ int select = JOptionPane.showConfirmDialog(null,
+ yBox, "Add Ortholog",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(select == JOptionPane.CANCEL_OPTION)
+ return;
+
+ add("ortholog", ((String)dbs.getSelectedItem())+":"+
+ accession.getText().trim(), feature);
+ }
+ });
+ xBox.add(addOrthoButton);
+
+ if(orthoQualifier != null)
+ {
+ StringVector orthologs = orthoQualifier.getValues();
+ for(int i=0; i<orthologs.size(); i++)
+ {
+ JTextField ortholog = new JTextField( (String)orthologs.get(i) );
+ xBox.add(ortholog);
+ }
}
+ //
+ // paralog
+ JButton addParaButton = new JButton("ADD PARALOG");
+ addParaButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ JExtendedComboBox dbs = new JExtendedComboBox(databases);
+ JTextField accession = new JTextField(15);
+
+ Box yBox = Box.createHorizontalBox();
+ yBox.add(dbs);
+ yBox.add(accession);
+
+ int select = JOptionPane.showConfirmDialog(null,
+ yBox, "Add Paralog",
+ JOptionPane.OK_CANCEL_OPTION);
+ if(select == JOptionPane.CANCEL_OPTION)
+ return;
+
+ add("paralog", ((String)dbs.getSelectedItem())+":"+
+ accession.getText().trim(), feature);
+ }
+ });
+ xBox.add(addParaButton);
+ if(paraQualifier != null)
+ {
+ StringVector paralogs = paraQualifier.getValues();
+ for(int i=0; i<paralogs.size(); i++)
+ {
+ JTextField paralog = new JTextField( (String)paralogs.get(i) );
+ xBox.add(paralog);
+ }
+ }
- gffBox.add(gridPanel);
- return gffBox;
+ return xBox;
}
+ /**
+ * Update ortho/paralogs for a feature
+ * @param feature
+ */
public void updateFromFeature(final Feature feature)
{
removeAll();
- if(orthologQualifiers != null)
+ if(ortho_para_logQualifiers != null)
feature.removeFeatureChangeListener(this);
- orthologQualifiers = feature.getQualifiers().copy();
+ ortho_para_logQualifiers = feature.getQualifiers().copy();
- orthologQualifiers = new QualifierVector();
+ ortho_para_logQualifiers = new QualifierVector();
final QualifierVector qualifiers = feature.getQualifiers();
for(int i = 0 ; i < qualifiers.size(); ++i)
{
Qualifier qualifier = (Qualifier)qualifiers.elementAt(i);
if(isOrthologTag(qualifier))
- orthologQualifiers.addElement(qualifier.copy());
+ ortho_para_logQualifiers.addElement(qualifier.copy());
}
feature.addFeatureChangeListener(this);
- add(createOrthologQualifiersComponent());
+ add(createOrthoParaLogQualifiersComponent(feature));
repaint();
revalidate();
}
+ /**
+ * Add ortholog/paralog
+ * @param name ortholog or paralog
+ * @param value
+ */
+ public void add(final String name, final String value, final Feature feature)
+ {
+ final int index;
+
+ Qualifier qualifier = ortho_para_logQualifiers.getQualifierByName(name);
+
+ if(qualifier == null)
+ {
+ qualifier = new Qualifier(name);
+ index = -1;
+ }
+ else
+ index = ortho_para_logQualifiers.indexOf(qualifier);
+
+ qualifier.addValue(value);
+
+ if(index > -1)
+ {
+ ortho_para_logQualifiers.remove(index);
+ ortho_para_logQualifiers.add(index, qualifier);
+ }
+ else
+ ortho_para_logQualifiers.add(qualifier);
+
+ removeAll();
+ add(createOrthoParaLogQualifiersComponent(feature));
+ repaint();
+ revalidate();
+ }
+
/**
* Get the latest (edited) controlled vocab qualifiers
* @return
*/
public QualifierVector getOrthologQualifiers()
{
- // check editable components for changes
-
- //
-
- return orthologQualifiers;
+ return ortho_para_logQualifiers;
}
public void featureChanged(FeatureChangeEvent event)