From 3aa725b66b162b84fe8b4ccfbc64d0aa2b99b670 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 20 Jun 2007 15:23:29 +0000
Subject: [PATCH] implement opening gene editors for linked features in a
cluster
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6131 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../ortholog/AbstractMatchTable.java | 122 +++++++++++++++++-
.../genebuilder/ortholog/MatchPanel.java | 8 +-
.../genebuilder/ortholog/OrthologTable.java | 74 +++++------
3 files changed, 157 insertions(+), 47 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/AbstractMatchTable.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/AbstractMatchTable.java
index 745c5d008..b2a2d6b3a 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/AbstractMatchTable.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/AbstractMatchTable.java
@@ -48,7 +48,11 @@ import javax.swing.table.DefaultTableModel;
import javax.swing.table.TableCellRenderer;
import javax.swing.table.TableColumn;
+import uk.ac.sanger.artemis.components.genebuilder.GeneEdit;
+import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.QualifierVector;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
abstract class AbstractMatchTable
{
@@ -212,12 +216,11 @@ abstract class AbstractMatchTable
{
public void actionPerformed(ActionEvent e)
{
- fireEditingStopped();
-
+ fireEditingStopped();
}
});
}
-
+
public Component getTableCellEditorComponent(JTable table, Object value,
boolean isSelected, int row, int column)
{
@@ -264,6 +267,119 @@ abstract class AbstractMatchTable
catch(ArrayIndexOutOfBoundsException e){}
}
}
+
+
+
+
+
+
+
+ /**
+ *
+ */
+ protected class LinkEditor extends DefaultCellEditor
+ {
+ /** */
+ private static final long serialVersionUID = 1L;
+ protected JButton linkButton = new JButton();
+ private boolean isPushed;
+ private Color fgLinkColor = Color.BLUE;
+ private DatabaseDocument doc;
+
+ public LinkEditor(JCheckBox checkBox, final DefaultTableModel tableModel,
+ DatabaseDocument doc)
+ {
+ super(checkBox);
+ this.doc = doc;
+
+ linkButton.setBorderPainted(false);
+ linkButton.setOpaque(false);
+
+
+ linkButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ fireEditingStopped();
+ }
+ });
+ }
+
+ private DatabaseDocumentEntry makeEntry(final String schema,
+ final String uniquename)
+ {
+ DatabaseDocumentEntry db_entry = null;
+ DatabaseDocument newdoc = new DatabaseDocument(doc,
+ uniquename, schema, true);
+
+ try
+ {
+ db_entry = new DatabaseDocumentEntry(newdoc, null);
+ }
+ catch(EntryInformationException e)
+ {
+ e.printStackTrace();
+ }
+ catch(IOException e)
+ {
+ e.printStackTrace();
+ }
+ return db_entry;
+ }
+
+ public Component getTableCellEditorComponent(JTable table, Object value,
+ boolean isSelected, int row, int column)
+ {
+ linkButton.setText((String)value);
+ if (isSelected)
+ {
+ linkButton.setForeground(fgLinkColor);
+ linkButton.setBackground(table.getSelectionBackground());
+ }
+ else
+ {
+ linkButton.setForeground(fgLinkColor);
+ linkButton.setBackground(table.getBackground());
+ }
+
+ isPushed = true;
+ return linkButton;
+ }
+
+ public Object getCellEditorValue()
+ {
+ String link = linkButton.getText();
+ if(isPushed)
+ {
+ // open gene editor for this link
+
+ String reference[] = link.split(":");
+ DatabaseDocumentEntry entry = makeEntry(reference[0], reference[1]);
+ entry.setReadOnly(true);
+ GeneEdit.showGeneEditor(reference[0], reference[1], entry);
+
+ isChanged = true;
+ return link;
+ }
+ isPushed = false;
+ return link;
+ }
+
+ public boolean stopCellEditing()
+ {
+ isPushed = false;
+ return super.stopCellEditing();
+ }
+
+ protected void fireEditingStopped()
+ {
+ try
+ {
+ super.fireEditingStopped();
+ }
+ catch(ArrayIndexOutOfBoundsException e){}
+ }
+ }
//
//http://java.sun.com/docs/books/tutorial/uiswing/dnd/intro.html
diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
index 1155b3cc1..ad9afe538 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java
@@ -17,7 +17,7 @@
* 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/genebuilder/ortholog/MatchPanel.java,v 1.6 2007-06-13 14:17:32 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java,v 1.7 2007-06-20 15:23:29 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder.ortholog;
@@ -151,7 +151,11 @@ public class MatchPanel extends JPanel
//{
if(hide_show_ortho == null)
hide_show_ortho = new JButton("-");
- orthologTable = new OrthologTable(orthoQualifier);
+
+ DocumentEntry entry = (DocumentEntry)feature.getEmblFeature().getEntry();
+ DatabaseDocument doc = (DatabaseDocument)entry.getDocument();
+
+ orthologTable = new OrthologTable(doc, orthoQualifier);
addHideShowButton(orthologTable.getTable(), hide_show_ortho);
xBox.add(hide_show_ortho);
editableComponents.add(orthologTable);
diff --git a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
index a482f3c03..8d735e86a 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java
@@ -43,17 +43,18 @@ import javax.swing.table.TableModel;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.QualifierVector;
+import uk.ac.sanger.artemis.util.DatabaseDocument;
public class OrthologTable extends AbstractMatchTable
{
- private int NUMBER_COLUMNS = 4;
+ private int NUMBER_COLUMNS = 3;
private Vector rowData = new Vector();
private Vector tableData = new Vector(NUMBER_COLUMNS);
private JTable orthologTable;
private JButton infoLevelButton = new JButton("Details");
private Qualifier origQualifier;
private boolean isChanged = false;
-
+
//
// column headings
final static String ORGANISM_COL = "Organism";
@@ -66,32 +67,29 @@ public class OrthologTable extends AbstractMatchTable
* @param similarity
* @param similarityString
*/
- protected OrthologTable(final Qualifier origQualifier)
+ protected OrthologTable(final DatabaseDocument doc,
+ final Qualifier origQualifier)
{
this.origQualifier = origQualifier;
infoLevelButton.setOpaque(false);
tableData.setSize(NUMBER_COLUMNS);
- tableData.setElementAt(ORGANISM_COL,0);
- tableData.setElementAt(ORTHO_COL,1);
- tableData.setElementAt(DESCRIPTION_COL,2);
- tableData.setElementAt(REMOVE_BUTTON_COL,3);
+ tableData.setElementAt(ORTHO_COL,0);
+ tableData.setElementAt(DESCRIPTION_COL,1);
+ tableData.setElementAt(REMOVE_BUTTON_COL,2);
// add row data
Vector thisRowData = new Vector();
- thisRowData.add("organism");
- thisRowData.add("blah");
+ thisRowData.add("Bpseudomallei:BPSL0003");
thisRowData.add("blah blah");
rowData.add(thisRowData);
Vector thisRowData2 = new Vector();
- thisRowData2.add("organism2");
- thisRowData2.add("blah2");
+ thisRowData2.add("Bpseudomallei:BPSL2915");
thisRowData2.add("blah blah2");
rowData.add(thisRowData2);
Vector thisRowData3 = new Vector();
- thisRowData3.add("organism3");
- thisRowData3.add("blah3");
+ thisRowData3.add("schema:id");
thisRowData3.add("blah blah3");
rowData.add(thisRowData3);
@@ -124,6 +122,11 @@ public class OrthologTable extends AbstractMatchTable
col = orthologTable.getColumn(REMOVE_BUTTON_COL);
col.setCellEditor(new ButtonEditor(new JCheckBox(),
(DefaultTableModel)orthologTable.getModel()));
+
+ // orthologue link
+ col = orthologTable.getColumn(ORTHO_COL);
+ col.setCellEditor(new LinkEditor(new JCheckBox(),
+ (DefaultTableModel)orthologTable.getModel(), doc));
}
protected boolean isQualifierChanged()
@@ -148,20 +151,15 @@ public class OrthologTable extends AbstractMatchTable
private static final long serialVersionUID = 1L;
private int minHeight = -1;
- private final JTextArea orthologTextArea = new JTextArea();
- private final JTextArea organismTextArea = new JTextArea();
+ private final JLabel orthologLabel = new JLabel();
private final JTextArea descriptionTextArea = new JTextArea();
private final JLabel buttRemove = new JLabel("X");
private Color fgColor = new Color(139,35,35);
+ private Color fgLinkColor = Color.BLUE;
public OrthologRenderer()
{
-
- organismTextArea.setLineWrap(true);
- organismTextArea.setWrapStyleWord(true);
-
- orthologTextArea.setLineWrap(true);
- orthologTextArea.setWrapStyleWord(true);
+ orthologLabel.setForeground(Color.BLUE);
descriptionTextArea.setLineWrap(true);
descriptionTextArea.setWrapStyleWord(true);
@@ -191,29 +189,21 @@ public class OrthologTable extends AbstractMatchTable
Dimension dim;
TableColumn tableCol;
- if(column == getColumnIndex(ORGANISM_COL))
- {
- organismTextArea.setText(text);
-
- tableCol = table.getColumnModel().getColumn(column);
- organismTextArea.setSize(tableCol.getWidth(), table.getRowHeight(row));
-
- dim = organismTextArea.getPreferredSize();
- minHeight = Math.max(minHeight, dim.height);
-
- c = organismTextArea;
- }
- else if(column == getColumnIndex(ORTHO_COL))
+ if(column == getColumnIndex(ORTHO_COL))
{
- orthologTextArea.setText(text);
-
- tableCol = table.getColumnModel().getColumn(column);
- orthologTextArea.setSize(tableCol.getWidth(), table.getRowHeight(row));
-
- dim = orthologTextArea.getPreferredSize();
- minHeight = Math.max(minHeight, dim.height);
+ orthologLabel.setText(text);
+ if(isSelected)
+ {
+ orthologLabel.setForeground(fgLinkColor);
+ orthologLabel.setBackground(table.getSelectionBackground());
+ }
+ else
+ {
+ orthologLabel.setForeground(fgLinkColor);
+ orthologLabel.setBackground(UIManager.getColor("Button.background"));
+ }
- c = orthologTextArea;
+ c = orthologLabel;
}
else if(column == getColumnIndex(DESCRIPTION_COL))
{
--
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