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

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
 {
@@ -213,7 +217,6 @@ abstract class AbstractMatchTable
        public void actionPerformed(ActionEvent e) 
        {
          fireEditingStopped(); 
-         
        }
      });
    }
@@ -265,6 +268,119 @@ abstract class AbstractMatchTable
    }
  }
   
+  
+  
+  
+  
+  
+  
+  /**
+  *
+  */
+  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
   //

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);

uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthologTable.java

@@ -43,10 +43,11 @@ 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;
@@ -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))
+      if(column == getColumnIndex(ORTHO_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;
+        orthologLabel.setText(text);
+        if(isSelected) 
+        {
+          orthologLabel.setForeground(fgLinkColor);
+          orthologLabel.setBackground(table.getSelectionBackground());
         } 
-      else if(column == getColumnIndex(ORTHO_COL))
+        else
         {
-        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.setForeground(fgLinkColor);
+          orthologLabel.setBackground(UIManager.getColor("Button.background"));
+        }
         
-        c = orthologTextArea;
+        c = orthologLabel;
       }
       else if(column == getColumnIndex(DESCRIPTION_COL))
       {