X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=ef688f7b6327f695b76c1f89f75844cbdb25245f;hb=8240aa86ee94d4c372af7deb1452a8294ff8800b;hp=ce88b90118c1336147836fcc1103f23a07b100ee;hpb=8f759d39bf8d95e5657eccda618b65ad31171fcf;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index ce88b90..ef688f7 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -31,8 +31,6 @@ import jalview.io.JalviewFileChooser;
 import java.awt.BorderLayout;
 import java.awt.Font;
 import java.awt.Color;
-import jalview.biojava.dasobert.dasregistry.DasSource;
-import jalview.biojava.dasobert.dasregistry.DasCoordinateSystem;
 
 public class FeatureSettings extends JPanel
 {
@@ -50,7 +48,6 @@ public class FeatureSettings extends JPanel
   JSlider transparency = new JSlider();
 
   JPanel transPanel = new JPanel(new FlowLayout());
-  boolean alignmentHasFeatures = false;
 
   public FeatureSettings(AlignFrame af)
   {
@@ -68,6 +65,54 @@ public class FeatureSettings extends JPanel
      ex.printStackTrace();
    }
 
+   table = new JTable();
+   table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
+   table.setFont(new Font("Verdana", Font.PLAIN, 12));
+   table.setDefaultRenderer(Color.class,
+                            new ColorRenderer());
+
+   table.setDefaultEditor(Color.class,
+                          new ColorEditor());
+
+   table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+   table.addMouseListener(new MouseAdapter()
+   {
+     public void mousePressed(MouseEvent evt)
+     {
+       selectedRow = table.rowAtPoint(evt.getPoint());
+     }
+   });
+
+   table.addMouseMotionListener(new MouseMotionAdapter()
+   {
+     public void mouseDragged(MouseEvent evt)
+     {
+       int newRow = table.rowAtPoint(evt.getPoint());
+       if (newRow != selectedRow
+           && selectedRow != -1
+           && newRow != -1)
+       {
+         Object[] temp = new Object[3];
+         temp[0] = table.getValueAt(selectedRow, 0);
+         temp[1] = table.getValueAt(selectedRow, 1);
+         temp[2] = table.getValueAt(selectedRow, 2);
+
+         table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
+         table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
+         table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
+
+         table.setValueAt(temp[0], newRow, 0);
+         table.setValueAt(temp[1], newRow, 1);
+         table.setValueAt(temp[2], newRow, 2);
+
+         selectedRow = newRow;
+       }
+     }
+   });
+
+   scrollPane.setViewportView(table);
+
     dassourceBrowser = new DasSourceBrowser();
     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 
@@ -76,7 +121,6 @@ public class FeatureSettings extends JPanel
     if (af.getViewport().featuresDisplayed == null || fr.renderOrder==null)
        fr.findAllFeatures();
 
-
     setTableData();
 
     frame = new JInternalFrame();
@@ -85,10 +129,8 @@ public class FeatureSettings extends JPanel
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
-  public void setTableData()
+  synchronized public void setTableData()
   {
-    alignmentHasFeatures = false;
-
     if (fr.featureGroups == null)
       fr.featureGroups = new Hashtable();
 
@@ -102,8 +144,6 @@ public class FeatureSettings extends JPanel
       if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)
         continue;
 
-      alignmentHasFeatures = true;
-
       tmpfeatures = af.getViewport().alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
 
       int index = 0;
@@ -127,14 +167,28 @@ public class FeatureSettings extends JPanel
              {
                visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();
              }
-             else
-             {
-               fr.featureGroups.put(group, new Boolean(visible));
+
                if (groupPanel == null)
                {
                  groupPanel = new JPanel();
                }
 
+               boolean alreadyAdded = false;
+               for(int g=0; g<groupPanel.getComponentCount(); g++)
+               {
+                 if(((JCheckBox)groupPanel.getComponent(g))
+                    .getText().equals(group))
+                 {
+                   alreadyAdded = true;
+                   break;
+                 }
+               }
+
+               if(alreadyAdded)
+                 continue;
+
+               fr.featureGroups.put(group, new Boolean(visible));
+
                final JCheckBox check = new JCheckBox(group, visible);
                check.setFont(new Font("Serif", Font.BOLD, 12));
                check.addItemListener(new ItemListener()
@@ -152,8 +206,6 @@ public class FeatureSettings extends JPanel
                });
                groupPanel.add(check);
              }
-           }
-
        }
 
        if (!allFeatures.contains(tmpfeatures[index].getType()))
@@ -164,20 +216,9 @@ public class FeatureSettings extends JPanel
     }
   }
 
-
-    if(!alignmentHasFeatures)
-     {
-    //   try
-     //  { frame.setClosed(true);  }
-    //   catch (Exception ex){}
-
-    //   JOptionPane.showInternalMessageDialog(
-    ///       Desktop.desktop, "No features have been added to this alignment!",
-    //
-   //    return;
-     }
-
      resetTable(false);
+
+     validate();
   }
 
 
@@ -262,54 +303,9 @@ public class FeatureSettings extends JPanel
       System.arraycopy(data,0,originalData,0,data.length);
     }
 
-    table = new JTable(new FeatureTableModel(data));
-    scrollPane.setViewportView(table);
-    table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
-    table.setFont(new Font("Verdana", Font.PLAIN, 12));
-    table.setDefaultRenderer(Color.class,
-                         new ColorRenderer());
-
-    table.setDefaultEditor(Color.class,
-                      new ColorEditor());
-
+    table.setModel(new FeatureTableModel(data));
     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 
-    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-
-    table.addMouseListener(new MouseAdapter()
-        {
-          public void mousePressed(MouseEvent evt)
-          {
-            selectedRow = table.rowAtPoint(evt.getPoint());
-          }
-        });
-
-    table.addMouseMotionListener(new MouseMotionAdapter()
-        {
-          public void mouseDragged(MouseEvent evt)
-          {
-            int newRow = table.rowAtPoint(evt.getPoint());
-            if(newRow!=selectedRow
-               && selectedRow!=-1
-               && newRow!=-1)
-            {
-              Object[] temp = new Object[3];
-              temp[0] = table.getValueAt(selectedRow, 0);
-              temp[1] = table.getValueAt(selectedRow, 1);
-              temp[2] = table.getValueAt(selectedRow, 2);
-
-              table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-              table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-              table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-              table.setValueAt(temp[0], newRow, 0);
-              table.setValueAt(temp[1], newRow, 1);
-              table.setValueAt(temp[2], newRow, 2);
-
-              selectedRow = newRow;
-            }
-          }
-    });
 
     if (groupPanel != null)
     {
@@ -537,7 +533,7 @@ public class FeatureSettings extends JPanel
     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
     dasSettingsPane.setBorder(null);
     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
-    tabbedPane.addTab("Display Settings", settingsPane );
+    tabbedPane.addTab("Feature Settings", settingsPane );
     tabbedPane.addTab("DAS Settings", dasSettingsPane);
     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
     transPanel.add(transparency);