X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=7c95ed78e19dd96e5aa029bfcd0292b057dcd16d;hb=4263dac5b885f760215fa599eb453e1221767d04;hp=532518055cb689c1996d07b18a60b9a2a08053c4;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 5325180..7c95ed7 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.gui;
 
 import jalview.datamodel.*;
@@ -17,10 +35,12 @@ public class FeatureSettings extends JPanel
   final FeatureRenderer fr;
   final AlignmentPanel ap;
   final AlignViewport av;
+  Hashtable allFeatures;
   Object [][] originalData;
   final JInternalFrame frame;
   JScrollPane scrollPane = new JScrollPane();
   JTable table;
+  JPanel groupPanel;
 
   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)
   {
@@ -104,7 +124,13 @@ public class FeatureSettings extends JPanel
     JPanel bigPanel = new JPanel(new BorderLayout());
     bigPanel.add(transPanel, BorderLayout.SOUTH);
     bigPanel.add(scrollPane, BorderLayout.CENTER);
-
+    if(groupPanel!=null)
+    {
+      groupPanel.setLayout(
+          new GridLayout(groupPanel.getComponentCount()/3, 4));
+      groupPanel.validate();
+      bigPanel.add(groupPanel, BorderLayout.NORTH);
+    }
     add(bigPanel, BorderLayout.CENTER);
     add(buttonPanel, BorderLayout.SOUTH);
 
@@ -113,116 +139,179 @@ public class FeatureSettings extends JPanel
 
   void setTableData()
   {
-    Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
+    if (fr.featureGroups == null)
+      fr.featureGroups = new Hashtable();
+    else
+      fr.featureGroups.clear();
 
-    for(int i=0; i< av.alignment.getHeight(); i++)
-    {
-       features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
-       if(features==null)
-         continue;
+    allFeatures = new Hashtable();
+    SequenceFeature[] features;
+
+  for (int i = 0; i < av.alignment.getHeight(); i++)
+  {
+    features = av.alignment.getSequenceAt(i).getDatasetSequence().
+        getSequenceFeatures();
 
-       e = features.elements();
-       while(e.hasMoreElements())
+    if (features == null)
+      continue;
+
+    int index = 0;
+    while (index < features.length)
+    {
+      if(features[index].getFeatureGroup()!=null
+          && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))
        {
-         sf = (SequenceFeature)e.nextElement();
-         if(!allFeatures.contains(sf.getType()))
-         {
-           allFeatures.addElement(sf.getType());
-         }
+         fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));
+         if(groupPanel==null)
+            groupPanel = new JPanel();
+
+          final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);
+          check.setFont(new Font("Serif", Font.BOLD, 12));
+          check.addItemListener(new ItemListener()
+              {
+                public void itemStateChanged(ItemEvent evt)
+                {
+                  if (fr.featureGroups.containsKey(check.getText()))
+                  {
+                    fr.featureGroups.put(check.getText(),
+                                         new Boolean(check.isSelected()));
+                    ap.seqPanel.seqCanvas.repaint();
+                    if (ap.overviewPanel != null)
+                      ap.overviewPanel.updateOverviewImage();
+                  }
+                  resetTable();
+                }
+              });
+          groupPanel.add(check);
        }
+      if (!allFeatures.contains(features[index].getType()))
+      {
+        if(features[index].featureGroup!=null)
+          allFeatures.put(features[index].getType(), features[index].featureGroup);
+        else
+          allFeatures.put(features[index].getType(), "NOGROUP");
+      }
+      index++;
     }
+  }
     if(allFeatures.size()<1)
      {
-       try{
-         frame.setClosed(true);
-       }catch(Exception ex){}
+       try
+       { frame.setClosed(true);  }
+       catch (Exception ex){}
+
+       JOptionPane.showInternalMessageDialog(
+           Desktop.desktop, "No features have been added to this alignment!",
+           "No Sequence Features", JOptionPane.WARNING_MESSAGE);
+
        return;
      }
 
+     resetTable();
+  }
+
+  void resetTable()
+  {
     int fSize = allFeatures.size();
 
     String type;
     boolean originalExists = false;
-    if(originalData!=null)
+    if (originalData != null)
       originalExists = true;
     else
       originalData = new Object[fSize][3];
 
-    Object [][] data = new Object[fSize][3];
-    for(int i=0; i<fSize; i++)
+    Object[][] tmp = new Object[fSize][3];
+    int tmpIndex = 0;
+
+    Enumeration en = allFeatures.keys();
+    int i=0;
+    while(en.hasMoreElements())
     {
-      type = allFeatures.elementAt(i).toString();
+      type = en.nextElement().toString();
       Color col = fr.getColour(type);
-      data[i][0]=type;
-      data[i][1]=col;
-      if(fr.featuresDisplayed!=null)
-         data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-      else
-        data[i][2] = new Boolean(true);
-
-      if(!originalExists)
+
+      //This will ignore any features which are in groups not shown
+     Object visibleGroup =  fr.featureGroups.get(allFeatures.get(type));
+     if(visibleGroup == null
+           || ((Boolean)(visibleGroup)).booleanValue())
+      {
+        tmp[tmpIndex][0] = type;
+        tmp[tmpIndex][1] = col;
+        if (av.featuresDisplayed != null)
+          tmp[tmpIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));
+        else
+          tmp[tmpIndex][2] = new Boolean(true);
+
+        tmpIndex++;
+      }
+
+
+      if (!originalExists)
       {
         originalData[i][0] = type;
         originalData[i][1] = col;
-        if (fr.featuresDisplayed != null)
-          originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
+        if (av.featuresDisplayed != null)
+          originalData[i][2] = new Boolean(av.featuresDisplayed.contains(type));
         else
           originalData[i][2] = new Boolean(true);
       }
+      i++;
     }
-    ////////////////////////////////////
-        //Now build the table
-        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());
+    Object [][]data = new Object[tmpIndex][3];
+    System.arraycopy(tmp, 0, data,0, tmpIndex);
 
-        table.getColumnModel().getColumn(0).setPreferredWidth(200);
+    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.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+    table.setDefaultEditor(Color.class,
+                      new ColorEditor());
 
-        table.addMouseListener(new MouseAdapter()
-            {
-              public void mousePressed(MouseEvent evt)
-              {
-                selectedRow = table.rowAtPoint(evt.getPoint());
-              }
-            });
+    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()
+    table.addMouseMotionListener(new MouseMotionAdapter()
+        {
+          public void mouseDragged(MouseEvent evt)
+          {
+            int newRow = table.rowAtPoint(evt.getPoint());
+            if(newRow!=selectedRow
+               && selectedRow!=-1
+               && newRow!=-1)
             {
-              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);
+              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(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);
+              table.setValueAt(temp[0], newRow, 0);
+              table.setValueAt(temp[1], newRow, 1);
+              table.setValueAt(temp[2], newRow, 2);
 
-                  selectedRow = newRow;
-                }
-              }
-        });
+              selectedRow = newRow;
+            }
+          }
+    });
+
+    updateFeatureRenderer(data);
 
   }
 
@@ -315,6 +404,9 @@ public class FeatureSettings extends JPanel
   {
     fr.setFeaturePriority( data );
     ap.repaint();
+
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
   int selectedRow =-1;