X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=7c95ed78e19dd96e5aa029bfcd0292b057dcd16d;hb=4263dac5b885f760215fa599eb453e1221767d04;hp=eb744544ea74f33a4f33f8ed75037db17453a67f;hpb=22b9e04a8351aef1cb23a66d898502601499b673;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index eb74454..7c95ed7 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -35,6 +35,7 @@ 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();
@@ -124,8 +125,12 @@ public class FeatureSettings extends JPanel
     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);
 
@@ -139,30 +144,28 @@ public class FeatureSettings extends JPanel
     else
       fr.featureGroups.clear();
 
-    Vector allFeatures = new Vector();
-    Vector features;
-    Enumeration e;
-    SequenceFeature sf;
+    allFeatures = new Hashtable();
+    SequenceFeature[] features;
 
   for (int i = 0; i < av.alignment.getHeight(); i++)
   {
     features = av.alignment.getSequenceAt(i).getDatasetSequence().
         getSequenceFeatures();
+
     if (features == null)
       continue;
 
-    e = features.elements();
-    while (e.hasMoreElements())
+    int index = 0;
+    while (index < features.length)
     {
-      sf = (SequenceFeature) e.nextElement();
-      if(sf.getFeatureGroup()!=null
-          && !fr.featureGroups.containsKey(sf.getFeatureGroup()))
+      if(features[index].getFeatureGroup()!=null
+          && !fr.featureGroups.containsKey(features[index].getFeatureGroup()))
        {
-         fr.featureGroups.put(sf.getFeatureGroup(), new Boolean(true));
+         fr.featureGroups.put(features[index].getFeatureGroup(), new Boolean(true));
          if(groupPanel==null)
             groupPanel = new JPanel();
 
-          final JCheckBox check = new JCheckBox(sf.getFeatureGroup(), true);
+          final JCheckBox check = new JCheckBox(features[index].getFeatureGroup(), true);
           check.setFont(new Font("Serif", Font.BOLD, 12));
           check.addItemListener(new ItemListener()
               {
@@ -176,15 +179,19 @@ public class FeatureSettings extends JPanel
                     if (ap.overviewPanel != null)
                       ap.overviewPanel.updateOverviewImage();
                   }
-
+                  resetTable();
                 }
               });
           groupPanel.add(check);
        }
-      if (!allFeatures.contains(sf.getType()))
+      if (!allFeatures.contains(features[index].getType()))
       {
-        allFeatures.addElement(sf.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)
@@ -200,87 +207,111 @@ public class FeatureSettings extends JPanel
        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.addMouseMotionListener(new MouseMotionAdapter()
+    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)
             {
-              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);
 
   }