X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=489cbb145d0bf7941f320502430479403782f43a;hb=71b8b157747abb849fb50316450a22d4559873da;hp=5e15364d48c229f1f90bb65b762328007c14c758;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 5e15364..489cbb1 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -23,8 +23,9 @@ package jalview.appletgui;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
 import java.awt.BorderLayout;
 import java.awt.Button;
@@ -56,17 +57,16 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.Vector;
 
 public class FeatureSettings extends Panel
         implements ItemListener, MouseListener, MouseMotionListener,
-        ActionListener, AdjustmentListener, FeatureSettingsControllerI
+        AdjustmentListener, FeatureSettingsControllerI
 {
   FeatureRenderer fr;
 
@@ -121,8 +121,17 @@ public class FeatureSettings extends Panel
       add(scrollPane, BorderLayout.CENTER);
     }
 
-    Button invert = new Button("Invert Selection");
-    invert.addActionListener(this);
+    Button invert = new Button(
+            MessageManager.getString("label.invert_selection"));
+    invert.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSelection();
+      }
+    });
 
     Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
     lowerPanel.add(invert);
@@ -378,36 +387,38 @@ public class FeatureSettings extends Panel
   // Group selection states
   void resetTable(boolean groupsChanged)
   {
-    SequenceFeature[] tmpfeatures;
-    String group = null, type;
-    Vector<String> visibleChecks = new Vector<String>();
-    Set<String> foundGroups = new HashSet<String>();
+    List<String> displayableTypes = new ArrayList<>();
+    Set<String> foundGroups = new HashSet<>();
+
     AlignmentI alignment = av.getAlignment();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
-      if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
-      {
-        continue;
-      }
+      SequenceI seq = alignment.getSequenceAt(i);
 
-      tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
-      int index = 0;
-      while (index < tmpfeatures.length)
+      /*
+       * get the sequence's groups for positional features
+       * and keep track of which groups are visible
+       */
+      Set<String> groups = seq.getFeatures().getFeatureGroups(true);
+      Set<String> visibleGroups = new HashSet<>();
+      for (String group : groups)
       {
-        group = tmpfeatures[index].featureGroup;
-        foundGroups.add(group);
-
+        // if (group == null || fr.checkGroupVisibility(group, true))
         if (group == null || checkGroupState(group))
         {
-          type = tmpfeatures[index].getType();
-          if (!visibleChecks.contains(type))
-          {
-            visibleChecks.addElement(type);
-          }
+          visibleGroups.add(group);
         }
-        index++;
       }
+      foundGroups.addAll(groups);
+
+      /*
+       * get distinct feature types for visible groups
+       * record distinct visible types
+       */
+      Set<String> types = seq.getFeatures().getFeatureTypesForGroups(true,
+              visibleGroups.toArray(new String[visibleGroups.size()]));
+      displayableTypes.addAll(types);
     }
 
     /*
@@ -424,7 +435,7 @@ public class FeatureSettings extends Panel
     {
       comps = featurePanel.getComponents();
       check = (MyCheckbox) comps[i];
-      if (!visibleChecks.contains(check.type))
+      if (!displayableTypes.contains(check.type))
       {
         featurePanel.remove(i);
         cSize--;
@@ -441,24 +452,24 @@ public class FeatureSettings extends Panel
       {
         String item = rol.get(ro);
 
-        if (!visibleChecks.contains(item))
+        if (!displayableTypes.contains(item))
         {
           continue;
         }
 
-        visibleChecks.removeElement(item);
+        displayableTypes.remove(item);
 
         addCheck(false, item);
       }
     }
 
-    // now add checkboxes which should be visible,
-    // if they have not already been added
-    Enumeration<String> en = visibleChecks.elements();
-
-    while (en.hasMoreElements())
+    /*
+     * now add checkboxes which should be visible,
+     * if they have not already been added
+     */
+    for (String type : displayableTypes)
     {
-      addCheck(groupsChanged, en.nextElement().toString());
+      addCheck(groupsChanged, type);
     }
 
     featurePanel.setLayout(
@@ -544,8 +555,7 @@ public class FeatureSettings extends Panel
     }
   }
 
-  @Override
-  public void actionPerformed(ActionEvent evt)
+  protected void invertSelection()
   {
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
     {
@@ -582,24 +592,21 @@ public class FeatureSettings extends Panel
   {
     Component[] comps = featurePanel.getComponents();
     int cSize = comps.length;
-
-    Object[][] tmp = new Object[cSize][3];
-    int tmpSize = 0;
-    for (int i = 0; i < cSize; i++)
-    {
-      MyCheckbox check = (MyCheckbox) comps[i];
-      tmp[tmpSize][0] = check.type;
-      tmp[tmpSize][1] = fr.getFeatureStyle(check.type);
-      tmp[tmpSize][2] = new Boolean(check.getState());
-      tmpSize++;
+    FeatureSettingsBean[] rowData = new FeatureSettingsBean[cSize];
+    int i = 0;
+    for (Component comp : comps)
+    {
+      MyCheckbox check = (MyCheckbox) comp;
+      // feature filter set to null as not (yet) offered in applet
+      FeatureColourI colour = fr.getFeatureStyle(check.type);
+      rowData[i] = new FeatureSettingsBean(check.type, colour, null,
+              check.getState());
+      i++;
     }
 
-    Object[][] data = new Object[tmpSize][3];
-    System.arraycopy(tmp, 0, data, 0, tmpSize);
-
-    fr.setFeaturePriority(data);
+    fr.setFeaturePriority(rowData);
 
-    ap.paintAlignment(updateOverview);
+    ap.paintAlignment(updateOverview, updateOverview);
   }
 
   MyCheckbox selectedCheck;
@@ -679,7 +686,7 @@ public class FeatureSettings extends Panel
   {
     featurePanel.removeAll();
     resetTable(false);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -696,7 +703,7 @@ public class FeatureSettings extends Panel
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
     {
       this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
     }
@@ -731,7 +738,7 @@ public class FeatureSettings extends Panel
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     fr.setTransparency((100 - transparency.getValue()) / 100f);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   class MyCheckbox extends Checkbox