JAL-2808 JAL-2069 FeatureTypeSettings (with new Filters tab) replaces FeatureColourCh...

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 5e15364..39a2747 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -20,10 +20,14 @@
  */
 package jalview.appletgui;
 
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
+import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
+
 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 java.awt.BorderLayout;
@@ -56,13 +60,12 @@ 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,
@@ -378,36 +381,38 @@ 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 +429,7 @@ 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 +446,24 @@ 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(
@@ -583,23 +588,28 @@ public class FeatureSettings extends Panel
     Component[] comps = featurePanel.getComponents();
     int cSize = comps.length;
 
-    Object[][] tmp = new Object[cSize][3];
+    /*
+     * temporary! leave column[2] empty - used for Filter in
+     * gui.FeatureSettings
+     */
+    int columnCount = 4;
+    Object[][] tmp = new Object[cSize][columnCount];
     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());
+      tmp[tmpSize][TYPE_COLUMN /* 0 */] = check.type;
+      tmp[tmpSize][COLOUR_COLUMN /* 1 */] = fr.getFeatureStyle(check.type);
+      tmp[tmpSize][SHOW_COLUMN /* 3 */] = new Boolean(check.getState());
       tmpSize++;
     }
 
-    Object[][] data = new Object[tmpSize][3];
+    Object[][] data = new Object[tmpSize][columnCount];
     System.arraycopy(tmp, 0, data, 0, tmpSize);
 
     fr.setFeaturePriority(data);
 
-    ap.paintAlignment(updateOverview);
+    ap.paintAlignment(updateOverview, updateOverview);
   }
 
   MyCheckbox selectedCheck;
@@ -679,7 +689,7 @@ public class FeatureSettings extends Panel
   {
     featurePanel.removeAll();
     resetTable(false);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -731,7 +741,7 @@ 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