JAL-2630 applet update overview on release of threshold slider

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 6c162e1..f460389 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -46,53 +46,81 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
-import java.util.Hashtable;
 
 public class FeatureColourChooser extends Panel implements ActionListener,
         AdjustmentListener, ItemListener, MouseListener
 {
+  /*
+   * the absolute min-max range of a feature score is scaled to 
+   * 1000 positions on the colour threshold slider
+   */
   private static final int SCALE_FACTOR_1K = 1000;
 
-  JVDialog frame;
+  private JVDialog frame;
 
-  Frame owner;
+  private Frame owner;
 
-  FeatureRenderer fr;
+  private FeatureRenderer fr;
 
-  FeatureSettings fs = null;
+  private FeatureSettings fs = null;
 
-  // AlignmentPanel ap;
+  private FeatureColourI cs;
 
-  FeatureColourI cs;
+  private FeatureColourI oldcs;
 
-  FeatureColourI oldcs;
-
-  Hashtable oldgroupColours;
-
-  boolean adjusting = false;
+  private boolean adjusting = false;
 
   private float min, max;
 
-  String type = null;
+  private String type = null;
 
   private AlignFrame af = null;
 
-  public FeatureColourChooser(AlignFrame af, String type)
+  private Panel minColour = new Panel();
+
+  private Panel maxColour = new Panel();
+
+  private Choice threshold = new Choice();
+
+  private Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+
+  private TextField thresholdValue = new TextField(20);
+
+  private Checkbox thresholdIsMin = new Checkbox();
+
+  private Checkbox colourFromLabel = new Checkbox();
+
+  private GraphLine threshline;
+
+  /**
+   * Constructor given a context AlignFrame and a feature type. This is used
+   * when opening the graduated colour dialog from the Amend Feature dialog.
+   * 
+   * @param alignFrame
+   * @param featureType
+   */
+  public FeatureColourChooser(AlignFrame alignFrame, String featureType)
   {
-    this.af = af;
-    init(af.getSeqcanvas().getFeatureRenderer(), type);
+    this.af = alignFrame;
+    init(alignFrame.getSeqcanvas().getFeatureRenderer(), featureType);
   }
 
-  public FeatureColourChooser(FeatureSettings fsettings, String type)
+  /**
+   * Constructor given a context FeatureSettings and a feature type. This is
+   * used when opening the graduated colour dialog from Feature Settings.
+   * 
+   * @param fsettings
+   * @param featureType
+   */
+  public FeatureColourChooser(FeatureSettings fsettings, String featureType)
   {
     this.fs = fsettings;
-    init(fsettings.fr, type);
-    // this.ap = fsettings.ap;
+    init(fsettings.fr, featureType);
   }
 
-  private void init(FeatureRenderer frenderer, String type)
+  private void init(FeatureRenderer frenderer, String featureType)
   {
-    this.type = type;
+    this.type = featureType;
     fr = frenderer;
     float mm[] = fr.getMinMax().get(type)[0];
     min = mm[0];
@@ -132,7 +160,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
             : 0));
 
     adjusting = false;
-    changeColour();
+    changeColour(true);
     colourFromLabel.addItemListener(this);
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
@@ -145,7 +173,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     frame.setVisible(true);
     if (frame.accept)
     {
-      changeColour();
+      changeColour(true);
     }
     else
     {
@@ -185,9 +213,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     thresholdIsMin.addItemListener(this);
 
     this.setLayout(new GridLayout(4, 1));
+    Panel jPanel1 = new Panel();
     jPanel1.setLayout(new FlowLayout());
+    Panel jPanel2 = new Panel();
     jPanel2.setLayout(new FlowLayout());
+    Panel jPanel3 = new Panel();
     jPanel3.setLayout(new GridLayout(1, 1));
+    Panel jPanel4 = new Panel();
     jPanel4.setLayout(new FlowLayout());
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
@@ -235,32 +267,6 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     this.add(jPanel4);// , java.awt.BorderLayout.CENTER);
   }
 
-  Panel minColour = new Panel();
-
-  Panel maxColour = new Panel();
-
-  Panel jPanel1 = new Panel();
-
-  Panel jPanel2 = new Panel();
-
-  Choice threshold = new Choice();
-
-  Panel jPanel3 = new Panel();
-
-  Panel jPanel4 = new Panel();
-
-  Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
-
-  TextField thresholdValue = new TextField(20);
-
-  // BorderLayout borderLayout1 = new BorderLayout();
-
-  Checkbox thresholdIsMin = new Checkbox();
-
-  Checkbox colourFromLabel = new Checkbox();
-
-  private GraphLine threshline;
-
   @Override
   public void actionPerformed(ActionEvent evt)
   {
@@ -285,7 +291,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
     else
     {
-      changeColour();
+      changeColour(true);
     }
   }
 
@@ -294,9 +300,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     maxColour.setEnabled(!colourFromLabel.getState());
     minColour.setEnabled(!colourFromLabel.getState());
-    changeColour();
+    changeColour(true);
   }
 
+  /**
+   * Handler called when the value of the threshold slider changes, either by
+   * user action or programmatically
+   */
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
@@ -307,29 +317,32 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     }
   }
 
+  /**
+   * Responds to a change of colour threshold by computing the absolute value
+   * and refreshing the alignment.
+   */
   protected void valueChanged()
   {
     threshline.value = slider.getValue() / 1000f;
     cs.setThreshold(threshline.value);
-    changeColour();
+    changeColour(false);
     PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
-    // ap.paintAlignment(false);
   }
 
   public void minColour_actionPerformed(Color newCol)
   {
     if (newCol == null)
     {
-      UserDefinedColours udc = new UserDefinedColours(this,
+      new UserDefinedColours(this,
               minColour.getBackground(), owner,
-              MessageManager.getString("label.select_colour_minimum_value")); // frame.owner,
+              MessageManager.getString("label.select_colour_minimum_value"));
     }
     else
     {
       minColour.setBackground(newCol);
       minColour.setForeground(newCol);
       minColour.repaint();
-      changeColour();
+      changeColour(true);
     }
 
   }
@@ -338,10 +351,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     if (newCol == null)
     {
-
-      // UserDefinedColours udc = new UserDefinedColours(this,
-      // "Select Colour for Maximum Value",maxColour.getBackground(),true);
-      UserDefinedColours udc = new UserDefinedColours(this,
+      new UserDefinedColours(this,
               maxColour.getBackground(), owner,
               MessageManager.getString("label.select_colour_maximum_value"));
     }
@@ -350,11 +360,11 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       maxColour.setBackground(newCol);
       maxColour.setForeground(newCol);
       maxColour.repaint();
-      changeColour();
+      changeColour(true);
     }
   }
 
-  void changeColour()
+  void changeColour(boolean updateOverview)
   {
     // Check if combobox is still adjusting
     if (adjusting)
@@ -417,13 +427,13 @@ public class FeatureColourChooser extends Panel implements ActionListener,
 
     fr.setColour(type, acg);
     cs = acg;
-    fs.selectionChanged();
+    fs.selectionChanged(updateOverview);
   }
 
   void reset()
   {
     fr.setColour(type, oldcs);
-    fs.selectionChanged();
+    fs.selectionChanged(true);
   }
 
   @Override
@@ -439,16 +449,19 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
-    if (evt.getSource() == minColour || evt.getSource() == maxColour)
+    if (evt.getSource() == minColour)
     {
-      // relay the event
-      actionPerformed(new ActionEvent(evt.getSource(), 1, "Clicked"));
+      minColour_actionPerformed(null);
+    }
+    else if (evt.getSource() == maxColour)
+    {
+      maxColour_actionPerformed(null);
     }
     else
     {
-      PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
+      changeColour(true);
+      // PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
     }
-    // ap.paintAlignment(true);
   }
 
   @Override

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 9d2f601..7d00afd 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -544,7 +544,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       Checkbox check = (Checkbox) featurePanel.getComponent(i);
       check.setState(!check.getState());
     }
-    selectionChanged();
+    selectionChanged(true);
   }
 
   private ItemListener groupItemListener = new ItemListener()
@@ -567,10 +567,10 @@ public class FeatureSettings extends Panel implements ItemListener,
   @Override
   public void itemStateChanged(ItemEvent evt)
   {
-    selectionChanged();
+    selectionChanged(true);
   }
 
-  void selectionChanged()
+  void selectionChanged(boolean updateOverview)
   {
     Component[] comps = featurePanel.getComponents();
     int cSize = comps.length;
@@ -591,7 +591,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     fr.setFeaturePriority(data);
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(updateOverview);
   }
 
   MyCheckbox selectedCheck;

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 7c6fad0..32507fe 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -27,6 +27,7 @@ import java.awt.Component;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 /**
@@ -37,7 +38,7 @@ import java.util.Vector;
  */
 public class PaintRefresher
 {
-  static Hashtable components;
+  static Map<String, Vector<Component>> components;
 
   /**
    * DOCUMENT ME!
@@ -51,12 +52,12 @@ public class PaintRefresher
   {
     if (components == null)
     {
-      components = new Hashtable();
+      components = new Hashtable<String, Vector<Component>>();
     }
 
     if (components.containsKey(seqSetId))
     {
-      Vector comps = (Vector) components.get(seqSetId);
+      Vector<Component> comps = components.get(seqSetId);
       if (!comps.contains(comp))
       {
         comps.addElement(comp);
@@ -64,7 +65,7 @@ public class PaintRefresher
     }
     else
     {
-      Vector vcoms = new Vector();
+      Vector<Component> vcoms = new Vector<>();
       vcoms.addElement(comp);
       components.put(seqSetId, vcoms);
     }
@@ -77,11 +78,9 @@ public class PaintRefresher
       return;
     }
 
-    Enumeration en = components.keys();
-    while (en.hasMoreElements())
+    for (String id : components.keySet())
     {
-      String id = en.nextElement().toString();
-      Vector comps = (Vector) components.get(id);
+      Vector<Component> comps = components.get(id);
       comps.removeElement(comp);
       if (comps.size() == 0)
       {
@@ -104,17 +103,17 @@ public class PaintRefresher
     }
 
     Component comp;
-    Vector comps = (Vector) components.get(id);
+    Vector<Component> comps = components.get(id);
 
     if (comps == null)
     {
       return;
     }
 
-    Enumeration e = comps.elements();
+    Enumeration<Component> e = comps.elements();
     while (e.hasMoreElements())
     {
-      comp = (Component) e.nextElement();
+      comp = e.nextElement();
 
       if (comp == source)
       {
@@ -240,8 +239,8 @@ public class PaintRefresher
 
   public static AlignmentPanel[] getAssociatedPanels(String id)
   {
-    Vector comps = (Vector) components.get(id);
-    Vector tmp = new Vector();
+    Vector<Component> comps = components.get(id);
+    Vector<Component> tmp = new Vector<>();
     int i, iSize = comps.size();
     for (i = 0; i < iSize; i++)
     {