JAL-1421 typed map / lists, explicit imports, method refactoring

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

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 1c156dc..40a2ce5 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -57,9 +57,10 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.util.Arrays;
 import java.util.Enumeration;
-import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 public class FeatureSettings extends Panel implements ItemListener,
@@ -165,6 +166,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     final FeatureSettings me = this;
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent e)
       {
         if (me.av.featureSettings == me)
@@ -185,6 +187,7 @@ public class FeatureSettings extends Panel implements ItemListener,
             width, height);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     g.setColor(Color.black);
@@ -198,7 +201,8 @@ public class FeatureSettings extends Panel implements ItemListener,
             60);
   }
 
-  protected void popupSort(final MyCheckbox check, final Hashtable minmax,
+  protected void popupSort(final MyCheckbox check,
+          final Map<String, float[][]> minmax,
           int x, int y)
   {
     final String type = check.type;
@@ -212,10 +216,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     scr.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc
-                .sortAlignmentByFeatureScore(new String[] { type });
+        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -224,17 +229,18 @@ public class FeatureSettings extends Panel implements ItemListener,
     dens.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc
-                .sortAlignmentByFeatureDensity(new String[] { type });
+        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays
+                .asList(new String[] { type }));
       }
 
     });
     men.add(dens);
     if (minmax != null)
     {
-      final Object typeMinMax = minmax.get(type);
+      final float[][] typeMinMax = minmax.get(type);
       /*
        * final java.awt.CheckboxMenuItem chb = new
        * java.awt.CheckboxMenuItem("Vary Height"); // this is broken at the
@@ -247,7 +253,7 @@ public class FeatureSettings extends Panel implements ItemListener,
        * 
        * }); men.add(chb);
        */
-      if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+      if (typeMinMax != null && typeMinMax[0] != null)
       {
         // graduated colourschemes for those where minmax exists for the
         // positional features
@@ -258,6 +264,7 @@ public class FeatureSettings extends Panel implements ItemListener,
         mxcol.addActionListener(new ActionListener()
         {
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (typeCol instanceof Color)
@@ -312,9 +319,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     for (String group : fr.getFeatureGroups())
     {
       boolean vis = fr.checkGroupVisibility(group, false);
-      Checkbox check = new MyCheckbox(group, vis,
-              (fr.featureLinks != null && fr.featureLinks
-                      .containsKey(group)));
+      Checkbox check = new MyCheckbox(group, vis, false);
       check.addMouseListener(this);
       check.setFont(new Font("Serif", Font.BOLD, 12));
       check.addItemListener(groupItemListener);
@@ -334,7 +339,7 @@ public class FeatureSettings extends Panel implements ItemListener,
   {
     SequenceFeature[] tmpfeatures;
     String group = null, type;
-    Vector visibleChecks = new Vector();
+    Vector<String> visibleChecks = new Vector<String>();
     AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -400,7 +405,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     // now add checkboxes which should be visible,
     // if they have not already been added
-    Enumeration en = visibleChecks.elements();
+    Enumeration<String> en = visibleChecks.elements();
 
     while (en.hasMoreElements())
     {
@@ -452,10 +457,7 @@ public class FeatureSettings extends Panel implements ItemListener,
         selected = true;
       }
 
-      check = new MyCheckbox(
-              type,
-              selected,
-              (fr.featureLinks != null && fr.featureLinks.containsKey(type)),
+      check = new MyCheckbox(type, selected, false,
               fr.getFeatureStyle(type));
 
       check.addMouseListener(this);
@@ -474,6 +476,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -486,6 +489,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   private ItemListener groupItemListener = new ItemListener()
   {
+    @Override
     public void itemStateChanged(ItemEvent evt)
     {
       Checkbox source = (Checkbox) evt.getSource();
@@ -500,6 +504,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     };
   };
 
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     selectionChanged();
@@ -533,22 +538,7 @@ public class FeatureSettings extends Panel implements ItemListener,
 
   boolean dragging = false;
 
-  public void mousePressed(MouseEvent evt)
-  {
-
-    selectedCheck = (MyCheckbox) evt.getSource();
-
-    if (fr.featureLinks != null
-            && fr.featureLinks.containsKey(selectedCheck.type))
-    {
-      if (evt.getX() > selectedCheck.stringWidth + 20)
-      {
-        evt.consume();
-      }
-    }
-
-  }
-
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (((Component) evt.getSource()).getParent() != featurePanel)
@@ -558,6 +548,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     dragging = true;
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     if (((Component) evt.getSource()).getParent() != featurePanel)
@@ -633,14 +624,17 @@ public class FeatureSettings extends Panel implements ItemListener,
     ap.paintAlignment(true);
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
@@ -648,16 +642,6 @@ public class FeatureSettings extends Panel implements ItemListener,
     {
       this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
     }
-    if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type))
-    {
-      if (evt.getX() > check.stringWidth + 20)
-      {
-        evt.consume();
-        String link = fr.featureLinks.get(check.type).toString();
-        ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1),
-                link.substring(0, link.indexOf("|")));
-      }
-    }
 
     if (check.getParent() != featurePanel)
     {
@@ -680,10 +664,12 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     fr.setTransparency((100 - transparency.getValue()) / 100f);
@@ -764,6 +750,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       updateColor(featureStyle);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       Dimension d = getSize();
@@ -802,4 +789,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+  }
+
 }