Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport

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

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index b51906d..584a69a 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -57,6 +57,7 @@ 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;
@@ -64,7 +65,7 @@ import java.util.Vector;
 
 public class FeatureSettings extends Panel implements ItemListener,
         MouseListener, MouseMotionListener, ActionListener,
-        AdjustmentListener
+        AdjustmentListener, FeatureSettingsControllerI
 {
   FeatureRenderer fr;
 
@@ -114,12 +115,13 @@ public class FeatureSettings extends Panel implements ItemListener,
       fr.findAllFeatures(true); // was default - now true to make all visible
     }
 
-    setTableData();
+    discoverAllFeatureData();
 
     this.setLayout(new BorderLayout());
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       add(scrollPane, BorderLayout.CENTER);
     }
@@ -150,10 +152,11 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     if (groupPanel != null)
     {
-      groupPanel
-              .setLayout(new GridLayout(
-                      (fr.getFeatureGroupsSize()) / 4 + 1,
-                      4)); // JBPNote - this was scaled on number of visible groups. seems broken
+      groupPanel.setLayout(new GridLayout(
+              (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+                                                        // scaled on number of
+                                                        // visible groups. seems
+                                                        // broken
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -163,6 +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)
@@ -179,10 +183,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     height = Math.min(400, height);
     int width = 300;
     jalview.bin.JalviewLite.addFrame(frame,
-            MessageManager.getString("label.feature_settings"), width,
-            height);
+            MessageManager.getString("label.sequence_feature_settings"),
+            width, height);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     g.setColor(Color.black);
@@ -202,8 +207,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     final String type = check.type;
     final Object typeCol = fr.getFeatureStyle(type);
     java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
-            "label.settings_for_type", new String[]
-            { type }));
+            "label.settings_for_type", new String[] { type }));
     java.awt.MenuItem scr = new MenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -211,10 +215,11 @@ 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 }));
       }
 
     });
@@ -223,10 +228,11 @@ 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 }));
       }
 
     });
@@ -257,6 +263,7 @@ public class FeatureSettings extends Panel implements ItemListener,
         mxcol.addActionListener(new ActionListener()
         {
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (typeCol instanceof Color)
@@ -279,9 +286,11 @@ public class FeatureSettings extends Panel implements ItemListener,
     men.show(this.featurePanel, x, y);
   }
 
-  public void setTableData()
+  @Override
+  public void discoverAllFeatureData()
   {
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       rebuildGroups();
 
@@ -306,12 +315,10 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     // TODO: JAL-964 - smoothly incorporate new group entries if panel already
     // displayed and new groups present
-    for (String group:fr.getFeatureGroups())
+    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);
@@ -324,6 +331,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       groupPanel.validate();
     }
   }
+
   // This routine adds and removes checkboxes depending on
   // Group selection states
   void resetTable(boolean groupsChanged)
@@ -448,10 +456,7 @@ 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);
@@ -470,6 +475,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
@@ -480,11 +486,13 @@ public class FeatureSettings extends Panel implements ItemListener,
     selectionChanged();
   }
 
-  private ItemListener groupItemListener = new ItemListener() {
-    public void itemStateChanged(ItemEvent evt) {
+  private ItemListener groupItemListener = new ItemListener()
+  {
+    @Override
+    public void itemStateChanged(ItemEvent evt)
+    {
       Checkbox source = (Checkbox) evt.getSource();
-      fr.setGroupVisibility(source.getLabel(),
-              source.getState());
+      fr.setGroupVisibility(source.getLabel(), source.getState());
       ap.seqPanel.seqCanvas.repaint();
       if (ap.overviewPanel != null)
       {
@@ -494,6 +502,8 @@ public class FeatureSettings extends Panel implements ItemListener,
       return;
     };
   };
+
+  @Override
   public void itemStateChanged(ItemEvent evt)
   {
     selectionChanged();
@@ -527,22 +537,7 @@ 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)
@@ -552,6 +547,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     dragging = true;
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     if (((Component) evt.getSource()).getParent() != featurePanel)
@@ -613,7 +609,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     else
     {
-      throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_unsupported_feature_colour_object"));
     }
     refreshTable();
   }
@@ -625,14 +623,17 @@ 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();
@@ -640,16 +641,6 @@ 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)
     {
@@ -672,10 +663,12 @@ 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);
@@ -709,7 +702,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_colour_for_mycheckbox"));
       }
       if (col != null)
       {
@@ -754,6 +749,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       updateColor(featureStyle);
     }
 
+    @Override
     public void paint(Graphics g)
     {
       Dimension d = getSize();
@@ -792,4 +788,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
   }
 
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+  }
+
 }