Merge branch 'feature/JAL-674_dssp' into features/JAL-1264_showHideAnnotations

[jalview.git] / src / jalview / gui / AnnotationLabels.java

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index fdb3975..0c29840 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,19 +20,42 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.util.regex.Pattern;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.MediaTracker;
+import java.awt.RenderingHints;
+import java.awt.Toolkit;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
-import java.awt.image.*;
-import javax.swing.*;
+import java.awt.image.BufferedImage;
+import java.util.Vector;
+import java.util.regex.Pattern;
 
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.util.MessageManager;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
 
 /**
  * DOCUMENT ME!
@@ -115,7 +138,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Graphics2D g = (Graphics2D) bi.getGraphics();
     g.rotate(Math.toRadians(90));
     g.drawImage(temp, 0, -bi.getWidth(this), this);
-    image = (Image) bi;
+    image = bi;
 
     addMouseListener(this);
     addMouseMotionListener(this);
@@ -249,11 +272,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
     }
 
+    refresh();
+
+  }
+
+  /**
+   * Redraw sensibly.
+   */
+  protected void refresh()
+  {
     ap.validateAnnotationDimensions(false);
     ap.addNotify();
     ap.repaint();
-    // validate();
-    // ap.paintAlignment(true);
   }
 
   /**
@@ -480,7 +510,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
    */
   public void mouseClicked(MouseEvent evt)
   {
-    AlignmentAnnotation[] aa = ap.av.getAlignment()
+    final AlignmentAnnotation[] aa = ap.av.getAlignment()
             .getAlignmentAnnotation();
     if (SwingUtilities.isLeftMouseButton(evt))
     {
@@ -579,6 +609,35 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     item = new JMenuItem(HIDE);
     item.addActionListener(this);
     pop.add(item);
+    // JAL-1264 hide all sequence-specific annotations of this type
+    final String label = aa[selectedRow].label;
+    if (selectedRow < aa.length)
+    {
+      if (aa[selectedRow].sequenceRef != null)
+      {
+        JMenuItem hideType = new JMenuItem();
+        String text = MessageManager.getString("label.hide_all") + " " + label;
+        hideType.setText(text);
+        hideType.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            for (AlignmentAnnotation ann : ap.av.getAlignment()
+                    .getAlignmentAnnotation())
+            {
+              if (ann.sequenceRef != null && ann.label != null
+                      && ann.label.equals(label))
+              {
+                ann.visible = false;
+              }
+            }
+            refresh();
+          }
+        });
+        pop.add(hideType);
+      }
+    }
     item = new JMenuItem(DELETE);
     item.addActionListener(this);
     pop.add(item);
@@ -608,7 +667,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           pop.add(item);
         }
       }
-      else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+      else if (label.indexOf("Consensus") > -1)
       {
         pop.addSeparator();
         // av and sequencegroup need to implement same interface for