Merge branch 'develop' into developtomchmmer

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index c049326..07c3e0a 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -51,13 +52,22 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Vector;
 
 public class AnnotationLabels extends Panel
         implements ActionListener, MouseListener, MouseMotionListener
 {
   Image image;
 
+  /**
+   * width in pixels within which height adjuster arrows are shown and active
+   */
+  private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+  /**
+   * height in pixels for allowing height adjuster to be active
+   */
+  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
   boolean active = false;
 
   AlignmentPanel ap;
@@ -93,23 +103,6 @@ public class AnnotationLabels extends Panel
     this.ap = ap;
     this.av = ap.av;
     setLayout(null);
-
-    /**
-     * this retrieves the adjustable height glyph from resources. we don't use
-     * it at the moment. java.net.URL url =
-     * getClass().getResource("/images/idwidth.gif"); Image temp = null;
-     * 
-     * if (url != null) { temp =
-     * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
-     * 
-     * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
-     * mt.waitForID(0); } catch (Exception ex) { }
-     * 
-     * BufferedImage bi = new BufferedImage(temp.getHeight(this),
-     * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
-     * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
-     * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
-     */
     addMouseListener(this);
     addMouseMotionListener(this);
   }
@@ -209,7 +202,9 @@ public class AnnotationLabels extends Panel
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      SequenceI cons = av.getConsensusSeq();
+      SequenceGroup group = aa[selectedRow].groupRef;
+      SequenceI cons = group == null ? av.getConsensusSeq()
+              : group.getConsensusSeq();
       if (cons != null)
       {
         copy_annotseqtoclipboard(cons);
@@ -269,7 +264,8 @@ public class AnnotationLabels extends Panel
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    resizePanel = evt.getY() < 10 && evt.getX() < 14;
+    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+            && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
     setCursor(Cursor.getPredefinedCursor(
             resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
     int row = getSelectedRow(evt.getY() + scrollOffset);
@@ -461,8 +457,8 @@ public class AnnotationLabels extends Panel
             .getAlignmentAnnotation();
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
 
       PopupMenu popup = new PopupMenu(
@@ -538,7 +534,7 @@ public class AnnotationLabels extends Panel
                     MessageManager.getString("label.ignore_gaps_consensus"),
                     (aa[selectedRow].groupRef != null)
                             ? aa[selectedRow].groupRef
-                                    .getIgnoreGapsConsensus()
+                                    .isIgnoreGapsConsensus()
                             : ap.av.isIgnoreGapsConsensus());
             final AlignmentAnnotation aaa = aa[selectedRow];
             cbmi.addItemListener(new ItemListener()
@@ -849,8 +845,8 @@ public class AnnotationLabels extends Panel
                     + "\t" + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
-              av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
   }
 
@@ -909,14 +905,8 @@ public class AnnotationLabels extends Panel
       }
     }
     g.translate(0, +scrollOffset);
-    if (resizePanel)
-    {
-      // g.setColor(Color.red);
-      // g.setPaintMode();
-      // g.drawLine(2, 8, 5, 2);
-      // g.drawLine(5, 2, 8, 8);
-    }
-    else if (!dragCancelled && dragEvent != null && aa != null)
+
+    if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),