patch for JAL-695 - need to test if this is observed in applet

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 62ed93c..2184851 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -57,6 +57,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
   Tooltip tooltip;
 
+  private boolean hasHiddenRows;
+
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -77,24 +79,29 @@ public class AnnotationLabels extends Panel implements ActionListener,
     repaint();
   }
 
+  /**
+   * 
+   * @param y
+   * @return -2 if no rows are visible at all, -1 if no visible rows were
+   *         selected
+   */
   int getSelectedRow(int y)
   {
-    int row = -1;
+    int row = -2;
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
     if (aa == null)
     {
       return row;
     }
-
     int height = 0;
     for (int i = 0; i < aa.length; i++)
     {
+      row = -1;
       if (!aa[i].visible)
       {
         continue;
       }
-
       height += aa[i].height;
       if (y < height)
       {
@@ -201,8 +208,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       if (tooltip == null)
       {
-        tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row]
-                .getDescription(true), this);
+        tooltip = new Tooltip(
+                ap.av.alignment.getAlignmentAnnotation()[row]
+                        .getDescription(true),
+                this);
       }
       else
       {
@@ -240,17 +249,28 @@ public class AnnotationLabels extends Panel implements ActionListener,
   public void mousePressed(MouseEvent evt)
   {
     selectedRow = getSelectedRow(evt.getY() - scrollOffset);
-
     AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
 
+    // DETECT RIGHT MOUSE BUTTON IN AWT
+    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    {
+
+
     PopupMenu popup = new PopupMenu("Annotations");
 
     MenuItem item = new MenuItem(ADDNEW);
     item.addActionListener(this);
     popup.add(item);
-    if (aa == null)
+    if (selectedRow < 0)
     {
-
+      // this never happens at moment: - see comment on JAL-563
+      if (hasHiddenRows)
+      {
+        item = new MenuItem(SHOWALL);
+        item.addActionListener(this);
+        popup.add(item);
+      }
+      this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
       return;
     }
@@ -261,9 +281,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
     item = new MenuItem(HIDE);
     item.addActionListener(this);
     popup.add(item);
-    item = new MenuItem(SHOWALL);
-    item.addActionListener(this);
-    popup.add(item);
+    if (hasHiddenRows)
+    {
+      item = new MenuItem(SHOWALL);
+      item.addActionListener(this);
+      popup.add(item);
+    }
     this.add(popup);
     item = new MenuItem(OUTPUT_TEXT);
     item.addActionListener(this);
@@ -290,7 +313,53 @@ public class AnnotationLabels extends Panel implements ActionListener,
     }
 
     popup.show(this, evt.getX(), evt.getY());
+    } else {
+      // selection action.
+      if (selectedRow > -1 && selectedRow < aa.length)
+      {
+        if (aa[selectedRow].groupRef != null)
+        {
+          if (evt.getClickCount() >= 2)
+          {
+            // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            ap.av.setSelectionGroup(// new SequenceGroup(
+            aa[selectedRow].groupRef); // );
+            ap.av.sendSelection();
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+          }
+          else
+          {
+            ap.seqPanel.ap.idPanel
+                    .highlightSearchResults(aa[selectedRow].groupRef
+                            .getSequences(null));
+          }
+          return;
+        }
+        else if (aa[selectedRow].sequenceRef != null)
+        {
+          Vector sr = new Vector();
+          sr.addElement(aa[selectedRow].sequenceRef);
+          if (evt.getClickCount() == 1)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+          }
+          else if (evt.getClickCount() >= 2)
+          {
+            ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+            SequenceGroup sg = new SequenceGroup();
+            sg.addSequence(aa[selectedRow].sequenceRef, false);
+            ap.av.setSelectionGroup(sg);
+            ap.paintAlignment(false);
+            PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
+          }
+
+        }
+      }
 
+    }
   }
 
   /**
@@ -352,35 +421,26 @@ public class AnnotationLabels extends Panel implements ActionListener,
     g.setColor(Color.black);
 
     AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-    int y = g.getFont().getSize();
-    int x = 0;
+    int y = 0, fy = g.getFont().getSize();
+    int x = 0, offset;
 
     if (aa != null)
     {
+      hasHiddenRows = false;
       for (int i = 0; i < aa.length; i++)
       {
         if (!aa[i].visible)
         {
+          hasHiddenRows = true;
           continue;
         }
 
         x = width - fm.stringWidth(aa[i].label) - 3;
 
-        if (aa[i].graph > 0)
-        {
-          y += (aa[i].height / 3);
-        }
-
-        g.drawString(aa[i].label, x, y);
+        y += aa[i].height;
+        offset = -(aa[i].height - fy) / 2;
 
-        if (aa[i].graph > 0)
-        {
-          y += (2 * aa[i].height / 3);
-        }
-        else
-        {
-          y += aa[i].height;
-        }
+        g.drawString(aa[i].label, x, y + offset);
       }
     }
   }