Jalview 2.6 source licence

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 28270c9..8a377cc 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.appletgui;
 
@@ -58,6 +57,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
   Tooltip tooltip;
 
+  private boolean hasHiddenRows;
+
   public AnnotationLabels(AlignmentPanel ap)
   {
     this.ap = ap;
@@ -78,24 +79,28 @@ 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)
       {
@@ -249,15 +254,31 @@ public class AnnotationLabels extends Panel implements ActionListener,
     MenuItem item = new MenuItem(ADDNEW);
     item.addActionListener(this);
     popup.add(item);
+    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;
+    }
+    // add the rest if there are actually rows to show
     item = new MenuItem(EDITNAME);
     item.addActionListener(this);
     popup.add(item);
     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);
@@ -291,7 +312,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   protected void copy_annotseqtoclipboard(SequenceI sq)
   {
@@ -346,35 +367,26 @@ 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);
       }
     }
   }