JAL-1432 updated copyright notices

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index d0af0a5..8a22288 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -376,10 +377,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         anot[index].displayCharacter = label;
       }
     }
-    aa[activeRow].validateRangeAndDisplay();
-
-    adjustPanelHeight();
+    av.getAlignment().validateAnnotation(aa[activeRow]);
     ap.alignmentChanged();
+    
+    adjustPanelHeight();
     repaint();
 
     return;
@@ -699,16 +700,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseClicked(MouseEvent evt)
   {
-    if (activeRow != -1)
-    {
-      AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-      AlignmentAnnotation anot = aa[activeRow];
-
-      if (anot.description.equals("secondary structure"))
-      {
-        // System.out.println(anot.description+" "+anot.getRNAStruc());
-      }
-    }
+//    if (activeRow != -1)
+//    {
+//      AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+//      AlignmentAnnotation anot = aa[activeRow];
+//    }
   }
 
   // TODO mouseClicked-content and drawCursor are quite experimental!
@@ -760,7 +756,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
     if (imgWidth < 1)
       return;
-    if (image == null || imgWidth != image.getWidth()
+    if (image == null || imgWidth != image.getWidth(this)
             || image.getHeight(this) != getHeight())
     {
       try
@@ -800,7 +796,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
-
+  /**
+   * set true to enable redraw timing debug output on stderr
+   */
+  private final boolean debugRedraw = false;
   /**
    * non-Thread safe repaint
    * 
@@ -809,7 +808,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void fastPaint(int horizontal)
   {
-
     if ((horizontal == 0) || gg == null
             || av.getAlignment().getAlignmentAnnotation() == null
             || av.getAlignment().getAlignmentAnnotation().length < 1
@@ -818,8 +816,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
       return;
     }
+    long stime=System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
+    long mtime=System.currentTimeMillis();
     int sr = av.startRes;
     int er = av.endRes + 1;
     int transX = 0;
@@ -839,9 +838,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     drawComponent(gg, sr, er);
 
     gg.translate(-transX, 0);
-
+    long dtime=System.currentTimeMillis();
     fastPaint = true;
     repaint();
+    long rtime=System.currentTimeMillis();
+    if (debugRedraw) {
+      System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+    }
 
   }
 
@@ -902,7 +905,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       fadedImage = null;
     }
-
+    
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -950,4 +953,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   {
     return imgWidth;
   }
+  private int[] bounds = new int[2];
+  @Override
+  public int[] getVisibleVRange()
+  {
+    if (ap!=null && ap.alabels!=null)
+    {
+    int sOffset=-ap.alabels.scrollOffset;
+    int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
+    bounds[0] = sOffset; bounds[1]=visHeight;
+    return bounds;
+    } else return null;
+  }
 }