formatting

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

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 23d8341..ffb8e4e 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -27,7 +27,9 @@ import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 
 /**
- * AnnotationPanel displays visible portion of annotation rows below unwrapped alignment 
+ * AnnotationPanel displays visible portion of annotation rows below unwrapped
+ * alignment
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -99,7 +101,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * Creates a new AnnotationPanel object.
-   *
+   * 
    * @param ap
    *          DOCUMENT ME!
    */
@@ -118,7 +120,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     addMouseMotionListener(this);
     ap.annotationScroller.getVerticalScrollBar()
             .addAdjustmentListener(this);
-    // save any wheel listeners on the scroller, so we can propagate scroll events to them.
+    // save any wheel listeners on the scroller, so we can propagate scroll
+    // events to them.
     _mwl = ap.annotationScroller.getMouseWheelListeners();
     // and then set our own listener to consume all mousewheel events
     ap.annotationScroller.addMouseWheelListener(this);
@@ -148,7 +151,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
     else
     {
-      // TODO: find the correct way to let the event bubble up to ap.annotationScroller
+      // TODO: find the correct way to let the event bubble up to
+      // ap.annotationScroller
       for (MouseWheelListener mwl : _mwl)
       {
         if (mwl != null)
@@ -197,7 +201,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /*
    * (non-Javadoc)
-   * @see java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event.AdjustmentEvent)
+   * 
+   * @see
+   * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
+   * .AdjustmentEvent)
    */
   @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
@@ -210,7 +217,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    * Calculates the height of the annotation displayed in the annotation panel.
    * Callers should normally call the ap.adjustAnnotationHeight method to ensure
    * all annotation associated components are updated correctly.
-   *
+   * 
    */
   public int adjustPanelHeight()
   {
@@ -227,7 +234,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -383,7 +390,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   {
     String collatedInput = "";
     String last = "";
-    ColumnSelection viscols=av.getColumnSelection();
+    ColumnSelection viscols = av.getColumnSelection();
     // TODO: refactor and save av.getColumnSelection for efficiency
     for (int i = 0; i < columnSelection.size(); i++)
     {
@@ -426,7 +433,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -519,7 +526,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -534,7 +541,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -546,7 +553,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -558,7 +565,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -585,7 +592,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -685,7 +692,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param evt
    *          DOCUMENT ME!
    */
@@ -725,10 +732,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     }
 
   }
-  private volatile boolean imageFresh=false;
+
+  private volatile boolean imageFresh = false;
+
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
    *          DOCUMENT ME!
    */
@@ -754,15 +763,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (image == null || imgWidth != image.getWidth()
             || image.getHeight(this) != getHeight())
     {
-      try {
-      image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
-              BufferedImage.TYPE_INT_RGB);
+      try
+      {
+        image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
+                BufferedImage.TYPE_INT_RGB);
       } catch (OutOfMemoryError oom)
       {
-        try {
+        try
+        {
           System.gc();
-        } catch (Exception x){};
-        new OOMWarning("Couldn't allocate memory to redraw screen. Please restart Jalview", oom);
+        } catch (Exception x)
+        {
+        }
+        ;
+        new OOMWarning(
+                "Couldn't allocate memory to redraw screen. Please restart Jalview",
+                oom);
         return;
       }
       gg = (Graphics2D) image.getGraphics();
@@ -777,17 +793,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       fm = gg.getFontMetrics();
       gg.setColor(Color.white);
       gg.fillRect(0, 0, imgWidth, image.getHeight());
-      imageFresh=true;
+      imageFresh = true;
     }
 
     drawComponent(gg, av.startRes, av.endRes + 1);
-    imageFresh=false;
+    imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
 
   /**
    * non-Thread safe repaint
-   *
+   * 
    * @param horizontal
    *          repaint with horizontal shift in alignment
    */
@@ -828,10 +844,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     repaint();
 
   }
-  private volatile boolean lastImageGood=false;
+
+  private volatile boolean lastImageGood = false;
+
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
    *          DOCUMENT ME!
    * @param startRes
@@ -841,21 +859,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public void drawComponent(Graphics g, int startRes, int endRes)
   {
-    BufferedImage oldFaded=fadedImage;
+    BufferedImage oldFaded = fadedImage;
     if (av.isCalcInProgress())
     {
       if (image == null)
       {
-        lastImageGood=false;
+        lastImageGood = false;
         return;
       }
       // We'll keep a record of the old image,
       // and draw a faded image until the calculation
       // has completed
-      if (lastImageGood && (fadedImage == null || fadedImage.getWidth() != imgWidth
-              || fadedImage.getHeight() != image.getHeight()))
+      if (lastImageGood
+              && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage
+                      .getHeight() != image.getHeight()))
       {
-//        System.err.println("redraw faded image ("+(fadedImage==null ? "null image" : "") + " lastGood="+lastImageGood+")");
+        // System.err.println("redraw faded image ("+(fadedImage==null ?
+        // "null image" : "") + " lastGood="+lastImageGood+")");
         fadedImage = new BufferedImage(imgWidth, image.getHeight(),
                 BufferedImage.TYPE_INT_RGB);
 
@@ -869,15 +889,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         fadedG.drawImage(image, 0, 0, this);
 
       }
-      // make sure we don't overwrite the last good faded image until all calculations have finished
-      lastImageGood=false;
+      // make sure we don't overwrite the last good faded image until all
+      // calculations have finished
+      lastImageGood = false;
 
     }
     else
     {
-      if (fadedImage!=null)
+      if (fadedImage != null)
       {
-        oldFaded=fadedImage;
+        oldFaded = fadedImage;
       }
       fadedImage = null;
     }
@@ -904,10 +925,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       return;
     }
-    lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
-    if (!lastImageGood && fadedImage==null)
+    lastImageGood = renderer.drawComponent(this, av, g, activeRow,
+            startRes, endRes);
+    if (!lastImageGood && fadedImage == null)
     {
-      fadedImage=oldFaded;
+      fadedImage = oldFaded;
     }
   }