formatting

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 475f0c7..cad0fc1 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -26,7 +26,7 @@ import javax.swing.*;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -39,6 +39,7 @@ public class OverviewPanel extends JPanel implements Runnable
   AlignmentPanel ap;
 
   final AnnotationRenderer renderer = new AnnotationRenderer();
+
   float scalew = 1f;
 
   float scaleh = 1f;
@@ -67,7 +68,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * Creates a new OverviewPanel object.
-   *
+   * 
    * @param ap
    *          DOCUMENT ME!
    */
@@ -86,7 +87,7 @@ public class OverviewPanel extends JPanel implements Runnable
     float initialScale = (float) av.getAlignment().getWidth()
             / (float) av.getAlignment().getHeight();
 
-    if (av.getAlignmentConservationAnnotation()== null)
+    if (av.getAlignmentConservationAnnotation() == null)
     {
       graphHeight = 0;
     }
@@ -204,8 +205,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.hasHiddenRows())
     {
-      row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
-              row);
+      row = av.getAlignment().getHiddenSequences()
+              .findIndexWithoutHiddenSeqs(row);
     }
 
     ap.setScrollValues(col, row);
@@ -300,7 +301,8 @@ public class OverviewPanel extends JPanel implements Runnable
       hiddenRow = false;
       if (av.hasHiddenRows())
       {
-        seq = av.getAlignment().getHiddenSequences().getHiddenSequence(lastrow);
+        seq = av.getAlignment().getHiddenSequences()
+                .getHiddenSequence(lastrow);
         if (seq == null)
         {
           int index = av.getAlignment().getHiddenSequences()
@@ -361,7 +363,7 @@ public class OverviewPanel extends JPanel implements Runnable
       }
     }
 
-    if (av.getAlignmentConservationAnnotation()!= null)
+    if (av.getAlignmentConservationAnnotation() != null)
     {
       renderer.updateFromAlignViewport(av);
       for (col = 0; col < width; col++)
@@ -369,7 +371,8 @@ public class OverviewPanel extends JPanel implements Runnable
         lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
-          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),av.getAlignmentConservationAnnotation().annotations,
+          renderer.drawGraph(mg, av.getAlignmentConservationAnnotation(),
+                  av.getAlignmentConservationAnnotation().annotations,
                   (int) (sampleCol) + 1, graphHeight,
                   (int) (col * sampleCol), (int) (col * sampleCol) + 1);
           mg.translate(-col, -sequencesHeight);
@@ -396,7 +399,8 @@ public class OverviewPanel extends JPanel implements Runnable
   {
     int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
     int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
-            .getHiddenSequences().getSize()) * av.getCharHeight();
+            .getHiddenSequences().getSize())
+            * av.getCharHeight();
 
     int startRes = av.getStartRes();
     int endRes = av.getEndRes();
@@ -412,8 +416,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     if (av.hasHiddenRows())
     {
-      startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
-              startSeq);
+      startSeq = av.getAlignment().getHiddenSequences()
+              .adjustForHiddenSeqs(startSeq);
 
       endSeq = av.getAlignment().getHiddenSequences()
               .adjustForHiddenSeqs(endSeq);
@@ -442,7 +446,7 @@ public class OverviewPanel extends JPanel implements Runnable
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param g
    *          DOCUMENT ME!
    */