JAL-3253 miscellaneous tidying up before merge to JS-develop

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

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 9245104..05f6afc 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -79,7 +79,7 @@ public class OverviewPanel extends JPanel
 
   private Dimension dim;
 
-  private boolean showProgress = !Platform.isJS(); // Jalview.getInstance().getShowStatus()
+  private boolean showProgress = !Platform.isJS();
 
   /**
    * Creates a new OverviewPanel object.
@@ -220,15 +220,17 @@ public class OverviewPanel extends JPanel
     });
   }
 
+  /***
+   * Resize is called on the initial display of the Overview. This code adjusts
+   * sizes to account for the progress bar if it has not already been accounted
+   * for, which triggers another resize call for the correct sizing, at which
+   * point the overview image is updated. (This avoids a double recalculation of
+   * the image.)
+   */
   protected void resizePanel()
   {
     int ph = (progressPanel.getParent() == null ? 0
             : progressPanel.getHeight());
-    // Resize is called on the initial display of the overview.
-    // This code adjusts sizes to account for the progress bar if it has not
-    // already been accounted for, which triggers another resize call for
-    // the correct sizing, at which point the overview image is updated.
-    // (This avoids a double recalculation of the image.)
     if (getWidth() == od.getWidth() && getHeight() == od.getHeight() + ph)
     {
       if (canvas.lastMiniMe == null)
@@ -254,7 +256,7 @@ public class OverviewPanel extends JPanel
   }
 
   /**
-   * Create the appropriate type of OverViewDimensions, with the desired size.
+   * Creates the appropriate type of OverviewDimensions, with the desired size
    */
   private void createOverviewDimensions()
   {
@@ -270,7 +272,6 @@ public class OverviewPanel extends JPanel
       od = new OverviewDimensionsHideHidden(av.getRanges(), showAnnotation,
               dim);
     }
-
   }
 
   /**
@@ -312,20 +313,7 @@ public class OverviewPanel extends JPanel
   }
 
   /**
-   * Updates the overview image when the related alignment panel is updated.
-   * 
-   * Cases:
-   * 
-   * AlignFrame.setFeatureGroupState
-   * 
-   * AlignmentPanel.paintAlignment(true,...) (117 references)
-   * 
-   * OverviewPanel..componentResized() OverviewPanel.toggleHiddenColumns()
-   * 
-   * PopupMenu for action.reveal_sequences, action.reveal_all
-   * 
-   * SliderPanel.mouseReleased()
-   * 
+   * Updates the overview image when the related alignment panel is updated
    */
   public void updateOverviewImage()
   {
@@ -373,7 +361,6 @@ public class OverviewPanel extends JPanel
   /**
    * Update the overview panel box when the associated alignment panel is
    * changed
-   * 
    */
   private void setBoxPositionOnly()
   {