From 9b692e0079f05e5e0bf1fca16d9b305c719d7dfb Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 10 Oct 2019 15:15:26 +0100
Subject: [PATCH] JAL-3383 javadoc

---
 src/jalview/renderer/OverviewRenderer.java    |   24 ++++++++++++++----------
 src/jalview/viewmodel/OverviewDimensions.java |   15 +++++++++++++++
 2 files changed, 29 insertions(+), 10 deletions(-)

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 82e89e5..9f966e2 100644
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -148,8 +148,14 @@ public class OverviewRenderer
 
   private BitSet bscol;
 
+  /*
+   * Overview width in pixels
+   */
   private final int w;
 
+  /*
+   * Overview height in pixels
+   */
   private final int h;
 
   public OverviewRenderer(AlignmentViewPanel panel,
@@ -277,7 +283,7 @@ public class OverviewRenderer
       columnsToShow = calcColumnsToShow();
     }
 
-    Platform.timeCheck(null, Platform.TIME_MARK);
+    // Platform.timeCheck(null, Platform.TIME_MARK);
   }
 
   private void nextRow()
@@ -470,13 +476,13 @@ public class OverviewRenderer
 
   private void done()
   {
-    if (!redraw)
-    {
-      Platform.timeCheck(
-              "overviewrender " + ndone + " pixels row:" + row + " redraw:"
-                      + redraw,
-              Platform.TIME_MARK);
-    }
+    // if (!redraw)
+    // {
+//      Platform.timeCheck(
+//              "overviewrender " + ndone + " pixels row:" + row + " redraw:"
+//                      + redraw,
+//              Platform.TIME_MARK);
+    // }
 
     overlayHiddenRegions();
     if (showProgress)
@@ -625,8 +631,6 @@ public class OverviewRenderer
         // get details of this alignment row
         if (rows.isHidden(alignmentRow))
         {
-          // BH 2019.09.24 fixes JAL-3440 Java+JavaScript off by one row in
-          // height
           g2d.fillRect(0, pixelRow, w, endRow - pixelRow);
         }
         pixelRow = endRow;
diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 8dc7dd8..39d0098 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -151,16 +151,31 @@ public abstract class OverviewDimensions
     return boxHeight;
   }
 
+  /**
+   * Returns the width of the Overview in pixels
+   * 
+   * @return
+   */
   public int getWidth()
   {
     return width;
   }
 
+  /**
+   * Returns the height of the Overview in pixels
+   * 
+   * @return
+   */
   public int getHeight()
   {
     return sequencesHeight + graphHeight;
   }
 
+  /**
+   * Returns the height of the sequence alignment in the Overview in pixels
+   * 
+   * @return
+   */
   public int getSequencesHeight()
   {
     return sequencesHeight;
-- 
1.7.10.2