JAL-2034 notes on efficiency

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 9be4fdb..c2a401d 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -295,6 +295,9 @@ public class OverviewPanel extends JPanel implements Runnable
     final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
             .hasHiddenColumns();
     boolean hiddenRow = false;
+    // get hidden row and hidden column map once at beginning.
+    // clone featureRenderer settings to avoid race conditions... if state is
+    // updated just need to refresh again
     for (row = 0; row < sequencesHeight; row++)
     {
       if (resizeAgain)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 258a229..17d69f4 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -91,6 +91,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   @Override
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
+    // rate limiting step when rendering overview for lots of groups
     allGroups = av.getAlignment().findAllGroups(seq);
 
     if (inCurrentSequenceGroup(i))