From 43141b2f7afda8dbb88090d0630574b1cdefb0eb Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Sat, 24 Jun 2017 06:48:27 +0100
Subject: [PATCH] JAL-1858 refactored method to redraw previous/new
 highlighted positions

---
 src/jalview/gui/SeqCanvas.java |   72 +++++++++++++++++++++++++---------------
 1 file changed, 45 insertions(+), 27 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 7035142..52e5849 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -1000,20 +999,43 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     fastpainting = true;
     fastPaint = true;
 
-    /*
-     * to avoid redrawing the whole visible region, we instead
-     * calculate the minimal redraw to remove previous highlights
-     * and add new ones;
-     * first make a temporary SearchResults that includes 
-     * both the new and any existing search results
-     */
-    SearchResultsI combined = results;
-    SearchResultsI previous = av.getSearchResults();
-    if (previous != null)
+    try
+    {
+      /*
+       * to avoid redrawing the whole visible region, we instead
+       * redraw just the minimal regions to remove previous highlights
+       * and add new ones
+       */
+      SearchResultsI previous = av.getSearchResults();
+      av.setSearchResults(results);
+      boolean redrawn = drawMappedPositions(previous);
+      redrawn |= drawMappedPositions(results);
+      if (redrawn)
+      {
+        repaint();
+      }
+    } finally
+    {
+      fastpainting = false;
+    }
+  }
+
+  /**
+   * Redraws the minimal rectangle in the visible region (if any) that includes
+   * mapped positions of the given search results. Whether or not positions are
+   * highlighted depends on the SearchResults set on the Viewport. This allows
+   * this method to be called to either clear or set highlighting. Answers true
+   * if any positions were drawn (in which case a repaint is still required),
+   * else false.
+   * 
+   * @param results
+   * @return
+   */
+  protected boolean drawMappedPositions(SearchResultsI results)
+  {
+    if (results == null)
     {
-      combined = new SearchResults();
-      combined.addSearchResults(results);
-      combined.addSearchResults(previous);
+      return false;
     }
 
     /*
@@ -1029,20 +1051,21 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     ViewportRanges ranges = av.getRanges();
     int firstVisibleColumn = ranges.getStartRes();
     int lastVisibleColumn = ranges.getEndRes();
+    AlignmentI alignment = av.getAlignment();
     if (av.hasHiddenColumns())
     {
-      firstVisibleColumn = av.getAlignment().getHiddenColumns()
+      firstVisibleColumn = alignment.getHiddenColumns()
               .adjustForHiddenColumns(firstVisibleColumn);
-      lastVisibleColumn = av.getAlignment().getHiddenColumns()
+      lastVisibleColumn = alignment.getHiddenColumns()
               .adjustForHiddenColumns(lastVisibleColumn);
     }
 
     for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
             .getEndSeq(); seqNo++)
     {
-      SequenceI seq = av.getAlignment().getSequenceAt(seqNo);
+      SequenceI seq = alignment.getSequenceAt(seqNo);
 
-      int[] visibleResults = combined.getResults(seq, firstVisibleColumn,
+      int[] visibleResults = results.getResults(seq, firstVisibleColumn,
               lastVisibleColumn);
       if (visibleResults != null)
       {
@@ -1072,27 +1095,22 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       }
     }
 
-    av.setSearchResults(results);
-
     if (matchFound)
     {
       if (av.hasHiddenColumns())
       {
-        firstCol = av.getAlignment().getHiddenColumns()
+        firstCol = alignment.getHiddenColumns()
                 .findColumnPosition(firstCol);
-        lastCol = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(lastCol);
+        lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
       }
-      int transX = (firstCol - firstVisibleColumn) * av.getCharWidth();
+      int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
       int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
       gg.translate(transX, transY);
       drawPanel(gg, firstCol, lastCol, firstSeq, lastSeq, 0);
       gg.translate(-transX, -transY);
-
-      repaint();
     }
 
-    fastpainting = false; // todo in finally block?
+    return matchFound;
   }
 
   @Override
-- 
1.7.10.2