From b1f1dafab890809e47d9b3e7b54aa300ebe6d7a1 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Thu, 18 Apr 2019 12:55:55 -0500
Subject: [PATCH] Adds check for gap padding to disallow fast paint upon
 pasting if alignment has been modified.

---
 src/jalview/gui/SeqCanvas.java               |   24 +++++++-----------------
 src/jalview/viewmodel/AlignmentViewport.java |   21 ++++++++++++++++++++-
 2 files changed, 27 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index d1046f8..c99041b 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -287,6 +287,7 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
    */
   public void fastPaint(int horizontal, int vertical)
   {
+
     // System.err.println("<<SeqCanvas fastPaint " + fastpainting + " "
     // + horizontal + " " + vertical);
     // effectively:
@@ -395,6 +396,10 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     int startSeq = ranges.getStartSeq();
     int endRes = ranges.getEndRes();
     int endSeq = ranges.getEndSeq();
+    if (av.isFastPaintDisabled())
+    {
+      fastPaint = false;
+    }
 
     // System.err.println(">>SeqCanvas paintComponent " + fastPaint + "\n"
     // + getVisibleRect() + "\n" + g.getClipBounds());
@@ -412,12 +417,11 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
       drawSelectionGroup((Graphics2D) g, startRes, endRes, startSeq,
               endSeq);
       fastPaint = false;
-      //System.out.println("SeqCanvas fast paint");
+      // System.out.println("SeqCanvas fast paint");
     }
     else
     {
-
-      System.out.println("SeqCanvas full paint");
+      // System.out.println("SeqCanvas full paint");
       /*
        * img is a cached version of the last view we drew.
        * If we have no img or the size has changed, make a new one
@@ -2160,18 +2164,4 @@ public class SeqCanvas extends JPanel implements ViewportListenerI
     return labelWidthWest;
   }
 
-  /**
-   * Ensure that a full paint is done next, for whatever reason. This was
-   * necessary for JavaScript; apparently in Java the timing is just right on
-   * multiple threads (EventQueue-0, Consensus, Conservation) that we can get
-   * away with one fast paint before the others, but this ensures that in the
-   * end we get a full paint. Problem arose in relation to copy/paste, where the
-   * paste was not finalized with a full paint.
-   * 
-   * @author hansonr 2019.04.17
-   */
-  public void clearFastPaint()
-  {
-    fastPaint = false;
-  }
 }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 5a99c3d..f2ab8a6 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1323,6 +1323,21 @@ public abstract class AlignmentViewport
    */
   private boolean followHighlight = true;
 
+  private boolean disableFastPaint; // BH 2019.04.18
+
+  /**
+   * BH 2019.04.18 When gap filling is on and a modification is made to fill
+   * those, we need to disallow fast painting for paste just once
+   * 
+   * @return
+   */
+  public boolean isFastPaintDisabled()
+  {
+    boolean ret = disableFastPaint;
+    disableFastPaint = false;
+    return ret;
+  }
+
   /**
    * Property change listener for changes in alignment
    * 
@@ -1857,7 +1872,11 @@ public abstract class AlignmentViewport
   {
     if (isPadGaps())
     {
-      alignment.padGaps();
+      if (alignment.padGaps())
+      {
+        // the new alignment has been modified -- can't fast paint
+        disableFastPaint = true;
+      }
     }
     if (autoCalculateConsensus)
     {
-- 
1.7.10.2