From 5f01d4060ac01ebac24998f906e1e52959d568ec Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 16 Jun 2020 12:47:12 +0100
Subject: [PATCH 1/1] JAL-3446 defer size calculations until panel added to
 window

---
 src/jalview/gui/AlignmentPanel.java |   30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cf45483..7758dae 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -602,18 +602,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   /**
    * update alignment layout for viewport settings
-   * 
-   * @param wrap
-   *          DOCUMENT ME!
    */
   public void updateLayout()
   {
-    // BH 2020.06.09 avoid negative values for SequencePanel and SeqCanvas dimensions
-//    if (getTopLevelAncestor() == null)
-//    {
-//      return;
-//    }
-
     ViewportRanges ranges = av.getRanges();
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
@@ -632,9 +623,24 @@ public class AlignmentPanel extends GAlignmentPanel implements
     {
       annotationScroller.setVisible(true);
       annotationSpaceFillerHolder.setVisible(true);
-      validateAnnotationDimensions(false);
     }
 
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    /*
+     * defer dimension calculations if panel not yet added to a Window
+     * BH 2020.06.09
+     */
+    if (getTopLevelAncestor() == null)
+    {
+      repaint();
+      return;
+    }
+
+    if (!wrap && av.isShowAnnotation())
+    {
+      validateAnnotationDimensions(false);
+    }
     int canvasWidth = getSeqPanel().seqCanvas.getWidth();
     if (canvasWidth > 0)
     { // may not yet be laid out
@@ -655,12 +661,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
     }
 
-    idSpaceFillerPanel1.setVisible(!wrap);
-
     // System.out.println("ap dim = " + getSize());
-
     // these values will go negative if getSize() returns (0,0):
-
     // System.out.println("seqpan dim = " + getSeqPanel().getSize());
     // System.out.println("seqcan dim = " + getSeqPanel().seqCanvas.getSize());
 
-- 
1.7.10.2