From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 3 Oct 2023 13:18:08 +0000 (+0100)
Subject: Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpai... 
X-Git-Tag: Release_2_11_3_0~3^2~27^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5d225e1798ef42d0c49784f9ef24e76e2d0cf014;hp=639553df9be00842fb12ad4ddfc39a65cb3a60bd;p=jalview.git

Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint
---

diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html
index efadf91..8d180ee 100644
--- a/help/help/html/features/paematrices.html
+++ b/help/help/html/features/paematrices.html
@@ -56,10 +56,11 @@
 			href="../features/structurechooser.html">Jalview's structure
 			chooser</a> GUI. If you have produced your own models and accompanying
 		PAE matrices using a pipeline such as ColabFold, then you can load
-		them both together via the <a
-			href="../features/structurechooser.html#loadpdbfile">Load PDB
-			File</a> dropdown menu in the 3D structure chooser. in a <a
-			href="../io/paematrixformat.html">supported PAE format</a>.
+		them both together via the
+		<a href="../features/structurechooser.html#loadpdbfile">Load PDB
+			File</a> dropdown menu in the 3D structure chooser, providing it is
+		in a
+		<a href="../io/paematrixformat.html">supported PAE format</a>.
 	</p>
 	<p>
 		The <a href="../features/clarguments-basic.html">Command Line
diff --git a/help/help/html/structures/epas1_annotdetail.png b/help/help/html/structures/epas1_annotdetail.png
new file mode 100644
index 0000000..45118a0
Binary files /dev/null and b/help/help/html/structures/epas1_annotdetail.png differ
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ae561e7..3127731 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1051,6 +1051,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
 
+    alignmentGraphics.setColor(Color.white);
+    alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight);
+
     /*
      * draw the Scale at horizontal offset, then reset to top left (0, 0)
      */