Merge branch 'develop' into bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpai...

diff --git a/help/help/html/features/paematrices.html b/help/help/html/features/paematrices.html
index efadf91..8d180ee 100644 (file)
--- 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 (file)
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 (file)
--- 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)
      */