comments re JAL-823 legacy issue

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 147a68d..2df51b1 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2574,12 +2574,11 @@ public class Jalview2XML
                 { x, y, width, height }, "",
                     new Hashtable<String, Object[]>(), new boolean[]
                     { false, false } });
-                // Legacy->2.7 conversion: if there is no attribute for
-                // colouring with the alignPanel then by default we set the
-                // first encountered view to be the default source of colour
-                // information.
+                // Legacy pre-2.7 conversion JAL-823 : 
+                // do not assume any view has to be linked for colour by sequence
               }
-              // TODO: assemble String[] { pdb files }, String[] { id for each
+              
+              // assemble String[] { pdb files }, String[] { id for each
               // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
               // seqs_file 2}, boolean[] {
               // linkAlignPanel,superposeWithAlignpanel}} from hash
@@ -2587,7 +2586,7 @@ public class Jalview2XML
               ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
                       .hasAlignwithAlignPanel() ? ids[p].getStructureState(
                       s).getAlignwithAlignPanel() : false;
-              // always colour by linked panel if not specified
+              // never colour by linked panel if not specified
               ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
                       .hasColourwithAlignPanel() ? ids[p]
                       .getStructureState(s).getColourwithAlignPanel()