From 725d892788e2e4e64ba98c2ee4f0c21d631612fe Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 22 Apr 2011 11:40:53 +0000 Subject: [PATCH] comments re JAL-823 legacy issue --- src/jalview/gui/Jalview2XML.java | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 147a68d..2df51b1 100755 --- 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(), 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() -- 1.7.10.2