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comments re JAL-823 legacy issue
author
jprocter
<Jim Procter>
Fri, 22 Apr 2011 11:40:53 +0000
(11:40 +0000)
committer
jprocter
<Jim Procter>
Fri, 22 Apr 2011 11:40:53 +0000
(11:40 +0000)
src/jalview/gui/Jalview2XML.java
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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 } });
{ 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
// 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;
((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()
((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
.hasColourwithAlignPanel() ? ids[p]
.getStructureState(s).getColourwithAlignPanel()