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JAL-766 JAL-733 - new alignment->jmol associations are automatically used to colour...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Wed, 14 Sep 2011 10:41:31 +0000
(11:41 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Wed, 14 Sep 2011 10:41:31 +0000
(11:41 +0100)
src/jalview/gui/AppJmol.java
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diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
5c5e3e8
..
e500240
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-236,7
+236,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
* @param ap
*/
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
* @param ap
*/
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ final AlignmentPanel ap)
{
progressBar = ap.alignFrame;
// ////////////////////////////////
{
progressBar = ap.alignFrame;
// ////////////////////////////////
@@
-271,7
+271,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
if (frames[i] instanceof AppJmol)
{
{
if (frames[i] instanceof AppJmol)
{
- AppJmol topJmol = ((AppJmol) frames[i]);
+ final AppJmol topJmol = ((AppJmol) frames[i]);
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
// JBPNOTE: this looks like a binding routine, rather than a gui
// routine
for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
@@
-280,7
+280,10
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
{
topJmol.jmb.addSequence(pe, seq);
topJmol.addAlignmentPanel(ap);
+ // add it to the set used for colouring
+ topJmol.useAlignmentPanelForColourbyseq(ap);
topJmol.buildJmolActionMenu();
topJmol.buildJmolActionMenu();
+ ap.getStructureSelectionManager().sequenceColoursChanged(ap);
break;
}
}
break;
}
}