From 77ab7d6694e27575261ab58c098eee76e68c2228 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 14 Sep 2011 11:41:31 +0100 Subject: [PATCH] JAL-766 JAL-733 - new alignment->jmol associations are automatically used to colour structure --- src/jalview/gui/AppJmol.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 5c5e3e8..e500240 100644 --- 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, - AlignmentPanel ap) + final AlignmentPanel ap) { progressBar = ap.alignFrame; // //////////////////////////////// @@ -271,7 +271,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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++) @@ -280,7 +280,10 @@ public class AppJmol extends GStructureViewer implements Runnable, { topJmol.jmb.addSequence(pe, seq); topJmol.addAlignmentPanel(ap); + // add it to the set used for colouring + topJmol.useAlignmentPanelForColourbyseq(ap); topJmol.buildJmolActionMenu(); + ap.getStructureSelectionManager().sequenceColoursChanged(ap); break; } } -- 1.7.10.2