From 9de0507352a9bc6573ec8ac0bac5d2b42c124e0d Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 22 Apr 2011 11:39:27 +0000 Subject: [PATCH] moved loadingFromArchive flag modification to after GUI refreshes are completed and javadoc. --- src/jalview/ext/jmol/JalviewJmolBinding.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 67327c1..8ea1c5d 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -1270,7 +1270,6 @@ public abstract class JalviewJmolBinding implements StructureListener, { viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); } - setLoadingFromArchive(false); // register ourselves as a listener and notify the gui that it needs to // update itself. ssm.addStructureViewerListener(this); @@ -1284,6 +1283,7 @@ public abstract class JalviewJmolBinding implements StructureListener, refreshGUI(); loadNotifiesHandled++; } + setLoadingFromArchive(false); } public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) @@ -1324,6 +1324,13 @@ public abstract class JalviewJmolBinding implements StructureListener, } + /** + * function to colour all structures using the given Jalview colourscheme. + * This disables the colourBySequence flag but does not record the + * colourscheme used for use later. + * + * @param cs + */ public void setJalviewColourScheme(ColourSchemeI cs) { colourBySequence = false; @@ -1419,6 +1426,9 @@ public abstract class JalviewJmolBinding implements StructureListener, String commandOptions, final Container consolePanel, String buttonsToShow) { + if (commandOptions==null) { + commandOptions=""; + } viewer = JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null), htmlName + ((Object) this).toString(), documentBase, codeBase, -- 1.7.10.2