From b94df7cbe375db4a0df5c351dda035ae8e9c10f7 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 28 Aug 2008 13:10:47 +0000 Subject: [PATCH] bugfix for Jmol and new classloader reading capability --- src/jalview/appletgui/AppletJmol.java | 8 +++++--- src/jalview/bin/JalviewLite.java | 7 ++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index aa81764..e272f97 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -690,7 +690,6 @@ public class AppletJmol extends EmbmenuFrame "select backbone;restrict;cartoon;wireframe off;spacefill off"); ssm = StructureSelectionManager.getStructureSelectionManager(); - MCview.PDBfile pdb; if (loadedInline) { @@ -701,9 +700,12 @@ public class AppletJmol extends EmbmenuFrame } else { - pdb = ssm.setMapping(sequence,chains, + // TODO: Jmol can in principle retrieve from CLASSLOADER but this needs to be tested. See mantis bug https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 + + pdb = ssm.setMapping(sequence,chains, pdbentry.getFile(), - protocol); + AppletFormatAdapter.URL); + } pdbentry.setId(pdb.id); diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 8f2b3d4..7a4b6bc 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -829,10 +829,11 @@ public class JalviewLite extends Applet } param = setProtocolState(param); - if (!jmolAvailable - && protocol == AppletFormatAdapter.CLASSLOADER) + if (//!jmolAvailable + // && + protocol == AppletFormatAdapter.CLASSLOADER) { - // TODO: pass PDB file in classloader on to Jmol + // TODO: verify this Re: https://mantis.lifesci.dundee.ac.uk/view.php?id=36605 // This exception preserves the current behaviour where, even if // the local pdb file was identified in the class loader protocol = AppletFormatAdapter.URL; // this is probably NOT -- 1.7.10.2