X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=f3bc42e27fd3d0891a96d985054a8cbd5c610d77;hb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;hp=a1a009de2b9c841c7f64c148da3c8ac431301575;hpb=3fd44a9b8f3e44b671ee26be26a8c1d541de3028;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a1a009d..f3bc42e 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -30,6 +32,7 @@ import javax.swing.*;
import org.exolab.castor.xml.*;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
@@ -1793,7 +1796,7 @@ public class Jalview2XML
try
{
// create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector();
+ newStructureViewers = new Vector();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
@@ -1924,8 +1927,7 @@ public class Jalview2XML
if (object.getJalviewModelSequence().getViewportCount() > 0)
{
af = _af;
- if (object.getJalviewModelSequence().getViewportCount() > 1
- && af.viewport.gatherViewsHere)
+ if (af.viewport.gatherViewsHere)
{
gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
}
@@ -3131,10 +3133,11 @@ public class Jalview2XML
@Override
public void run()
{
- AppJmol sview = null;
+ JalviewStructureDisplayI sview = null;
try
{
- sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+ sview = new StructureViewer(alf.alignPanel.getStructureSelectionManager()).createView(StructureViewer.Viewer.JMOL, pdbf, id, sq, alf.alignPanel,
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
addNewStructureViewer(sview);
@@ -3210,15 +3213,18 @@ public class Jalview2XML
/**
*
- * @param supported - minimum version we are comparing against
- * @param version - version of data being processsed.
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed.
* @return true if version is development/null or evaluates to the same or
* later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
*/
private boolean isVersionStringLaterThan(String supported, String version)
{
if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
- || version.equalsIgnoreCase("Test"))
+ || version.equalsIgnoreCase("Test")
+ || version.equalsIgnoreCase("AUTOMATED BUILD"))
{
System.err.println("Assuming project file with "
+ (version == null ? "null" : version)
@@ -3261,13 +3267,13 @@ public class Jalview2XML
return true;
}
- Vector newStructureViewers = null;
+ Vector newStructureViewers = null;
- protected void addNewStructureViewer(AppJmol sview)
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
{
if (newStructureViewers != null)
{
- sview.jmb.setFinishedLoadingFromArchive(false);
+ sview.getBinding().setFinishedLoadingFromArchive(false);
newStructureViewers.add(sview);
}
}
@@ -3276,9 +3282,9 @@ public class Jalview2XML
{
if (newStructureViewers != null)
{
- for (AppJmol sview : newStructureViewers)
+ for (JalviewStructureDisplayI sview : newStructureViewers)
{
- sview.jmb.setFinishedLoadingFromArchive(true);
+ sview.getBinding().setFinishedLoadingFromArchive(true);
}
newStructureViewers.clear();
newStructureViewers = null;