* 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
* 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.
*
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
- 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);
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
addNewStructureViewer(sview);
- * @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")
* @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")