+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.structure.StructureSelectionManager;
-
import java.util.List;
import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.ChimeraXCommands;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureSelectionManager;
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
+ public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, DataSourceType protocol)
{
super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
+ setStructureCommands(new ChimeraXCommands());
}
@Override
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- executeCommand(command, false);
+ executeCommand(new StructureCommand(command), false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
}
/**
- * {@inheritDoc}
+ * Returns the file extension to use for a saved viewer session file (.cxs)
*
* @return
+ * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
*/
@Override
- protected String getOpenCommandFileCommand(String path)
+ public String getSessionFileExtension()
{
- return "open " + path;
+ return CHIMERAX_SESSION_EXTENSION;
}
- /**
- * {@inheritDoc}
- */
@Override
- protected String getSaveSessionCommand(String filepath)
+ public String getHelpURL()
{
- return "save session " + filepath;
+ return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
}
- /**
- * Returns the file extension to use for a saved viewer session file
- *
- * @return
- */
@Override
- public String getSessionFileExtension()
+ protected ViewerType getViewerType()
{
- return ".cxs";
+ return ViewerType.CHIMERAX;
}
@Override
- public String getHelpURL()
+ protected String getModelId(int pdbfnum, String file)
{
- return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
+ return String.valueOf(pdbfnum + 1);
+ }
+
+ /**
+ * Returns a model of the structure positions described by the ChimeraX format
+ * atomspec
+ *
+ * @param atomSpec
+ * @return
+ */
+ @Override
+ protected AtomSpec parseAtomSpec(String atomSpec)
+ {
+ return AtomSpec.fromChimeraXAtomspec(atomSpec);
}
}