Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / gui / JalviewChimeraXBindingModel.java

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index e2aaa65..737e72a 100644 (file)
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,18 +1,124 @@
+/*
+ * 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 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
+  protected List<String> getChimeraPaths()
+  {
+    return StructureManager.getChimeraPaths(true);
+  }
+
+  @Override
+  protected void addChimeraModel(PDBEntry pe,
+          List<ChimeraModel> modelsToMap)
+  {
+    /*
+     * ChimeraX hack: force chimera model name to pdbId here
+     */
+    int modelNumber = chimeraMaps.size() + 1;
+    String command = "setattr #" + modelNumber + " models name "
+            + pe.getId();
+    executeCommand(new StructureCommand(command), false);
+    modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
+            modelNumber, 0));
+  }
+
+  /**
+   * {@inheritDoc}
+   * 
+   * @return
+   */
+  @Override
+  protected String getCommandFileExtension()
+  {
+    return ".cxc";
+  }
+
+  /**
+   * 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
+  public String getSessionFileExtension()
+  {
+    return CHIMERAX_SESSION_EXTENSION;
+  }
+
+  @Override
+  public String getHelpURL()
+  {
+    return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
+  }
+
+  @Override
+  protected ViewerType getViewerType()
+  {
+    return ViewerType.CHIMERAX;
+  }
+
+  @Override
+  protected String getModelId(int pdbfnum, String file)
+  {
+    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);
   }
 
 }