Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
new file mode 100644 (file)
index 0000000..cfd44c7
--- /dev/null
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
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+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);
+  }
+
+}