JAL-3829 alternative UX: need to select 3d-beacons from dropdown if db-refs need...

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

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index 3a6c89c..cfd44c7 100644 (file)
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,20 +1,22 @@
 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;
 
-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;
-
 public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
 {
+  public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
 
   public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
@@ -40,7 +42,7 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
     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));
   }
@@ -57,14 +59,15 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
   }
 
   /**
-   * Returns the file extension to use for a saved viewer session file
+   * 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 ".cxs";
+    return CHIMERAX_SESSION_EXTENSION;
   }
 
   @Override
@@ -79,4 +82,21 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
     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);
+  }
+
 }