X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalviewChimeraXBindingModel.java;h=cfd44c7f8806ccec41a71b887af8b37e17fa87c6;hb=2d9d76a0d2350007aa5cdac2a7720ca2a37cfcfe;hp=0779bef30925efad7740c3a4622d75ba88b96f90;hpb=6cb920bb7a7f285a165cd34b3429dabba71f7518;p=jalview.git

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index 0779bef..cfd44c7 100644
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,24 +1,29 @@
 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
@@ -37,7 +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));
   }
@@ -54,40 +59,44 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
   }
 
   /**
-   * {@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;
+  }
+
+  @Override
+  public String getHelpURL()
+  {
+    return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
   }
 
-  /**
-   * {@inheritDoc}
-   */
   @Override
-  protected String getSaveSessionCommand(String filepath)
+  protected ViewerType getViewerType()
   {
-    return "save session " + filepath;
+    return ViewerType.CHIMERAX;
   }
 
-  /**
-   * Returns the file extension to use for a saved viewer session file
-   * 
-   * @return
-   */
   @Override
-  public String getSessionFileExtension()
+  protected String getModelId(int pdbfnum, String file)
   {
-    return ".cxs";
+    return String.valueOf(pdbfnum + 1);
   }
 
+  /**
+   * Returns a model of the structure positions described by the ChimeraX format atomspec
+   * @param atomSpec
+   * @return
+   */
   @Override
-  public String getHelpURL()
+  protected AtomSpec parseAtomSpec(String atomSpec)
   {
-    return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
+    return AtomSpec.fromChimeraXAtomspec(atomSpec);
   }
 
 }