JAL-3551 null pointer defence while structure files loading; comments

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

diff --git a/src/jalview/gui/JalviewChimeraXBindingModel.java b/src/jalview/gui/JalviewChimeraXBindingModel.java
index 0779bef..c685f0f 100644 (file)
--- 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.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 +59,33 @@ 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;
   }
 
-  /**
-   * {@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);
   }
 
 }