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 0779bef..737e72a 100644 (file)
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,24 +1,49 @@
+/*
+ * 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 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 +62,7 @@ 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 +79,46 @@ 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);
+  }
+
+  /**
+   * 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);
   }
 
 }