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 d7b5a94..737e72a 100644 (file)
--- a/src/jalview/gui/JalviewChimeraXBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraXBindingModel.java
@@ -1,3 +1,23 @@
+/*
+ * 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 java.util.List;
@@ -10,11 +30,13 @@ 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,
@@ -65,7 +87,7 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
   @Override
   public String getSessionFileExtension()
   {
-    return ".cxs";
+    return CHIMERAX_SESSION_EXTENSION;
   }
 
   @Override
@@ -86,4 +108,17 @@ public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
     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);
+  }
+
 }