X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommands.java;h=4e45ac82236bdce841f7851e924664fabf859200;hb=a777a323d548a3e63025c911ccc35f86a2a01cee;hp=f1a8b5fd64051001d6ba4c634d1aba63c3d2385b;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index f1a8b5f..4e45ac8 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -28,24 +28,35 @@ import java.util.List;
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
 import jalview.structure.StructureCommandI;
-import jalview.util.ColorUtils;
 
 /**
  * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
  */
 public class ChimeraXCommands extends ChimeraCommands
 {
-  private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
+  private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+          "info resattr");
 
-  private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
+  private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
+          "exit");
 
-  private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
+  private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+          "info notify stop selection jalview");
 
-  private static final StructureCommand GET_SELECTION = new StructureCommand("info selection level residue");
+  private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+          "info notify stop models jalview");
+
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
+  private static final StructureCommand GET_SELECTION = new StructureCommand(
+          "info selection level residue");
 
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
           "~display all;~ribbon;show @CA|P atoms");
 
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
   private static final StructureCommand FOCUS_VIEW = new StructureCommand(
           "view");
 
@@ -76,7 +87,6 @@ public class ChimeraXCommands extends ChimeraCommands
   @Override
   public StructureCommandI focusView()
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
     return FOCUS_VIEW;
   }
 
@@ -92,8 +102,8 @@ public class ChimeraXCommands extends ChimeraCommands
   }
 
   /**
-   * Returns a viewer command to set the given residue attribute value on
-   * residues specified by the AtomSpecModel, for example
+   * Returns a viewer command to set the given residue attribute value on residues
+   * specified by the AtomSpecModel, for example
    * 
    * <pre>
    * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
@@ -135,6 +145,10 @@ public class ChimeraXCommands extends ChimeraCommands
    * Returns the range(s) formatted as a ChimeraX atomspec, for example
    * <p>
    * #1/A:2-20,30-40/B:10-20|#2/A:12-30
+   * <p>
+   * Note there is no need to explicitly exclude ALTLOC atoms when
+   * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
+   * change from Chimera)
    * 
    * @return
    */
@@ -156,7 +170,6 @@ public class ChimeraXCommands extends ChimeraCommands
         // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
         sb.append("@CA");
       }
-      // todo: is there ChimeraX syntax to exclude altlocs?
     }
     return sb.toString();
   }
@@ -236,24 +249,25 @@ public class ChimeraXCommands extends ChimeraCommands
   @Override
   public StructureCommandI closeViewer()
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
     return CLOSE_CHIMERAX;
   }
 
   @Override
   public List<StructureCommandI> startNotifications(String uri)
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
     List<StructureCommandI> cmds = new ArrayList<>();
-    cmds.add(new StructureCommand("info notify start models prefix ModelChanged jalview url " + uri));
-    cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
+    cmds.add(new StructureCommand(
+            "info notify start models jalview prefix ModelChanged url "
+                    + uri));
+    cmds.add(new StructureCommand(
+            "info notify start selection jalview prefix SelectionChanged url "
+                    + uri));
     return cmds;
   }
 
   @Override
   public List<StructureCommandI> stopNotifications()
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
     List<StructureCommandI> cmds = new ArrayList<>();
     cmds.add(STOP_NOTIFY_MODELS);
     cmds.add(STOP_NOTIFY_SELECTION);
@@ -265,4 +279,10 @@ public class ChimeraXCommands extends ChimeraCommands
   {
     return GET_SELECTION;
   }
+
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return LIST_RESIDUE_ATTRIBUTES;
+  }
 }