JAL-1761 need to pass molecule type when generating superposition commands

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraXCommands.java

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index 314e6db..74e7f08 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -28,7 +28,6 @@ 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
@@ -36,15 +35,19 @@ import jalview.util.ColorUtils;
 public class ChimeraXCommands extends ChimeraCommands
 {
   // 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 LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+          "info resattr");
 
   // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
-  private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+  private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
+          "exit");
 
   // 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 STOP_NOTIFY_SELECTION = new StructureCommand(
+          "info notify stop selection jalview");
 
-  private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
+  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(
@@ -99,8 +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
@@ -142,6 +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
    */
@@ -163,7 +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();
   }
@@ -207,7 +213,7 @@ public class ChimeraXCommands extends ChimeraCommands
 
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
-          AtomSpecModel spec)
+          AtomSpecModel spec, boolean isNucleotide)
   {
     /*
      * Form ChimeraX match command to match spec to ref
@@ -250,8 +256,12 @@ public class ChimeraXCommands extends ChimeraCommands
   public List<StructureCommandI> startNotifications(String uri)
   {
     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;
   }