JAL-2422 a fix and a fudge for two failing ChimeraX 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 b7d9ce3..ad04fc9 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -20,23 +20,39 @@
  */
 package jalview.ext.rbvi.chimera;
 
-import jalview.structure.AtomSpecModel;
-import jalview.structure.StructureCommand;
-import jalview.structure.StructureCommandI;
-import jalview.util.ColorUtils;
-
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+
 /**
  * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
  */
 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");
+
+  // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
+  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_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");
 
@@ -56,13 +72,6 @@ public class ChimeraXCommands extends ChimeraCommands
   }
 
   @Override
-  public StructureCommandI setBackgroundColour(Color col)
-  {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/set.html
-    return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
-  }
-
-  @Override
   public StructureCommandI colourResidues(String atomSpec, Color colour)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
@@ -74,7 +83,6 @@ public class ChimeraXCommands extends ChimeraCommands
   @Override
   public StructureCommandI focusView()
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
     return FOCUS_VIEW;
   }
 
@@ -125,7 +133,8 @@ public class ChimeraXCommands extends ChimeraCommands
   public StructureCommandI saveSession(String filepath)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
-    return new StructureCommand("save session " + filepath);
+    // note ChimeraX will append ".cxs" to the filepath!
+    return new StructureCommand("save " + filepath + " format session");
   }
 
   /**
@@ -222,4 +231,47 @@ public class ChimeraXCommands extends ChimeraCommands
     return Arrays.asList(new StructureCommand(cmd.toString()));
   }
 
+  @Override
+  public StructureCommandI openSession(String filepath)
+  {
+    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite
+    // this version of the command has no dependency on file extension
+    return new StructureCommand("open " + filepath + " format session");
+  }
+
+  @Override
+  public StructureCommandI closeViewer()
+  {
+    return CLOSE_CHIMERAX;
+  }
+
+  @Override
+  public List<StructureCommandI> startNotifications(String uri)
+  {
+    List<StructureCommandI> cmds = new ArrayList<>();
+    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()
+  {
+    List<StructureCommandI> cmds = new ArrayList<>();
+    cmds.add(STOP_NOTIFY_MODELS);
+    cmds.add(STOP_NOTIFY_SELECTION);
+    return cmds;
+  }
+
+  @Override
+  public StructureCommandI getSelectedResidues()
+  {
+    return GET_SELECTION;
+  }
+
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return LIST_RESIDUE_ATTRIBUTES;
+  }
 }