X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommands.java;h=f1a8b5fd64051001d6ba4c634d1aba63c3d2385b;hb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;hp=9636a6a2a089fb9c8e4f7b24e1625217ccd59637;hpb=42f4227ed213d422a87d3b22fc9e85d14ffaf53f;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index 9636a6a..f1a8b5f 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -20,22 +20,31 @@
  */
 package jalview.ext.rbvi.chimera;
 
+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;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.util.Arrays;
-import java.util.List;
-
 /**
  * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
  */
 public class ChimeraXCommands extends ChimeraCommands
 {
+  private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+
+  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 GET_SELECTION = new StructureCommand("info selection level residue");
+
   private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
-          "~display all;show @CA|P pbonds");
+          "~display all;~ribbon;show @CA|P atoms");
 
   private static final StructureCommand FOCUS_VIEW = new StructureCommand(
           "view");
@@ -56,14 +65,7 @@ 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 getColourCommand(String atomSpec, Color colour)
+  public StructureCommandI colourResidues(String atomSpec, Color colour)
   {
     // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
     String colourCode = getColourString(colour);
@@ -125,7 +127,8 @@ 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");
   }
 
   /**
@@ -150,7 +153,8 @@ public class ChimeraXCommands extends ChimeraCommands
       appendModel(sb, model, atomSpec);
       if (alphaOnly)
       {
-        sb.append("@CA|P");
+        // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
+        sb.append("@CA");
       }
       // todo: is there ChimeraX syntax to exclude altlocs?
     }
@@ -195,16 +199,15 @@ public class ChimeraXCommands extends ChimeraCommands
   }
 
   @Override
-  public List<StructureCommandI> superposeStructures(AtomSpecModel spec,
-          AtomSpecModel ref)
+  public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
+          AtomSpecModel spec)
   {
     /*
      * Form ChimeraX match command to match spec to ref
      * 
      * match #1/A:2-94 toAtoms #2/A:1-93
      * 
-     * @see
-     * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
+     * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
      */
     StringBuilder cmd = new StringBuilder();
     String atomSpec = getAtomSpec(spec, true);
@@ -222,4 +225,44 @@ 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()
+  {
+    // 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));
+    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);
+    return cmds;
+  }
+
+  @Override
+  public StructureCommandI getSelectedResidues()
+  {
+    return GET_SELECTION;
+  }
 }