X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommands.java;h=66ecaeafb653deb1c0dea064d959d217c9082686;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d0c5671eba9745da99c9ecb9f5858a0835469a1f;hpb=15684417a64007046f10d193d5c9363be8f88ea7;p=jalview.git

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
index d0c5671..66ecaea 100644
--- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java
@@ -21,22 +21,43 @@
 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 jalview.structure.StructureCommandsI.AtomSpecType;
 
 /**
  * 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 +77,6 @@ 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 +88,6 @@ public class ChimeraXCommands extends ChimeraCommands
   @Override
   public StructureCommandI focusView()
   {
-    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
     return FOCUS_VIEW;
   }
 
@@ -107,7 +120,8 @@ public class ChimeraXCommands extends ChimeraCommands
           String attributeValue, AtomSpecModel atomSpecModel)
   {
     StringBuilder sb = new StringBuilder(128);
-    sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
+    sb.append("setattr ")
+            .append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
     sb.append(" res ").append(attributeName).append(" '")
             .append(attributeValue).append("'");
     sb.append(" create true");
@@ -125,7 +139,8 @@ 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");
   }
 
   /**
@@ -140,7 +155,7 @@ public class ChimeraXCommands extends ChimeraCommands
    * @return
    */
   @Override
-  public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+  public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
   {
     StringBuilder sb = new StringBuilder(128);
     boolean firstModel = true;
@@ -152,11 +167,14 @@ public class ChimeraXCommands extends ChimeraCommands
       }
       firstModel = false;
       appendModel(sb, model, atomSpec);
-      if (alphaOnly)
+      if (specType == AtomSpecType.ALPHA)
       {
-        // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
         sb.append("@CA");
       }
+      if (specType == AtomSpecType.PHOSPHATE)
+      {
+        sb.append("@P");
+      }
     }
     return sb.toString();
   }
@@ -200,7 +218,7 @@ public class ChimeraXCommands extends ChimeraCommands
 
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
-          AtomSpecModel spec)
+          AtomSpecModel spec, AtomSpecType backbone)
   {
     /*
      * Form ChimeraX match command to match spec to ref
@@ -210,8 +228,8 @@ public class ChimeraXCommands extends ChimeraCommands
      * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
      */
     StringBuilder cmd = new StringBuilder();
-    String atomSpec = getAtomSpec(spec, true);
-    String refSpec = getAtomSpec(ref, true);
+    String atomSpec = getAtomSpec(spec, backbone);
+    String refSpec = getAtomSpec(ref, backbone);
     cmd.append("align ").append(atomSpec).append(" toAtoms ")
             .append(refSpec);
 
@@ -219,10 +237,58 @@ public class ChimeraXCommands extends ChimeraCommands
      * show superposed residues as ribbon, others as chain
      */
     cmd.append("; ribbon ");
-    cmd.append(getAtomSpec(spec, false)).append("|");
-    cmd.append(getAtomSpec(ref, false)).append("; view");
+    cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
+    cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY))
+            .append("; view");
 
     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;
+  }
 }