JAL-2422 proof of concept adaptations for ChimeraX commands

[jalview.git] / src / ext / edu / ucsf / rbvi / strucviz2 / ChimeraManager.java

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index a322f0b..1a8bd76 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -334,7 +334,11 @@ public class ChimeraManager
 
   public void stopListening()
   {
-    sendChimeraCommand("listen stop models ; listen stop selection ", false);
+    // TODO send this command when viewer connection is closed in Jalview
+    String command = isChimeraX
+            ? "info notify stop models jalview; info notify stop selection jalview"
+            : "listen stop models ; listen stop selection ";
+    sendChimeraCommand(command, false);
   }
 
   /**
@@ -344,9 +348,15 @@ public class ChimeraManager
    */
   public void startListening(String uri)
   {
-    sendChimeraCommand("listen start models url " + uri
-            + ";listen start select prefix SelectionChanged url " + uri,
-            false);
+    String command = isChimeraX
+            ? ("info notify start models prefix ModelChanged jalview url "
+                    + uri
+                    + "; info notify start selection jalview prefix SelectionChanged url "
+                    + uri)
+            : ("listen start models url " + uri
+                    + ";listen start select prefix SelectionChanged url "
+                    + uri);
+    sendChimeraCommand(command, false);
   }
 
   /**
@@ -420,19 +430,33 @@ public class ChimeraManager
   public List<String> getSelectedResidueSpecs()
   {
     List<String> selectedResidues = new ArrayList<>();
-    List<String> chimeraReply = sendChimeraCommand(
-            "list selection level residue", true);
+
+    /*
+     * skip for now if ChimeraX - times out
+     */
+    if (isChimeraX)
+    {
+      return selectedResidues;
+    }
+
+    // in fact 'listinfo' (undocumented) works in ChimeraX
+    String command = (isChimeraX ? "info" : "list")
+            + " selection level residue";
+    List<String> chimeraReply = sendChimeraCommand(command, true);
     if (chimeraReply != null)
     {
       /*
-       * expect 0, 1 or more lines of the format
+       * expect 0, 1 or more lines of the format either
+       * Chimera:
        * residue id #0:43.A type GLY
-       * where we are only interested in the atomspec #0.43.A
+       * ChimeraX:
+       * residue id /A:89 name THR index 88
+       * We are only interested in the atomspec (third token of the reply)
        */
       for (String inputLine : chimeraReply)
       {
         String[] inputLineParts = inputLine.split("\\s+");
-        if (inputLineParts.length == 5)
+        if (inputLineParts.length >= 5)
         {
           selectedResidues.add(inputLineParts[2]);
         }
@@ -722,7 +746,8 @@ public class ChimeraManager
   public List<String> getAttrList()
   {
     List<String> attributes = new ArrayList<>();
-    final List<String> reply = sendChimeraCommand("list resattr", true);
+    String command = (isChimeraX ? "info " : "list") + "resattr";
+    final List<String> reply = sendChimeraCommand(command, true);
     if (reply != null)
     {
       for (String inputLine : reply)