Merge branch 'develop' into feature/JAL-3551Pymol

[jalview.git] / src / jalview / ext / jmol / JalviewJmolBinding.java

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index c3a22fb..54eb599 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -40,6 +40,7 @@ import org.jmol.c.CBK;
 import org.jmol.viewer.Viewer;
 
 import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.IProgressIndicator;
@@ -111,6 +112,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return getViewerTitle("Jmol", true);
   }
 
+  private String jmolScript(String script)
+  {
+    Cache.log.debug(">>Jmol>> " + script);
+    String s = jmolViewer.evalStringQuiet(script);
+    Cache.log.debug("<<Jmol<< " + s);
+
+    return s;
+  }
+
   @Override
   public List<String> executeCommand(StructureCommandI command,
           boolean getReply)
@@ -123,7 +133,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(cmd))
     {
-      jmolViewer.evalStringQuiet(cmd + "\n");
+      jmolScript(cmd + "\n");
     }
     jmolHistory(true);
     lastCommand = cmd;
@@ -235,7 +245,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     {
       if (resetLastRes.length() > 0)
       {
-        jmolViewer.evalStringQuiet(resetLastRes.toString());
+        jmolScript(resetLastRes.toString());
         resetLastRes.setLength(0);
       }
       for (AtomSpec atom : atoms)
@@ -274,7 +284,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     resetLastRes.append(selection).append(";wireframe 0;").append(selection)
             .append(" and not hetero; spacefill 0;");
 
-    jmolViewer.evalStringQuiet(cmd.toString());
+    jmolScript(cmd.toString());
     jmolHistory(true);
   }
 
@@ -282,7 +292,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   private void jmolHistory(boolean enable)
   {
-    jmolViewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+    jmolScript("History " + ((debug || enable) ? "on" : "off"));
   }
 
   public void loadInline(String string)
@@ -428,7 +438,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     /**
      * this implements the toggle label behaviour copied from the original
-     * structure viewer, MCView
+     * structure viewer, mc_view
      */
     if (strData != null)
     {
@@ -459,7 +469,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     if (!atomsPicked.contains(picked))
     {
-      jmolViewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+      jmolScript("select " + picked + ";label %n %r:%c");
       atomsPicked.addElement(picked);
     }
     else
@@ -645,8 +655,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
           // see JAL-623 - need method of matching pasted data up
           {
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, DataSourceType.PASTE,
-                    getIProgressIndicator());
+                    pdbfile, DataSourceType.PASTE, getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -714,7 +723,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     // }
     if (!isLoadingFromArchive())
     {
-      jmolViewer.evalStringQuiet(
+      jmolScript(
               "model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
     }
     // register ourselves as a listener and notify the gui that it needs to
@@ -779,7 +788,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   public void showHelp()
   {
-    showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+    showUrl("http://wiki.jmol.org"
+    // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+            , "jmolHelp");
   }
 
   /**
@@ -796,7 +807,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   public abstract void showConsole(boolean show);
 
+  public static Viewer getJmolData(JmolParser jmolParser)
+  {
+    return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null,
+            "-x -o -n", jmolParser);
+  }
+
   /**
+   * 
+   * 
+   * 
    * @param renderPanel
    * @param jmolfileio
    *          - when true will initialise jmol's file IO system (should be false
@@ -827,13 +847,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * @param consolePanel
    *          - panel to contain Jmol console
    * @param buttonsToShow
-   *          - buttons to show on the console, in ordr
+   *          - buttons to show on the console, in order
    */
   public void allocateViewer(Container renderPanel, boolean jmolfileio,
           String htmlName, URL documentBase, URL codeBase,
           String commandOptions, final Container consolePanel,
           String buttonsToShow)
   {
+
+    System.err.println("Allocating Jmol Viewer: " + commandOptions);
+
     if (commandOptions == null)
     {
       commandOptions = "";
@@ -845,7 +868,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
 
-    console = createJmolConsole(consolePanel, buttonsToShow);
+    try
+    {
+      console = createJmolConsole(consolePanel, buttonsToShow);
+    } catch (Throwable e)
+    {
+      System.err.println("Could not create Jmol application console. "
+              + e.getMessage());
+      e.printStackTrace();
+    }
     if (consolePanel != null)
     {
       consolePanel.addComponentListener(this);
@@ -857,6 +888,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   protected abstract JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow);
 
+  // BH 2018 -- Jmol console is not working due to problems with styled
+  // documents.
+
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
   @Override