From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 17 Nov 2021 13:39:31 +0000 (+0000)
Subject: JAL-3922 convert selection events in Jmol to highlights in Jalview - still need to... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2Fr2_11_2%2FJAL-3922_jmolSelectionHighlighting;p=jalview.git

JAL-3922 convert selection events in Jmol to highlights in Jalview - still need to ignore selection events performed as part of Jalview manipulating Jmol.
---

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 903d9b7..6ee0fa7 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -39,6 +39,8 @@ import org.jmol.api.JmolSelectionListener;
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
+import org.jmol.modelset.Atom;
+import org.jmol.modelset.Model;
 import org.jmol.viewer.Viewer;
 
 import jalview.api.AlignmentViewPanel;
@@ -246,6 +248,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     // jmolpopup.jpiShow(x, y);
   }
 
+  private List<AtomSpec> lastHighlight = new ArrayList<AtomSpec>();
+  private List<AtomSpec> resetLastHighlight = new ArrayList<AtomSpec>();
   /**
    * Highlight zero, one or more atoms on the structure
    */
@@ -254,6 +258,11 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     if (atoms != null)
     {
+      // make sure we ignore the next few selection events for these
+      lastHighlight.addAll(resetLastHighlight);
+      lastHighlight.addAll(atoms);
+      resetLastHighlight.clear();
+      resetLastHighlight.addAll(atoms);
       if (resetLastRes.length() > 0)
       {
         jmolScript(resetLastRes.toString());
@@ -281,6 +290,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
     StringBuilder selection = new StringBuilder(32);
     StringBuilder cmd = new StringBuilder(64);
+    // save existing selection.
+    // display halo
     selection.append("select ").append(String.valueOf(pdbResNum));
     selection.append(":");
     if (!chain.equals(" "))
@@ -906,7 +917,29 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             commandOptions, this);
 
     jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
-
+    
+    jmolViewer.addSelectionListener(new JmolSelectionListener()
+    {
+      
+      @Override
+      public void selectionChanged(BS arg0)
+      {
+        if (!isLoadingFinished())
+        {
+          return;
+        }
+        List<AtomSpec> lastH = lastHighlight;
+        lastHighlight = new ArrayList<AtomSpec>();
+        final AtomSpec[] lastHighlighted = lastH.toArray(new AtomSpec[0]); // copy of the int[] array
+        SwingUtilities.invokeLater(new Runnable() {
+          
+          public void run() {
+            
+            processselectionChanged(arg0, lastHighlighted);
+          }
+        });
+      }
+    });
     try
     {
       console = createJmolConsole(consolePanel, buttonsToShow);
@@ -924,6 +957,53 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   }
 
+  protected void processselectionChanged(BS arg0, AtomSpec[] lastHighlighted)
+  {
+    int atom = arg0.nextSetBit(0);
+    int modelNo=-1,resNo=-1;
+    String chainCode="NOCHAIN";
+    List<AtomSpec> toSelect = new ArrayList<AtomSpec>();
+    while (atom>-1 && arg0.get(atom)){
+      //
+      Model atomModel = jmolViewer.getModelForAtomIndex(atom);
+      Atom firstAtom = atomModel.ms.getAtom(atom);
+      String chcode = firstAtom.getChainIDStr();
+      if (atomModel.modelIndex!=modelNo || resNo != firstAtom.getResno() || !chainCode.equals(chcode))
+      {
+        resNo = firstAtom.getResno();
+        modelNo = atomModel.modelIndex;
+        chainCode = chcode;
+        boolean ignore=false;
+        String modelFile = getPdbEntry(modelNo).getFile();
+        if (lastHighlighted!=null)
+        {
+          
+          for (AtomSpec hgh:lastHighlighted)
+          {
+            if (hgh.getPdbResNum() == resNo && chainCode.equals(hgh.getChain()) && hgh.getPdbFile().equals(modelFile))
+            {
+              ignore=true;
+              break;
+            }
+          }
+        }
+        if (!ignore)
+        {
+          AtomSpec atomspec = new AtomSpec(modelFile, chainCode, resNo, atomModel.firstAtomIndex);
+          toSelect.add(atomspec);
+        }
+      }
+      // look for next selected atom
+      atom = arg0.nextSetBit(++atom);
+    } 
+    if (toSelect.size()>0 || arg0.isEmpty())
+    {
+      // if we have ignored everything we don't clear the existing highlight
+      getSsm().mouseOverStructure(toSelect);
+    }
+  }
+
+
   protected abstract JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow);
 
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 6b06e56..c581317 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -27,8 +27,12 @@ import java.util.List;
 import java.util.Map;
 
 import javax.swing.JComponent;
+import javax.swing.SwingUtilities;
 
+import org.jmol.api.AtomIndexIterator;
 import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.modelset.Atom;
+import org.jmol.modelset.Model;
 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 import jalview.api.AlignmentViewPanel;
@@ -39,6 +43,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
 import jalview.io.DataSourceType;
+import jalview.structure.AtomSpec;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -142,8 +147,12 @@ public class AppJmolBinding extends JalviewJmolBinding
   @Override
   public void selectionChanged(BS arg0)
   {
+    SwingUtilities.invokeLater(new Runnable() {
+      public void run() {
+      }
+    });
   }
-
+  
   @Override
   public void showConsole(boolean b)
   {