Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_R...

[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 e85d387..b2224ab 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -22,11 +22,13 @@ package jalview.ext.jmol;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -37,6 +39,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -44,7 +47,6 @@ import java.awt.event.ComponentEvent;
 import java.awt.event.ComponentListener;
 import java.io.File;
 import java.net.URL;
-import java.security.AccessControlException;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.Hashtable;
@@ -615,74 +617,6 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-  // ////////////////////////////////
-  // /StructureListener
-  // @Override
-  public synchronized String[] getPdbFilex()
-  {
-    if (viewer == null)
-    {
-      return new String[0];
-    }
-    if (modelFileNames == null)
-    {
-      List<String> mset = new ArrayList<>();
-      _modelFileNameMap = new int[viewer.ms.mc];
-      String m = viewer.ms.getModelFileName(0);
-      if (m != null)
-      {
-        String filePath = m;
-        try
-        {
-          filePath = new File(m).getAbsolutePath();
-        } catch (AccessControlException x)
-        {
-          // usually not allowed to do this in applet
-          System.err.println(
-                  "jmolBinding: Using local file string from Jmol: " + m);
-        }
-        if (filePath.indexOf("/file:") != -1)
-        {
-          // applet path with docroot - discard as format won't match pdbfile
-          filePath = m;
-        }
-        mset.add(filePath);
-        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
-      }
-      int j = 1;
-      for (int i = 1; i < viewer.ms.mc; i++)
-      {
-        m = viewer.ms.getModelFileName(i);
-        String filePath = m;
-        if (m != null)
-        {
-          try
-          {
-            filePath = new File(m).getAbsolutePath();
-          } catch (AccessControlException x)
-          {
-            // usually not allowed to do this in applet, so keep raw handle
-            // System.err.println("jmolBinding: Using local file string from
-            // Jmol: "+m);
-          }
-        }
-
-        /*
-         * add this model unless it is read from a structure file we have
-         * already seen (example: 2MJW is an NMR structure with 10 models)
-         */
-        if (!mset.contains(filePath))
-        {
-          mset.add(filePath);
-          _modelFileNameMap[j] = i; // record the model index for the filename
-          j++;
-        }
-      }
-      modelFileNames = mset.toArray(new String[mset.size()]);
-    }
-    return modelFileNames;
-  }
-
   @Override
   public synchronized String[] getStructureFiles()
   {
@@ -914,6 +848,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             pdbfilename);
     if (label != null)
     {
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
       StringTokenizer toks = new StringTokenizer(strInfo, " ");
       StringBuilder sb = new StringBuilder();
       sb.append("select ").append(String.valueOf(pdbResNum)).append(":")
@@ -1257,7 +1193,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;