Merge branch 'bug/JAL-2634' into develop

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 0990b56..db0b47e 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -29,12 +29,14 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.util.MappingUtils;
@@ -384,6 +386,7 @@ public class StructureSelectionManager
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
+      sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(pdbFile, sourceType);
 
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
@@ -739,7 +742,7 @@ public class StructureSelectionManager
       if (listeners.elementAt(i) instanceof StructureListener)
       {
         sl = (StructureListener) listeners.elementAt(i);
-        for (String pdbfile : sl.getPdbFile())
+        for (String pdbfile : sl.getStructureFiles())
         {
           pdbs.remove(pdbfile);
         }
@@ -1201,13 +1204,14 @@ public class StructureSelectionManager
 
   public synchronized void sendSelection(
           jalview.datamodel.SequenceGroup selection,
-          jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+          jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+          SelectionSource source)
   {
     for (SelectionListener slis : sel_listeners)
     {
       if (slis != source)
       {
-        slis.selection(selection, colsel, source);
+        slis.selection(selection, colsel, hidden, source);
       }
     }
   }