Merge remote-tracking branch 'origin/develop' into imp/JAL-2774

[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 96dfcfe..41bc116 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.schemes.ColourSchemeI;
@@ -72,7 +73,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private boolean associateNewStructs = false;
 
-  Vector<String> atomsPicked = new Vector<String>();
+  Vector<String> atomsPicked = new Vector<>();
 
   private List<String> chainNames;
 
@@ -610,7 +611,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     }
     if (modelFileNames == null)
     {
-      List<String> mset = new ArrayList<String>();
+      List<String> mset = new ArrayList<>();
       _modelFileNameMap = new int[viewer.ms.mc];
       String m = viewer.ms.getModelFileName(0);
       if (m != null)
@@ -670,7 +671,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   @Override
   public synchronized String[] getStructureFiles()
   {
-    List<String> mset = new ArrayList<String>();
+    List<String> mset = new ArrayList<>();
     if (viewer == null)
     {
       return new String[0];
@@ -975,6 +976,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
         notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
                 (String) data[0]);
         // also highlight in alignment
+        // deliberate fall through
       case HOVER:
         notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
                 (String) data[0]);
@@ -1059,8 +1061,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new ArrayList<String>();
-    chainFile = new Hashtable<String, String>();
+    chainNames = new ArrayList<>();
+    chainFile = new Hashtable<>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getStructureFiles();
     // first check if we've lost any structures
@@ -1126,7 +1128,8 @@ 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);
+                    pdbfile, DataSourceType.PASTE,
+                    getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
@@ -1158,7 +1161,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             }
             // Explicitly map to the filename used by Jmol ;
             pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    fileName, protocol);
+                    fileName, protocol, getIProgressIndicator());
             // pdbentry[pe].getFile(), protocol);
 
           }
@@ -1226,6 +1229,8 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     return chainNames;
   }
 
+  protected abstract IProgressIndicator getIProgressIndicator();
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);