JAL-3446 breaking change redacted

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 4a8a7d8..c30d8c7 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -145,7 +145,7 @@ public class StructureChooser extends GStructureChooser
    */
   private void discoverStructureViews()
   {
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
       targetView.removeAllItems();
       if (lastTargetedView != null && !lastTargetedView.isVisible())
@@ -153,7 +153,7 @@ public class StructureChooser extends GStructureChooser
         lastTargetedView = null;
       }
       int linkedViewsAt = 0;
-      for (StructureViewerBase view : Desktop.instance
+      for (StructureViewerBase view : Desktop.getInstance()
               .getStructureViewers(null, null))
       {
         StructureViewer viewHandler = (lastTargetedView != null
@@ -886,11 +886,9 @@ public class StructureChooser extends GStructureChooser
   public void showStructures(boolean waitUntilFinished)
   {
 
-    final StructureSelectionManager ssm = ap.getStructureSelectionManager();
-
     final int preferredHeight = pnl_filter.getHeight();
 
-    final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+    final StructureViewer theViewer = getTargetedStructureViewer();
     boolean superimpose = chk_superpose.isSelected();
 
     Runnable viewStruc = new Runnable()
@@ -929,9 +927,7 @@ public class StructureChooser extends GStructureChooser
 
             if (pdbEntry == null)
             {
-              pdbEntry = new PDBEntry();
-              pdbEntry.setId(pdbIdStr);
-              pdbEntry.setType(PDBEntry.Type.PDB);
+              pdbEntry = new PDBEntry(pdbIdStr, null, "pdb");
               selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
             }
             pdbEntriesToView[count++] = pdbEntry;
@@ -1005,10 +1001,8 @@ public class StructureChooser extends GStructureChooser
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
+          PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true);
           sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
                   new SequenceI[]
                   { selectedSequence }, superimpose, theViewer,
@@ -1066,11 +1060,9 @@ public class StructureChooser extends GStructureChooser
    * @param ssm
    * @return
    */
-  StructureViewer getTargetedStructureViewer(StructureSelectionManager ssm)
+  StructureViewer getTargetedStructureViewer()
   {
-    Object sv = targetView.getSelectedItem();
-
-    return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
+    return (StructureViewer) targetView.getSelectedItem();
   }
 
   /**