Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2af17a9..97b0cfb 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,24 +21,6 @@
 
 package jalview.gui;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.io.DataSourceType;
-import jalview.jbgui.GStructureChooser;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -56,6 +38,23 @@ import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.io.DataSourceType;
+import jalview.jbgui.GStructureChooser;
+import jalview.util.MessageManager;
+
 /**
  * Provides the behaviors for the Structure chooser Panel
  * 
@@ -886,11 +885,9 @@ 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 +926,7 @@ 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 +1000,8 @@ public class StructureChooser extends GStructureChooser
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.getInstance());
+          PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true);
           sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
                   new SequenceI[]
                   { selectedSequence }, superimpose, theViewer,
@@ -1066,11 +1059,9 @@ 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();
   }
 
   /**
@@ -1292,6 +1283,12 @@ public class StructureChooser extends GStructureChooser
   {
     progressBar.setProgressBar(message, id);
   }
+  
+  @Override
+  public void removeProgressBar(long id)
+  {
+    progressBar.removeProgressBar(id);
+  }
 
   @Override
   public void registerHandler(long id, IProgressIndicatorHandler handler)