Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index ce57373..a8ce659 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -41,7 +41,6 @@ import javax.swing.JPopupMenu;
 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;
@@ -119,13 +118,11 @@ public class StructureChooser extends GStructureChooser
     // which FTS engine to use
     data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
     initDialog();
-
     this.ap = ap;
     this.selectedSequence = selectedSeq;
     this.selectedSequences = selectedSeqs;
     this.progressIndicator = (ap == null) ? null : ap.alignFrame;
     init();
-
   }
 
   /**
@@ -215,7 +212,6 @@ public class StructureChooser extends GStructureChooser
 
     // ensure a filter option is in force for search
     populateFilterComboBox(true, cachedPDBExists);
-
     // looks for any existing structures already loaded
     // for the sequences (the cached ones)
     // then queries the StructureChooserQuerySource to
@@ -362,7 +358,7 @@ public class StructureChooser extends GStructureChooser
    */
   private void discoverStructureViews()
   {
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
       targetView.removeAllItems();
       if (lastTargetedView != null && !lastTargetedView.isVisible())
@@ -370,7 +366,7 @@ 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
@@ -435,13 +431,10 @@ public class StructureChooser extends GStructureChooser
 
     discoveredStructuresSet = new LinkedHashSet<>();
     HashSet<String> errors = new HashSet<>();
-
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
-
     for (SequenceI seq : selectedSequences)
     {
-
       FTSRestResponse resultList;
       try
       {
@@ -475,7 +468,6 @@ public class StructureChooser extends GStructureChooser
     {
       getResultTable()
               .setModel(data.getTableModel(discoveredStructuresSet));
-
       noOfStructuresFound = discoveredStructuresSet.size();
       lastDiscoveredStructuresSet = discoveredStructuresSet;
       mainFrame.setTitle(MessageManager.formatMessage(
@@ -533,7 +525,6 @@ public class StructureChooser extends GStructureChooser
   {
     Thread filterThread = new Thread(new Runnable()
     {
-
       @Override
       public void run()
       {
@@ -546,14 +537,12 @@ public class StructureChooser extends GStructureChooser
 
         for (SequenceI seq : selectedSequences)
         {
-
           FTSRestResponse resultList;
           try
           {
             resultList = data.selectFirstRankedQuery(seq,
                     discoveredStructuresSet, wantedFields, fieldToFilterBy,
                     !chk_invertFilter.isSelected());
-
           } catch (Exception e)
           {
             e.printStackTrace();
@@ -659,11 +648,11 @@ public class StructureChooser extends GStructureChooser
   protected void populateFilterComboBox(boolean haveData,
           boolean cachedPDBExist, FilterOption lastSel)
   {
-
     /*
      * temporarily suspend the change listener behaviour
      */
     cmb_filterOption.removeItemListener(this);
+
     int selSet = -1;
     cmb_filterOption.removeAllItems();
     if (haveData)
@@ -683,7 +672,6 @@ public class StructureChooser extends GStructureChooser
         cmb_filterOption.addItem(filter);
       }
     }
-
     cmb_filterOption.addItem(
             new FilterOption(MessageManager.getString("label.enter_pdb_id"),
                     "-", VIEWS_ENTER_ID, false, null));
@@ -706,6 +694,7 @@ public class StructureChooser extends GStructureChooser
         cmb_filterOption.setSelectedItem(cachedOption);
       }
     }
+
     if (selSet > -1)
     {
       cmb_filterOption.setSelectedIndex(selSet);
@@ -729,7 +718,6 @@ public class StructureChooser extends GStructureChooser
     // otherwise, record selection
     // and update the layout and dialog accordingly
     lastSelected = selectedFilterOpt;
-
     layout_switchableViews.show(pnl_switchableViews,
             selectedFilterOpt.getView());
     String filterTitle = mainFrame.getTitle();
@@ -923,6 +911,7 @@ public class StructureChooser extends GStructureChooser
   {
     validateSelections();
   }
+
   private FilterOption lastSelected=null;
   /**
    * Handles the state change event for the 'filter' combo-box and 'invert'
@@ -983,7 +972,6 @@ public class StructureChooser extends GStructureChooser
     }
     return found;
   }
-
   /**
    * Handles the 'New View' action
    */
@@ -1053,7 +1041,6 @@ public class StructureChooser extends GStructureChooser
           {
             PDBEntry pdbEntry = ((PDBEntryTableModel) tbl_local_pdb
                     .getModel()).getPDBEntryAt(row).getPdbEntry();
-
             pdbEntriesToView[count++] = pdbEntry;
             SequenceI selectedSeq = (SequenceI) tbl_local_pdb
                     .getValueAt(row, refSeqColIndex);
@@ -1106,7 +1093,7 @@ public class StructureChooser extends GStructureChooser
           PDBEntry fileEntry = new AssociatePdbFileWithSeq()
                   .associatePdbWithSeq(selectedPdbFileName,
                           DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
+                          Desktop.getInstance());
 
           sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
                   ap, new SequenceI[]
@@ -1355,7 +1342,6 @@ public class StructureChooser extends GStructureChooser
         {
           fetchStructuresMetaData();
           // populateFilterComboBox(true, cachedPDBExists);
-
           filterResultSet(
                   ((FilterOption) cmb_filterOption.getSelectedItem())
                           .getValue());
@@ -1481,6 +1467,12 @@ 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)