JAL-3368 JAL-2365 JAL-2642

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index cb09b7c..d9bac9e 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -72,7 +72,7 @@ public class StructureChooser extends GStructureChooser
 
   protected SequenceI selectedSequence;
 
-  public SequenceI[] selectedSequences;
+  SequenceI[] selectedSequences;
 
   private IProgressIndicator progressIndicator;
 
@@ -143,20 +143,22 @@ public class StructureChooser extends GStructureChooser
    */
   protected void discoverStructureViews()
   {
-    if (Desktop.getInstance() != null)
+    Desktop desktop = Desktop.getInstance();
+    if (desktop != null)
     {
       targetView.removeAllItems();
-      Desktop d = Desktop.getInstance();
-      if (d.lastTargetedView != null && !d.lastTargetedView.isVisible())
+      if (desktop.lastTargetedView != null
+              && !desktop.lastTargetedView.isVisible())
       {
-        d.lastTargetedView = null;
+        desktop.lastTargetedView = null;
       }
       int linkedViewsAt = 0;
-      for (StructureViewerBase view : Desktop.getInstance()
+      for (StructureViewerBase view : desktop
               .getStructureViewers(null, null))
       {
-        StructureViewer viewHandler = (d.lastTargetedView != null
-                && d.lastTargetedView.sview == view) ? d.lastTargetedView
+        StructureViewer viewHandler = (desktop.lastTargetedView != null
+                && desktop.lastTargetedView.sview == view)
+                        ? desktop.lastTargetedView
                         : StructureViewer.reconfigure(view);
 
         if (view.isLinkedWith(ap))
@@ -177,9 +179,9 @@ public class StructureChooser extends GStructureChooser
       if (targetView.getItemCount() > 0)
       {
         targetView.setVisible(true);
-        if (d.lastTargetedView != null)
+        if (desktop.lastTargetedView != null)
         {
-          targetView.setSelectedItem(d.lastTargetedView);
+          targetView.setSelectedItem(desktop.lastTargetedView);
         }
         else
         {
@@ -1125,53 +1127,53 @@ public class StructureChooser extends GStructureChooser
   protected void txt_search_ActionPerformed()
   {
     String text = txt_search.getText().trim();
-       if (text.length() >= PDB_ID_MIN)
-  {
-    new Thread()
+    if (text.length() >= PDB_ID_MIN)
     {
-
-       @Override
-      public void run()
+      new Thread()
       {
-        errorWarning.setLength(0);
-        isValidPBDEntry = false;
-        if (text.length() > 0)
+
+        @Override
+        public void run()
         {
-          String searchTerm = text.toLowerCase();
-          searchTerm = searchTerm.split(":")[0];
-          // System.out.println(">>>>> search term : " + searchTerm);
-          List<FTSDataColumnI> wantedFields = new ArrayList<>();
-          FTSRestRequest pdbRequest = new FTSRestRequest();
-          pdbRequest.setAllowEmptySeq(false);
-          pdbRequest.setResponseSize(1);
-          pdbRequest.setFieldToSearchBy("(pdb_id:");
-          pdbRequest.setWantedFields(wantedFields);
-          pdbRequest.setSearchTerm(searchTerm + ")");
-          pdbRequest.setAssociatedSequence(selectedSequence);
-          pdbRestClient = PDBFTSRestClient.getInstance();
-          wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
-          FTSRestResponse resultList;
-          try
-          {
-            resultList = pdbRestClient.executeRequest(pdbRequest);
-          } catch (Exception e)
+          errorWarning.setLength(0);
+          isValidPBDEntry = false;
+          if (text.length() > 0)
           {
-            errorWarning.append(e.getMessage());
-            return;
-          } finally
-          {
-            validateSelections();
-          }
-          if (resultList.getSearchSummary() != null
-                  && resultList.getSearchSummary().size() > 0)
-          {
-            isValidPBDEntry = true;
+            String searchTerm = text.toLowerCase();
+            searchTerm = searchTerm.split(":")[0];
+            // System.out.println(">>>>> search term : " + searchTerm);
+            List<FTSDataColumnI> wantedFields = new ArrayList<>();
+            FTSRestRequest pdbRequest = new FTSRestRequest();
+            pdbRequest.setAllowEmptySeq(false);
+            pdbRequest.setResponseSize(1);
+            pdbRequest.setFieldToSearchBy("(pdb_id:");
+            pdbRequest.setWantedFields(wantedFields);
+            pdbRequest.setSearchTerm(searchTerm + ")");
+            pdbRequest.setAssociatedSequence(selectedSequence);
+            pdbRestClient = PDBFTSRestClient.getInstance();
+            wantedFields.add(pdbRestClient.getPrimaryKeyColumn());
+            FTSRestResponse resultList;
+            try
+            {
+              resultList = pdbRestClient.executeRequest(pdbRequest);
+            } catch (Exception e)
+            {
+              errorWarning.append(e.getMessage());
+              return;
+            } finally
+            {
+              validateSelections();
+            }
+            if (resultList.getSearchSummary() != null
+                    && resultList.getSearchSummary().size() > 0)
+            {
+              isValidPBDEntry = true;
+            }
           }
+          validateSelections();
         }
-        validateSelections();
-      }
-    }.start();
-  }
+      }.start();
+    }
   }
 
   @Override