JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 510ce78..347c1b2 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -75,7 +75,6 @@ public class StructureChooser extends GStructureChooser
 
   private boolean isValidPBDEntry;
 
-
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -210,7 +209,8 @@ public class StructureChooser extends GStructureChooser
       if (seq.getDatasetSequence() != null
               && seq.getDatasetSequence().getAllPDBEntries() != null)
       {
-        for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
+        for (PDBEntry pdbEntry : seq.getDatasetSequence()
+                .getAllPDBEntries())
         {
           if (pdbEntry.getFile() != null)
           {
@@ -224,7 +224,6 @@ public class StructureChooser extends GStructureChooser
     tbl_local_pdb.setModel(tableModelx);
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -390,14 +389,12 @@ public class StructureChooser extends GStructureChooser
           // Update table selection model here
           tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
           mainFrame.setTitle(MessageManager.formatMessage(
-                  "label.structure_chooser_filter_time",
- totalTime));
+                  "label.structure_chooser_filter_time", totalTime));
         }
         else
         {
           mainFrame.setTitle(MessageManager.formatMessage(
-                  "label.structure_chooser_filter_time",
- totalTime));
+                  "label.structure_chooser_filter_time", totalTime));
           if (errors.size() > 0)
           {
             StringBuilder errorMsg = new StringBuilder();
@@ -405,7 +402,9 @@ public class StructureChooser extends GStructureChooser
             {
               errorMsg.append(error).append("\n");
             }
-            JOptionPane.showMessageDialog(null, errorMsg.toString(),
+            JOptionPane.showMessageDialog(
+                    null,
+                    errorMsg.toString(),
                     MessageManager.getString("label.pdb_web-service_error"),
                     JOptionPane.ERROR_MESSAGE);
           }
@@ -546,9 +545,9 @@ public class StructureChooser extends GStructureChooser
     lbl_pdbManualFetchStatus.setToolTipText("");
     if (txt_search.getText().length() > 0)
     {
-      lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
-              true, MessageManager.formatMessage(
-                      "info.no_pdb_entry_found_for",
+      lbl_pdbManualFetchStatus
+              .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+                      .formatMessage("info.no_pdb_entry_found_for",
                               txt_search.getText())));
     }
 
@@ -715,11 +714,9 @@ public class StructureChooser extends GStructureChooser
         selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
       }
 
-      PDBEntry[] pdbEntriesToView = new PDBEntry[]
-      { pdbEntry };
+      PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
       launchStructureViewer(ap.getStructureSelectionManager(),
-              pdbEntriesToView, ap, new SequenceI[]
-              { selectedSequence });
+              pdbEntriesToView, ap, new SequenceI[] { selectedSequence });
     }
     else if (currentView == VIEWS_FROM_FILE)
     {
@@ -735,9 +732,8 @@ public class StructureChooser extends GStructureChooser
                       selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
-              new PDBEntry[]
-              { fileEntry }, ap, new SequenceI[]
-              { selectedSequence });
+              new PDBEntry[] { fileEntry }, ap,
+              new SequenceI[] { selectedSequence });
     }
     mainFrame.dispose();
   }
@@ -756,8 +752,7 @@ public class StructureChooser extends GStructureChooser
           ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
           for (SequenceI seq : sequences)
           {
-            seqsMap.add(new SequenceI[]
-            { seq });
+            seqsMap.add(new SequenceI[] { seq });
           }
           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
           sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
@@ -820,40 +815,40 @@ public class StructureChooser extends GStructureChooser
     {
       public void run()
       {
-    errorWarning.setLength(0);
-    isValidPBDEntry = false;
-    if (txt_search.getText().length() > 0)
-    {
-      List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
-      wantedFields.add(PDBDocField.PDB_ID);
-      PDBRestRequest pdbRequest = new PDBRestRequest();
-      pdbRequest.setAllowEmptySeq(false);
-      pdbRequest.setResponseSize(1);
-      pdbRequest.setFieldToSearchBy("(pdb_id:");
-      pdbRequest.setWantedFields(wantedFields);
-      pdbRequest.setSearchTerm(txt_search.getText() + ")");
-      pdbRequest.setAssociatedSequence(selectedSequence);
-      pdbRestCleint = new PDBRestClient();
-      PDBRestResponse resultList;
-      try
-      {
-        resultList = pdbRestCleint.executeRequest(pdbRequest);
-      } catch (Exception e)
-      {
-        errorWarning.append(e.getMessage());
-        return;
-      } finally
-      {
+        errorWarning.setLength(0);
+        isValidPBDEntry = false;
+        if (txt_search.getText().length() > 0)
+        {
+          List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+          wantedFields.add(PDBDocField.PDB_ID);
+          PDBRestRequest pdbRequest = new PDBRestRequest();
+          pdbRequest.setAllowEmptySeq(false);
+          pdbRequest.setResponseSize(1);
+          pdbRequest.setFieldToSearchBy("(pdb_id:");
+          pdbRequest.setWantedFields(wantedFields);
+          pdbRequest.setSearchTerm(txt_search.getText() + ")");
+          pdbRequest.setAssociatedSequence(selectedSequence);
+          pdbRestCleint = new PDBRestClient();
+          PDBRestResponse resultList;
+          try
+          {
+            resultList = pdbRestCleint.executeRequest(pdbRequest);
+          } catch (Exception e)
+          {
+            errorWarning.append(e.getMessage());
+            return;
+          } finally
+          {
+            validateSelections();
+          }
+          if (resultList.getSearchSummary() != null
+                  && resultList.getSearchSummary().size() > 0)
+          {
+            isValidPBDEntry = true;
+          }
+        }
         validateSelections();
       }
-      if (resultList.getSearchSummary() != null
-              && resultList.getSearchSummary().size() > 0)
-      {
-        isValidPBDEntry = true;
-      }
-    }
-    validateSelections();
-      }
     }.start();
   }
 
@@ -878,8 +873,7 @@ public class StructureChooser extends GStructureChooser
 
   public class PDBEntryTableModel extends AbstractTableModel
   {
-    String[] columns =
-    { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+    String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
 
     private List<CachedPDB> pdbEntries;