From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 5 Aug 2015 17:11:15 +0000 (+0100)
Subject: JAL-1821 formatting
X-Git-Tag: Release_2_10_0~549^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=85f67b4d7015ad29dca4ccc2fef961439b784cb0;p=jalview.git

JAL-1821 formatting
---

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5e7ea48..23b688c 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -49,7 +49,6 @@ import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
-
 /**
  * Provides the behaviors for the Structure chooser Panel
  * 
@@ -189,8 +188,7 @@ public class StructureChooser extends GStructureChooser
     }
     else
     {
-      mainFrame
-.setTitle("Structure Chooser - Manual association");
+      mainFrame.setTitle("Structure Chooser - Manual association");
       if (errors.size() > 0)
       {
         StringBuilder errorMsg = new StringBuilder();
@@ -232,16 +230,13 @@ public class StructureChooser extends GStructureChooser
           String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                   .getChainCode();
           Object[] pdbEntryRowData = new Object[]
-          { seq, pdbEntry.getId(),
- chain,
-              pdbEntry.getType(),
+          { seq, pdbEntry.getId(), chain, pdbEntry.getType(),
               pdbEntry.getFile() };
           if (pdbEntry.getFile() != null)
           {
             tableModel.addRow(pdbEntryRowData);
           }
-          cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
-                  pdbEntry);
+          cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry);
         }
       }
     }
@@ -461,7 +456,6 @@ public class StructureChooser extends GStructureChooser
     filterThread.start();
   }
 
-
   /**
    * Handles action event for btn_pdbFromFile
    */
@@ -628,8 +622,7 @@ public class StructureChooser extends GStructureChooser
             .getCmb_assSeq().getSelectedItem();
     lbl_fromFileStatus.setIcon(errorImage);
     if (selectedSequences.length == 1
-            || (assSeqOpt != null
-            && !assSeqOpt.getName().equalsIgnoreCase(
+            || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
                     "-Select Associated Seq-")))
     {
       btn_pdbFromFile.setEnabled(true);
@@ -713,7 +706,8 @@ public class StructureChooser extends GStructureChooser
       launchStructureViewer(ap.getStructureSelectionManager(),
               pdbEntriesToView, ap, selectedSeqs);
     }
-    else if(currentView == VIEWS_LOCAL_PDB){
+    else if (currentView == VIEWS_LOCAL_PDB)
+    {
       int[] selectedRows = tbl_local_pdb.getSelectedRows();
       PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
       int count = 0;
@@ -725,8 +719,7 @@ public class StructureChooser extends GStructureChooser
       for (int row : selectedRows)
       {
         String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
-                .toString()
-                .toLowerCase();
+                .toString().toLowerCase();
         pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
         SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
                 refSeqColIndex);
@@ -771,9 +764,9 @@ public class StructureChooser extends GStructureChooser
         selectedSequence = userSelectedSeq;
       }
       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-              .associatePdbWithSeq(
-              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
-              selectedSequence, true, Desktop.instance);
+              .associatePdbWithSeq(selectedPdbFileName,
+                      jalview.io.AppletFormatAdapter.FILE,
+                      selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
               new PDBEntry[]