From b1613533d44e86c95bb2ae1e1428330b314df1f6 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@STO24954W.ad.stolaf.edu>
Date: Mon, 8 Apr 2019 23:38:21 -0500
Subject: [PATCH] code formatting only

---
 .../fts/service/uniprot/UniProtFTSRestClient.java  |    5 +-
 src/jalview/gui/FeatureSettings.java               |  158 ++++++++++----------
 2 files changed, 85 insertions(+), 78 deletions(-)

diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index ae8f6e5..3f0b8a4 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -47,10 +47,11 @@ public class UniProtFTSRestClient extends FTSRestClient
 {
   private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
 
-  static {
+  static
+  {
     Platform.addJ2SDirectDatabaseCall(DEFAULT_UNIPROT_DOMAIN);
   }
-  
+
   private static FTSRestClientI instance = null;
 
   public final String uniprotSearchEndpoint;
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 872fe15..f81ecce 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -131,7 +131,8 @@ public class FeatureSettings extends JPanel
 
   private static final int MIN_HEIGHT = 400;
 
-  private final static String BASE_TOOLTIP = MessageManager.getString("label.click_to_edit");
+  private final static String BASE_TOOLTIP = MessageManager
+          .getString("label.click_to_edit");
 
   final FeatureRenderer fr;
 
@@ -231,10 +232,9 @@ public class FeatureSettings extends JPanel
         default:
           break;
         }
-        
+
         return tip;
       }
-      
 
       /**
        * Position the tooltip near the bottom edge of, and half way across, the
@@ -261,7 +261,7 @@ public class FeatureSettings extends JPanel
 
     table.setDefaultEditor(FeatureMatcherSet.class, new FilterEditor());
     table.setDefaultRenderer(FeatureMatcherSet.class, new FilterRenderer());
-    
+
     TableColumn colourColumn = new TableColumn(COLOUR_COLUMN, 75,
             new ColorRenderer(), new ColorEditor());
     table.addColumn(colourColumn);
@@ -385,15 +385,15 @@ public class FeatureSettings extends JPanel
     inConstruction = false;
   }
 
-  	/**
-	 * Constructs and shows a popup menu of possible actions on the selected row and
-	 * feature type
-	 * 
-	 * @param rowSelected
-	 * @param type
-	 * @param typeCol
-	 * @param pt
-	 */
+  /**
+   * Constructs and shows a popup menu of possible actions on the selected row
+   * and feature type
+   * 
+   * @param rowSelected
+   * @param type
+   * @param typeCol
+   * @param pt
+   */
   protected void showPopupMenu(final int rowSelected, final String type,
           final Object typeCol, final Point pt)
   {
@@ -409,7 +409,7 @@ public class FeatureSettings extends JPanel
             MessageManager.getString("label.variable_colour"));
     variableColourCB.setSelected(!featureColour.isSimpleColour());
     men.add(variableColourCB);
-    
+
     /*
      * checkbox action listener doubles up as listener to OK
      * from the variable colour / filters dialog
@@ -421,8 +421,10 @@ public class FeatureSettings extends JPanel
       {
         if (e.getSource() == variableColourCB)
         {
-          men.setVisible(true); // BH 2018 for JavaScript because this is a checkbox
-          men.setVisible(false); // BH 2018 for JavaScript because this is a checkbox
+          men.setVisible(true); // BH 2018 for JavaScript because this is a
+                                // checkbox
+          men.setVisible(false); // BH 2018 for JavaScript because this is a
+                                 // checkbox
           if (featureColour.isSimpleColour())
           {
             /*
@@ -436,7 +438,8 @@ public class FeatureSettings extends JPanel
             /*
              * toggle variable to simple colour - show colour chooser
              */
-            String title = MessageManager.formatMessage("label.select_colour_for", type);
+            String title = MessageManager
+                    .formatMessage("label.select_colour_for", type);
             ColourChooserListener listener = new ColourChooserListener()
             {
               @Override
@@ -450,11 +453,11 @@ public class FeatureSettings extends JPanel
                         false);
               }
             };
-            JalviewColourChooser.showColourChooser(FeatureSettings.this, title,
-            	featureColour.getMaxColour(), listener);
+            JalviewColourChooser.showColourChooser(FeatureSettings.this,
+                    title, featureColour.getMaxColour(), listener);
           }
         }
-        else    
+        else
         {
           if (e.getSource() instanceof FeatureTypeSettings)
           {
@@ -465,13 +468,13 @@ public class FeatureSettings extends JPanel
             FeatureColourI fci = fr.getFeatureColours().get(type);
             table.setValueAt(fci, rowSelected, COLOUR_COLUMN);
             // BH 2018 setting a table value does not invalidate it.
-//	            System.out.println("FeatureSettings is valied" + table.isValid());
-//	            table.validate();
+            // System.out.println("FeatureSettings is valied" +
+            // table.validate();
           }
         }
       }
     });
-    
+
     men.addSeparator();
 
     JMenuItem scr = new JMenuItem(
@@ -760,8 +763,8 @@ public class FeatureSettings extends JPanel
   }
 
   /**
-   * Updates 'originalData' (used for restore on Cancel) if we detect that changes
-   * have been made outwith this dialog
+   * Updates 'originalData' (used for restore on Cancel) if we detect that
+   * changes have been made outwith this dialog
    * <ul>
    * <li>a new feature type added (and made visible)</li>
    * <li>a feature colour changed (in the Amend Features dialog)</li>
@@ -825,8 +828,8 @@ public class FeatureSettings extends JPanel
 
   /**
    * Remove from the groups panel any checkboxes for groups that are not in the
-   * foundGroups set. This enables removing a group from the display when the last
-   * feature in that group is deleted.
+   * foundGroups set. This enables removing a group from the display when the
+   * last feature in that group is deleted.
    * 
    * @param foundGroups
    */
@@ -883,13 +886,13 @@ public class FeatureSettings extends JPanel
     chooser.setToolTipText(MessageManager.getString("action.load"));
     chooser.setResponseHandler(0, new Runnable()
     {
-	  @Override
-	  public void run() 
-	  {
-	    File file = chooser.getSelectedFile();
-		load(file);
-	  }
-	});
+      @Override
+      public void run()
+      {
+        File file = chooser.getSelectedFile();
+        load(file);
+      }
+    });
     chooser.showOpenDialog(this);
   }
 
@@ -950,8 +953,7 @@ public class FeatureSettings extends JPanel
       if (table != null)
       {
         resetTable(null);
-        Object[][] data = ((FeatureTableModel) table.getModel())
-                .getData();
+        Object[][] data = ((FeatureTableModel) table.getModel()).getData();
         ensureOrder(data);
         updateFeatureRenderer(data, false);
         table.repaint();
@@ -975,11 +977,11 @@ public class FeatureSettings extends JPanel
             MessageManager.getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
     int option = chooser.showSaveDialog(this);
-	if (option == JalviewFileChooser.APPROVE_OPTION) 
-	{
-	  File file = chooser.getSelectedFile();
-	  save(file);
-	}
+    if (option == JalviewFileChooser.APPROVE_OPTION)
+    {
+      File file = chooser.getSelectedFile();
+      save(file);
+    }
   }
 
   /**
@@ -993,8 +995,8 @@ public class FeatureSettings extends JPanel
     ucs.setSchemeName("Sequence Features");
     try
     {
-      PrintWriter out = new PrintWriter(new OutputStreamWriter(
-              new FileOutputStream(file), "UTF-8"));
+      PrintWriter out = new PrintWriter(
+              new OutputStreamWriter(new FileOutputStream(file), "UTF-8"));
 
       /*
        * sort feature types by colour order, from 0 (highest)
@@ -1031,11 +1033,11 @@ public class FeatureSettings extends JPanel
         FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
         if (filter != null && !filter.isEmpty())
         {
-          Iterator<FeatureMatcherI> iterator = filter.getMatchers().iterator();
+          Iterator<FeatureMatcherI> iterator = filter.getMatchers()
+                  .iterator();
           FeatureMatcherI firstMatcher = iterator.next();
           jalview.xml.binding.jalview.FeatureMatcherSet ms = jalview.project.Jalview2XML
-                  .marshalFilter(firstMatcher, iterator,
-                  filter.isAnded());
+                  .marshalFilter(firstMatcher, iterator, filter.isAnded());
           Filter filterModel = new Filter();
           filterModel.setFeatureType(featureType);
           filterModel.setMatcherSet(ms);
@@ -1117,7 +1119,8 @@ public class FeatureSettings extends JPanel
       else
       {
         width[i] /= max; // normalize
-        fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for later
+        fr.setOrder(data[i][TYPE_COLUMN].toString(), width[i]); // store for
+                                                                // later
       }
       if (i > 0)
       {
@@ -1151,8 +1154,8 @@ public class FeatureSettings extends JPanel
   }
 
   /**
-   * Update the priority order of features; only repaint if this changed the order
-   * of visible features
+   * Update the priority order of features; only repaint if this changed the
+   * order of visible features
    * 
    * @param data
    * @param visibleNew
@@ -1389,7 +1392,7 @@ public class FeatureSettings extends JPanel
   {
     boolean thr = false;
     StringBuilder tx = new StringBuilder();
-  
+
     if (gcol.isColourByAttribute())
     {
       tx.append(FeatureMatcher
@@ -1647,7 +1650,7 @@ public class FeatureSettings extends JPanel
   }
 
   @SuppressWarnings("serial")
-class ColorEditor extends AbstractCellEditor
+  class ColorEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
     FeatureColourI currentColor;
@@ -1688,8 +1691,9 @@ class ColorEditor extends AbstractCellEditor
           /*
            * simple colour chooser
            */
-          String ttl = MessageManager.formatMessage("label.select_colour_for", type);
-          ColourChooserListener listener = new ColourChooserListener() 
+          String ttl = MessageManager
+                  .formatMessage("label.select_colour_for", type);
+          ColourChooserListener listener = new ColourChooserListener()
           {
             @Override
             public void colourSelected(Color c)
@@ -1698,13 +1702,15 @@ class ColorEditor extends AbstractCellEditor
               table.setValueAt(currentColor, rowSelected, COLOUR_COLUMN);
               fireEditingStopped();
             }
-			@Override
-			public void cancel() 
-			{
-	          fireEditingStopped();
-			}
+
+            @Override
+            public void cancel()
+            {
+              fireEditingStopped();
+            }
           };
-          JalviewColourChooser.showColourChooser(button,  ttl,  currentColor.getColour(), listener);
+          JalviewColourChooser.showColourChooser(button, ttl,
+                  currentColor.getColour(), listener);
         }
         else
         {
@@ -1744,7 +1750,7 @@ class ColorEditor extends AbstractCellEditor
         data[COLOUR_COLUMN] = currentColor;
         data[FILTER_COLUMN] = currentFilter;
         fireEditingStopped();
-        // SwingJS needs an explicit repaint() here, 
+        // SwingJS needs an explicit repaint() here,
         // rather than relying upon no validation having
         // occurred since the stopEditing call was made.
         // Its laying out has not been stopped by the modal frame
@@ -1754,15 +1760,15 @@ class ColorEditor extends AbstractCellEditor
     }
 
     /**
-     * Override allows access to this method from anonymous inner classes 
+     * Override allows access to this method from anonymous inner classes
      */
     @Override
-	protected void fireEditingStopped() 
+    protected void fireEditingStopped()
     {
-	    super.fireEditingStopped();
-	}
+      super.fireEditingStopped();
+    }
 
-	// Implement the one CellEditor method that AbstractCellEditor doesn't.
+    // Implement the one CellEditor method that AbstractCellEditor doesn't.
     @Override
     public Object getCellEditorValue()
     {
@@ -1771,8 +1777,8 @@ class ColorEditor extends AbstractCellEditor
 
     // Implement the one method defined by TableCellEditor.
     @Override
-    public Component getTableCellEditorComponent(JTable theTable, Object value,
-            boolean isSelected, int row, int column)
+    public Component getTableCellEditorComponent(JTable theTable,
+            Object value, boolean isSelected, int row, int column)
     {
       currentColor = (FeatureColourI) value;
       this.rowSelected = row;
@@ -1800,12 +1806,12 @@ class ColorEditor extends AbstractCellEditor
 
   /**
    * The cell editor for the Filter column. It displays the text of any filters
-   * for the feature type in that row (in full as a tooltip, possible abbreviated
-   * as display text). On click in the cell, opens the Feature Display Settings
-   * dialog at the Filters tab.
+   * for the feature type in that row (in full as a tooltip, possible
+   * abbreviated as display text). On click in the cell, opens the Feature
+   * Display Settings dialog at the Filters tab.
    */
   @SuppressWarnings("serial")
-class FilterEditor extends AbstractCellEditor
+  class FilterEditor extends AbstractCellEditor
           implements TableCellEditor, ActionListener
   {
 
@@ -1864,13 +1870,13 @@ class FilterEditor extends AbstractCellEditor
         {
           currentFilter = new FeatureMatcherSet();
         }
-        
+
         Object[] data = ((FeatureTableModel) table.getModel())
                 .getData()[rowSelected];
         data[COLOUR_COLUMN] = currentColor;
         data[FILTER_COLUMN] = currentFilter;
         fireEditingStopped();
-        // SwingJS needs an explicit repaint() here, 
+        // SwingJS needs an explicit repaint() here,
         // rather than relying upon no validation having
         // occurred since the stopEditing call was made.
         // Its laying out has not been stopped by the modal frame
@@ -1886,8 +1892,8 @@ class FilterEditor extends AbstractCellEditor
     }
 
     @Override
-    public Component getTableCellEditorComponent(JTable theTable, Object value,
-            boolean isSelected, int row, int column)
+    public Component getTableCellEditorComponent(JTable theTable,
+            Object value, boolean isSelected, int row, int column)
     {
       currentFilter = (FeatureMatcherSetI) value;
       this.rowSelected = row;
@@ -1978,7 +1984,7 @@ class FeatureIcon implements Icon
         g.fillRect(s1, 0, e1 - s1, height);
       }
       g.setColor(gcol.getMaxColour());
-//      g.fillRect(0, e1, width - e1, height);  // BH 2018
+      // g.fillRect(0, e1, width - e1, height); // BH 2018
       g.fillRect(e1, 0, width - e1, height);
     }
   }
-- 
1.7.10.2