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Merge branch 'develop' into features/JAL-2446NCList
[jalview.git] / src / jalview / gui / Preferences.java
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index cccdd2e..c3c9239 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -213,18 +213,18 @@ public class Preferences extends GPreferences
     showUnconserved
             .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
     showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
-    showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
-            false));
-    showGroupConservation.setSelected(Cache.getDefault(
-            "SHOW_GROUP_CONSERVATION", false));
-    showConsensHistogram.setSelected(Cache.getDefault(
-            "SHOW_CONSENSUS_HISTOGRAM", true));
-    showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
-            false));
-    showNpTooltip.setSelected(Cache
-            .getDefault("SHOW_NPFEATS_TOOLTIP", true));
-    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
-            true));
+    showGroupConsensus
+            .setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS", false));
+    showGroupConservation.setSelected(
+            Cache.getDefault("SHOW_GROUP_CONSERVATION", false));
+    showConsensHistogram.setSelected(
+            Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
+    showConsensLogo
+            .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+    showNpTooltip
+            .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip
+            .setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
 
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
@@ -244,12 +244,12 @@ public class Preferences extends GPreferences
 
     fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
     fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
-    fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
-            + ""));
+    fontStyleCB.setSelectedItem(
+            Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
-    scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
-            false));
+    scaleProteinToCdna
+            .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
@@ -303,10 +303,10 @@ public class Preferences extends GPreferences
     protColour.setSelectedItem(newProp != null ? newProp : oldProp);
     newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
     nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
-    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
-            Color.orange));
-    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
-            Color.red));
+    minColour.setBackground(
+            Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(
+            Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 
     /*
      * Set Structure tab defaults.
@@ -319,8 +319,8 @@ public class Preferences extends GPreferences
     addSecondaryStructure.setEnabled(structSelected);
     addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
     addTempFactor.setEnabled(structSelected);
-    structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
-            ViewerType.JMOL.name()));
+    structViewer.setSelectedItem(
+            Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
     chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
     chimeraPath.addActionListener(new ActionListener()
     {
@@ -359,12 +359,12 @@ public class Preferences extends GPreferences
             SortOrder.DESCENDING));
     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
             SortOrder.DESCENDING));
-    sortKeys.add(new RowSorter.SortKey(m.getNameColumn(),
-            SortOrder.ASCENDING));
+    sortKeys.add(
+            new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 
     sorter.setSortKeys(sortKeys);
     sorter.sort();
-    
+
     // set up filtering
     ActionListener onReset;
     onReset = new ActionListener()
@@ -413,35 +413,35 @@ public class Preferences extends GPreferences
       @Override
       public void changedUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
 
       @Override
       public void removeUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
 
       @Override
       public void insertUpdate(DocumentEvent e)
       {
-        sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag
-                + filterTB.getText()));
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
       }
     });
 
     // set up list selection functionality
-    linkUrlTable.getSelectionModel().addListSelectionListener(
-            new UrlListSelectionHandler());
+    linkUrlTable.getSelectionModel()
+            .addListSelectionListener(new UrlListSelectionHandler());
 
     // set up radio buttons
     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
             .getPrimaryColumn();
     String onClickName = linkUrlTable.getColumnName(onClickCol);
-    linkUrlTable.getColumn(onClickName).setCellRenderer(
-               new RadioButtonRenderer());
+    linkUrlTable.getColumn(onClickName)
+            .setCellRenderer(new RadioButtonRenderer());
     linkUrlTable.getColumn(onClickName)
             .setCellEditor(new RadioButtonEditor());
 
@@ -451,8 +451,8 @@ public class Preferences extends GPreferences
       if (linkUrlTable.getModel().getColumnClass(column)
               .equals(Boolean.class))
       {
-        TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn(
-                column);
+        TableColumn tableColumn = linkUrlTable.getColumnModel()
+                .getColumn(column);
         int preferredWidth = tableColumn.getMinWidth();
 
         TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
@@ -512,14 +512,14 @@ public class Preferences extends GPreferences
     pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
     pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
     modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
-    embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
-            true));
+    embbedBioJSON
+            .setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON", true));
 
     /*
      * Set Editing tab defaults
      */
-    autoCalculateConsCheck.setSelected(Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
+    autoCalculateConsCheck
+            .setSelected(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
     sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
 
@@ -561,15 +561,15 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.toString(identity.isSelected()));
 
-    Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("GAP_SYMBOL",
+            gapSymbolCB.getSelectedItem().toString());
 
-    Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_NAME",
+            fontNameCB.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_STYLE",
+            fontStyleCB.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("FONT_SIZE",
+            fontSizeCB.getSelectedItem().toString());
 
     Cache.applicationProperties.setProperty("ID_ITALICS",
             Boolean.toString(idItalics.isSelected()));
@@ -602,8 +602,8 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
             Boolean.toString(startupCheckbox.isSelected()));
 
-    Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty("SORT_ALIGNMENT",
+            sortby.getSelectedItem().toString());
 
     // convert description of sort order to enum name for save
     SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
@@ -615,16 +615,16 @@ public class Preferences extends GPreferences
     }
 
     final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
-    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
-            .valueOf(showAutocalcFirst).toString());
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE,
+            Boolean.valueOf(showAutocalcFirst).toString());
 
     /*
      * Save Colours settings
      */
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
-            .getSelectedItem().toString());
-    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT,
+            protColour.getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC,
+            nucColour.getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
@@ -641,8 +641,8 @@ public class Preferences extends GPreferences
             Boolean.toString(useRnaView.isSelected()));
     Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
             Boolean.toString(structFromPdb.isSelected()));
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
-            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
+            structViewer.getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
@@ -804,11 +804,11 @@ public class Preferences extends GPreferences
   public void startupFileTextfield_mouseClicked()
   {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-    JalviewFileChooser chooser = JalviewFileChooser.forRead(
-            Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+    JalviewFileChooser chooser = JalviewFileChooser
+            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager
-            .getString("label.select_startup_file"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_startup_file"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -820,8 +820,8 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
                 format.getName());
       }
-      startupFileTextfield.setText(chooser.getSelectedFile()
-              .getAbsolutePath());
+      startupFileTextfield
+              .setText(chooser.getSelectedFile().getAbsolutePath());
     }
   }
 
@@ -874,15 +874,16 @@ public class Preferences extends GPreferences
     {
       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.new_sequence_url_link"),
-              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
           if (((UrlLinkTableModel) linkUrlTable.getModel())
                   .isUniqueName(link.getName()))
           {
-            ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow(
-                    link.getName(), link.getURL());
+            ((UrlLinkTableModel) linkUrlTable.getModel())
+                    .insertRow(link.getName(), link.getURL());
             valid = true;
           }
           else
@@ -925,7 +926,8 @@ public class Preferences extends GPreferences
     {
       if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
               MessageManager.getString("label.edit_sequence_url_link"),
-              JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION)
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -971,13 +973,12 @@ public class Preferences extends GPreferences
     ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
   }
 
-
   @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(MessageManager
-            .getString("label.select_default_browser"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_default_browser"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -1050,8 +1051,9 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
-              .getString("warn.user_defined_width_requirements"),
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager
+                      .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
               JvOptionPane.WARNING_MESSAGE);
       userIdWidth.setText("");
@@ -1115,8 +1117,7 @@ public class Preferences extends GPreferences
     if (!found)
     {
       String[] options = { "OK", "Help" };
-      int showHelp = JvOptionPane.showInternalOptionDialog(
-              Desktop.desktop,
+      int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
                       MessageManager.getString("label.chimera_missing")),
               "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
@@ -1188,7 +1189,7 @@ public class Preferences extends GPreferences
       return name.hashCode() + code.hashCode();
     }
   }
-  
+
   private class UrlListSelectionHandler implements ListSelectionListener
   {
 
@@ -1228,5 +1229,5 @@ public class Preferences extends GPreferences
         editLink.setEnabled(false);
       }
     }
-}
+  }
 }