JAL-1479 implemented preferences for SIFTs / Needleman & Wunsch selection in structur...

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 54370d8..e576678 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1279,3 +1279,6 @@ exception.pdb_rest_service_no_longer_available = PDB rest services no longer ava
 exception.resource_not_be_found = The requested resource could not be found
 exception.pdb_server_error = There seems to be an error from the PDB server
 exception.pdb_server_unreachable = Jalview is unable to reach the PDBe Solr server. \nPlease ensure that you are connected to the internet and try again.
+label.nw_mapping = Needleman & Wunsch Alignment
+label.sifts_mapping = SIFTs Mapping
+label.mapping_method = Sequence \u27f7 Structure mapping method
\ No newline at end of file

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 5cb6512..885a62f 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -313,6 +313,15 @@ public class Preferences extends GPreferences
       }
     });
 
+    if (Cache.getDefault("MAP_WITH_SIFTS", false))
+    {
+      siftsMapping.setSelected(true);
+    }
+    else
+    {
+      nwMapping.setSelected(true);
+    }
+
     /*
      * Set Connections tab defaults
      */
@@ -384,6 +393,7 @@ public class Preferences extends GPreferences
    * 
    * @param e
    */
+  @Override
   public void ok_actionPerformed(ActionEvent e)
   {
     if (!validateSettings())
@@ -492,6 +502,8 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
             .getSelectedItem().toString());
     Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
+            Boolean.toString(siftsMapping.isSelected()));
 
     /*
      * Save Output settings
@@ -647,6 +659,7 @@ public class Preferences extends GPreferences
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void startupFileTextfield_mouseClicked()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -676,6 +689,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
@@ -694,6 +708,7 @@ public class Preferences extends GPreferences
    * @param e
    *          DOCUMENT ME!
    */
+  @Override
   public void annotations_actionPerformed(ActionEvent e)
   {
     conservation.setEnabled(annotations.isSelected());
@@ -707,6 +722,7 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
   }
 
+  @Override
   public void newLink_actionPerformed(ActionEvent e)
   {
 
@@ -733,6 +749,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void editLink_actionPerformed(ActionEvent e)
   {
     GSequenceLink link = new GSequenceLink();
@@ -774,6 +791,7 @@ public class Preferences extends GPreferences
     }
   }
 
+  @Override
   public void deleteLink_actionPerformed(ActionEvent e)
   {
     int index = linkNameList.getSelectedIndex();
@@ -796,6 +814,7 @@ public class Preferences extends GPreferences
     linkURLList.setListData(urlLinks);
   }
 
+  @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
@@ -818,6 +837,7 @@ public class Preferences extends GPreferences
    * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+  @Override
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index b12355a..b5c1804 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -44,6 +44,7 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 
 import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
 import javax.swing.DefaultListCellRenderer;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
@@ -52,6 +53,7 @@ import javax.swing.JFileChooser;
 import javax.swing.JLabel;
 import javax.swing.JList;
 import javax.swing.JPanel;
+import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
 import javax.swing.JTextField;
@@ -156,6 +158,12 @@ public class GPreferences extends JPanel
 
   protected JTextField chimeraPath = new JTextField();
 
+  protected ButtonGroup mappingMethod = new ButtonGroup();
+
+  protected JRadioButton siftsMapping = new JRadioButton();
+
+  protected JRadioButton nwMapping = new JRadioButton();
+
   /*
    * Colours tab components
    */
@@ -509,6 +517,7 @@ public class GPreferences extends JPanel
     newLink.setText(MessageManager.getString("action.new"));
     newLink.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         newLink_actionPerformed(e);
@@ -518,6 +527,7 @@ public class GPreferences extends JPanel
     editLink.setText(MessageManager.getString("action.edit"));
     editLink.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         editLink_actionPerformed(e);
@@ -527,6 +537,7 @@ public class GPreferences extends JPanel
     deleteLink.setText(MessageManager.getString("action.delete"));
     deleteLink.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         deleteLink_actionPerformed(e);
@@ -535,6 +546,7 @@ public class GPreferences extends JPanel
 
     linkURLList.addListSelectionListener(new ListSelectionListener()
     {
+      @Override
       public void valueChanged(ListSelectionEvent e)
       {
         int index = linkURLList.getSelectedIndex();
@@ -544,6 +556,7 @@ public class GPreferences extends JPanel
 
     linkNameList.addListSelectionListener(new ListSelectionListener()
     {
+      @Override
       public void valueChanged(ListSelectionEvent e)
       {
         int index = linkNameList.getSelectedIndex();
@@ -571,6 +584,7 @@ public class GPreferences extends JPanel
 
     defaultBrowser.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseClicked(MouseEvent e)
       {
         if (e.getClickCount() > 1)
@@ -585,6 +599,7 @@ public class GPreferences extends JPanel
     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
     useProxy.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         useProxy_actionPerformed();
@@ -653,6 +668,7 @@ public class GPreferences extends JPanel
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_actionPerformed(e);
@@ -662,6 +678,7 @@ public class GPreferences extends JPanel
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancel_actionPerformed(e);
@@ -693,6 +710,7 @@ public class GPreferences extends JPanel
     minColour.setPreferredSize(new Dimension(40, 20));
     minColour.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         minColour_actionPerformed(minColour);
@@ -707,6 +725,7 @@ public class GPreferences extends JPanel
     maxColour.setPreferredSize(new Dimension(40, 20));
     maxColour.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         maxColour_actionPerformed(maxColour);
@@ -764,7 +783,7 @@ public class GPreferences extends JPanel
     final int width = 400;
     final int height = 22;
     final int lineSpacing = 25;
-    int ypos = 30;
+    int ypos = 15;
 
     structFromPdb.setFont(LABEL_FONT);
     structFromPdb
@@ -859,13 +878,30 @@ public class GPreferences extends JPanel
     structureTab.add(chimeraPath);
 
     ypos += lineSpacing;
-    // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
-    // scrl_pdbDocFieldConfig
-    // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
-    // scrl_pdbDocFieldConfig.setBounds();
+    nwMapping.setFont(LABEL_FONT);
+    nwMapping.setText(MessageManager.getString("label.nw_mapping"));
+    siftsMapping.setFont(LABEL_FONT);
+    siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
+    mappingMethod.add(nwMapping);
+    mappingMethod.add(siftsMapping);
+    JPanel mappingPanel = new JPanel();
+    mappingPanel.setFont(LABEL_FONT);
+    TitledBorder mmTitledBorder = new TitledBorder(
+            MessageManager.getString("label.mapping_method"));
+    mmTitledBorder.setTitleFont(LABEL_FONT);
+    mappingPanel.setBorder(mmTitledBorder);
+    mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
+    // GridLayout mappingLayout = new GridLayout();
+    mappingPanel.setLayout(new GridLayout());
+    mappingPanel.add(nwMapping);
+    mappingPanel.add(siftsMapping);
+    structureTab.add(mappingPanel);
+
+    ypos += lineSpacing;
+    ypos += lineSpacing;
     PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
             PreferenceSource.PREFERENCES);
-    docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+    docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
     structureTab.add(docFieldPref);
 
     return structureTab;
@@ -1018,6 +1054,7 @@ public class GPreferences extends JPanel
     annotations.setBounds(new Rectangle(169, 12, 200, 23));
     annotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotations_actionPerformed(e);
@@ -1025,6 +1062,7 @@ public class GPreferences extends JPanel
     });
     identity.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotations_actionPerformed(e);
@@ -1032,6 +1070,7 @@ public class GPreferences extends JPanel
     });
     showGroupConsensus.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotations_actionPerformed(e);
@@ -1045,6 +1084,7 @@ public class GPreferences extends JPanel
             .getString("action.show_unconserved"));
     showUnconserved.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showunconserved_actionPerformed(e);
@@ -1112,6 +1152,7 @@ public class GPreferences extends JPanel
     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
     startupFileTextfield.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseClicked(MouseEvent e)
       {
         if (e.getClickCount() > 1)