JAL-2527 Started adding overview preferences

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 162f10f..9c6f75b 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1311,3 +1311,10 @@ label.occupancy_descr = Number of aligned positions
 label.show_experimental = Enable experimental features
 label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
 label.warning_hidden = Warning: {0} {1} is currently hidden
+label.overview_settings = Overview settings
+label.ov_legacy_gap = Use legacy gap colouring (gaps are white)
+label.gap_colour = Gap colour
+label.ov_show_hide_default = Show hidden regions when opening overview
+label.hidden_colour = Hidden colour
+label.select_gap_colour = Gap colour
+label.select_hidden_colour = Hidden colour

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 8385142..9fb2fc5 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1311,3 +1311,10 @@ label.togglehidden = Mostrar regiones ocultas
 label.show_experimental = Habilitar funciones experimentales
 label.show_experimental_tip = Habilitar funciones nuevas y experimentales (ver Latest Release Notes para más detalles)
 label.warning_hidden = Advertencia: {0} {1} está actualmente oculto
+label.overview_settings = Overview settings
+label.ov_legacy_gap = Use legacy gap colouring (gaps are white)
+label.gap_colour = Gap colour
+label.ov_show_hide_default = Show hidden regions when opening overview
+label.hidden_colour = Hidden colour
+label.select_gap_colour = Gap colour
+label.select_hidden_colour = Hidden colour
\ No newline at end of file

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c3c9239..6fdaa0d 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -54,6 +54,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import javax.help.HelpSetException;
+import javax.swing.JButton;
 import javax.swing.JColorChooser;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
@@ -155,7 +156,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<String>();
+    groupURLLinks = new ArrayList<>();
   }
 
   JInternalFrame frame;
@@ -307,6 +308,10 @@ public class Preferences extends GPreferences
             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
     maxColour.setBackground(
             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+    gapColour.setBackground(
+            Cache.getDefaultColour("GAP_COLOUR", Color.lightGray));
+    hiddenColour.setBackground(
+            Cache.getDefaultColour("HIDDEN_COLOUR", Color.darkGray));
 
     /*
      * Set Structure tab defaults.
@@ -1035,6 +1040,32 @@ public class Preferences extends GPreferences
   }
 
   @Override
+  public void gapColour_actionPerformed(JButton btn)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_gap_colour"),
+            gapColour.getForeground());
+    if (col != null)
+    {
+      btn.setForeground(col);
+    }
+    btn.repaint();
+  }
+
+  @Override
+  public void hiddenColour_actionPerformed(JButton btn)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_hidden_colour"),
+            hiddenColour.getForeground());
+    if (col != null)
+    {
+      btn.setForeground(col);
+    }
+    btn.repaint();
+  }
+
+  @Override
   protected void userIdWidth_actionPerformed()
   {
     try

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 633d2b8..a58569a 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -95,11 +95,11 @@ public class GPreferences extends JPanel
 
   protected JCheckBox rightAlign = new JCheckBox();
 
-  protected JComboBox<String> fontSizeCB = new JComboBox<String>();
+  protected JComboBox<String> fontSizeCB = new JComboBox<>();
 
-  protected JComboBox<String> fontStyleCB = new JComboBox<String>();
+  protected JComboBox<String> fontStyleCB = new JComboBox<>();
 
-  protected JComboBox<String> fontNameCB = new JComboBox<String>();
+  protected JComboBox<String> fontNameCB = new JComboBox<>();
 
   protected JCheckBox showOccupancy = new JCheckBox();
 
@@ -111,15 +111,15 @@ public class GPreferences extends JPanel
 
   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 
-  protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
+  protected JComboBox<String> gapSymbolCB = new JComboBox<>();
 
   protected JCheckBox wrap = new JCheckBox();
 
-  protected JComboBox<String> sortby = new JComboBox<String>();
+  protected JComboBox<String> sortby = new JComboBox<>();
 
-  protected JComboBox<String> sortAnnBy = new JComboBox<String>();
+  protected JComboBox<String> sortAnnBy = new JComboBox<>();
 
-  protected JComboBox<String> sortAutocalc = new JComboBox<String>();
+  protected JComboBox<String> sortAutocalc = new JComboBox<>();
 
   protected JCheckBox startupCheckbox = new JCheckBox();
 
@@ -159,7 +159,7 @@ public class GPreferences extends JPanel
 
   protected JCheckBox addTempFactor = new JCheckBox();
 
-  protected JComboBox<String> structViewer = new JComboBox<String>();
+  protected JComboBox<String> structViewer = new JComboBox<>();
 
   protected JTextField chimeraPath = new JTextField();
 
@@ -176,9 +176,13 @@ public class GPreferences extends JPanel
 
   protected JPanel maxColour = new JPanel();
 
-  protected JComboBox<String> protColour = new JComboBox<String>();
+  protected JComboBox<String> protColour = new JComboBox<>();
 
-  protected JComboBox<String> nucColour = new JComboBox<String>();
+  protected JComboBox<String> nucColour = new JComboBox<>();
+
+  protected JButton gapColour = new JButton();
+
+  protected JButton hiddenColour = new JButton();
 
   /*
    * Connections tab components
@@ -216,7 +220,7 @@ public class GPreferences extends JPanel
   /*
    * Output tab components
    */
-  protected JComboBox<Object> epsRendering = new JComboBox<Object>();
+  protected JComboBox<Object> epsRendering = new JComboBox<>();
 
   protected JLabel userIdWidthlabel = new JLabel();
 
@@ -888,9 +892,10 @@ public class GPreferences extends JPanel
   private JPanel initColoursTab()
   {
     JPanel coloursTab = new JPanel();
-    coloursTab.setBorder(new TitledBorder(
+    JPanel alignmentPanel = new JPanel();
+    alignmentPanel.setBorder(new TitledBorder(
             MessageManager.getString("action.open_new_alignment")));
-    coloursTab.setLayout(new FlowLayout());
+    alignmentPanel.setLayout(new FlowLayout());
     JLabel mincolourLabel = new JLabel();
     mincolourLabel.setFont(LABEL_FONT);
     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -929,7 +934,7 @@ public class GPreferences extends JPanel
     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     protColourLabel.setText(
             MessageManager.getString("label.prot_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    JvSwingUtils.addtoLayout(alignmentPanel,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             protColourLabel, protColour);
@@ -941,7 +946,7 @@ public class GPreferences extends JPanel
     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     nucColourLabel.setText(
             MessageManager.getString("label.nuc_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    JvSwingUtils.addtoLayout(alignmentPanel,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             nucColourLabel, nucColour);
@@ -958,7 +963,107 @@ public class GPreferences extends JPanel
             MessageManager.getString(
                     "label.default_maximum_colour_annotation_shading"),
             maxcolourLabel, maxColour);
-    coloursTab.add(annotationShding); // , FlowLayout.LEFT);
+    alignmentPanel.add(annotationShding); // , FlowLayout.LEFT);
+
+    JPanel overviewPanel = new JPanel();
+    overviewPanel.setBorder(new TitledBorder(
+            MessageManager.getString("label.overview_settings")));
+    overviewPanel.setLayout(new FlowLayout());
+
+    gapColour.setFont(LABEL_FONT);
+    gapColour.setBorder(BorderFactory.createEtchedBorder());
+    gapColour.setPreferredSize(new Dimension(40, 20));
+    gapColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        gapColour_actionPerformed(gapColour);
+      }
+    });
+
+    hiddenColour.setFont(LABEL_FONT);
+    hiddenColour.setBorder(BorderFactory.createEtchedBorder());
+    hiddenColour.setPreferredSize(new Dimension(40, 20));
+    hiddenColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        hiddenColour_actionPerformed(hiddenColour);
+      }
+    });
+    
+    JCheckBox gapSetting = new JCheckBox(
+            MessageManager.getString("label.ov_legacy_gap"));
+    gapSetting.setFont(LABEL_FONT);
+    gapSetting.setHorizontalAlignment(SwingConstants.LEFT);
+    JLabel gapLabel = new JLabel(
+            MessageManager.getString("label.gap_colour"));
+    gapLabel.setFont(LABEL_FONT);
+    gapLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    JCheckBox hiddenSetting = new JCheckBox(
+            MessageManager.getString("label.ov_show_hide_default"));
+    hiddenSetting.setFont(LABEL_FONT);
+    hiddenSetting.setHorizontalAlignment(SwingConstants.LEFT);
+    JLabel hiddenLabel = new JLabel(
+            MessageManager.getString("label.hidden_colour"));
+    hiddenLabel.setFont(LABEL_FONT);
+    hiddenLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+    overviewPanel.setLayout(new GridBagLayout());
+    GridBagConstraints c1 = new GridBagConstraints();
+
+    c1.fill = GridBagConstraints.HORIZONTAL;
+    c1.gridx = 0;
+    c1.gridy = 0;
+    c1.weightx = 1;
+    c1.anchor = GridBagConstraints.FIRST_LINE_START;
+    overviewPanel.add(gapSetting, c1);
+
+    GridBagConstraints c2 = new GridBagConstraints();
+    c2.fill = GridBagConstraints.HORIZONTAL;
+    c2.gridx = 1;
+    c2.gridy = 0;
+    c2.insets = new Insets(0, 5, 0, 5);
+    overviewPanel.add(gapLabel, c2);
+
+    GridBagConstraints c3 = new GridBagConstraints();
+    c3.fill = GridBagConstraints.HORIZONTAL;
+    c3.gridx = 2;
+    c3.gridy = 0;
+    overviewPanel.add(gapColour, c3);
+
+    GridBagConstraints c4 = new GridBagConstraints();
+    c4.fill = GridBagConstraints.HORIZONTAL;
+    c4.gridx = 0;
+    c4.gridy = 1;
+    c4.weightx = 1;
+    overviewPanel.add(hiddenSetting, c4);
+
+    GridBagConstraints c5 = new GridBagConstraints();
+    c5.fill = GridBagConstraints.HORIZONTAL;
+    c5.gridx = 1;
+    c5.gridy = 1;
+    c5.insets = new Insets(0, 5, 0, 5);
+    overviewPanel.add(hiddenLabel, c5);
+
+    GridBagConstraints c6 = new GridBagConstraints();
+    c6.fill = GridBagConstraints.HORIZONTAL;
+    c6.gridx = 2;
+    c6.gridy = 1;
+    overviewPanel.add(hiddenColour, c6);
+
+    // Add padding so the panel doesn't look ridiculous
+    JPanel spacePanel = new JPanel();
+    overviewPanel.add(spacePanel,
+            new GridBagConstraints(0, 2, 1, 1, 1.0, 1.0,
+                    GridBagConstraints.WEST, GridBagConstraints.BOTH,
+                    new Insets(0, 0, 0, 5), 0, 0));
+
+    coloursTab.setLayout(new GridLayout(2, 1));
+    coloursTab.add(alignmentPanel);
+    coloursTab.add(overviewPanel);
     return coloursTab;
   }
 
@@ -1494,6 +1599,14 @@ public class GPreferences extends JPanel
   {
   }
 
+  protected void gapColour_actionPerformed(JButton btn)
+  {
+  }
+
+  protected void hiddenColour_actionPerformed(JButton btn)
+  {
+  }
+
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub