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jog pixels for OSX
[jalview.git] / src / jalview / jbgui / GPreferences.java
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 7b2e5c4..105f28f 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -136,7 +136,11 @@ public class GPreferences extends JPanel
 
   GridLayout gridLayout2 = new GridLayout();
 
-  JPanel jPanel3 = new JPanel();
+
+  JPanel annsettingsPanel = new JPanel();
+  JPanel autoAnnotSettings1 = new JPanel();
+  JPanel autoAnnotSettings2 = new JPanel();
+  JPanel autoAnnotSettings3 = new JPanel();
 
   JPanel exportTab = new JPanel();
 
@@ -189,6 +193,8 @@ public class GPreferences extends JPanel
   protected JCheckBox rightAlign = new JCheckBox();
 
   protected JCheckBox showUnconserved = new JCheckBox();
+  protected JCheckBox showDbRefTooltip = new JCheckBox();
+  protected JCheckBox showNpTooltip = new JCheckBox();
 
   protected JCheckBox idItalics = new JCheckBox();
 
@@ -196,6 +202,15 @@ public class GPreferences extends JPanel
   protected JCheckBox usagestats = new JCheckBox(); 
   protected JCheckBox questionnaire = new JCheckBox();
   protected JCheckBox versioncheck = new JCheckBox();
+  protected JLabel showGroupbits = new JLabel();
+  protected JLabel showConsensbits = new JLabel();
+  protected JCheckBox showConsensLogo = new JCheckBox();
+  protected JCheckBox showConsensHistogram = new JCheckBox();
+  protected JCheckBox showGroupConsensus = new JCheckBox();
+  protected JCheckBox showGroupConservation = new JCheckBox();
+  protected JCheckBox shareSelections = new JCheckBox();
+  protected JCheckBox followHighlight = new JCheckBox();
+  
 
   /**
    * Creates a new GPreferences object.
@@ -260,11 +275,56 @@ public class GPreferences extends JPanel
     identity.setHorizontalTextPosition(SwingConstants.LEFT);
     identity.setSelected(true);
     identity.setText("Consensus");
+    showGroupbits.setFont(verdana11);
+    showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
+    showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
+    showGroupbits.setText("Show group:");
+    showConsensbits.setFont(verdana11);
+    showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
+    showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
+    showConsensbits.setText("Consensus:");
+    showConsensHistogram.setEnabled(false);
+    showConsensHistogram.setFont(verdana11);
+    showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
+    showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
+    showConsensHistogram.setSelected(true);
+    showConsensHistogram.setText("Histogram");
+    showConsensLogo.setEnabled(false);
+    showConsensLogo.setFont(verdana11);
+    showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
+    showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
+    showConsensLogo.setSelected(true);
+    showConsensLogo.setText("Logo");
+    showGroupConsensus.setEnabled(false);
+    showGroupConsensus.setFont(verdana11);
+    showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
+    showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
+    showGroupConsensus.setSelected(true);
+    showGroupConsensus.setText("Consensus");
+    showGroupConservation.setEnabled(false);
+    showGroupConservation.setFont(verdana11);
+    showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
+    showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
+    showGroupConservation.setSelected(true);
+    showGroupConservation.setText("Conservation");
+    showNpTooltip.setEnabled(true);
+    showNpTooltip.setFont(verdana11);
+    showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+    showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+    showNpTooltip.setSelected(true);
+    showNpTooltip.setText("Non-positional Features");
+    showDbRefTooltip.setEnabled(true);
+    showDbRefTooltip.setFont(verdana11);
+    showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
+    showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
+    showDbRefTooltip.setSelected(true);
+    showDbRefTooltip.setText("Database References");
     annotations.setFont(verdana11);
     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
-    annotations.setHorizontalTextPosition(SwingConstants.LEFT);
+    annotations.setHorizontalTextPosition(SwingConstants.LEADING);
     annotations.setSelected(true);
     annotations.setText("Show Annotations");
+    annotations.setBounds(new Rectangle(169, 14, 200, 23));
     annotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -272,10 +332,23 @@ public class GPreferences extends JPanel
         annotations_actionPerformed(e);
       }
     });
+    identity.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          annotations_actionPerformed(e);
+        }
+      }); 
+    showGroupConsensus.addActionListener(new ActionListener()
+      {
+        public void actionPerformed(ActionEvent e)
+        {
+          annotations_actionPerformed(e);
+        }
+      });
     showUnconserved.setFont(verdana11);
     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
-    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
     showUnconserved.setSelected(true);
     showUnconserved.setText("Show Unconserved");
     showUnconserved.addActionListener(new ActionListener()
@@ -285,6 +358,18 @@ public class GPreferences extends JPanel
         showunconserved_actionPerformed(e);
       }
     });
+    /// TODO: fit these in to preferences panel!!!!!
+    shareSelections.setFont(verdana11);
+    shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
+    shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
+    shareSelections.setSelected(true);
+    shareSelections.setText("Share selection across views");
+    followHighlight.setFont(verdana11);
+    followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
+    followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
+    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+    followHighlight.setSelected(true);
+    followHighlight.setText("Scroll to highlighted regions");
     
     gapLabel.setFont(verdana11);
     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -434,7 +519,6 @@ public class GPreferences extends JPanel
     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
     jPanel2.setLayout(gridLayout2);
     gridLayout2.setRows(13);
-    jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
     exportTab.setLayout(null);
     epsLabel.setFont(verdana11);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -508,11 +592,10 @@ public class GPreferences extends JPanel
     openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     openoverv.setActionCommand("Open Overview");
     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
-    openoverv.setHorizontalTextPosition(SwingConstants.LEADING);
-    openoverv.setText("Open Overview Window");
-    openoverv.setBounds(new Rectangle(169, 17, 200, 23));
+    openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
+    openoverv.setText("Open Overview");
     jPanel2.add(fullScreen);
-    jPanel2.add(annotations);
+    jPanel2.add(openoverv);
     jPanel2.add(seqLimit);
     jPanel2.add(rightAlign);
     jPanel2.add(fontLabel);
@@ -524,18 +607,51 @@ public class GPreferences extends JPanel
     jPanel2.add(colourLabel);
     jPanel2.add(sortLabel);
     jPanel2.add(startupCheckbox);
-    visualTab.add(openoverv);
+    visualTab.add(annotations);
     visualTab.add(startupFileTextfield);
     visualTab.add(sortby);
     visualTab.add(colour);
     visualTab.add(gapSymbolCB);
-    visualTab.add(jPanel3);
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
-    jPanel3.add(conservation);
-    jPanel3.add(identity);
-    jPanel3.add(quality);
+    annsettingsPanel.setBounds(new Rectangle(173,34,300,61));
+    annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT,0,0));
+    annsettingsPanel.add(autoAnnotSettings1);
+    annsettingsPanel.add(autoAnnotSettings2);
+    annsettingsPanel.add(autoAnnotSettings3);
+    autoAnnotSettings1.setLayout(new GridLayout(3,1,0,0));
+  autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
+  autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
+    visualTab.add(annsettingsPanel);
+    Border jb = new EmptyBorder(1,1,4,5);
+    quality.setBorder(jb);
+    conservation.setBorder(jb);
+    identity.setBorder(jb);
+    showConsensbits.setBorder(jb);
+    showGroupbits.setBorder(jb);
+    showGroupConsensus.setBorder(jb);
+    showGroupConservation.setBorder(jb);
+    showConsensHistogram.setBorder(jb);
+    showConsensLogo.setBorder(jb);
+    
+    autoAnnotSettings2.add(conservation);
+    autoAnnotSettings1.add(quality);
+    autoAnnotSettings3.add(identity);
+autoAnnotSettings1.add(showGroupbits);
+    autoAnnotSettings3.add(showGroupConsensus);
+    autoAnnotSettings2.add(showGroupConservation);
+    autoAnnotSettings1.add(showConsensbits);
+    autoAnnotSettings2.add(showConsensHistogram);
+    autoAnnotSettings3.add(showConsensLogo);
+
+    JPanel tooltipSettings = new JPanel();
+    tooltipSettings.setBorder(new TitledBorder("Sequence ID Tooltip"));
+    tooltipSettings.setBounds(173, 130, 200,62);
+    tooltipSettings.setLayout(new GridLayout(2,1));
+    tooltipSettings.add(showDbRefTooltip);
+    tooltipSettings.add(showNpTooltip);
+    visualTab.add(tooltipSettings);
     visualTab.add(jPanel2);
 
     linkPanel.add(editLinkButtons, BorderLayout.EAST);