osx pixel tweak

[jalview.git] / src / jalview / jbgui / GPreferences.java

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 7bd8f53..c6e9bf7 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -193,6 +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();
 
@@ -305,12 +307,24 @@ public class GPreferences extends JPanel
     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.LEADING);
     annotations.setSelected(true);
     annotations.setText("Show Annotations");
-    annotations.setBounds(new Rectangle(169, 16, 200, 23));
+    annotations.setBounds(new Rectangle(169, 12, 200, 23));
     annotations.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -335,7 +349,6 @@ public class GPreferences extends JPanel
     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()
@@ -345,10 +358,10 @@ 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);
-    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
     shareSelections.setSelected(true);
     shareSelections.setText("Share selection across views");
     followHighlight.setFont(verdana11);
@@ -370,13 +383,13 @@ public class GPreferences extends JPanel
     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     fontLabel.setText("Font ");
     fontSizeCB.setFont(verdana11);
-    fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
+    fontSizeCB.setBounds(new Rectangle(319, 104, 49, 23));
     fontStyleCB.setFont(verdana11);
-    fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
+    fontStyleCB.setBounds(new Rectangle(367, 104, 70, 23));
     fontNameCB.setFont(verdana11);
-    fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
+    fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
     gapSymbolCB.setFont(verdana11);
-    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
+    gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -506,11 +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));
-    //jPanel3.setBounds(new Rectangle(173, 35, 274, 78));
-    //jPanel3.setLayout(new GridLayout(3,3));
-//    autoAnnotSettings1.setBounds(new Rectangle(173,53,274,26));// new Rectangle(173, 116, 274, 78));
-//    autoAnnotSettings2.setBounds(new Rectangle(173,72,274,26));
     exportTab.setLayout(null);
     epsLabel.setFont(verdana11);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -607,18 +615,15 @@ public class GPreferences extends JPanel
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
-    annsettingsPanel.setBounds(new Rectangle(173,39,300,62));
+    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));
-//  autoAnnotSettings1.setPreferredSize(new Dimensions())
   autoAnnotSettings2.setLayout(new GridLayout(3,1,0,0));
   autoAnnotSettings3.setLayout(new GridLayout(3,1,0,0));
     visualTab.add(annsettingsPanel);
-    //visualTab.add(autoAnnotSettings1);
-    //visualTab.add(autoAnnotSettings2);
     Border jb = new EmptyBorder(1,1,4,5);
     quality.setBorder(jb);
     conservation.setBorder(jb);
@@ -633,19 +638,20 @@ public class GPreferences extends JPanel
     autoAnnotSettings2.add(conservation);
     autoAnnotSettings1.add(quality);
     autoAnnotSettings3.add(identity);
-
-    /*FlowLayout fl = new FlowLayout();
-    fl.setAlignment(FlowLayout.LEFT);
-    autoAnnotSettings1.setLayout(fl);
-    fl = new FlowLayout();
-    fl.setAlignment(FlowLayout.LEFT);
-    autoAnnotSettings2.setLayout(fl); */
-    autoAnnotSettings1.add(showGroupbits);
+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);