JAL-2050 only hide introns if exons are present! Removed 'hide introns'

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

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 0aafe50..b5c1804 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -110,8 +110,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox wrap = new JCheckBox();
 
-  protected JCheckBox hideIntrons = new JCheckBox();
-
   protected JComboBox<String> sortby = new JComboBox<String>();
 
   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
@@ -1151,7 +1149,7 @@ public class GPreferences extends JPanel
     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
     startupCheckbox.setSelected(true);
     startupFileTextfield.setFont(LABEL_FONT);
-    startupFileTextfield.setBounds(new Rectangle(173, 328, 330, 20));
+    startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
     startupFileTextfield.addMouseListener(new MouseAdapter()
     {
       @Override
@@ -1165,19 +1163,19 @@ public class GPreferences extends JPanel
     });
 
     sortby.setFont(LABEL_FONT);
-    sortby.setBounds(new Rectangle(172, 280, 155, 20));
+    sortby.setBounds(new Rectangle(172, 260, 155, 21));
     JLabel sortLabel = new JLabel();
     sortLabel.setFont(LABEL_FONT);
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     sortLabel.setText(MessageManager.getString("label.sort_by"));
     sortAnnBy.setFont(LABEL_FONT);
-    sortAnnBy.setBounds(new Rectangle(172, 305, 110, 20));
+    sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
     JLabel sortAnnLabel = new JLabel();
     sortAnnLabel.setFont(LABEL_FONT);
     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
     sortAutocalc.setFont(LABEL_FONT);
-    sortAutocalc.setBounds(new Rectangle(290, 305, 165, 20));
+    sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
 
     JPanel annsettingsPanel = new JPanel();
     annsettingsPanel.setBounds(new Rectangle(173, 34, 320, 75));
@@ -1221,12 +1219,6 @@ public class GPreferences extends JPanel
     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
     wrap.setText(MessageManager.getString("label.wrap_alignment"));
-    hideIntrons.setFont(LABEL_FONT);
-    hideIntrons.setHorizontalAlignment(SwingConstants.TRAILING);
-    hideIntrons.setHorizontalTextPosition(SwingConstants.LEADING);
-    hideIntrons.setText(MessageManager.getString("label.hide_introns"));
-    hideIntrons.setToolTipText(MessageManager
-            .getString("label.hide_introns_tip"));
     rightAlign.setFont(LABEL_FONT);
     rightAlign.setForeground(Color.black);
     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -1244,8 +1236,8 @@ public class GPreferences extends JPanel
     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
     openoverv.setText(MessageManager.getString(("label.open_overview")));
     JPanel jPanel2 = new JPanel();
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 330));
-    jPanel2.setLayout(new GridLayout(15, 1));
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
+    jPanel2.setLayout(new GridLayout(14, 1));
     jPanel2.add(fullScreen);
     jPanel2.add(openoverv);
     jPanel2.add(seqLimit);
@@ -1257,7 +1249,6 @@ public class GPreferences extends JPanel
     jPanel2.add(scaleProteinToCdna);
     jPanel2.add(gapLabel);
     jPanel2.add(wrap);
-    jPanel2.add(hideIntrons);
     jPanel2.add(sortLabel);
     jPanel2.add(sortAnnLabel);
     jPanel2.add(startupCheckbox);