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[jalview.git] / src / jalview / jbgui / GPreferences.java
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 58c7743..27a54d7 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -24,7 +24,9 @@ import javax.swing.*;
 import javax.swing.border.TitledBorder;\r
 import java.awt.event.*;\r
 import javax.swing.event.*;\r
-\r
+import java.awt.Font;\r
+import java.awt.Rectangle;\r
+import java.awt.Insets;\r
 \r
 /**\r
  * DOCUMENT ME!\r
@@ -106,6 +108,11 @@ public class GPreferences extends JPanel
   protected JCheckBox smoothFont = new JCheckBox();\r
   JPanel calcTab = new JPanel();\r
   protected JCheckBox autoCalculateConsCheck = new JCheckBox();\r
+  protected JCheckBox padGaps = new JCheckBox();\r
+  protected JCheckBox modellerOutput = new JCheckBox();\r
+  protected JPanel dasPanel = new JPanel();\r
+  BorderLayout borderLayout4 = new BorderLayout();\r
+  protected JCheckBox wrap = new JCheckBox();\r
   /**\r
      * Creates a new GPreferences object.\r
      */\r
@@ -173,7 +180,7 @@ public class GPreferences extends JPanel
     annotations.setFont(verdana11);\r
         annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
         annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
-    annotations.setMargin(new Insets(2, 4, 2, 0));\r
+    annotations.setMargin(new Insets(2, 2, 2, 0));\r
     annotations.setSelected(true);\r
         annotations.setText("Show Annotations");\r
     annotations.addActionListener(new ActionListener()\r
@@ -187,7 +194,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         gapLabel.setText("Gap Symbol ");\r
     colour.setFont(verdana11);\r
-        colour.setBounds(new Rectangle(171, 180, 155, 21));\r
+        colour.setBounds(new Rectangle(172, 188, 155, 21));\r
         colourLabel.setFont(verdana11);\r
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         colourLabel.setText("Colour ");\r
@@ -195,13 +202,13 @@ public class GPreferences extends JPanel
         fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         fontLabel.setText("Font ");\r
     fontSizeCB.setFont(verdana11);\r
-        fontSizeCB.setBounds(new Rectangle(318, 100, 49, 21));\r
+        fontSizeCB.setBounds(new Rectangle(317, 92, 49, 21));\r
         fontStyleCB.setFont(verdana11);\r
-        fontStyleCB.setBounds(new Rectangle(366, 100, 70, 21));\r
+        fontStyleCB.setBounds(new Rectangle(364, 92, 70, 21));\r
         fontNameCB.setFont(verdana11);\r
-        fontNameCB.setBounds(new Rectangle(171, 100, 147, 21));\r
+        fontNameCB.setBounds(new Rectangle(171, 92, 147, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(171, 153, 69, 21));\r
+        gapSymbolCB.setBounds(new Rectangle(172, 163, 69, 21));\r
         startupCheckbox.setText("Open file");\r
     startupCheckbox.setFont(verdana11);\r
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -306,14 +313,14 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(171, 208, 155, 21));\r
+    sortby.setBounds(new Rectangle(171, 213, 155, 21));\r
     sortLabel.setFont(verdana11);\r
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
     sortLabel.setText("Sort by ");\r
     jPanel2.setBounds(new Rectangle(7, 17, 158, 245));\r
     jPanel2.setLayout(gridLayout2);\r
-    gridLayout2.setRows(9);\r
-    jPanel3.setBounds(new Rectangle(167, 41, 274, 26));\r
+    gridLayout2.setRows(10);\r
+    jPanel3.setBounds(new Rectangle(169, 39, 274, 26));\r
     exportTab.setLayout(null);\r
     epsLabel.setFont(verdana11);\r
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
@@ -353,6 +360,7 @@ public class GPreferences extends JPanel
     seqLimit.setFont(verdana11);\r
     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);\r
+    seqLimit.setMargin(new Insets(2, 2, 2, 0));\r
     seqLimit.setText("Full Sequence Id");\r
     gridLayout3.setRows(8);\r
     smoothFont.setFont(verdana11);\r
@@ -360,26 +368,39 @@ public class GPreferences extends JPanel
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);\r
     smoothFont.setText("Smooth Font");\r
     calcTab.setLayout(null);\r
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
     autoCalculateConsCheck.setText("AutoCalculate Consensus");\r
-    autoCalculateConsCheck.setBounds(new Rectangle(16, 29, 209, 23));\r
+    autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));\r
+    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    padGaps.setText("Pad gaps when editing");\r
+    padGaps.setBounds(new Rectangle(22, 94, 168, 23));\r
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    modellerOutput.setText("Use Modeller Output");\r
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));\r
+    dasPanel.setLayout(borderLayout4);\r
+    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    wrap.setHorizontalAlignment(SwingConstants.TRAILING);\r
+    wrap.setHorizontalTextPosition(SwingConstants.LEADING);\r
+    wrap.setText("Wrap Alignment");\r
     jPanel2.add(fullScreen);\r
 \r
     jPanel2.add(annotations);\r
     jPanel2.add(seqLimit);\r
     jPanel2.add(fontLabel);\r
     jPanel2.add(smoothFont);\r
+    jPanel2.add(wrap);\r
     jPanel2.add(gapLabel);\r
     jPanel2.add(colourLabel);\r
     jPanel2.add(sortLabel);\r
     jPanel2.add(startupCheckbox);\r
-    visualTab.add(colour);\r
-    visualTab.add(gapSymbolCB);\r
-    visualTab.add(startupFileTextfield);\r
     visualTab.add(sortby);\r
+    visualTab.add(gapSymbolCB);\r
+    visualTab.add(colour);\r
     visualTab.add(fontNameCB);\r
     visualTab.add(fontSizeCB);\r
     visualTab.add(fontStyleCB);\r
     visualTab.add(jPanel3);\r
+    visualTab.add(startupFileTextfield);\r
     jPanel3.add(conservation);\r
     jPanel3.add(identity);\r
     jPanel3.add(quality);\r
@@ -444,8 +465,11 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);\r
     jPanel11.add(pileupjv);\r
     jPanel11.add(pirjv);\r
-    tabbedPane.add(calcTab, "Calculations");\r
+    exportTab.add(modellerOutput);\r
+    tabbedPane.add(calcTab, "Editing");\r
     calcTab.add(autoCalculateConsCheck);\r
+    calcTab.add(padGaps);\r
+    tabbedPane.add(dasPanel, "DAS Settings");\r
 \r
     exportTab.add(epsLabel);\r
     exportTab.add(epsRendering);\r