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imported Vamsas bindings and alpha vamsas client code from VamJalview cvs branch...
[jalview.git] / src / jalview / jbgui / GPreferences.java
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 2001efd..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
@@ -103,6 +105,14 @@ public class GPreferences extends JPanel
   Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
   protected JCheckBox seqLimit = new JCheckBox();\r
   GridLayout gridLayout3 = new GridLayout();\r
+  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
@@ -170,7 +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
@@ -184,7 +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(170, 170, 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
@@ -192,20 +202,20 @@ public class GPreferences extends JPanel
         fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
         fontLabel.setText("Font ");\r
     fontSizeCB.setFont(verdana11);\r
-        fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));\r
+        fontSizeCB.setBounds(new Rectangle(317, 92, 49, 21));\r
         fontStyleCB.setFont(verdana11);\r
-        fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
+        fontStyleCB.setBounds(new Rectangle(364, 92, 70, 21));\r
         fontNameCB.setFont(verdana11);\r
-        fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));\r
+        fontNameCB.setBounds(new Rectangle(171, 92, 147, 21));\r
         gapSymbolCB.setFont(verdana11);\r
-        gapSymbolCB.setBounds(new Rectangle(170, 141, 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
         startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
         startupCheckbox.setSelected(true);\r
         startupFileTextfield.setFont(verdana11);\r
-        startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));\r
+        startupFileTextfield.setBounds(new Rectangle(171, 236, 270, 20));\r
         startupFileTextfield.addMouseListener(new MouseAdapter()\r
             {\r
                 public void mouseClicked(MouseEvent e)\r
@@ -273,7 +283,7 @@ public class GPreferences extends JPanel
     linkPanel.setLayout(borderLayout2);\r
     editLinkButtons.setLayout(gridLayout1);\r
     gridLayout1.setRows(3);\r
-    linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+    linkNameList.setFont(verdana11);\r
     linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
     linkPanel2.setLayout(borderLayout3);\r
     linkURLList.setFont(verdana11);\r
@@ -303,14 +313,14 @@ public class GPreferences extends JPanel
     jPanel1.setBorder(titledBorder1);\r
     jPanel1.setLayout(gridBagLayout1);\r
     sortby.setFont(verdana11);\r
-    sortby.setBounds(new Rectangle(170, 200, 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, 242));\r
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 245));\r
     jPanel2.setLayout(gridLayout2);\r
-    gridLayout2.setRows(8);\r
-    jPanel3.setBounds(new Rectangle(168, 47, 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
@@ -333,7 +343,7 @@ public class GPreferences extends JPanel
     msfjv.setFont(verdana11);\r
     msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     pirjv.setText("PIR     ");\r
-    jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    jPanel11.setFont(verdana11);\r
     jPanel11.setBorder(titledBorder2);\r
     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
     jPanel11.setLayout(gridLayout3);\r
@@ -347,30 +357,53 @@ public class GPreferences extends JPanel
     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
     pirjv.setFont(verdana11);\r
     pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
-    seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+    seqLimit.setFont(verdana11);\r
     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
-    seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);\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
+    smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);\r
+    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(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(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
-    visualTab.add(sortby);\r
-    visualTab.add(startupFileTextfield);\r
-    visualTab.add(fontNameCB);\r
-    visualTab.add(fontSizeCB);\r
-    visualTab.add(fontStyleCB);\r
     visualTab.add(jPanel2);\r
     linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
     editLinkButtons.add(newLink, null);\r
@@ -432,6 +465,12 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);\r
     jPanel11.add(pileupjv);\r
     jPanel11.add(pirjv);\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
     exportTab.add(jPanel11);\r