X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=92f5055fecd2e3709d165d564ef4a7222f326366;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c52972814bd672dea17b763e033c21ece981c68e;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index c529728..92f5055 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,24 +20,38 @@
  */
 package jalview.jbgui;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.Insets;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+
 public class GFinder extends JPanel
 {
-  JLabel jLabel1 = new JLabel();
+  JLabel jLabelFind = new JLabel();
 
   protected JButton findAll = new JButton();
 
   protected JButton findNext = new JButton();
 
-  JPanel jPanel1 = new JPanel();
+  JPanel actionsPanel = new JPanel();
 
   GridLayout gridLayout1 = new GridLayout();
 
@@ -47,7 +61,7 @@ public class GFinder extends JPanel
 
   protected JTextArea textfield = new JTextArea();
 
-  BorderLayout borderLayout1 = new BorderLayout();
+  BorderLayout mainBorderLayout = new BorderLayout();
 
   JPanel jPanel2 = new JPanel();
 
@@ -61,6 +75,10 @@ public class GFinder extends JPanel
 
   protected JCheckBox caseSensitive = new JCheckBox();
 
+  protected JCheckBox searchDescription = new JCheckBox();
+
+  GridLayout optionsGridLayout = new GridLayout();
+
   public GFinder()
   {
     try
@@ -74,9 +92,9 @@ public class GFinder extends JPanel
 
   private void jbInit() throws Exception
   {
-    jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
-    jLabel1.setText(MessageManager.getString("action.find"));
-    this.setLayout(borderLayout1);
+    jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
+    jLabelFind.setText(MessageManager.getString("label.find"));
+    this.setLayout(mainBorderLayout);
     findAll.setFont(new java.awt.Font("Verdana", 0, 12));
     findAll.setText(MessageManager.getString("action.find_all"));
     findAll.addActionListener(new java.awt.event.ActionListener()
@@ -95,7 +113,7 @@ public class GFinder extends JPanel
         findNext_actionPerformed(e);
       }
     });
-    jPanel1.setLayout(gridLayout1);
+    actionsPanel.setLayout(gridLayout1);
     gridLayout1.setHgap(0);
     gridLayout1.setRows(3);
     gridLayout1.setVgap(2);
@@ -128,25 +146,38 @@ public class GFinder extends JPanel
       }
     });
 
-    borderLayout1.setHgap(5);
-    borderLayout1.setVgap(5);
+    mainBorderLayout.setHgap(5);
+    mainBorderLayout.setVgap(5);
     jPanel4.setLayout(borderLayout2);
     jPanel2.setPreferredSize(new Dimension(10, 1));
     jPanel3.setPreferredSize(new Dimension(10, 1));
     caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
     caseSensitive.setText(MessageManager.getString("label.match_case"));
-    jPanel1.add(findNext, null);
-    jPanel1.add(findAll, null);
-    jPanel1.add(createNewGroup, null);
-    this.add(jLabel1, java.awt.BorderLayout.WEST);
-    this.add(jPanel1, java.awt.BorderLayout.EAST);
+
+    searchDescription.setText(MessageManager
+            .getString("label.include_description"));
+
+    actionsPanel.add(findNext, null);
+    actionsPanel.add(findAll, null);
+    actionsPanel.add(createNewGroup, null);
+    this.add(jLabelFind, java.awt.BorderLayout.WEST);
+    this.add(actionsPanel, java.awt.BorderLayout.EAST);
     this.add(jPanel2, java.awt.BorderLayout.SOUTH);
     this.add(jPanel3, java.awt.BorderLayout.NORTH);
     this.add(jPanel4, java.awt.BorderLayout.CENTER);
-    jPanel4.add(jScrollPane1, java.awt.BorderLayout.CENTER);
+    jPanel4.add(jScrollPane1, java.awt.BorderLayout.NORTH);
     jScrollPane1.getViewport().add(textfield);
-    jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
-    jPanel4.add(caseSensitive, java.awt.BorderLayout.SOUTH);
+
+    JPanel optionsPanel = new JPanel();
+
+    optionsGridLayout.setHgap(0);
+    optionsGridLayout.setRows(2);
+    optionsGridLayout.setVgap(2);
+    optionsPanel.setLayout(optionsGridLayout);
+    optionsPanel.add(caseSensitive, null);
+    optionsPanel.add(searchDescription, null);
+
+    jPanel4.add(optionsPanel, java.awt.BorderLayout.WEST);
   }
 
   protected void findNext_actionPerformed(ActionEvent e)
@@ -179,7 +210,7 @@ public class GFinder extends JPanel
         public void run()
         {
           String str = textfield.getText();
-          Alignment al = null;
+          AlignmentI al = null;
           try
           {
             al = new FormatAdapter().readFile(str, "Paste", "FASTA");