X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=78ae0a83d9033f03b192b3b7c27f2639f49e36b9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=b8dcad3ac50e91885b9cea589aa50c7e5906a6e6;hpb=3f9c1d052c8fe2e92ae0d7a1c3088ccb82c58ba5;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index b8dcad3..78ae0a8 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.jbgui;
 
@@ -22,42 +21,54 @@ import java.awt.*;
 import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.Alignment;
-import java.awt.BorderLayout;
 
-public class GFinder
-    extends JPanel
+import jalview.datamodel.*;
+import jalview.io.*;
+
+public class GFinder extends JPanel
 {
   JLabel jLabel1 = new JLabel();
+
   protected JButton findAll = new JButton();
+
   protected JButton findNext = new JButton();
+
   JPanel jPanel1 = new JPanel();
+
   GridLayout gridLayout1 = new GridLayout();
+
   protected JButton createNewGroup = new JButton();
+
   JScrollPane jScrollPane1 = new JScrollPane();
+
   protected JTextArea textfield = new JTextArea();
+
   BorderLayout borderLayout1 = new BorderLayout();
+
   JPanel jPanel2 = new JPanel();
+
   JPanel jPanel3 = new JPanel();
+
   JPanel jPanel4 = new JPanel();
+
   BorderLayout borderLayout2 = new BorderLayout();
+
   JPanel jPanel6 = new JPanel();
+
   protected JCheckBox caseSensitive = new JCheckBox();
+
   public GFinder()
   {
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
   }
 
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
     jLabel1.setText("Find");
@@ -105,10 +116,12 @@ public class GFinder
         textfield_caretUpdate(e);
       }
     });
-    textfield.addKeyListener(new java.awt.event.KeyAdapter() {
-        public void keyPressed(KeyEvent e) {
-            textfield_keyPressed(e);
-        }
+    textfield.addKeyListener(new java.awt.event.KeyAdapter()
+    {
+      public void keyPressed(KeyEvent e)
+      {
+        textfield_keyPressed(e);
+      }
     });
 
     borderLayout1.setHgap(5);
@@ -140,10 +153,9 @@ public class GFinder
   {
   }
 
-
   protected void textfield_keyPressed(KeyEvent e)
   {
-    if(e.getKeyCode()==KeyEvent.VK_ENTER)
+    if (e.getKeyCode() == KeyEvent.VK_ENTER)
     {
       e.consume();
       findNext_actionPerformed(null);
@@ -164,13 +176,17 @@ public class GFinder
         {
           String str = textfield.getText();
           Alignment al = null;
-          try{al = new FormatAdapter().readFile(str, "Paste", "FASTA");}
-          catch(Exception ex){}
-          if(al!=null && al.getHeight()>0)
+          try
+          {
+            al = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          } catch (Exception ex)
+          {
+          }
+          if (al != null && al.getHeight() > 0)
           {
             str = jalview.analysis.AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars,
-                al.getSequenceAt(0).getSequenceAsString());
+                    jalview.util.Comparison.GapChars, al.getSequenceAt(0)
+                            .getSequenceAsString());
 
             textfield.setText(str);
           }