X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=70606a1e33c3178719233b1faa7717566b8e715e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=9d72d264a1f9f4472320bd4ed2792197bbae7516;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index 9d72d26..70606a1 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.jbgui;
 
@@ -26,38 +26,50 @@ import javax.swing.event.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 
-public class GFinder
-    extends JPanel
+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");
@@ -168,14 +180,14 @@ public class GFinder
           try
           {
             al = new FormatAdapter().readFile(str, "Paste", "FASTA");
+          } catch (Exception ex)
+          {
           }
-          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);
           }