/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
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");
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);
}