-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.jbgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-import javax.swing.event.CaretListener;\r
-import javax.swing.event.CaretEvent;\r
-\r
-public class GFinder extends JPanel {\r
- JLabel jLabel1 = new JLabel();\r
- protected JButton findAll = new JButton();\r
- protected JButton findNext = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- GridLayout gridLayout1 = new GridLayout();\r
- protected JButton createNewGroup = new JButton();\r
- JScrollPane jScrollPane1 = new JScrollPane();\r
- protected JTextArea textfield = new JTextArea();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- JPanel jPanel2 = new JPanel();\r
- JPanel jPanel3 = new JPanel();\r
- JPanel jPanel4 = new JPanel();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- JPanel jPanel5 = new JPanel();\r
- JPanel jPanel6 = new JPanel();\r
- public GFinder() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("Find");\r
- this.setLayout(borderLayout1);\r
- findAll.setFont(new java.awt.Font("Verdana", 0, 12));\r
- findAll.setText("Find all");\r
- findAll.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- findAll_actionPerformed(e);\r
- }\r
- });\r
- findNext.setEnabled(false);\r
- findNext.setFont(new java.awt.Font("Verdana", 0, 12));\r
- findNext.setText("Find Next");\r
- findNext.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- findNext_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.setLayout(gridLayout1);\r
- gridLayout1.setHgap(0);\r
- gridLayout1.setRows(3);\r
- gridLayout1.setVgap(2);\r
- createNewGroup.setEnabled(false);\r
- createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));\r
- createNewGroup.setToolTipText("");\r
- createNewGroup.setMargin(new Insets(0, 0, 0, 0));\r
- createNewGroup.setText("Create new group");\r
- createNewGroup.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- createNewGroup_actionPerformed(e);\r
- }\r
- });\r
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));\r
- textfield.setText("");\r
- textfield.setLineWrap(true);\r
- textfield.addCaretListener(new CaretListener()\r
- {\r
- public void caretUpdate(CaretEvent e)\r
- {\r
- textfield_caretUpdate(e);\r
- }\r
- });\r
- borderLayout1.setHgap(5);\r
- borderLayout1.setVgap(5);\r
- jPanel4.setLayout(borderLayout2);\r
- jPanel2.setPreferredSize(new Dimension(10, 1));\r
- jPanel3.setPreferredSize(new Dimension(10, 1));\r
- jPanel1.add(findNext, null);\r
- jPanel1.add(findAll, null);\r
- jPanel1.add(createNewGroup, null);\r
- this.add(jLabel1, java.awt.BorderLayout.WEST);\r
- this.add(jPanel1, java.awt.BorderLayout.EAST);\r
- this.add(jPanel2, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel3, java.awt.BorderLayout.NORTH);\r
- this.add(jPanel4, java.awt.BorderLayout.CENTER);\r
- jPanel4.add(jScrollPane1, java.awt.BorderLayout.CENTER);\r
- jPanel4.add(jPanel5, java.awt.BorderLayout.SOUTH);\r
- jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);\r
- jScrollPane1.getViewport().add(textfield);\r
- }\r
-\r
- protected void findNext_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void findAll_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void textfield_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- void textfield_keyTyped(KeyEvent e) {\r
- findNext.setEnabled(true);\r
- }\r
-\r
- public void createNewGroup_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- public void textfield_caretUpdate(CaretEvent e)\r
- {\r
- if (textfield.getText().indexOf("\t")>-1)\r
- {\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- String text = textfield.getText();\r
- text = text.substring(text.lastIndexOf("\t") + 1).trim();\r
- text = jalview.analysis.AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars, text);\r
- textfield.setText(text);\r
- }\r
- });\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+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)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel1.setText("Find");
+ this.setLayout(borderLayout1);
+ findAll.setFont(new java.awt.Font("Verdana", 0, 12));
+ findAll.setText("Find all");
+ findAll.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findAll_actionPerformed(e);
+ }
+ });
+ findNext.setFont(new java.awt.Font("Verdana", 0, 12));
+ findNext.setText("Find Next");
+ findNext.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ findNext_actionPerformed(e);
+ }
+ });
+ jPanel1.setLayout(gridLayout1);
+ gridLayout1.setHgap(0);
+ gridLayout1.setRows(3);
+ gridLayout1.setVgap(2);
+ createNewGroup.setEnabled(false);
+ createNewGroup.setFont(new java.awt.Font("Verdana", 0, 12));
+ createNewGroup.setMargin(new Insets(0, 0, 0, 0));
+ createNewGroup.setText("New Feature");
+ createNewGroup.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ createNewGroup_actionPerformed(e);
+ }
+ });
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
+ textfield.setText("");
+ textfield.setLineWrap(true);
+ textfield.addCaretListener(new CaretListener()
+ {
+ public void caretUpdate(CaretEvent e)
+ {
+ textfield_caretUpdate(e);
+ }
+ });
+ textfield.addKeyListener(new java.awt.event.KeyAdapter()
+ {
+ public void keyPressed(KeyEvent e)
+ {
+ textfield_keyPressed(e);
+ }
+ });
+
+ borderLayout1.setHgap(5);
+ borderLayout1.setVgap(5);
+ jPanel4.setLayout(borderLayout2);
+ jPanel2.setPreferredSize(new Dimension(10, 1));
+ jPanel3.setPreferredSize(new Dimension(10, 1));
+ caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
+ caseSensitive.setText("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);
+ 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);
+ jScrollPane1.getViewport().add(textfield);
+ jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);
+ jPanel4.add(caseSensitive, java.awt.BorderLayout.SOUTH);
+ }
+
+ protected void findNext_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void findAll_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void textfield_keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ e.consume();
+ findNext_actionPerformed(null);
+ }
+ }
+
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+ }
+
+ public void textfield_caretUpdate(CaretEvent e)
+ {
+ if (textfield.getText().indexOf(">") > -1)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ String str = textfield.getText();
+ Alignment al = null;
+ 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());
+
+ textfield.setText(str);
+ }
+ }
+ });
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff