-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import jalview.io.FormatAdapter;\r
-import jalview.datamodel.SequenceI;\r
-import java.awt.BorderLayout;\r
-\r
-public class GFinder\r
- extends JPanel\r
-{\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 jPanel6 = new JPanel();\r
- protected JCheckBox caseSensitive = new JCheckBox();\r
- public GFinder()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\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
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\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
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\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.setMargin(new Insets(0, 0, 0, 0));\r
- createNewGroup.setText("New Feature");\r
- createNewGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\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
- textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
- public void keyPressed(KeyEvent e) {\r
- textfield_keyPressed(e);\r
- }\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
- caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);\r
- caseSensitive.setText("Match Case");\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
- jScrollPane1.getViewport().add(textfield);\r
- jPanel4.add(jPanel6, java.awt.BorderLayout.NORTH);\r
- jPanel4.add(caseSensitive, java.awt.BorderLayout.SOUTH);\r
- }\r
-\r
- protected void findNext_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- protected void findAll_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
-\r
- protected void textfield_keyPressed(KeyEvent e)\r
- {\r
-\r
- if(e.getKeyCode()==KeyEvent.VK_ENTER)\r
- {\r
- e.consume();\r
- findNext_actionPerformed(null);\r
- }\r
- findNext.setEnabled(true);\r
- }\r
-\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
- public void textfield_caretUpdate(CaretEvent e)\r
- {\r
- if (textfield.getText().indexOf(">") > -1)\r
- {\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- {\r
- String str = textfield.getText();\r
- SequenceI[] sequences = null;\r
- try{sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");}\r
- catch(Exception ex){}\r
- if(sequences!=null && sequences.length>0)\r
- {\r
- str = jalview.analysis.AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars,\r
- sequences[0].getSequenceAsString());\r
-\r
- textfield.setText(str);\r
- }\r
- }\r
- });\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
+
+import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.io.cache.JvCacheableInputBox;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.SwingConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.event.CaretEvent;
+import javax.swing.event.CaretListener;
+import javax.swing.text.JTextComponent;
+
+public class GFinder extends JPanel
+{
+ private static final java.awt.Font VERDANA_12 = new Font("Verdana",
+ Font.PLAIN, 12);
+
+ private static final String FINDER_CACHE_KEY = "CACHE.FINDER";
+
+ protected JButton createFeatures;
+
+ protected JvCacheableInputBox<String> searchBox;
+
+ protected JCheckBox caseSensitive;
+
+ protected JCheckBox searchDescription;
+
+ protected JCheckBox ignoreHidden;
+
+ public GFinder()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Constructs the widgets and adds them to the layout
+ */
+ private void jbInit() throws Exception
+ {
+ /*
+ * border layout
+ * West: 4 rows
+ * first row 'Find'
+ * remaining rows empty
+ * Center: 4 rows
+ * first row search box
+ * second row 'match case' checkbox
+ * third row 'include description' checkbox
+ * fourth row 'ignore hidden' checkbox
+ * East: four rows
+ * first row 'find next' button
+ * second row 'find all' button
+ * third row 'new feature' button
+ * fourth row empty
+ */
+ this.setLayout(new BorderLayout());
+ JPanel eastPanel = new JPanel();
+ eastPanel.setLayout(new GridLayout(4, 1));
+ this.add(eastPanel, BorderLayout.EAST);
+ JPanel centrePanel = new JPanel();
+ centrePanel.setLayout(new GridLayout(4, 1));
+ this.add(centrePanel, BorderLayout.CENTER);
+ JPanel westPanel = new JPanel();
+ westPanel.setLayout(new GridLayout(4, 1));
+ this.add(westPanel, BorderLayout.WEST);
+
+ /*
+ * 'Find' prompt goes top left
+ */
+ JLabel findLabel = new JLabel(
+ " " + MessageManager.getString("label.find") + " ");
+ findLabel.setFont(VERDANA_12);
+ westPanel.add(findLabel);
+
+ /*
+ * search box
+ */
+ searchBox = new JvCacheableInputBox<>(FINDER_CACHE_KEY, 25);
+ searchBox.setFont(VERDANA_12);
+ ((JTextComponent) searchBox.getEditor().getEditorComponent())
+ .addCaretListener(new CaretListener()
+ {
+ @Override
+ public void caretUpdate(CaretEvent e)
+ {
+ textfield_caretUpdate();
+ }
+ });
+ searchBox.getEditor().getEditorComponent()
+ .addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ textfield_keyPressed(e);
+ }
+ });
+ centrePanel.add(searchBox);
+
+ /*
+ * search options checkboxes
+ */
+ caseSensitive = new JCheckBox();
+ caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
+ caseSensitive.setText(MessageManager.getString("label.match_case"));
+
+ searchDescription = new JCheckBox();
+ searchDescription
+ .setText(MessageManager.getString("label.include_description"));
+
+ ignoreHidden = new JCheckBox();
+ ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
+ ignoreHidden.setToolTipText(
+ MessageManager.getString("label.ignore_hidden_tooltip"));
+
+ centrePanel.add(caseSensitive);
+ centrePanel.add(searchDescription);
+ centrePanel.add(ignoreHidden);
+
+ /*
+ * action buttons
+ */
+ JButton findAll = new JButton(
+ MessageManager.getString("action.find_all"));
+ findAll.setFont(VERDANA_12);
+ findAll.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ findAll_actionPerformed();
+ }
+ });
+ JButton findNext = new JButton(
+ MessageManager.getString("action.find_next"));
+ findNext.setFont(VERDANA_12);
+ findNext.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ findNext_actionPerformed();
+ }
+ });
+ createFeatures = new JButton();
+ createFeatures.setEnabled(false);
+ createFeatures.setFont(VERDANA_12);
+ createFeatures.setText(MessageManager.getString("label.new_feature"));
+ createFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createFeatures_actionPerformed();
+ }
+ });
+ eastPanel.add(findNext);
+ eastPanel.add(findAll);
+ eastPanel.add(createFeatures);
+ }
+
+ protected void textfield_keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ if (!searchBox.isPopupVisible())
+ {
+ e.consume();
+ findNext_actionPerformed();
+ }
+ }
+ }
+
+ protected void findNext_actionPerformed()
+ {
+ }
+
+ protected void findAll_actionPerformed()
+ {
+ }
+
+ public void createFeatures_actionPerformed()
+ {
+ }
+
+ public void textfield_caretUpdate()
+ {
+ // disabled as appears to be running a non-functional
+ if (false && searchBox.getUserInput().indexOf(">") > -1)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ String str = searchBox.getUserInput();
+ AlignmentI al = null;
+ try
+ {
+ al = new FormatAdapter().readFile(str, DataSourceType.PASTE,
+ FileFormat.Fasta);
+ } catch (Exception ex)
+ {
+ }
+ if (al != null && al.getHeight() > 0)
+ {
+ str = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ al.getSequenceAt(0).getSequenceAsString());
+ // todo and what? set str as searchBox text?
+ }
+ }
+ });
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff