X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGFinder.java;h=57beaeeafbc487bec199c0a6bfcccdf0ba882e90;hb=b7014049e421026d0f2d57179af9688472cd78f2;hp=b9bccc00f28ebdd6c66414ec642cde3be396ffb3;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index b9bccc0..57beaee 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -1,184 +1,258 @@
-/*
- * 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
- */
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import jalview.io.FormatAdapter;
-import jalview.datamodel.SequenceI;
-import java.awt.BorderLayout;
-
-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.setEnabled(false);
- 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);
- }
- findNext.setEnabled(true);
- }
-
- 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();
- SequenceI[] sequences = null;
- try{sequences = new FormatAdapter().readFile(str, "Paste", "FASTA");}
- catch(Exception ex){}
- if(sequences!=null && sequences.length>0)
- {
- str = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- sequences[0].getSequenceAsString());
-
- textfield.setText(str);
- }
- }
- });
- }
- }
-}
+/*
+ * 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 .
+ * 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 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?
+ }
+ }
+ });
+ }
+ }
+
+}