src/jalview/jbgui/GFinder.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.datamodel.AlignmentI;
  24 import jalview.io.DataSourceType;
  25 import jalview.io.FileFormat;
  26 import jalview.io.FormatAdapter;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Dimension;
  31 import java.awt.Font;
  32 import java.awt.GridLayout;
  33 import java.awt.Insets;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.KeyEvent;
  36
  37 import javax.swing.JButton;
  38 import javax.swing.JCheckBox;
  39 import javax.swing.JLabel;
  40 import javax.swing.JPanel;
  41 import javax.swing.JScrollPane;
  42 import javax.swing.JTextArea;
  43 import javax.swing.SwingConstants;
  44 import javax.swing.SwingUtilities;
  45 import javax.swing.event.CaretEvent;
  46 import javax.swing.event.CaretListener;
  47
  48 public class GFinder extends JPanel
  49 {
  50   JLabel jLabelFind = new JLabel();
  51
  52   protected JButton findAll = new JButton();
  53
  54   protected JButton findNext = new JButton();
  55
  56   JPanel actionsPanel = new JPanel();
  57
  58   GridLayout gridLayout1 = new GridLayout();
  59
  60   protected JButton createFeatures = new JButton();
  61
  62   JScrollPane jScrollPane1 = new JScrollPane();
  63
  64   protected JTextArea textfield = new JTextArea();
  65
  66   BorderLayout mainBorderLayout = new BorderLayout();
  67
  68   JPanel jPanel2 = new JPanel();
  69
  70   JPanel jPanel3 = new JPanel();
  71
  72   JPanel jPanel4 = new JPanel();
  73
  74   BorderLayout borderLayout2 = new BorderLayout();
  75
  76   JPanel jPanel6 = new JPanel();
  77
  78   protected JCheckBox caseSensitive = new JCheckBox();
  79
  80   protected JCheckBox searchDescription = new JCheckBox();
  81
  82   GridLayout optionsGridLayout = new GridLayout();
  83
  84   public GFinder()
  85   {
  86     try
  87     {
  88       jbInit();
  89     } catch (Exception e)
  90     {
  91       e.printStackTrace();
  92     }
  93   }
  94
  95   private void jbInit() throws Exception
  96   {
  97     jLabelFind.setFont(new java.awt.Font("Verdana", 0, 12));
  98     jLabelFind.setText(MessageManager.getString("label.find"));
  99     this.setLayout(mainBorderLayout);
 100     findAll.setFont(new java.awt.Font("Verdana", 0, 12));
 101     findAll.setText(MessageManager.getString("action.find_all"));
 102     findAll.addActionListener(new java.awt.event.ActionListener()
 103     {
 104       @Override
 105       public void actionPerformed(ActionEvent e)
 106       {
 107         findAll_actionPerformed(e);
 108       }
 109     });
 110     findNext.setFont(new java.awt.Font("Verdana", 0, 12));
 111     findNext.setText(MessageManager.getString("action.find_next"));
 112     findNext.addActionListener(new java.awt.event.ActionListener()
 113     {
 114       @Override
 115       public void actionPerformed(ActionEvent e)
 116       {
 117         findNext_actionPerformed(e);
 118       }
 119     });
 120     actionsPanel.setLayout(gridLayout1);
 121     gridLayout1.setHgap(0);
 122     gridLayout1.setRows(3);
 123     gridLayout1.setVgap(2);
 124     createFeatures.setEnabled(false);
 125     createFeatures.setFont(new java.awt.Font("Verdana", 0, 12));
 126     createFeatures.setMargin(new Insets(0, 0, 0, 0));
 127     createFeatures.setText(MessageManager.getString("label.new_feature"));
 128     createFeatures.addActionListener(new java.awt.event.ActionListener()
 129     {
 130       @Override
 131       public void actionPerformed(ActionEvent e)
 132       {
 133         createFeatures_actionPerformed();
 134       }
 135     });
 136     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 12));
 137     textfield.setText("");
 138     textfield.setLineWrap(true);
 139     textfield.addCaretListener(new CaretListener()
 140     {
 141       @Override
 142       public void caretUpdate(CaretEvent e)
 143       {
 144         textfield_caretUpdate(e);
 145       }
 146     });
 147     textfield.addKeyListener(new java.awt.event.KeyAdapter()
 148     {
 149       @Override
 150       public void keyPressed(KeyEvent e)
 151       {
 152         textfield_keyPressed(e);
 153       }
 154     });
 155
 156     mainBorderLayout.setHgap(5);
 157     mainBorderLayout.setVgap(5);
 158     jPanel4.setLayout(borderLayout2);
 159     jPanel2.setPreferredSize(new Dimension(10, 1));
 160     jPanel3.setPreferredSize(new Dimension(10, 1));
 161     caseSensitive.setHorizontalAlignment(SwingConstants.LEFT);
 162     caseSensitive.setText(MessageManager.getString("label.match_case"));
 163
 164     searchDescription.setText(MessageManager
 165             .getString("label.include_description"));
 166
 167     actionsPanel.add(findNext, null);
 168     actionsPanel.add(findAll, null);
 169     actionsPanel.add(createFeatures, null);
 170     this.add(jLabelFind, java.awt.BorderLayout.WEST);
 171     this.add(actionsPanel, java.awt.BorderLayout.EAST);
 172     this.add(jPanel2, java.awt.BorderLayout.SOUTH);
 173     this.add(jPanel3, java.awt.BorderLayout.NORTH);
 174     this.add(jPanel4, java.awt.BorderLayout.CENTER);
 175     jPanel4.add(jScrollPane1, java.awt.BorderLayout.NORTH);
 176     jScrollPane1.getViewport().add(textfield);
 177
 178     JPanel optionsPanel = new JPanel();
 179
 180     optionsGridLayout.setHgap(0);
 181     optionsGridLayout.setRows(2);
 182     optionsGridLayout.setVgap(2);
 183     optionsPanel.setLayout(optionsGridLayout);
 184     optionsPanel.add(caseSensitive, null);
 185     optionsPanel.add(searchDescription, null);
 186
 187     jPanel4.add(optionsPanel, java.awt.BorderLayout.WEST);
 188   }
 189
 190   protected void findNext_actionPerformed(ActionEvent e)
 191   {
 192   }
 193
 194   protected void findAll_actionPerformed(ActionEvent e)
 195   {
 196   }
 197
 198   protected void textfield_keyPressed(KeyEvent e)
 199   {
 200     if (e.getKeyCode() == KeyEvent.VK_ENTER)
 201     {
 202       e.consume();
 203       findNext_actionPerformed(null);
 204     }
 205   }
 206
 207   public void createFeatures_actionPerformed()
 208   {
 209   }
 210
 211   public void textfield_caretUpdate(CaretEvent e)
 212   {
 213     if (textfield.getText().indexOf(">") > -1)
 214     {
 215       SwingUtilities.invokeLater(new Runnable()
 216       {
 217         @Override
 218         public void run()
 219         {
 220           String str = textfield.getText();
 221           AlignmentI al = null;
 222           try
 223           {
 224             al = new FormatAdapter().readFile(str, DataSourceType.PASTE,
 225                     FileFormat.Fasta);
 226           } catch (Exception ex)
 227           {
 228           }
 229           if (al != null && al.getHeight() > 0)
 230           {
 231             str = jalview.analysis.AlignSeq.extractGaps(
 232                     jalview.util.Comparison.GapChars, al.getSequenceAt(0)
 233                             .getSequenceAsString());
 234
 235             textfield.setText(str);
 236           }
 237         }
 238       });
 239     }
 240   }
 241 }