src/jalview/gui/FeatureSettings.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 import javax.swing.*;\r
  23 import javax.swing.event.*;\r
  24 import java.awt.*;\r
  25 import java.util.*;\r
  26 import javax.swing.BorderFactory;\r
  27 import java.awt.event.*;\r
  28 import javax.swing.table.*;\r
  29 import java.io.*;\r
  30 import jalview.io.JalviewFileChooser;\r
  31 \r
  32 public class FeatureSettings extends JPanel\r
  33 {\r
  34 \r
  35   final FeatureRenderer fr;\r
  36   final AlignmentPanel ap;\r
  37   final AlignViewport av;\r
  38   Object [][] originalData;\r
  39   final JInternalFrame frame;\r
  40   JScrollPane scrollPane = new JScrollPane();\r
  41   JTable table;\r
  42 \r
  43   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
  44   {\r
  45     this.ap = ap;\r
  46     this.av = av;\r
  47     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
  48     av.alignment.getSequences();\r
  49     frame = new JInternalFrame();\r
  50     frame.setContentPane(this);\r
  51     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
  52 \r
  53     setTableData();\r
  54 \r
  55     final JSlider transparency = new JSlider(0, 70, 0);\r
  56     transparency.addChangeListener(new ChangeListener()\r
  57     {\r
  58       public void stateChanged(ChangeEvent evt)\r
  59       {\r
  60         fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
  61         ap.repaint();\r
  62       }\r
  63     });\r
  64 \r
  65     JPanel transPanel = new JPanel(new FlowLayout());\r
  66     transPanel.add(new JLabel("Transparency"));\r
  67     transPanel.add(transparency);\r
  68 \r
  69     //////////////////////////////////////////////\r
  70     //We're going to need those OK cancel buttons\r
  71     JPanel buttonPanel = new JPanel(new FlowLayout());\r
  72     JButton button = new JButton("OK");\r
  73     button.addActionListener(new ActionListener()\r
  74     {\r
  75       public void actionPerformed(ActionEvent evt)\r
  76       {\r
  77         try\r
  78         {\r
  79           frame.setClosed(true);\r
  80         }\r
  81         catch (Exception exe)\r
  82         {}\r
  83       }\r
  84     });\r
  85     buttonPanel.add(button);\r
  86     button = new JButton("Cancel");\r
  87     button.addActionListener(new ActionListener()\r
  88     {\r
  89       public void actionPerformed(ActionEvent evt)\r
  90       {\r
  91         try\r
  92         {\r
  93           updateFeatureRenderer(originalData);\r
  94           frame.setClosed(true);\r
  95         }\r
  96         catch (Exception exe)\r
  97         {}\r
  98       }\r
  99     });\r
 100     buttonPanel.add(button);\r
 101 \r
 102     button = new JButton("Load Colours");\r
 103     button.addActionListener(new ActionListener()\r
 104     {\r
 105       public void actionPerformed(ActionEvent evt)\r
 106       {\r
 107         load();\r
 108       }\r
 109     });\r
 110     buttonPanel.add(button);\r
 111     button = new JButton("Save Colours");\r
 112     button.addActionListener(new ActionListener()\r
 113     {\r
 114       public void actionPerformed(ActionEvent evt)\r
 115       {\r
 116         save();\r
 117       }\r
 118     });\r
 119     buttonPanel.add(button);\r
 120 \r
 121     this.setLayout(new BorderLayout());\r
 122     JPanel bigPanel = new JPanel(new BorderLayout());\r
 123     bigPanel.add(transPanel, BorderLayout.SOUTH);\r
 124     bigPanel.add(scrollPane, BorderLayout.CENTER);\r
 125 \r
 126     add(bigPanel, BorderLayout.CENTER);\r
 127     add(buttonPanel, BorderLayout.SOUTH);\r
 128 \r
 129 \r
 130   }\r
 131 \r
 132   void setTableData()\r
 133   {\r
 134     Vector allFeatures = new Vector();\r
 135     Vector features;\r
 136     Enumeration e;\r
 137     SequenceFeature sf;\r
 138 \r
 139     for(int i=0; i< av.alignment.getHeight(); i++)\r
 140     {\r
 141        features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 142        if(features==null)\r
 143          continue;\r
 144 \r
 145        e = features.elements();\r
 146        while(e.hasMoreElements())\r
 147        {\r
 148          sf = (SequenceFeature)e.nextElement();\r
 149          if(!allFeatures.contains(sf.getType()))\r
 150          {\r
 151            allFeatures.addElement(sf.getType());\r
 152          }\r
 153        }\r
 154     }\r
 155     if(allFeatures.size()<1)\r
 156      {\r
 157        try{\r
 158          frame.setClosed(true);\r
 159        }catch(Exception ex){}\r
 160        return;\r
 161      }\r
 162 \r
 163     int fSize = allFeatures.size();\r
 164 \r
 165     String type;\r
 166     boolean originalExists = false;\r
 167     if(originalData!=null)\r
 168       originalExists = true;\r
 169     else\r
 170       originalData = new Object[fSize][3];\r
 171 \r
 172     Object [][] data = new Object[fSize][3];\r
 173     for(int i=0; i<fSize; i++)\r
 174     {\r
 175       type = allFeatures.elementAt(i).toString();\r
 176       Color col = fr.getColour(type);\r
 177       data[i][0]=type;\r
 178       data[i][1]=col;\r
 179       if(fr.featuresDisplayed!=null)\r
 180          data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
 181       else\r
 182         data[i][2] = new Boolean(true);\r
 183 \r
 184       if(!originalExists)\r
 185       {\r
 186         originalData[i][0] = type;\r
 187         originalData[i][1] = col;\r
 188         if (fr.featuresDisplayed != null)\r
 189           originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
 190         else\r
 191           originalData[i][2] = new Boolean(true);\r
 192       }\r
 193     }\r
 194     ////////////////////////////////////\r
 195         //Now build the table\r
 196         table = new JTable(new FeatureTableModel(data));\r
 197         scrollPane.setViewportView(table);\r
 198         table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
 199         table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
 200         table.setDefaultRenderer(Color.class,\r
 201                              new ColorRenderer());\r
 202 \r
 203         table.setDefaultEditor(Color.class,\r
 204                           new ColorEditor());\r
 205 \r
 206         table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
 207 \r
 208         table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 209 \r
 210         table.addMouseListener(new MouseAdapter()\r
 211             {\r
 212               public void mousePressed(MouseEvent evt)\r
 213               {\r
 214                 selectedRow = table.rowAtPoint(evt.getPoint());\r
 215               }\r
 216             });\r
 217 \r
 218         table.addMouseMotionListener(new MouseMotionAdapter()\r
 219             {\r
 220               public void mouseDragged(MouseEvent evt)\r
 221               {\r
 222                 int newRow = table.rowAtPoint(evt.getPoint());\r
 223                 if(newRow!=selectedRow\r
 224                    && selectedRow!=-1\r
 225                    && newRow!=-1)\r
 226                 {\r
 227                   Object[] temp = new Object[3];\r
 228                   temp[0] = table.getValueAt(selectedRow, 0);\r
 229                   temp[1] = table.getValueAt(selectedRow, 1);\r
 230                   temp[2] = table.getValueAt(selectedRow, 2);\r
 231 \r
 232                   table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
 233                   table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
 234                   table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
 235 \r
 236                   table.setValueAt(temp[0], newRow, 0);\r
 237                   table.setValueAt(temp[1], newRow, 1);\r
 238                   table.setValueAt(temp[2], newRow, 2);\r
 239 \r
 240                   selectedRow = newRow;\r
 241                 }\r
 242               }\r
 243         });\r
 244 \r
 245   }\r
 246 \r
 247   void load()\r
 248   {\r
 249     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 250                  "LAST_DIRECTORY"), new String[] { "fc" },\r
 251              new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 252      chooser.setFileView(new jalview.io.JalviewFileView());\r
 253      chooser.setDialogTitle("Load Feature Colours");\r
 254      chooser.setToolTipText("Load");\r
 255 \r
 256      int value = chooser.showOpenDialog(this);\r
 257 \r
 258      if (value == JalviewFileChooser.APPROVE_OPTION)\r
 259      {\r
 260        File file = chooser.getSelectedFile();\r
 261 \r
 262        try\r
 263        {\r
 264          InputStreamReader in = new InputStreamReader(new FileInputStream(\r
 265              file), "UTF-8");\r
 266 \r
 267          jalview.binding.JalviewUserColours jucs = new jalview.binding.\r
 268              JalviewUserColours();\r
 269          jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
 270 \r
 271 \r
 272          for (int i = 0; i < jucs.getColourCount(); i++)\r
 273          {\r
 274            fr.setColour( jucs.getColour(i).getName(),\r
 275                           new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));\r
 276          }\r
 277 \r
 278          setTableData();\r
 279          ap.repaint();\r
 280        }\r
 281        catch (Exception ex)\r
 282        {\r
 283          System.out.println("Error loading User ColourFile\n" + ex);\r
 284        }\r
 285      }\r
 286   }\r
 287 \r
 288   void save()\r
 289   {\r
 290     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 291                 "LAST_DIRECTORY"), new String[] { "fc" },\r
 292             new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 293     chooser.setFileView(new jalview.io.JalviewFileView());\r
 294     chooser.setDialogTitle("Save Feature Colour Scheme");\r
 295     chooser.setToolTipText("Save");\r
 296 \r
 297     int value = chooser.showSaveDialog(this);\r
 298 \r
 299     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 300     {\r
 301         String choice = chooser.getSelectedFile().getPath();\r
 302         jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
 303         ucs.setSchemeName("Sequence Features");\r
 304         try\r
 305         {\r
 306             PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
 307                         new FileOutputStream(choice), "UTF-8"));\r
 308 \r
 309             Enumeration e = fr.featureColours.keys();\r
 310            while(e.hasMoreElements())\r
 311            {\r
 312 \r
 313 \r
 314                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 315                 col.setName(e.nextElement().toString());\r
 316                 col.setRGB(jalview.util.Format.getHexString(\r
 317                         fr.getColour(col.getName())));\r
 318                 ucs.addColour(col);\r
 319             }\r
 320 \r
 321             ucs.marshal(out);\r
 322             out.close();\r
 323         }\r
 324         catch (Exception ex)\r
 325         {\r
 326             ex.printStackTrace();\r
 327         }\r
 328     }\r
 329 \r
 330   }\r
 331 \r
 332   public void updateFeatureRenderer(Object [][] data)\r
 333   {\r
 334     fr.setFeaturePriority( data );\r
 335     ap.repaint();\r
 336   }\r
 337 \r
 338   int selectedRow =-1;\r
 339 \r
 340 \r
 341   /////////////////////////////////////////////////////////////////////////\r
 342   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
 343   /////////////////////////////////////////////////////////////////////////\r
 344   class FeatureTableModel\r
 345       extends AbstractTableModel\r
 346   {\r
 347     FeatureTableModel(Object[][] data)\r
 348     {\r
 349       this.data = data;\r
 350     }\r
 351 \r
 352     private String[] columnNames = {"Feature Type", "Colour","Display"};\r
 353           private Object[][] data;\r
 354 \r
 355           public Object[][] getData()\r
 356           {\r
 357             return data;\r
 358           }\r
 359 \r
 360           public int getColumnCount() {\r
 361               return columnNames.length;\r
 362           }\r
 363 \r
 364           public Object[] getRow(int row)\r
 365           {\r
 366             return data[row];\r
 367           }\r
 368 \r
 369           public int getRowCount() {\r
 370               return data.length;\r
 371           }\r
 372 \r
 373           public String getColumnName(int col) {\r
 374               return columnNames[col];\r
 375           }\r
 376 \r
 377           public Object getValueAt(int row, int col) {\r
 378               return data[row][col];\r
 379           }\r
 380 \r
 381           public Class getColumnClass(int c) {\r
 382               return getValueAt(0, c).getClass();\r
 383           }\r
 384 \r
 385           public boolean isCellEditable(int row, int col) {\r
 386               return col==0 ? false:true;\r
 387           }\r
 388 \r
 389           public void setValueAt(Object value, int row, int col) {\r
 390               data[row][col] = value;\r
 391               fireTableCellUpdated(row, col);\r
 392               updateFeatureRenderer(data);\r
 393           }\r
 394 \r
 395     }\r
 396     class ColorRenderer extends JLabel\r
 397                               implements TableCellRenderer {\r
 398        javax.swing.border.Border unselectedBorder = null;\r
 399        javax.swing.border.Border selectedBorder = null;\r
 400 \r
 401        public ColorRenderer() {\r
 402            setOpaque(true); //MUST do this for background to show up.\r
 403        }\r
 404 \r
 405        public Component getTableCellRendererComponent(\r
 406                                JTable table, Object color,\r
 407                                boolean isSelected, boolean hasFocus,\r
 408                                int row, int column) {\r
 409            Color newColor = (Color)color;\r
 410            setBackground(newColor);\r
 411                if (isSelected) {\r
 412                    if (selectedBorder == null) {\r
 413                        selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 414                                                  table.getSelectionBackground());\r
 415                    }\r
 416                    setBorder(selectedBorder);\r
 417                } else {\r
 418                    if (unselectedBorder == null) {\r
 419                        unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 420                                                  table.getBackground());\r
 421                    }\r
 422                    setBorder(unselectedBorder);\r
 423                }\r
 424 \r
 425            setToolTipText("RGB value: " + newColor.getRed() + ", "\r
 426                                         + newColor.getGreen() + ", "\r
 427                                         + newColor.getBlue());\r
 428            return this;\r
 429        }\r
 430    }\r
 431 }\r
 432 \r
 433  class ColorEditor extends AbstractCellEditor\r
 434                           implements TableCellEditor,\r
 435                                      ActionListener {\r
 436      Color currentColor;\r
 437      JButton button;\r
 438      JColorChooser colorChooser;\r
 439      JDialog dialog;\r
 440      protected static final String EDIT = "edit";\r
 441 \r
 442      public ColorEditor() {\r
 443          //Set up the editor (from the table's point of view),\r
 444          //which is a button.\r
 445          //This button brings up the color chooser dialog,\r
 446          //which is the editor from the user's point of view.\r
 447          button = new JButton();\r
 448          button.setActionCommand(EDIT);\r
 449          button.addActionListener(this);\r
 450          button.setBorderPainted(false);\r
 451          //Set up the dialog that the button brings up.\r
 452          colorChooser = new JColorChooser();\r
 453          dialog = JColorChooser.createDialog(button,\r
 454                                          "Select new Colour",\r
 455                                          true,  //modal\r
 456                                          colorChooser,\r
 457                                          this,  //OK button handler\r
 458                                          null); //no CANCEL button handler\r
 459      }\r
 460 \r
 461      /**\r
 462       * Handles events from the editor button and from\r
 463       * the dialog's OK button.\r
 464       */\r
 465      public void actionPerformed(ActionEvent e) {\r
 466 \r
 467           if (EDIT.equals(e.getActionCommand())) {\r
 468              //The user has clicked the cell, so\r
 469              //bring up the dialog.\r
 470              button.setBackground(currentColor);\r
 471              colorChooser.setColor(currentColor);\r
 472              dialog.setVisible(true);\r
 473 \r
 474              //Make the renderer reappear.\r
 475              fireEditingStopped();\r
 476 \r
 477          } else { //User pressed dialog's "OK" button.\r
 478              currentColor = colorChooser.getColor();\r
 479          }\r
 480      }\r
 481 \r
 482      //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
 483      public Object getCellEditorValue() {\r
 484          return currentColor;\r
 485      }\r
 486 \r
 487      //Implement the one method defined by TableCellEditor.\r
 488      public Component getTableCellEditorComponent(JTable table,\r
 489                                                   Object value,\r
 490                                                   boolean isSelected,\r
 491                                                   int row,\r
 492                                                   int column) {\r
 493          currentColor = (Color)value;\r
 494          return button;\r
 495      }\r
 496 }\r