src/jalview/gui/FeatureSettings.java

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