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().\r
 142         getSequenceFeatures();\r
 143     if (features == null)\r
 144       continue;\r
 145 \r
 146     e = features.elements();\r
 147     while (e.hasMoreElements())\r
 148     {\r
 149       sf = (SequenceFeature) e.nextElement();\r
 150       if (!allFeatures.contains(sf.getType()))\r
 151       {\r
 152         allFeatures.addElement(sf.getType());\r
 153       }\r
 154     }\r
 155   }\r
 156     if(allFeatures.size()<1)\r
 157      {\r
 158        try{\r
 159          frame.setClosed(true);\r
 160        }catch(Exception ex){}\r
 161        return;\r
 162      }\r
 163 \r
 164     int fSize = allFeatures.size();\r
 165 \r
 166     String type;\r
 167     boolean originalExists = false;\r
 168     if(originalData!=null)\r
 169       originalExists = true;\r
 170     else\r
 171       originalData = new Object[fSize][3];\r
 172 \r
 173     Object [][] data = new Object[fSize][3];\r
 174     for(int i=0; i<fSize; i++)\r
 175     {\r
 176       type = allFeatures.elementAt(i).toString();\r
 177       Color col = fr.getColour(type);\r
 178       data[i][0]=type;\r
 179       data[i][1]=col;\r
 180       if(fr.featuresDisplayed!=null)\r
 181          data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
 182       else\r
 183         data[i][2] = new Boolean(true);\r
 184 \r
 185       if(!originalExists)\r
 186       {\r
 187         originalData[i][0] = type;\r
 188         originalData[i][1] = col;\r
 189         if (fr.featuresDisplayed != null)\r
 190           originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
 191         else\r
 192           originalData[i][2] = new Boolean(true);\r
 193       }\r
 194     }\r
 195     ////////////////////////////////////\r
 196         //Now build the table\r
 197         table = new JTable(new FeatureTableModel(data));\r
 198         scrollPane.setViewportView(table);\r
 199         table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
 200         table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
 201         table.setDefaultRenderer(Color.class,\r
 202                              new ColorRenderer());\r
 203 \r
 204         table.setDefaultEditor(Color.class,\r
 205                           new ColorEditor());\r
 206 \r
 207         table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
 208 \r
 209         table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 210 \r
 211         table.addMouseListener(new MouseAdapter()\r
 212             {\r
 213               public void mousePressed(MouseEvent evt)\r
 214               {\r
 215                 selectedRow = table.rowAtPoint(evt.getPoint());\r
 216               }\r
 217             });\r
 218 \r
 219         table.addMouseMotionListener(new MouseMotionAdapter()\r
 220             {\r
 221               public void mouseDragged(MouseEvent evt)\r
 222               {\r
 223                 int newRow = table.rowAtPoint(evt.getPoint());\r
 224                 if(newRow!=selectedRow\r
 225                    && selectedRow!=-1\r
 226                    && newRow!=-1)\r
 227                 {\r
 228                   Object[] temp = new Object[3];\r
 229                   temp[0] = table.getValueAt(selectedRow, 0);\r
 230                   temp[1] = table.getValueAt(selectedRow, 1);\r
 231                   temp[2] = table.getValueAt(selectedRow, 2);\r
 232 \r
 233                   table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
 234                   table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
 235                   table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
 236 \r
 237                   table.setValueAt(temp[0], newRow, 0);\r
 238                   table.setValueAt(temp[1], newRow, 1);\r
 239                   table.setValueAt(temp[2], newRow, 2);\r
 240 \r
 241                   selectedRow = newRow;\r
 242                 }\r
 243               }\r
 244         });\r
 245 \r
 246   }\r
 247 \r
 248   void load()\r
 249   {\r
 250     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 251                  "LAST_DIRECTORY"), new String[] { "fc" },\r
 252              new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 253      chooser.setFileView(new jalview.io.JalviewFileView());\r
 254      chooser.setDialogTitle("Load Feature Colours");\r
 255      chooser.setToolTipText("Load");\r
 256 \r
 257      int value = chooser.showOpenDialog(this);\r
 258 \r
 259      if (value == JalviewFileChooser.APPROVE_OPTION)\r
 260      {\r
 261        File file = chooser.getSelectedFile();\r
 262 \r
 263        try\r
 264        {\r
 265          InputStreamReader in = new InputStreamReader(new FileInputStream(\r
 266              file), "UTF-8");\r
 267 \r
 268          jalview.binding.JalviewUserColours jucs = new jalview.binding.\r
 269              JalviewUserColours();\r
 270          jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
 271 \r
 272 \r
 273          for (int i = 0; i < jucs.getColourCount(); i++)\r
 274          {\r
 275            fr.setColour( jucs.getColour(i).getName(),\r
 276                           new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));\r
 277          }\r
 278 \r
 279          setTableData();\r
 280          ap.repaint();\r
 281        }\r
 282        catch (Exception ex)\r
 283        {\r
 284          System.out.println("Error loading User ColourFile\n" + ex);\r
 285        }\r
 286      }\r
 287   }\r
 288 \r
 289   void save()\r
 290   {\r
 291     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 292                 "LAST_DIRECTORY"), new String[] { "fc" },\r
 293             new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 294     chooser.setFileView(new jalview.io.JalviewFileView());\r
 295     chooser.setDialogTitle("Save Feature Colour Scheme");\r
 296     chooser.setToolTipText("Save");\r
 297 \r
 298     int value = chooser.showSaveDialog(this);\r
 299 \r
 300     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 301     {\r
 302         String choice = chooser.getSelectedFile().getPath();\r
 303         jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
 304         ucs.setSchemeName("Sequence Features");\r
 305         try\r
 306         {\r
 307             PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
 308                         new FileOutputStream(choice), "UTF-8"));\r
 309 \r
 310             Enumeration e = fr.featureColours.keys();\r
 311            while(e.hasMoreElements())\r
 312            {\r
 313 \r
 314 \r
 315                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 316                 col.setName(e.nextElement().toString());\r
 317                 col.setRGB(jalview.util.Format.getHexString(\r
 318                         fr.getColour(col.getName())));\r
 319                 ucs.addColour(col);\r
 320             }\r
 321 \r
 322             ucs.marshal(out);\r
 323             out.close();\r
 324         }\r
 325         catch (Exception ex)\r
 326         {\r
 327             ex.printStackTrace();\r
 328         }\r
 329     }\r
 330 \r
 331   }\r
 332 \r
 333   public void updateFeatureRenderer(Object [][] data)\r
 334   {\r
 335     fr.setFeaturePriority( data );\r
 336     ap.repaint();\r
 337 \r
 338     if(ap.overviewPanel!=null)\r
 339       ap.overviewPanel.updateOverviewImage();\r
 340   }\r
 341 \r
 342   int selectedRow =-1;\r
 343 \r
 344 \r
 345   /////////////////////////////////////////////////////////////////////////\r
 346   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
 347   /////////////////////////////////////////////////////////////////////////\r
 348   class FeatureTableModel\r
 349       extends AbstractTableModel\r
 350   {\r
 351     FeatureTableModel(Object[][] data)\r
 352     {\r
 353       this.data = data;\r
 354     }\r
 355 \r
 356     private String[] columnNames = {"Feature Type", "Colour","Display"};\r
 357           private Object[][] data;\r
 358 \r
 359           public Object[][] getData()\r
 360           {\r
 361             return data;\r
 362           }\r
 363 \r
 364           public int getColumnCount() {\r
 365               return columnNames.length;\r
 366           }\r
 367 \r
 368           public Object[] getRow(int row)\r
 369           {\r
 370             return data[row];\r
 371           }\r
 372 \r
 373           public int getRowCount() {\r
 374               return data.length;\r
 375           }\r
 376 \r
 377           public String getColumnName(int col) {\r
 378               return columnNames[col];\r
 379           }\r
 380 \r
 381           public Object getValueAt(int row, int col) {\r
 382               return data[row][col];\r
 383           }\r
 384 \r
 385           public Class getColumnClass(int c) {\r
 386               return getValueAt(0, c).getClass();\r
 387           }\r
 388 \r
 389           public boolean isCellEditable(int row, int col) {\r
 390               return col==0 ? false:true;\r
 391           }\r
 392 \r
 393           public void setValueAt(Object value, int row, int col) {\r
 394               data[row][col] = value;\r
 395               fireTableCellUpdated(row, col);\r
 396               updateFeatureRenderer(data);\r
 397           }\r
 398 \r
 399     }\r
 400     class ColorRenderer extends JLabel\r
 401                               implements TableCellRenderer {\r
 402        javax.swing.border.Border unselectedBorder = null;\r
 403        javax.swing.border.Border selectedBorder = null;\r
 404 \r
 405        public ColorRenderer() {\r
 406            setOpaque(true); //MUST do this for background to show up.\r
 407        }\r
 408 \r
 409        public Component getTableCellRendererComponent(\r
 410                                JTable table, Object color,\r
 411                                boolean isSelected, boolean hasFocus,\r
 412                                int row, int column) {\r
 413            Color newColor = (Color)color;\r
 414            setBackground(newColor);\r
 415                if (isSelected) {\r
 416                    if (selectedBorder == null) {\r
 417                        selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 418                                                  table.getSelectionBackground());\r
 419                    }\r
 420                    setBorder(selectedBorder);\r
 421                } else {\r
 422                    if (unselectedBorder == null) {\r
 423                        unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 424                                                  table.getBackground());\r
 425                    }\r
 426                    setBorder(unselectedBorder);\r
 427                }\r
 428 \r
 429            setToolTipText("RGB value: " + newColor.getRed() + ", "\r
 430                                         + newColor.getGreen() + ", "\r
 431                                         + newColor.getBlue());\r
 432            return this;\r
 433        }\r
 434    }\r
 435 }\r
 436 \r
 437  class ColorEditor extends AbstractCellEditor\r
 438                           implements TableCellEditor,\r
 439                                      ActionListener {\r
 440      Color currentColor;\r
 441      JButton button;\r
 442      JColorChooser colorChooser;\r
 443      JDialog dialog;\r
 444      protected static final String EDIT = "edit";\r
 445 \r
 446      public ColorEditor() {\r
 447          //Set up the editor (from the table's point of view),\r
 448          //which is a button.\r
 449          //This button brings up the color chooser dialog,\r
 450          //which is the editor from the user's point of view.\r
 451          button = new JButton();\r
 452          button.setActionCommand(EDIT);\r
 453          button.addActionListener(this);\r
 454          button.setBorderPainted(false);\r
 455          //Set up the dialog that the button brings up.\r
 456          colorChooser = new JColorChooser();\r
 457          dialog = JColorChooser.createDialog(button,\r
 458                                          "Select new Colour",\r
 459                                          true,  //modal\r
 460                                          colorChooser,\r
 461                                          this,  //OK button handler\r
 462                                          null); //no CANCEL button handler\r
 463      }\r
 464 \r
 465      /**\r
 466       * Handles events from the editor button and from\r
 467       * the dialog's OK button.\r
 468       */\r
 469      public void actionPerformed(ActionEvent e) {\r
 470 \r
 471           if (EDIT.equals(e.getActionCommand())) {\r
 472              //The user has clicked the cell, so\r
 473              //bring up the dialog.\r
 474              button.setBackground(currentColor);\r
 475              colorChooser.setColor(currentColor);\r
 476              dialog.setVisible(true);\r
 477 \r
 478              //Make the renderer reappear.\r
 479              fireEditingStopped();\r
 480 \r
 481          } else { //User pressed dialog's "OK" button.\r
 482              currentColor = colorChooser.getColor();\r
 483          }\r
 484      }\r
 485 \r
 486      //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
 487      public Object getCellEditorValue() {\r
 488          return currentColor;\r
 489      }\r
 490 \r
 491      //Implement the one method defined by TableCellEditor.\r
 492      public Component getTableCellEditorComponent(JTable table,\r
 493                                                   Object value,\r
 494                                                   boolean isSelected,\r
 495                                                   int row,\r
 496                                                   int column) {\r
 497          currentColor = (Color)value;\r
 498          return button;\r
 499      }\r
 500 }\r