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   JPanel groupPanel;\r
  43 \r
  44   boolean alignmentHasFeatures = false;\r
  45 \r
  46   public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
  47   {\r
  48     this.ap = ap;\r
  49     this.av = av;\r
  50     fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
  51     av.alignment.getSequences();\r
  52     frame = new JInternalFrame();\r
  53     frame.setContentPane(this);\r
  54     Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
  55     frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
  56 \r
  57     setTableData();\r
  58 \r
  59     final JSlider transparency = new JSlider(0, 70, 100 - (int)(fr.transparency*100)   );\r
  60     transparency.addChangeListener(new ChangeListener()\r
  61     {\r
  62       public void stateChanged(ChangeEvent evt)\r
  63       {\r
  64         fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
  65         ap.repaint();\r
  66       }\r
  67     });\r
  68 \r
  69     JPanel transPanel = new JPanel(new FlowLayout());\r
  70     transPanel.add(new JLabel("Transparency"));\r
  71     transPanel.add(transparency);\r
  72     JButton button = new JButton("Invert Selection");\r
  73     transPanel.add(button);\r
  74     button.addActionListener(new ActionListener()\r
  75         {\r
  76           public void actionPerformed(ActionEvent evt)\r
  77           {\r
  78             invertSelection();\r
  79           }\r
  80         });\r
  81 \r
  82     //////////////////////////////////////////////\r
  83     //We're going to need those OK cancel buttons\r
  84     JPanel buttonPanel = new JPanel(new FlowLayout());\r
  85     button = new JButton("OK");\r
  86     button.addActionListener(new ActionListener()\r
  87     {\r
  88       public void actionPerformed(ActionEvent evt)\r
  89       {\r
  90         try\r
  91         {\r
  92           frame.setClosed(true);\r
  93         }\r
  94         catch (Exception exe)\r
  95         {}\r
  96       }\r
  97     });\r
  98     buttonPanel.add(button);\r
  99     button = new JButton("Cancel");\r
 100     button.addActionListener(new ActionListener()\r
 101     {\r
 102       public void actionPerformed(ActionEvent evt)\r
 103       {\r
 104         try\r
 105         {\r
 106           updateFeatureRenderer(originalData);\r
 107           frame.setClosed(true);\r
 108         }\r
 109         catch (Exception exe)\r
 110         {}\r
 111       }\r
 112     });\r
 113     buttonPanel.add(button);\r
 114 \r
 115     button = new JButton("Load Colours");\r
 116     button.addActionListener(new ActionListener()\r
 117     {\r
 118       public void actionPerformed(ActionEvent evt)\r
 119       {\r
 120         load();\r
 121       }\r
 122     });\r
 123     buttonPanel.add(button);\r
 124     button = new JButton("Save Colours");\r
 125     button.addActionListener(new ActionListener()\r
 126     {\r
 127       public void actionPerformed(ActionEvent evt)\r
 128       {\r
 129         save();\r
 130       }\r
 131     });\r
 132     buttonPanel.add(button);\r
 133 \r
 134     this.setLayout(new BorderLayout());\r
 135     JPanel bigPanel = new JPanel(new BorderLayout());\r
 136     bigPanel.add(transPanel, BorderLayout.SOUTH);\r
 137     bigPanel.add(scrollPane, BorderLayout.CENTER);\r
 138     if(groupPanel!=null)\r
 139     {\r
 140       groupPanel.setLayout(\r
 141           new GridLayout(fr.featureGroups.size() / 4 + 1, 4));\r
 142 \r
 143       groupPanel.validate();\r
 144       bigPanel.add(groupPanel, BorderLayout.NORTH);\r
 145     }\r
 146     add(bigPanel, BorderLayout.CENTER);\r
 147     add(buttonPanel, BorderLayout.SOUTH);\r
 148 \r
 149 \r
 150   }\r
 151 \r
 152   void setTableData()\r
 153   {\r
 154     alignmentHasFeatures = false;\r
 155 \r
 156     if (fr.featureGroups == null)\r
 157       fr.featureGroups = new Hashtable();\r
 158 \r
 159     Vector allFeatures = new Vector();\r
 160     Vector allGroups = new Vector();\r
 161     SequenceFeature[] tmpfeatures;\r
 162     String group;\r
 163 \r
 164     for (int i = 0; i < av.alignment.getHeight(); i++)\r
 165     {\r
 166       if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
 167         continue;\r
 168 \r
 169       alignmentHasFeatures = true;\r
 170 \r
 171       tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 172 \r
 173       int index = 0;\r
 174       while (index < tmpfeatures.length)\r
 175       {\r
 176         if(tmpfeatures[index].begin == 0 && tmpfeatures[index].end ==0)\r
 177         {\r
 178           index++;\r
 179           continue;\r
 180         }\r
 181 \r
 182         if(tmpfeatures[index].getFeatureGroup()!=null)\r
 183         {\r
 184           group = tmpfeatures[index].featureGroup;\r
 185           if(!allGroups.contains(group))\r
 186            {\r
 187              allGroups.addElement(group);\r
 188 \r
 189              boolean visible = true;\r
 190              if (fr.featureGroups.containsKey(group))\r
 191              {\r
 192                visible = ( (Boolean) fr.featureGroups.get(group)).booleanValue();\r
 193              }\r
 194 \r
 195              fr.featureGroups.put(group, new Boolean(visible));\r
 196 \r
 197              if (groupPanel == null)\r
 198              {\r
 199                groupPanel = new JPanel();\r
 200              }\r
 201 \r
 202              final JCheckBox check = new JCheckBox(group, visible);\r
 203              check.setFont(new Font("Serif", Font.BOLD, 12));\r
 204              check.addItemListener(new ItemListener()\r
 205              {\r
 206                public void itemStateChanged(ItemEvent evt)\r
 207                {\r
 208                  fr.featureGroups.put(check.getText(),\r
 209                                       new Boolean(check.isSelected()));\r
 210                  ap.seqPanel.seqCanvas.repaint();\r
 211                  if (ap.overviewPanel != null)\r
 212                    ap.overviewPanel.updateOverviewImage();\r
 213 \r
 214                  resetTable(true);\r
 215                }\r
 216              });\r
 217              groupPanel.add(check);\r
 218 \r
 219            }\r
 220 \r
 221        }\r
 222 \r
 223        if (!allFeatures.contains(tmpfeatures[index].getType()))\r
 224        {\r
 225            allFeatures.addElement(tmpfeatures[index].getType());\r
 226        }\r
 227        index ++;\r
 228     }\r
 229   }\r
 230 \r
 231 \r
 232     if(!alignmentHasFeatures)\r
 233      {\r
 234        try\r
 235        { frame.setClosed(true);  }\r
 236        catch (Exception ex){}\r
 237 \r
 238        JOptionPane.showInternalMessageDialog(\r
 239            Desktop.desktop, "No features have been added to this alignment!",\r
 240            "No Sequence Features", JOptionPane.WARNING_MESSAGE);\r
 241 \r
 242        return;\r
 243      }\r
 244 \r
 245      resetTable(false);\r
 246   }\r
 247 \r
 248   void resetTable(boolean groupsChanged)\r
 249   {\r
 250    SequenceFeature [] tmpfeatures;\r
 251    String group=null, type;\r
 252    Vector visibleChecks = new Vector();\r
 253 \r
 254    //Find out which features should be visible depending on which groups\r
 255    //are selected / deselected\r
 256     for (int i = 0; i < av.alignment.getHeight(); i++)\r
 257     {\r
 258         if (av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures() == null)\r
 259           continue;\r
 260 \r
 261         tmpfeatures = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 262         int index = 0;\r
 263         while (index < tmpfeatures.length)\r
 264         {\r
 265           group = tmpfeatures[index].featureGroup;\r
 266 \r
 267           if(tmpfeatures[index].begin==0 && tmpfeatures[index].end==0)\r
 268           {\r
 269             index ++;\r
 270             continue;\r
 271           }\r
 272 \r
 273           if (group==null || fr.featureGroups.get(group)==null ||\r
 274               ((Boolean) fr.featureGroups.get(group)).booleanValue())\r
 275           {\r
 276             type = tmpfeatures[index].getType();\r
 277             if(!visibleChecks.contains(type) )\r
 278             {\r
 279               visibleChecks.addElement(type);\r
 280             }\r
 281           }\r
 282           index++;\r
 283         }\r
 284     }\r
 285 \r
 286     int fSize = visibleChecks.size();\r
 287     Object [][] data = new Object[fSize][3];\r
 288     int dataIndex = 0;\r
 289 \r
 290     if(fr.renderOrder!=null)\r
 291     {\r
 292       //First add the checks in the previous render order,\r
 293       //in case the window has been closed and reopened\r
 294       for(int ro=fr.renderOrder.length-1; ro>-1; ro--)\r
 295       {\r
 296            type = fr.renderOrder[ro];\r
 297 \r
 298            if(!visibleChecks.contains(type))\r
 299              continue;\r
 300 \r
 301            data[dataIndex][0] = type;\r
 302            data[dataIndex][1] = fr.getColour(type);\r
 303            data[dataIndex][2] = new Boolean(av.featuresDisplayed.containsKey(type));\r
 304            dataIndex++;\r
 305            visibleChecks.removeElement(type);\r
 306       }\r
 307     }\r
 308 \r
 309     fSize = visibleChecks.size();\r
 310     for(int i=0; i<fSize; i++)\r
 311     {\r
 312       //These must be extra features belonging to the group\r
 313       //which was just selected\r
 314       type = visibleChecks.elementAt(i).toString();\r
 315       data[dataIndex][0] = type;\r
 316 \r
 317       if(fr.getColour(type)==null)\r
 318         fr.createRandomColour(type);\r
 319 \r
 320       data[dataIndex][1] = fr.getColour(type);\r
 321       data[dataIndex][2] = new Boolean(true);\r
 322       dataIndex++;\r
 323     }\r
 324 \r
 325     if(originalData==null)\r
 326     {\r
 327       originalData = new Object[data.length][3];\r
 328       System.arraycopy(data,0,originalData,0,data.length);\r
 329     }\r
 330 \r
 331     table = new JTable(new FeatureTableModel(data));\r
 332     scrollPane.setViewportView(table);\r
 333     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
 334     table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
 335     table.setDefaultRenderer(Color.class,\r
 336                          new ColorRenderer());\r
 337 \r
 338     table.setDefaultEditor(Color.class,\r
 339                       new ColorEditor());\r
 340 \r
 341     table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
 342 \r
 343     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
 344 \r
 345     table.addMouseListener(new MouseAdapter()\r
 346         {\r
 347           public void mousePressed(MouseEvent evt)\r
 348           {\r
 349             selectedRow = table.rowAtPoint(evt.getPoint());\r
 350           }\r
 351         });\r
 352 \r
 353     table.addMouseMotionListener(new MouseMotionAdapter()\r
 354         {\r
 355           public void mouseDragged(MouseEvent evt)\r
 356           {\r
 357             int newRow = table.rowAtPoint(evt.getPoint());\r
 358             if(newRow!=selectedRow\r
 359                && selectedRow!=-1\r
 360                && newRow!=-1)\r
 361             {\r
 362               Object[] temp = new Object[3];\r
 363               temp[0] = table.getValueAt(selectedRow, 0);\r
 364               temp[1] = table.getValueAt(selectedRow, 1);\r
 365               temp[2] = table.getValueAt(selectedRow, 2);\r
 366 \r
 367               table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
 368               table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
 369               table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
 370 \r
 371               table.setValueAt(temp[0], newRow, 0);\r
 372               table.setValueAt(temp[1], newRow, 1);\r
 373               table.setValueAt(temp[2], newRow, 2);\r
 374 \r
 375               selectedRow = newRow;\r
 376             }\r
 377           }\r
 378     });\r
 379 \r
 380     updateFeatureRenderer(data);\r
 381 \r
 382   }\r
 383 \r
 384   void load()\r
 385   {\r
 386     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 387                  "LAST_DIRECTORY"), new String[] { "fc" },\r
 388              new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 389      chooser.setFileView(new jalview.io.JalviewFileView());\r
 390      chooser.setDialogTitle("Load Feature Colours");\r
 391      chooser.setToolTipText("Load");\r
 392 \r
 393      int value = chooser.showOpenDialog(this);\r
 394 \r
 395      if (value == JalviewFileChooser.APPROVE_OPTION)\r
 396      {\r
 397        File file = chooser.getSelectedFile();\r
 398 \r
 399        try\r
 400        {\r
 401          InputStreamReader in = new InputStreamReader(new FileInputStream(\r
 402              file), "UTF-8");\r
 403 \r
 404          jalview.binding.JalviewUserColours jucs = new jalview.binding.\r
 405              JalviewUserColours();\r
 406          jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
 407 \r
 408 \r
 409          for (int i = 0; i < jucs.getColourCount(); i++)\r
 410          {\r
 411            fr.setColour( jucs.getColour(i).getName(),\r
 412                           new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));\r
 413          }\r
 414 \r
 415          setTableData();\r
 416          ap.repaint();\r
 417        }\r
 418        catch (Exception ex)\r
 419        {\r
 420          System.out.println("Error loading User ColourFile\n" + ex);\r
 421        }\r
 422      }\r
 423   }\r
 424 \r
 425   void save()\r
 426   {\r
 427     JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 428                 "LAST_DIRECTORY"), new String[] { "fc" },\r
 429             new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
 430     chooser.setFileView(new jalview.io.JalviewFileView());\r
 431     chooser.setDialogTitle("Save Feature Colour Scheme");\r
 432     chooser.setToolTipText("Save");\r
 433 \r
 434     int value = chooser.showSaveDialog(this);\r
 435 \r
 436     if (value == JalviewFileChooser.APPROVE_OPTION)\r
 437     {\r
 438         String choice = chooser.getSelectedFile().getPath();\r
 439         jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
 440         ucs.setSchemeName("Sequence Features");\r
 441         try\r
 442         {\r
 443             PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
 444                         new FileOutputStream(choice), "UTF-8"));\r
 445 \r
 446             Enumeration e = fr.featureColours.keys();\r
 447            while(e.hasMoreElements())\r
 448            {\r
 449                 jalview.binding.Colour col = new jalview.binding.Colour();\r
 450                 col.setName(e.nextElement().toString());\r
 451                 col.setRGB(jalview.util.Format.getHexString(\r
 452                         fr.getColour(col.getName())));\r
 453                 ucs.addColour(col);\r
 454             }\r
 455 \r
 456             ucs.marshal(out);\r
 457             out.close();\r
 458         }\r
 459         catch (Exception ex)\r
 460         {\r
 461             ex.printStackTrace();\r
 462         }\r
 463     }\r
 464   }\r
 465 \r
 466   public void invertSelection()\r
 467   {\r
 468     for(int i=0; i<table.getRowCount(); i++)\r
 469     {\r
 470       Boolean value = (Boolean)table.getValueAt(i,2);\r
 471 \r
 472       table.setValueAt(\r
 473           new Boolean(!value.booleanValue()),\r
 474                        i,2);\r
 475     }\r
 476 \r
 477   }\r
 478 \r
 479   public void updateFeatureRenderer(Object [][] data)\r
 480   {\r
 481     fr.setFeaturePriority( data );\r
 482     ap.repaint();\r
 483 \r
 484     if(ap.overviewPanel!=null)\r
 485       ap.overviewPanel.updateOverviewImage();\r
 486   }\r
 487 \r
 488   int selectedRow =-1;\r
 489 \r
 490 \r
 491   /////////////////////////////////////////////////////////////////////////\r
 492   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
 493   /////////////////////////////////////////////////////////////////////////\r
 494   class FeatureTableModel\r
 495       extends AbstractTableModel\r
 496   {\r
 497     FeatureTableModel(Object[][] data)\r
 498     {\r
 499       this.data = data;\r
 500     }\r
 501 \r
 502     private String[] columnNames = {"Feature Type", "Colour","Display"};\r
 503           private Object[][] data;\r
 504 \r
 505           public Object[][] getData()\r
 506           {\r
 507             return data;\r
 508           }\r
 509 \r
 510           public void setData(Object[][] data)\r
 511           {\r
 512             this.data = data;\r
 513           }\r
 514 \r
 515           public int getColumnCount() {\r
 516               return columnNames.length;\r
 517           }\r
 518 \r
 519           public Object[] getRow(int row)\r
 520           {\r
 521             return data[row];\r
 522           }\r
 523 \r
 524           public int getRowCount() {\r
 525               return data.length;\r
 526           }\r
 527 \r
 528           public String getColumnName(int col) {\r
 529               return columnNames[col];\r
 530           }\r
 531 \r
 532           public Object getValueAt(int row, int col) {\r
 533               return data[row][col];\r
 534           }\r
 535 \r
 536           public Class getColumnClass(int c) {\r
 537               return getValueAt(0, c).getClass();\r
 538           }\r
 539 \r
 540           public boolean isCellEditable(int row, int col) {\r
 541               return col==0 ? false:true;\r
 542           }\r
 543 \r
 544           public void setValueAt(Object value, int row, int col) {\r
 545               data[row][col] = value;\r
 546               fireTableCellUpdated(row, col);\r
 547               updateFeatureRenderer(data);\r
 548           }\r
 549 \r
 550     }\r
 551     class ColorRenderer extends JLabel\r
 552                               implements TableCellRenderer {\r
 553        javax.swing.border.Border unselectedBorder = null;\r
 554        javax.swing.border.Border selectedBorder = null;\r
 555 \r
 556        public ColorRenderer() {\r
 557            setOpaque(true); //MUST do this for background to show up.\r
 558        }\r
 559 \r
 560        public Component getTableCellRendererComponent(\r
 561                                JTable table, Object color,\r
 562                                boolean isSelected, boolean hasFocus,\r
 563                                int row, int column) {\r
 564            Color newColor = (Color)color;\r
 565            setBackground(newColor);\r
 566                if (isSelected) {\r
 567                    if (selectedBorder == null) {\r
 568                        selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 569                                                  table.getSelectionBackground());\r
 570                    }\r
 571                    setBorder(selectedBorder);\r
 572                } else {\r
 573                    if (unselectedBorder == null) {\r
 574                        unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
 575                                                  table.getBackground());\r
 576                    }\r
 577                    setBorder(unselectedBorder);\r
 578                }\r
 579 \r
 580            setToolTipText("RGB value: " + newColor.getRed() + ", "\r
 581                                         + newColor.getGreen() + ", "\r
 582                                         + newColor.getBlue());\r
 583            return this;\r
 584        }\r
 585    }\r
 586 }\r
 587 \r
 588  class ColorEditor extends AbstractCellEditor\r
 589                           implements TableCellEditor,\r
 590                                      ActionListener {\r
 591      Color currentColor;\r
 592      JButton button;\r
 593      JColorChooser colorChooser;\r
 594      JDialog dialog;\r
 595      protected static final String EDIT = "edit";\r
 596 \r
 597      public ColorEditor() {\r
 598          //Set up the editor (from the table's point of view),\r
 599          //which is a button.\r
 600          //This button brings up the color chooser dialog,\r
 601          //which is the editor from the user's point of view.\r
 602          button = new JButton();\r
 603          button.setActionCommand(EDIT);\r
 604          button.addActionListener(this);\r
 605          button.setBorderPainted(false);\r
 606          //Set up the dialog that the button brings up.\r
 607          colorChooser = new JColorChooser();\r
 608          dialog = JColorChooser.createDialog(button,\r
 609                                          "Select new Colour",\r
 610                                          true,  //modal\r
 611                                          colorChooser,\r
 612                                          this,  //OK button handler\r
 613                                          null); //no CANCEL button handler\r
 614      }\r
 615 \r
 616      /**\r
 617       * Handles events from the editor button and from\r
 618       * the dialog's OK button.\r
 619       */\r
 620      public void actionPerformed(ActionEvent e) {\r
 621 \r
 622           if (EDIT.equals(e.getActionCommand())) {\r
 623              //The user has clicked the cell, so\r
 624              //bring up the dialog.\r
 625              button.setBackground(currentColor);\r
 626              colorChooser.setColor(currentColor);\r
 627              dialog.setVisible(true);\r
 628 \r
 629              //Make the renderer reappear.\r
 630              fireEditingStopped();\r
 631 \r
 632          } else { //User pressed dialog's "OK" button.\r
 633              currentColor = colorChooser.getColor();\r
 634          }\r
 635      }\r
 636 \r
 637      //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
 638      public Object getCellEditorValue() {\r
 639          return currentColor;\r
 640      }\r
 641 \r
 642      //Implement the one method defined by TableCellEditor.\r
 643      public Component getTableCellEditorComponent(JTable table,\r
 644                                                   Object value,\r
 645                                                   boolean isSelected,\r
 646                                                   int row,\r
 647                                                   int column) {\r
 648          currentColor = (Color)value;\r
 649          return button;\r
 650      }\r
 651 }\r