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