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