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