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