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