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