src/jalview/gui/FeatureSettings.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.api.FeatureColourI;
  24 import jalview.api.FeatureSettingsControllerI;
  25 import jalview.bin.Cache;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.Help.HelpId;
  29 import jalview.io.JalviewFileChooser;
  30 import jalview.schemabinding.version2.JalviewUserColours;
  31 import jalview.schemes.FeatureColour;
  32 import jalview.util.Format;
  33 import jalview.util.MessageManager;
  34 import jalview.util.Platform;
  35 import jalview.util.QuickSort;
  36 import jalview.viewmodel.AlignmentViewport;
  37 import jalview.ws.dbsources.das.api.jalviewSourceI;
  38
  39 import java.awt.BorderLayout;
  40 import java.awt.Color;
  41 import java.awt.Component;
  42 import java.awt.Font;
  43 import java.awt.Graphics;
  44 import java.awt.GridLayout;
  45 import java.awt.Rectangle;
  46 import java.awt.event.ActionEvent;
  47 import java.awt.event.ActionListener;
  48 import java.awt.event.ItemEvent;
  49 import java.awt.event.ItemListener;
  50 import java.awt.event.MouseAdapter;
  51 import java.awt.event.MouseEvent;
  52 import java.awt.event.MouseMotionAdapter;
  53 import java.beans.PropertyChangeEvent;
  54 import java.beans.PropertyChangeListener;
  55 import java.io.File;
  56 import java.io.FileInputStream;
  57 import java.io.FileOutputStream;
  58 import java.io.InputStreamReader;
  59 import java.io.OutputStreamWriter;
  60 import java.io.PrintWriter;
  61 import java.util.Arrays;
  62 import java.util.Hashtable;
  63 import java.util.Iterator;
  64 import java.util.List;
  65 import java.util.Map;
  66 import java.util.Set;
  67 import java.util.Vector;
  68
  69 import javax.help.HelpSetException;
  70 import javax.swing.AbstractCellEditor;
  71 import javax.swing.BorderFactory;
  72 import javax.swing.Icon;
  73 import javax.swing.JButton;
  74 import javax.swing.JCheckBox;
  75 import javax.swing.JCheckBoxMenuItem;
  76 import javax.swing.JColorChooser;
  77 import javax.swing.JDialog;
  78 import javax.swing.JInternalFrame;
  79 import javax.swing.JLabel;
  80 import javax.swing.JLayeredPane;
  81 import javax.swing.JMenuItem;
  82 import javax.swing.JOptionPane;
  83 import javax.swing.JPanel;
  84 import javax.swing.JPopupMenu;
  85 import javax.swing.JScrollPane;
  86 import javax.swing.JSlider;
  87 import javax.swing.JTabbedPane;
  88 import javax.swing.JTable;
  89 import javax.swing.ListSelectionModel;
  90 import javax.swing.SwingConstants;
  91 import javax.swing.SwingUtilities;
  92 import javax.swing.event.ChangeEvent;
  93 import javax.swing.event.ChangeListener;
  94 import javax.swing.table.AbstractTableModel;
  95 import javax.swing.table.TableCellEditor;
  96 import javax.swing.table.TableCellRenderer;
  97
  98 public class FeatureSettings extends JPanel implements
  99         FeatureSettingsControllerI
 100 {
 101   DasSourceBrowser dassourceBrowser;
 102
 103   jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
 104
 105   JPanel settingsPane = new JPanel();
 106
 107   JPanel dasSettingsPane = new JPanel();
 108
 109   final FeatureRenderer fr;
 110
 111   public final AlignFrame af;
 112
 113   Object[][] originalData;
 114
 115   private float originalTransparency;
 116
 117   final JInternalFrame frame;
 118
 119   JScrollPane scrollPane = new JScrollPane();
 120
 121   JTable table;
 122
 123   JPanel groupPanel;
 124
 125   JSlider transparency = new JSlider();
 126
 127   JPanel transPanel = new JPanel(new GridLayout(1, 2));
 128
 129   public FeatureSettings(AlignFrame af)
 130   {
 131     this.af = af;
 132     fr = af.getFeatureRenderer();
 133     // allow transparency to be recovered
 134     transparency.setMaximum(100 - (int) ((originalTransparency = fr
 135             .getTransparency()) * 100));
 136
 137     try
 138     {
 139       jbInit();
 140     } catch (Exception ex)
 141     {
 142       ex.printStackTrace();
 143     }
 144
 145     table = new JTable()
 146     {
 147       @Override
 148       public String getToolTipText(MouseEvent e)
 149       {
 150         if (table.columnAtPoint(e.getPoint()) == 0)
 151         {
 152           /*
 153            * Tooltip for feature name only
 154            */
 155           return JvSwingUtils.wrapTooltip(true, MessageManager
 156                   .getString("label.feature_settings_click_drag"));
 157         }
 158         return null;
 159       }
 160     };
 161     table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));
 162     table.setFont(new Font("Verdana", Font.PLAIN, 12));
 163     table.setDefaultRenderer(Color.class, new ColorRenderer());
 164
 165     table.setDefaultEditor(Color.class, new ColorEditor(this));
 166
 167     table.setDefaultEditor(FeatureColour.class, new ColorEditor(this));
 168     table.setDefaultRenderer(FeatureColour.class, new ColorRenderer());
 169     table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 170
 171     table.addMouseListener(new MouseAdapter()
 172     {
 173       @Override
 174       public void mousePressed(MouseEvent evt)
 175       {
 176         selectedRow = table.rowAtPoint(evt.getPoint());
 177         if (evt.isPopupTrigger())
 178         {
 179           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 180                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 181                   evt.getX(), evt.getY());
 182         }
 183         else if (evt.getClickCount() == 2)
 184         {
 185           boolean invertSelection = evt.isAltDown();
 186           boolean toggleSelection = Platform.isControlDown(evt);
 187           boolean extendSelection = evt.isShiftDown();
 188           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
 189                   invertSelection, extendSelection, toggleSelection,
 190                   (String) table.getValueAt(selectedRow, 0));
 191         }
 192       }
 193
 194       // isPopupTrigger fires on mouseReleased on Windows
 195       @Override
 196       public void mouseReleased(MouseEvent evt)
 197       {
 198         selectedRow = table.rowAtPoint(evt.getPoint());
 199         if (evt.isPopupTrigger())
 200         {
 201           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
 202                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
 203                   evt.getX(), evt.getY());
 204         }
 205       }
 206     });
 207
 208     table.addMouseMotionListener(new MouseMotionAdapter()
 209     {
 210       @Override
 211       public void mouseDragged(MouseEvent evt)
 212       {
 213         int newRow = table.rowAtPoint(evt.getPoint());
 214         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
 215         {
 216           /*
 217            * reposition 'selectedRow' to 'newRow' (the dragged to location)
 218            * this could be more than one row away for a very fast drag action
 219            * so just swap it with adjacent rows until we get it there
 220            */
 221           Object[][] data = ((FeatureTableModel) table.getModel())
 222                   .getData();
 223           int direction = newRow < selectedRow ? -1 : 1;
 224           for (int i = selectedRow; i != newRow; i += direction)
 225           {
 226             Object[] temp = data[i];
 227             data[i] = data[i + direction];
 228             data[i + direction] = temp;
 229           }
 230           updateFeatureRenderer(data);
 231           table.repaint();
 232           selectedRow = newRow;
 233         }
 234       }
 235     });
 236     // table.setToolTipText(JvSwingUtils.wrapTooltip(true,
 237     // MessageManager.getString("label.feature_settings_click_drag")));
 238     scrollPane.setViewportView(table);
 239
 240     dassourceBrowser = new DasSourceBrowser(this);
 241     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 242
 243     if (af.getViewport().isShowSequenceFeatures() || !fr.hasRenderOrder())
 244     {
 245       fr.findAllFeatures(true); // display everything!
 246     }
 247
 248     discoverAllFeatureData();
 249     final PropertyChangeListener change;
 250     final FeatureSettings fs = this;
 251     fr.addPropertyChangeListener(change = new PropertyChangeListener()
 252     {
 253       @Override
 254       public void propertyChange(PropertyChangeEvent evt)
 255       {
 256         if (!fs.resettingTable && !fs.handlingUpdate)
 257         {
 258           fs.handlingUpdate = true;
 259           fs.resetTable(null); // new groups may be added with new seuqence
 260           // feature types only
 261           fs.handlingUpdate = false;
 262         }
 263       }
 264
 265     });
 266
 267     frame = new JInternalFrame();
 268     frame.setContentPane(this);
 269     if (Platform.isAMac())
 270     {
 271       Desktop.addInternalFrame(frame,
 272               MessageManager.getString("label.sequence_feature_settings"),
 273               475, 480);
 274     }
 275     else
 276     {
 277       Desktop.addInternalFrame(frame,
 278               MessageManager.getString("label.sequence_feature_settings"),
 279               400, 450);
 280     }
 281
 282     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
 283     {
 284       @Override
 285       public void internalFrameClosed(
 286               javax.swing.event.InternalFrameEvent evt)
 287       {
 288         fr.removePropertyChangeListener(change);
 289         dassourceBrowser.fs = null;
 290       };
 291     });
 292     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 293   }
 294
 295   protected void popupSort(final int selectedRow, final String type,
 296           final Object typeCol, final Map<String, float[][]> minmax, int x,
 297           int y)
 298   {
 299     final FeatureColourI featureColour = (FeatureColourI) typeCol;
 300
 301     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
 302             "label.settings_for_param", new String[] { type }));
 303     JMenuItem scr = new JMenuItem(
 304             MessageManager.getString("label.sort_by_score"));
 305     men.add(scr);
 306     final FeatureSettings me = this;
 307     scr.addActionListener(new ActionListener()
 308     {
 309
 310       @Override
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         me.af.avc.sortAlignmentByFeatureScore(Arrays
 314                 .asList(new String[] { type }));
 315       }
 316
 317     });
 318     JMenuItem dens = new JMenuItem(
 319             MessageManager.getString("label.sort_by_density"));
 320     dens.addActionListener(new ActionListener()
 321     {
 322
 323       @Override
 324       public void actionPerformed(ActionEvent e)
 325       {
 326         me.af.avc.sortAlignmentByFeatureDensity(Arrays
 327                 .asList(new String[] { type }));
 328       }
 329
 330     });
 331     men.add(dens);
 332     if (minmax != null)
 333     {
 334       final float[][] typeMinMax = minmax.get(type);
 335       /*
 336        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
 337        * this is broken at the moment and isn't that useful anyway!
 338        * chb.setSelected(minmax.get(type) != null); chb.addActionListener(new
 339        * ActionListener() {
 340        *
 341        * public void actionPerformed(ActionEvent e) {
 342        * chb.setState(chb.getState()); if (chb.getState()) { minmax.put(type,
 343        * null); } else { minmax.put(type, typeMinMax); } }
 344        *
 345        * });
 346        *
 347        * men.add(chb);
 348        */
 349       if (typeMinMax != null && typeMinMax[0] != null)
 350       {
 351         // if (table.getValueAt(row, column));
 352         // graduated colourschemes for those where minmax exists for the
 353         // positional features
 354         final JCheckBoxMenuItem mxcol = new JCheckBoxMenuItem(
 355                 "Graduated Colour");
 356         mxcol.setSelected(!featureColour.isSimpleColour());
 357         men.add(mxcol);
 358         mxcol.addActionListener(new ActionListener()
 359         {
 360           JColorChooser colorChooser;
 361
 362           @Override
 363           public void actionPerformed(ActionEvent e)
 364           {
 365             if (e.getSource() == mxcol)
 366             {
 367               if (featureColour.isSimpleColour())
 368               {
 369                 FeatureColourChooser fc = new FeatureColourChooser(me.fr,
 370                         type);
 371                 fc.addActionListener(this);
 372               }
 373               else
 374               {
 375                 // bring up simple color chooser
 376                 colorChooser = new JColorChooser();
 377                 JDialog dialog = JColorChooser.createDialog(me,
 378                         "Select new Colour", true, // modal
 379                         colorChooser, this, // OK button handler
 380                         null); // no CANCEL button handler
 381                 colorChooser.setColor(featureColour.getMaxColour());
 382                 dialog.setVisible(true);
 383               }
 384             }
 385             else
 386             {
 387               if (e.getSource() instanceof FeatureColourChooser)
 388               {
 389                 FeatureColourChooser fc = (FeatureColourChooser) e
 390                         .getSource();
 391                 table.setValueAt(fc.getLastColour(), selectedRow, 1);
 392                 table.validate();
 393               }
 394               else
 395               {
 396                 // probably the color chooser!
 397                 table.setValueAt(
 398                         new FeatureColour(colorChooser.getColor()),
 399                         selectedRow, 1);
 400                 table.validate();
 401                 me.updateFeatureRenderer(
 402                         ((FeatureTableModel) table.getModel()).getData(),
 403                         false);
 404               }
 405             }
 406           }
 407
 408         });
 409       }
 410     }
 411     JMenuItem selCols = new JMenuItem(
 412             MessageManager.getString("label.select_columns_containing"));
 413     selCols.addActionListener(new ActionListener()
 414     {
 415       @Override
 416       public void actionPerformed(ActionEvent arg0)
 417       {
 418         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
 419                 false, type);
 420       }
 421     });
 422     JMenuItem clearCols = new JMenuItem(
 423             MessageManager.getString("label.select_columns_not_containing"));
 424     clearCols.addActionListener(new ActionListener()
 425     {
 426       @Override
 427       public void actionPerformed(ActionEvent arg0)
 428       {
 429         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
 430                 false, type);
 431       }
 432     });
 433     JMenuItem hideCols = new JMenuItem(
 434             MessageManager.getString("label.hide_columns_containing"));
 435     hideCols.addActionListener(new ActionListener()
 436     {
 437       @Override
 438       public void actionPerformed(ActionEvent arg0)
 439       {
 440         fr.ap.alignFrame.hideFeatureColumns(type, true);
 441       }
 442     });
 443     JMenuItem hideOtherCols = new JMenuItem(
 444             MessageManager.getString("label.hide_columns_not_containing"));
 445     hideOtherCols.addActionListener(new ActionListener()
 446     {
 447       @Override
 448       public void actionPerformed(ActionEvent arg0)
 449       {
 450         fr.ap.alignFrame.hideFeatureColumns(type, false);
 451       }
 452     });
 453     men.add(selCols);
 454     men.add(clearCols);
 455     men.add(hideCols);
 456     men.add(hideOtherCols);
 457     men.show(table, x, y);
 458   }
 459
 460   /**
 461    * true when Feature Settings are updating from feature renderer
 462    */
 463   private boolean handlingUpdate = false;
 464
 465   /**
 466    * contains a float[3] for each feature type string. created by setTableData
 467    */
 468   Map<String, float[]> typeWidth = null;
 469
 470   @Override
 471   synchronized public void discoverAllFeatureData()
 472   {
 473     Vector<String> allFeatures = new Vector<String>();
 474     Vector<String> allGroups = new Vector<String>();
 475     SequenceFeature[] tmpfeatures;
 476     String group;
 477     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 478     {
 479       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 480               .getSequenceFeatures();
 481       if (tmpfeatures == null)
 482       {
 483         continue;
 484       }
 485
 486       int index = 0;
 487       while (index < tmpfeatures.length)
 488       {
 489         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 490         {
 491           index++;
 492           continue;
 493         }
 494
 495         if (tmpfeatures[index].getFeatureGroup() != null)
 496         {
 497           group = tmpfeatures[index].featureGroup;
 498           if (!allGroups.contains(group))
 499           {
 500             allGroups.addElement(group);
 501             checkGroupState(group);
 502           }
 503         }
 504
 505         if (!allFeatures.contains(tmpfeatures[index].getType()))
 506         {
 507           allFeatures.addElement(tmpfeatures[index].getType());
 508         }
 509         index++;
 510       }
 511     }
 512
 513     resetTable(null);
 514
 515     validate();
 516   }
 517
 518   /**
 519    * Synchronise gui group list and check visibility of group
 520    *
 521    * @param group
 522    * @return true if group is visible
 523    */
 524   private boolean checkGroupState(String group)
 525   {
 526     boolean visible = fr.checkGroupVisibility(group, true);
 527
 528     if (groupPanel == null)
 529     {
 530       groupPanel = new JPanel();
 531     }
 532
 533     boolean alreadyAdded = false;
 534     for (int g = 0; g < groupPanel.getComponentCount(); g++)
 535     {
 536       if (((JCheckBox) groupPanel.getComponent(g)).getText().equals(group))
 537       {
 538         alreadyAdded = true;
 539         ((JCheckBox) groupPanel.getComponent(g)).setSelected(visible);
 540         break;
 541       }
 542     }
 543
 544     if (alreadyAdded)
 545     {
 546
 547       return visible;
 548     }
 549     final String grp = group;
 550     final JCheckBox check = new JCheckBox(group, visible);
 551     check.setFont(new Font("Serif", Font.BOLD, 12));
 552     check.addItemListener(new ItemListener()
 553     {
 554       @Override
 555       public void itemStateChanged(ItemEvent evt)
 556       {
 557         fr.setGroupVisibility(check.getText(), check.isSelected());
 558         af.alignPanel.getSeqPanel().seqCanvas.repaint();
 559         if (af.alignPanel.overviewPanel != null)
 560         {
 561           af.alignPanel.overviewPanel.updateOverviewImage();
 562         }
 563
 564         resetTable(new String[] { grp });
 565       }
 566     });
 567     groupPanel.add(check);
 568     return visible;
 569   }
 570
 571   boolean resettingTable = false;
 572
 573   synchronized void resetTable(String[] groupChanged)
 574   {
 575     if (resettingTable == true)
 576     {
 577       return;
 578     }
 579     resettingTable = true;
 580     typeWidth = new Hashtable<String, float[]>();
 581     // TODO: change avWidth calculation to 'per-sequence' average and use long
 582     // rather than float
 583     float[] avWidth = null;
 584     SequenceFeature[] tmpfeatures;
 585     String group = null, type;
 586     Vector<String> visibleChecks = new Vector<String>();
 587
 588     // Find out which features should be visible depending on which groups
 589     // are selected / deselected
 590     // and recompute average width ordering
 591     for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
 592     {
 593
 594       tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
 595               .getSequenceFeatures();
 596       if (tmpfeatures == null)
 597       {
 598         continue;
 599       }
 600
 601       int index = 0;
 602       while (index < tmpfeatures.length)
 603       {
 604         group = tmpfeatures[index].featureGroup;
 605
 606         if (tmpfeatures[index].begin == 0 && tmpfeatures[index].end == 0)
 607         {
 608           index++;
 609           continue;
 610         }
 611
 612         if (group == null || checkGroupState(group))
 613         {
 614           type = tmpfeatures[index].getType();
 615           if (!visibleChecks.contains(type))
 616           {
 617             visibleChecks.addElement(type);
 618           }
 619         }
 620         if (!typeWidth.containsKey(tmpfeatures[index].getType()))
 621         {
 622           typeWidth.put(tmpfeatures[index].getType(),
 623                   avWidth = new float[3]);
 624         }
 625         else
 626         {
 627           avWidth = typeWidth.get(tmpfeatures[index].getType());
 628         }
 629         avWidth[0]++;
 630         if (tmpfeatures[index].getBegin() > tmpfeatures[index].getEnd())
 631         {
 632           avWidth[1] += 1 + tmpfeatures[index].getBegin()
 633                   - tmpfeatures[index].getEnd();
 634         }
 635         else
 636         {
 637           avWidth[1] += 1 + tmpfeatures[index].getEnd()
 638                   - tmpfeatures[index].getBegin();
 639         }
 640         index++;
 641       }
 642     }
 643
 644     int fSize = visibleChecks.size();
 645     Object[][] data = new Object[fSize][3];
 646     int dataIndex = 0;
 647
 648     if (fr.hasRenderOrder())
 649     {
 650       if (!handlingUpdate)
 651       {
 652         fr.findAllFeatures(groupChanged != null); // prod to update
 653         // colourschemes. but don't
 654         // affect display
 655         // First add the checks in the previous render order,
 656         // in case the window has been closed and reopened
 657       }
 658       List<String> frl = fr.getRenderOrder();
 659       for (int ro = frl.size() - 1; ro > -1; ro--)
 660       {
 661         type = frl.get(ro);
 662
 663         if (!visibleChecks.contains(type))
 664         {
 665           continue;
 666         }
 667
 668         data[dataIndex][0] = type;
 669         data[dataIndex][1] = fr.getFeatureStyle(type);
 670         data[dataIndex][2] = new Boolean(af.getViewport()
 671                 .getFeaturesDisplayed().isVisible(type));
 672         dataIndex++;
 673         visibleChecks.removeElement(type);
 674       }
 675     }
 676
 677     fSize = visibleChecks.size();
 678     for (int i = 0; i < fSize; i++)
 679     {
 680       // These must be extra features belonging to the group
 681       // which was just selected
 682       type = visibleChecks.elementAt(i).toString();
 683       data[dataIndex][0] = type;
 684
 685       data[dataIndex][1] = fr.getFeatureStyle(type);
 686       if (data[dataIndex][1] == null)
 687       {
 688         // "Colour has been updated in another view!!"
 689         fr.clearRenderOrder();
 690         return;
 691       }
 692
 693       data[dataIndex][2] = new Boolean(true);
 694       dataIndex++;
 695     }
 696
 697     if (originalData == null)
 698     {
 699       originalData = new Object[data.length][3];
 700       for (int i = 0; i < data.length; i++)
 701       {
 702         System.arraycopy(data[i], 0, originalData[i], 0, 3);
 703       }
 704     }
 705
 706     table.setModel(new FeatureTableModel(data));
 707     table.getColumnModel().getColumn(0).setPreferredWidth(200);
 708
 709     if (groupPanel != null)
 710     {
 711       groupPanel.setLayout(new GridLayout(
 712               fr.getFeatureGroupsSize() / 4 + 1, 4));
 713
 714       groupPanel.validate();
 715       bigPanel.add(groupPanel, BorderLayout.NORTH);
 716     }
 717
 718     updateFeatureRenderer(data, groupChanged != null);
 719     resettingTable = false;
 720   }
 721
 722   /**
 723    * reorder data based on the featureRenderers global priority list.
 724    *
 725    * @param data
 726    */
 727   private void ensureOrder(Object[][] data)
 728   {
 729     boolean sort = false;
 730     float[] order = new float[data.length];
 731     for (int i = 0; i < order.length; i++)
 732     {
 733       order[i] = fr.getOrder(data[i][0].toString());
 734       if (order[i] < 0)
 735       {
 736         order[i] = fr.setOrder(data[i][0].toString(), i / order.length);
 737       }
 738       if (i > 1)
 739       {
 740         sort = sort || order[i - 1] > order[i];
 741       }
 742     }
 743     if (sort)
 744     {
 745       jalview.util.QuickSort.sort(order, data);
 746     }
 747   }
 748
 749   void load()
 750   {
 751     JalviewFileChooser chooser = new JalviewFileChooser(
 752             jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
 753             new String[] { "fc" },
 754             new String[] { "Sequence Feature Colours" },
 755             "Sequence Feature Colours");
 756     chooser.setFileView(new jalview.io.JalviewFileView());
 757     chooser.setDialogTitle(MessageManager
 758             .getString("label.load_feature_colours"));
 759     chooser.setToolTipText(MessageManager.getString("action.load"));
 760
 761     int value = chooser.showOpenDialog(this);
 762
 763     if (value == JalviewFileChooser.APPROVE_OPTION)
 764     {
 765       File file = chooser.getSelectedFile();
 766
 767       try
 768       {
 769         InputStreamReader in = new InputStreamReader(new FileInputStream(
 770                 file), "UTF-8");
 771
 772         JalviewUserColours jucs = JalviewUserColours.unmarshal(in);
 773
 774         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
 775         {
 776           String name;
 777           jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
 778           if (newcol.hasMax())
 779           {
 780             Color mincol = null, maxcol = null;
 781             try
 782             {
 783               mincol = new Color(Integer.parseInt(newcol.getMinRGB(), 16));
 784               maxcol = new Color(Integer.parseInt(newcol.getRGB(), 16));
 785
 786             } catch (Exception e)
 787             {
 788               Cache.log.warn("Couldn't parse out graduated feature color.",
 789                       e);
 790             }
 791             FeatureColourI gcol = new FeatureColour(mincol, maxcol,
 792                     newcol.getMin(), newcol.getMax());
 793             if (newcol.hasAutoScale())
 794             {
 795               gcol.setAutoScaled(newcol.getAutoScale());
 796             }
 797             if (newcol.hasColourByLabel())
 798             {
 799               gcol.setColourByLabel(newcol.getColourByLabel());
 800             }
 801             if (newcol.hasThreshold())
 802             {
 803               gcol.setThreshold(newcol.getThreshold());
 804             }
 805             if (newcol.getThreshType().length() > 0)
 806             {
 807               String ttyp = newcol.getThreshType();
 808               if (ttyp.equalsIgnoreCase("ABOVE"))
 809               {
 810                 gcol.setAboveThreshold(true);
 811               }
 812               if (ttyp.equalsIgnoreCase("BELOW"))
 813               {
 814                 gcol.setBelowThreshold(true);
 815               }
 816             }
 817             fr.setColour(name = newcol.getName(), gcol);
 818           }
 819           else
 820           {
 821             Color color = new Color(Integer.parseInt(jucs.getColour(i)
 822                     .getRGB(), 16));
 823             fr.setColour(name = jucs.getColour(i).getName(),
 824                     new FeatureColour(color));
 825           }
 826           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
 827         }
 828         if (table != null)
 829         {
 830           resetTable(null);
 831           Object[][] data = ((FeatureTableModel) table.getModel())
 832                   .getData();
 833           ensureOrder(data);
 834           updateFeatureRenderer(data, false);
 835           table.repaint();
 836         }
 837       } catch (Exception ex)
 838       {
 839         System.out.println("Error loading User Colour File\n" + ex);
 840       }
 841     }
 842   }
 843
 844   void save()
 845   {
 846     JalviewFileChooser chooser = new JalviewFileChooser(
 847             Cache.getProperty("LAST_DIRECTORY"), new String[] { "fc" },
 848             new String[] { "Sequence Feature Colours" },
 849             "Sequence Feature Colours");
 850     chooser.setFileView(new jalview.io.JalviewFileView());
 851     chooser.setDialogTitle(MessageManager
 852             .getString("label.save_feature_colours"));
 853     chooser.setToolTipText(MessageManager.getString("action.save"));
 854
 855     int value = chooser.showSaveDialog(this);
 856
 857     if (value == JalviewFileChooser.APPROVE_OPTION)
 858     {
 859       String choice = chooser.getSelectedFile().getPath();
 860       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 861       ucs.setSchemeName("Sequence Features");
 862       try
 863       {
 864         PrintWriter out = new PrintWriter(new OutputStreamWriter(
 865                 new FileOutputStream(choice), "UTF-8"));
 866
 867         Set<String> fr_colours = fr.getAllFeatureColours();
 868         Iterator<String> e = fr_colours.iterator();
 869         float[] sortOrder = new float[fr_colours.size()];
 870         String[] sortTypes = new String[fr_colours.size()];
 871         int i = 0;
 872         while (e.hasNext())
 873         {
 874           sortTypes[i] = e.next();
 875           sortOrder[i] = fr.getOrder(sortTypes[i]);
 876           i++;
 877         }
 878         QuickSort.sort(sortOrder, sortTypes);
 879         sortOrder = null;
 880         for (i = 0; i < sortTypes.length; i++)
 881         {
 882           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 883           col.setName(sortTypes[i]);
 884           FeatureColourI fcol = fr.getFeatureStyle(sortTypes[i]);
 885           if (fcol.isSimpleColour())
 886           {
 887             col.setRGB(Format.getHexString(fcol.getColour()));
 888           }
 889           else
 890           {
 891             col.setRGB(Format.getHexString(fcol.getMaxColour()));
 892             col.setMin(fcol.getMin());
 893             col.setMax(fcol.getMax());
 894             col.setMinRGB(jalview.util.Format.getHexString(fcol
 895                     .getMinColour()));
 896             col.setAutoScale(fcol.isAutoScaled());
 897             col.setThreshold(fcol.getThreshold());
 898             col.setColourByLabel(fcol.isColourByLabel());
 899             col.setThreshType(fcol.isAboveThreshold() ? "ABOVE" : (fcol
 900                     .isBelowThreshold() ? "BELOW" : "NONE"));
 901           }
 902           ucs.addColour(col);
 903         }
 904         ucs.marshal(out);
 905         out.close();
 906       } catch (Exception ex)
 907       {
 908         ex.printStackTrace();
 909       }
 910     }
 911   }
 912
 913   public void invertSelection()
 914   {
 915     for (int i = 0; i < table.getRowCount(); i++)
 916     {
 917       Boolean value = (Boolean) table.getValueAt(i, 2);
 918
 919       table.setValueAt(new Boolean(!value.booleanValue()), i, 2);
 920     }
 921   }
 922
 923   public void orderByAvWidth()
 924   {
 925     if (table == null || table.getModel() == null)
 926     {
 927       return;
 928     }
 929     Object[][] data = ((FeatureTableModel) table.getModel()).getData();
 930     float[] width = new float[data.length];
 931     float[] awidth;
 932     float max = 0;
 933     int num = 0;
 934     for (int i = 0; i < data.length; i++)
 935     {
 936       awidth = typeWidth.get(data[i][0]);
 937       if (awidth[0] > 0)
 938       {
 939         width[i] = awidth[1] / awidth[0];// *awidth[0]*awidth[2]; - better
 940         // weight - but have to make per
 941         // sequence, too (awidth[2])
 942         // if (width[i]==1) // hack to distinguish single width sequences.
 943         num++;
 944       }
 945       else
 946       {
 947         width[i] = 0;
 948       }
 949       if (max < width[i])
 950       {
 951         max = width[i];
 952       }
 953     }
 954     boolean sort = false;
 955     for (int i = 0; i < width.length; i++)
 956     {
 957       // awidth = (float[]) typeWidth.get(data[i][0]);
 958       if (width[i] == 0)
 959       {
 960         width[i] = fr.getOrder(data[i][0].toString());
 961         if (width[i] < 0)
 962         {
 963           width[i] = fr.setOrder(data[i][0].toString(), i / data.length);
 964         }
 965       }
 966       else
 967       {
 968         width[i] /= max; // normalize
 969         fr.setOrder(data[i][0].toString(), width[i]); // store for later
 970       }
 971       if (i > 0)
 972       {
 973         sort = sort || width[i - 1] > width[i];
 974       }
 975     }
 976     if (sort)
 977     {
 978       jalview.util.QuickSort.sort(width, data);
 979       // update global priority order
 980     }
 981
 982     updateFeatureRenderer(data, false);
 983     table.repaint();
 984   }
 985
 986   public void close()
 987   {
 988     try
 989     {
 990       frame.setClosed(true);
 991     } catch (Exception exe)
 992     {
 993     }
 994
 995   }
 996
 997   public void updateFeatureRenderer(Object[][] data)
 998   {
 999     updateFeatureRenderer(data, true);
1000   }
1001
1002   /**
1003    * Update the priority order of features; only repaint if this changed the
1004    * order of visible features
1005    *
1006    * @param data
1007    * @param visibleNew
1008    */
1009   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
1010   {
1011     if (fr.setFeaturePriority(data, visibleNew))
1012     {
1013       af.alignPanel.paintAlignment(true);
1014     }
1015   }
1016
1017   int selectedRow = -1;
1018
1019   JTabbedPane tabbedPane = new JTabbedPane();
1020
1021   BorderLayout borderLayout1 = new BorderLayout();
1022
1023   BorderLayout borderLayout2 = new BorderLayout();
1024
1025   BorderLayout borderLayout3 = new BorderLayout();
1026
1027   JPanel bigPanel = new JPanel();
1028
1029   BorderLayout borderLayout4 = new BorderLayout();
1030
1031   JButton invert = new JButton();
1032
1033   JPanel buttonPanel = new JPanel();
1034
1035   JButton cancel = new JButton();
1036
1037   JButton ok = new JButton();
1038
1039   JButton loadColours = new JButton();
1040
1041   JButton saveColours = new JButton();
1042
1043   JPanel dasButtonPanel = new JPanel();
1044
1045   JButton fetchDAS = new JButton();
1046
1047   JButton saveDAS = new JButton();
1048
1049   JButton cancelDAS = new JButton();
1050
1051   JButton optimizeOrder = new JButton();
1052
1053   JButton sortByScore = new JButton();
1054
1055   JButton sortByDens = new JButton();
1056
1057   JButton help = new JButton();
1058
1059   JPanel transbuttons = new JPanel(new GridLayout(5, 1));
1060
1061   private void jbInit() throws Exception
1062   {
1063     this.setLayout(borderLayout1);
1064     settingsPane.setLayout(borderLayout2);
1065     dasSettingsPane.setLayout(borderLayout3);
1066     bigPanel.setLayout(borderLayout4);
1067     invert.setFont(JvSwingUtils.getLabelFont());
1068     invert.setText(MessageManager.getString("label.invert_selection"));
1069     invert.addActionListener(new ActionListener()
1070     {
1071       @Override
1072       public void actionPerformed(ActionEvent e)
1073       {
1074         invertSelection();
1075       }
1076     });
1077     optimizeOrder.setFont(JvSwingUtils.getLabelFont());
1078     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
1079     optimizeOrder.addActionListener(new ActionListener()
1080     {
1081       @Override
1082       public void actionPerformed(ActionEvent e)
1083       {
1084         orderByAvWidth();
1085       }
1086     });
1087     sortByScore.setFont(JvSwingUtils.getLabelFont());
1088     sortByScore
1089             .setText(MessageManager.getString("label.seq_sort_by_score"));
1090     sortByScore.addActionListener(new ActionListener()
1091     {
1092       @Override
1093       public void actionPerformed(ActionEvent e)
1094       {
1095         af.avc.sortAlignmentByFeatureScore(null);
1096       }
1097     });
1098     sortByDens.setFont(JvSwingUtils.getLabelFont());
1099     sortByDens.setText(MessageManager
1100             .getString("label.sequence_sort_by_density"));
1101     sortByDens.addActionListener(new ActionListener()
1102     {
1103       @Override
1104       public void actionPerformed(ActionEvent e)
1105       {
1106         af.avc.sortAlignmentByFeatureDensity(null);
1107       }
1108     });
1109     help.setFont(JvSwingUtils.getLabelFont());
1110     help.setText(MessageManager.getString("action.help"));
1111     help.addActionListener(new ActionListener()
1112     {
1113       @Override
1114       public void actionPerformed(ActionEvent e)
1115       {
1116         try
1117         {
1118           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1119         } catch (HelpSetException e1)
1120         {
1121           e1.printStackTrace();
1122         }
1123       }
1124     });
1125     help.setFont(JvSwingUtils.getLabelFont());
1126     help.setText(MessageManager.getString("action.help"));
1127     help.addActionListener(new ActionListener()
1128     {
1129       @Override
1130       public void actionPerformed(ActionEvent e)
1131       {
1132         try
1133         {
1134           Help.showHelpWindow(HelpId.SequenceFeatureSettings);
1135         } catch (HelpSetException e1)
1136         {
1137           e1.printStackTrace();
1138         }
1139       }
1140     });
1141     cancel.setFont(JvSwingUtils.getLabelFont());
1142     cancel.setText(MessageManager.getString("action.cancel"));
1143     cancel.addActionListener(new ActionListener()
1144     {
1145       @Override
1146       public void actionPerformed(ActionEvent e)
1147       {
1148         fr.setTransparency(originalTransparency);
1149         updateFeatureRenderer(originalData);
1150         close();
1151       }
1152     });
1153     ok.setFont(JvSwingUtils.getLabelFont());
1154     ok.setText(MessageManager.getString("action.ok"));
1155     ok.addActionListener(new ActionListener()
1156     {
1157       @Override
1158       public void actionPerformed(ActionEvent e)
1159       {
1160         close();
1161       }
1162     });
1163     loadColours.setFont(JvSwingUtils.getLabelFont());
1164     loadColours.setText(MessageManager.getString("label.load_colours"));
1165     loadColours.addActionListener(new ActionListener()
1166     {
1167       @Override
1168       public void actionPerformed(ActionEvent e)
1169       {
1170         load();
1171       }
1172     });
1173     saveColours.setFont(JvSwingUtils.getLabelFont());
1174     saveColours.setText(MessageManager.getString("label.save_colours"));
1175     saveColours.addActionListener(new ActionListener()
1176     {
1177       @Override
1178       public void actionPerformed(ActionEvent e)
1179       {
1180         save();
1181       }
1182     });
1183     transparency.addChangeListener(new ChangeListener()
1184     {
1185       @Override
1186       public void stateChanged(ChangeEvent evt)
1187       {
1188         fr.setTransparency((100 - transparency.getValue()) / 100f);
1189         af.alignPanel.paintAlignment(true);
1190       }
1191     });
1192
1193     transparency.setMaximum(70);
1194     transparency.setToolTipText(MessageManager
1195             .getString("label.transparency_tip"));
1196     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
1197     fetchDAS.addActionListener(new ActionListener()
1198     {
1199       @Override
1200       public void actionPerformed(ActionEvent e)
1201       {
1202         fetchDAS_actionPerformed(e);
1203       }
1204     });
1205     saveDAS.setText(MessageManager.getString("action.save_as_default"));
1206     saveDAS.addActionListener(new ActionListener()
1207     {
1208       @Override
1209       public void actionPerformed(ActionEvent e)
1210       {
1211         saveDAS_actionPerformed(e);
1212       }
1213     });
1214     dasButtonPanel.setBorder(BorderFactory.createEtchedBorder());
1215     dasSettingsPane.setBorder(null);
1216     cancelDAS.setEnabled(false);
1217     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
1218     cancelDAS.addActionListener(new ActionListener()
1219     {
1220       @Override
1221       public void actionPerformed(ActionEvent e)
1222       {
1223         cancelDAS_actionPerformed(e);
1224       }
1225     });
1226     this.add(tabbedPane, java.awt.BorderLayout.CENTER);
1227     tabbedPane.addTab(MessageManager.getString("label.feature_settings"),
1228             settingsPane);
1229     tabbedPane.addTab(MessageManager.getString("label.das_settings"),
1230             dasSettingsPane);
1231     bigPanel.add(transPanel, java.awt.BorderLayout.SOUTH);
1232     transbuttons.add(optimizeOrder);
1233     transbuttons.add(invert);
1234     transbuttons.add(sortByScore);
1235     transbuttons.add(sortByDens);
1236     transbuttons.add(help);
1237     JPanel sliderPanel = new JPanel();
1238     sliderPanel.add(transparency);
1239     transPanel.add(transparency);
1240     transPanel.add(transbuttons);
1241     buttonPanel.add(ok);
1242     buttonPanel.add(cancel);
1243     buttonPanel.add(loadColours);
1244     buttonPanel.add(saveColours);
1245     bigPanel.add(scrollPane, java.awt.BorderLayout.CENTER);
1246     dasSettingsPane.add(dasButtonPanel, java.awt.BorderLayout.SOUTH);
1247     dasButtonPanel.add(fetchDAS);
1248     dasButtonPanel.add(cancelDAS);
1249     dasButtonPanel.add(saveDAS);
1250     settingsPane.add(bigPanel, java.awt.BorderLayout.CENTER);
1251     settingsPane.add(buttonPanel, java.awt.BorderLayout.SOUTH);
1252   }
1253
1254   public void fetchDAS_actionPerformed(ActionEvent e)
1255   {
1256     fetchDAS.setEnabled(false);
1257     cancelDAS.setEnabled(true);
1258     dassourceBrowser.setGuiEnabled(false);
1259     Vector<jalviewSourceI> selectedSources = dassourceBrowser
1260             .getSelectedSources();
1261     doDasFeatureFetch(selectedSources, true, true);
1262   }
1263
1264   /**
1265    * get the features from selectedSources for all or the current selection
1266    *
1267    * @param selectedSources
1268    * @param checkDbRefs
1269    * @param promptFetchDbRefs
1270    */
1271   private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
1272           boolean checkDbRefs, boolean promptFetchDbRefs)
1273   {
1274     SequenceI[] dataset, seqs;
1275     int iSize;
1276     AlignmentViewport vp = af.getViewport();
1277     if (vp.getSelectionGroup() != null
1278             && vp.getSelectionGroup().getSize() > 0)
1279     {
1280       iSize = vp.getSelectionGroup().getSize();
1281       dataset = new SequenceI[iSize];
1282       seqs = vp.getSelectionGroup().getSequencesInOrder(vp.getAlignment());
1283     }
1284     else
1285     {
1286       iSize = vp.getAlignment().getHeight();
1287       seqs = vp.getAlignment().getSequencesArray();
1288     }
1289
1290     dataset = new SequenceI[iSize];
1291     for (int i = 0; i < iSize; i++)
1292     {
1293       dataset[i] = seqs[i].getDatasetSequence();
1294     }
1295
1296     cancelDAS.setEnabled(true);
1297     dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
1298             this, selectedSources, checkDbRefs, promptFetchDbRefs);
1299     af.getViewport().setShowSequenceFeatures(true);
1300     af.showSeqFeatures.setSelected(true);
1301   }
1302
1303   /**
1304    * blocking call to initialise the das source browser
1305    */
1306   public void initDasSources()
1307   {
1308     dassourceBrowser.initDasSources();
1309   }
1310
1311   /**
1312    * examine the current list of das sources and return any matching the given
1313    * nicknames in sources
1314    *
1315    * @param sources
1316    *          Vector of Strings to resolve to DAS source nicknames.
1317    * @return sources that are present in source list.
1318    */
1319   public List<jalviewSourceI> resolveSourceNicknames(Vector<String> sources)
1320   {
1321     return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
1322   }
1323
1324   /**
1325    * get currently selected das sources. ensure you have called initDasSources
1326    * before calling this.
1327    *
1328    * @return vector of selected das source nicknames
1329    */
1330   public Vector<jalviewSourceI> getSelectedSources()
1331   {
1332     return dassourceBrowser.getSelectedSources();
1333   }
1334
1335   /**
1336    * properly initialise DAS fetcher and then initiate a new thread to fetch
1337    * features from the named sources (rather than any turned on by default)
1338    *
1339    * @param sources
1340    * @param block
1341    *          if true then runs in same thread, otherwise passes to the Swing
1342    *          executor
1343    */
1344   public void fetchDasFeatures(Vector<String> sources, boolean block)
1345   {
1346     initDasSources();
1347     List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry
1348             .resolveSourceNicknames(sources);
1349     if (resolved.size() == 0)
1350     {
1351       resolved = dassourceBrowser.getSelectedSources();
1352     }
1353     if (resolved.size() > 0)
1354     {
1355       final List<jalviewSourceI> dassources = resolved;
1356       fetchDAS.setEnabled(false);
1357       // cancelDAS.setEnabled(true); doDasFetch does this.
1358       Runnable fetcher = new Runnable()
1359       {
1360
1361         @Override
1362         public void run()
1363         {
1364           doDasFeatureFetch(dassources, true, false);
1365
1366         }
1367       };
1368       if (block)
1369       {
1370         fetcher.run();
1371       }
1372       else
1373       {
1374         SwingUtilities.invokeLater(fetcher);
1375       }
1376     }
1377   }
1378
1379   public void saveDAS_actionPerformed(ActionEvent e)
1380   {
1381     dassourceBrowser
1382             .saveProperties(jalview.bin.Cache.applicationProperties);
1383   }
1384
1385   public void complete()
1386   {
1387     fetchDAS.setEnabled(true);
1388     cancelDAS.setEnabled(false);
1389     dassourceBrowser.setGuiEnabled(true);
1390
1391   }
1392
1393   public void cancelDAS_actionPerformed(ActionEvent e)
1394   {
1395     if (dasFeatureFetcher != null)
1396     {
1397       dasFeatureFetcher.cancel();
1398     }
1399     complete();
1400   }
1401
1402   public void noDasSourceActive()
1403   {
1404     complete();
1405     JOptionPane
1406             .showInternalConfirmDialog(
1407                     Desktop.desktop,
1408                     MessageManager
1409                             .getString("label.no_das_sources_selected_warn"),
1410                     MessageManager
1411                             .getString("label.no_das_sources_selected_title"),
1412                     JOptionPane.DEFAULT_OPTION,
1413                     JOptionPane.INFORMATION_MESSAGE);
1414   }
1415
1416   // ///////////////////////////////////////////////////////////////////////
1417   // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html
1418   // ///////////////////////////////////////////////////////////////////////
1419   class FeatureTableModel extends AbstractTableModel
1420   {
1421     FeatureTableModel(Object[][] data)
1422     {
1423       this.data = data;
1424     }
1425
1426     private String[] columnNames = {
1427         MessageManager.getString("label.feature_type"),
1428         MessageManager.getString("action.colour"),
1429         MessageManager.getString("label.display") };
1430
1431     private Object[][] data;
1432
1433     public Object[][] getData()
1434     {
1435       return data;
1436     }
1437
1438     public void setData(Object[][] data)
1439     {
1440       this.data = data;
1441     }
1442
1443     @Override
1444     public int getColumnCount()
1445     {
1446       return columnNames.length;
1447     }
1448
1449     public Object[] getRow(int row)
1450     {
1451       return data[row];
1452     }
1453
1454     @Override
1455     public int getRowCount()
1456     {
1457       return data.length;
1458     }
1459
1460     @Override
1461     public String getColumnName(int col)
1462     {
1463       return columnNames[col];
1464     }
1465
1466     @Override
1467     public Object getValueAt(int row, int col)
1468     {
1469       return data[row][col];
1470     }
1471
1472     @Override
1473     public Class getColumnClass(int c)
1474     {
1475       return getValueAt(0, c).getClass();
1476     }
1477
1478     @Override
1479     public boolean isCellEditable(int row, int col)
1480     {
1481       return col == 0 ? false : true;
1482     }
1483
1484     @Override
1485     public void setValueAt(Object value, int row, int col)
1486     {
1487       data[row][col] = value;
1488       fireTableCellUpdated(row, col);
1489       updateFeatureRenderer(data);
1490     }
1491
1492   }
1493
1494   class ColorRenderer extends JLabel implements TableCellRenderer
1495   {
1496     javax.swing.border.Border unselectedBorder = null;
1497
1498     javax.swing.border.Border selectedBorder = null;
1499
1500     final String baseTT = "Click to edit, right/apple click for menu.";
1501
1502     public ColorRenderer()
1503     {
1504       setOpaque(true); // MUST do this for background to show up.
1505       setHorizontalTextPosition(SwingConstants.CENTER);
1506       setVerticalTextPosition(SwingConstants.CENTER);
1507     }
1508
1509     @Override
1510     public Component getTableCellRendererComponent(JTable tbl,
1511             Object color, boolean isSelected, boolean hasFocus, int row,
1512             int column)
1513     {
1514       FeatureColourI cellColour = (FeatureColourI) color;
1515       // JLabel comp = new JLabel();
1516       // comp.
1517       setOpaque(true);
1518       // comp.
1519       // setBounds(getBounds());
1520       Color newColor;
1521       setToolTipText(baseTT);
1522       setBackground(tbl.getBackground());
1523       if (!cellColour.isSimpleColour())
1524       {
1525         Rectangle cr = tbl.getCellRect(row, column, false);
1526         FeatureSettings.renderGraduatedColor(this, cellColour,
1527                 (int) cr.getWidth(), (int) cr.getHeight());
1528
1529       }
1530       else
1531       {
1532         this.setText("");
1533         this.setIcon(null);
1534         newColor = cellColour.getColour();
1535         setBackground(newColor);
1536       }
1537       if (isSelected)
1538       {
1539         if (selectedBorder == null)
1540         {
1541           selectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1542                   tbl.getSelectionBackground());
1543         }
1544         setBorder(selectedBorder);
1545       }
1546       else
1547       {
1548         if (unselectedBorder == null)
1549         {
1550           unselectedBorder = BorderFactory.createMatteBorder(2, 5, 2, 5,
1551                   tbl.getBackground());
1552         }
1553         setBorder(unselectedBorder);
1554       }
1555
1556       return this;
1557     }
1558   }
1559
1560   /**
1561    * update comp using rendering settings from gcol
1562    *
1563    * @param comp
1564    * @param gcol
1565    */
1566   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol)
1567   {
1568     int w = comp.getWidth(), h = comp.getHeight();
1569     if (w < 20)
1570     {
1571       w = (int) comp.getPreferredSize().getWidth();
1572       h = (int) comp.getPreferredSize().getHeight();
1573       if (w < 20)
1574       {
1575         w = 80;
1576         h = 12;
1577       }
1578     }
1579     renderGraduatedColor(comp, gcol, w, h);
1580   }
1581
1582   public static void renderGraduatedColor(JLabel comp, FeatureColourI gcol,
1583           int w, int h)
1584   {
1585     boolean thr = false;
1586     String tt = "";
1587     String tx = "";
1588     if (gcol.isAboveThreshold())
1589     {
1590       thr = true;
1591       tx += ">";
1592       tt += "Thresholded (Above " + gcol.getThreshold() + ") ";
1593     }
1594     if (gcol.isBelowThreshold())
1595     {
1596       thr = true;
1597       tx += "<";
1598       tt += "Thresholded (Below " + gcol.getThreshold() + ") ";
1599     }
1600     if (gcol.isColourByLabel())
1601     {
1602       tt = "Coloured by label text. " + tt;
1603       if (thr)
1604       {
1605         tx += " ";
1606       }
1607       tx += "Label";
1608       comp.setIcon(null);
1609     }
1610     else
1611     {
1612       Color newColor = gcol.getMaxColour();
1613       comp.setBackground(newColor);
1614       // System.err.println("Width is " + w / 2);
1615       Icon ficon = new FeatureIcon(gcol, comp.getBackground(), w, h, thr);
1616       comp.setIcon(ficon);
1617       // tt+="RGB value: Max (" + newColor.getRed() + ", "
1618       // + newColor.getGreen() + ", " + newColor.getBlue()
1619       // + ")\nMin (" + minCol.getRed() + ", " + minCol.getGreen()
1620       // + ", " + minCol.getBlue() + ")");
1621     }
1622     comp.setHorizontalAlignment(SwingConstants.CENTER);
1623     comp.setText(tx);
1624     if (tt.length() > 0)
1625     {
1626       if (comp.getToolTipText() == null)
1627       {
1628         comp.setToolTipText(tt);
1629       }
1630       else
1631       {
1632         comp.setToolTipText(tt + " " + comp.getToolTipText());
1633       }
1634     }
1635   }
1636 }
1637
1638 class FeatureIcon implements Icon
1639 {
1640   FeatureColourI gcol;
1641
1642   Color backg;
1643
1644   boolean midspace = false;
1645
1646   int width = 50, height = 20;
1647
1648   int s1, e1; // start and end of midpoint band for thresholded symbol
1649
1650   Color mpcolour = Color.white;
1651
1652   FeatureIcon(FeatureColourI gfc, Color bg, int w, int h, boolean mspace)
1653   {
1654     gcol = gfc;
1655     backg = bg;
1656     width = w;
1657     height = h;
1658     midspace = mspace;
1659     if (midspace)
1660     {
1661       s1 = width / 3;
1662       e1 = s1 * 2;
1663     }
1664     else
1665     {
1666       s1 = width / 2;
1667       e1 = s1;
1668     }
1669   }
1670
1671   @Override
1672   public int getIconWidth()
1673   {
1674     return width;
1675   }
1676
1677   @Override
1678   public int getIconHeight()
1679   {
1680     return height;
1681   }
1682
1683   @Override
1684   public void paintIcon(Component c, Graphics g, int x, int y)
1685   {
1686
1687     if (gcol.isColourByLabel())
1688     {
1689       g.setColor(backg);
1690       g.fillRect(0, 0, width, height);
1691       // need an icon here.
1692       g.setColor(gcol.getMaxColour());
1693
1694       g.setFont(new Font("Verdana", Font.PLAIN, 9));
1695
1696       // g.setFont(g.getFont().deriveFont(
1697       // AffineTransform.getScaleInstance(
1698       // width/g.getFontMetrics().stringWidth("Label"),
1699       // height/g.getFontMetrics().getHeight())));
1700
1701       g.drawString(MessageManager.getString("label.label"), 0, 0);
1702
1703     }
1704     else
1705     {
1706       Color minCol = gcol.getMinColour();
1707       g.setColor(minCol);
1708       g.fillRect(0, 0, s1, height);
1709       if (midspace)
1710       {
1711         g.setColor(Color.white);
1712         g.fillRect(s1, 0, e1 - s1, height);
1713       }
1714       g.setColor(gcol.getMaxColour());
1715       g.fillRect(0, e1, width - e1, height);
1716     }
1717   }
1718 }
1719
1720 class ColorEditor extends AbstractCellEditor implements TableCellEditor,
1721         ActionListener
1722 {
1723   FeatureSettings me;
1724
1725   FeatureColourI currentColor;
1726
1727   FeatureColourChooser chooser;
1728
1729   String type;
1730
1731   JButton button;
1732
1733   JColorChooser colorChooser;
1734
1735   JDialog dialog;
1736
1737   protected static final String EDIT = "edit";
1738
1739   int selectedRow = 0;
1740
1741   public ColorEditor(FeatureSettings me)
1742   {
1743     this.me = me;
1744     // Set up the editor (from the table's point of view),
1745     // which is a button.
1746     // This button brings up the color chooser dialog,
1747     // which is the editor from the user's point of view.
1748     button = new JButton();
1749     button.setActionCommand(EDIT);
1750     button.addActionListener(this);
1751     button.setBorderPainted(false);
1752     // Set up the dialog that the button brings up.
1753     colorChooser = new JColorChooser();
1754     dialog = JColorChooser.createDialog(button, "Select new Colour", true, // modal
1755             colorChooser, this, // OK button handler
1756             null); // no CANCEL button handler
1757   }
1758
1759   /**
1760    * Handles events from the editor button and from the dialog's OK button.
1761    */
1762   @Override
1763   public void actionPerformed(ActionEvent e)
1764   {
1765
1766     if (EDIT.equals(e.getActionCommand()))
1767     {
1768       // The user has clicked the cell, so
1769       // bring up the dialog.
1770       if (currentColor.isSimpleColour())
1771       {
1772         // bring up simple color chooser
1773         button.setBackground(currentColor.getColour());
1774         colorChooser.setColor(currentColor.getColour());
1775         dialog.setVisible(true);
1776       }
1777       else
1778       {
1779         // bring up graduated chooser.
1780         chooser = new FeatureColourChooser(me.fr, type);
1781         chooser.setRequestFocusEnabled(true);
1782         chooser.requestFocus();
1783         chooser.addActionListener(this);
1784       }
1785       // Make the renderer reappear.
1786       fireEditingStopped();
1787
1788     }
1789     else
1790     { // User pressed dialog's "OK" button.
1791       if (currentColor.isSimpleColour())
1792       {
1793         currentColor = new FeatureColour(colorChooser.getColor());
1794       }
1795       else
1796       {
1797         currentColor = chooser.getLastColour();
1798       }
1799       me.table.setValueAt(getCellEditorValue(), selectedRow, 1);
1800       fireEditingStopped();
1801       me.table.validate();
1802     }
1803   }
1804
1805   // Implement the one CellEditor method that AbstractCellEditor doesn't.
1806   @Override
1807   public Object getCellEditorValue()
1808   {
1809     return currentColor;
1810   }
1811
1812   // Implement the one method defined by TableCellEditor.
1813   @Override
1814   public Component getTableCellEditorComponent(JTable table, Object value,
1815           boolean isSelected, int row, int column)
1816   {
1817     currentColor = (FeatureColourI) value;
1818     this.selectedRow = row;
1819     type = me.table.getValueAt(row, 0).toString();
1820     button.setOpaque(true);
1821     button.setBackground(me.getBackground());
1822     if (!currentColor.isSimpleColour())
1823     {
1824       JLabel btn = new JLabel();
1825       btn.setSize(button.getSize());
1826       FeatureSettings.renderGraduatedColor(btn, currentColor);
1827       button.setBackground(btn.getBackground());
1828       button.setIcon(btn.getIcon());
1829       button.setText(btn.getText());
1830     }
1831     else
1832     {
1833       button.setText("");
1834       button.setIcon(null);
1835       button.setBackground(currentColor.getColour());
1836     }
1837     return button;
1838   }
1839 }