src/jalview/gui/UserDefinedColours.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21 import jalview.datamodel.*;
  22
  23 import jalview.io.*;
  24
  25 import jalview.jbgui.*;
  26
  27 import jalview.schemes.*;
  28
  29 import java.awt.*;
  30 import java.awt.event.*;
  31
  32 import java.io.*;
  33
  34 import java.util.*;
  35
  36 import javax.swing.*;
  37 import javax.swing.event.*;
  38
  39
  40
  41 /**
  42  * DOCUMENT ME!
  43  *
  44  * @author $author$
  45  * @version $Revision$
  46  */
  47 public class UserDefinedColours extends GUserDefinedColours
  48     implements ChangeListener
  49 {
  50     AlignmentPanel ap;
  51     SequenceGroup seqGroup;
  52     Vector selectedButtons;
  53     ColourSchemeI oldColourScheme;
  54     JInternalFrame frame;
  55     MCview.PDBCanvas pdbcanvas;
  56     Vector upperCaseButtons;
  57     Vector lowerCaseButtons;
  58
  59
  60     /**
  61      * Creates a new UserDefinedColours object.
  62      *
  63      * @param ap DOCUMENT ME!
  64      * @param sg DOCUMENT ME!
  65      */
  66     public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
  67     {
  68         super();
  69         lcaseColour.setEnabled(false);
  70
  71         this.ap = ap;
  72         seqGroup = sg;
  73
  74         if (seqGroup != null)
  75             oldColourScheme = seqGroup.cs;
  76         else
  77             oldColourScheme = ap.av.getGlobalColourScheme();
  78
  79         if (oldColourScheme instanceof UserColourScheme)
  80         {
  81           schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
  82           if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)
  83           {
  84             caseSensitive.setSelected(true);
  85             lcaseColour.setEnabled(true);
  86             resetButtonPanel(true);
  87           }
  88           else
  89             resetButtonPanel(false);
  90         }
  91         else
  92            resetButtonPanel(false);
  93
  94         showFrame();
  95     }
  96
  97     public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)
  98     {
  99         super();
 100         pdbcanvas = pdb;
 101
 102         colorChooser.getSelectionModel().addChangeListener(this);
 103
 104         oldColourScheme = oldcs;
 105
 106         if (oldColourScheme instanceof UserColourScheme)
 107         {
 108               schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());
 109         }
 110
 111         resetButtonPanel(false);
 112
 113         showFrame();
 114
 115     }
 116
 117     void showFrame()
 118     {
 119       colorChooser.getSelectionModel().addChangeListener(this);
 120       frame = new JInternalFrame();
 121       frame.setContentPane(this);
 122       Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);
 123
 124       if (seqGroup != null)
 125             frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
 126
 127       if (System.getProperty("os.name").startsWith("Mac"))
 128       {
 129         frame.setSize(760, 370);
 130       }
 131     }
 132
 133     void resetButtonPanel(boolean caseSensitive)
 134     {
 135       buttonPanel.removeAll();
 136
 137
 138       if(upperCaseButtons==null)
 139         upperCaseButtons = new Vector();
 140
 141       JButton button;
 142       String label;
 143       for (int i = 0; i < 20; i++)
 144       {
 145         if(caseSensitive)
 146           label = ResidueProperties.aa[i];
 147         else
 148           label = ResidueProperties.aa2Triplet.get
 149               (ResidueProperties.aa[i]).toString();
 150
 151         button = makeButton(label,
 152                               ResidueProperties.aa[i],
 153                               upperCaseButtons, i);
 154
 155         buttonPanel.add(button);
 156       }
 157
 158         buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));
 159         buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));
 160         buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));
 161         buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));
 162
 163       if(!caseSensitive)
 164       {
 165         gridLayout.setRows(6);
 166         gridLayout.setColumns(4);
 167       }
 168       else
 169       {
 170         gridLayout.setRows(7);
 171         int cols = 7;
 172         gridLayout.setColumns(cols+1);
 173
 174         if(lowerCaseButtons==null)
 175           lowerCaseButtons = new Vector();
 176
 177
 178           for (int i = 0; i < 20; i++)
 179           {
 180             int row = i / cols + 1;
 181             int index = (row * cols) + i;
 182             button = makeButton(
 183                 ResidueProperties.aa[i].toLowerCase(),
 184                 ResidueProperties.aa[i].toLowerCase(),
 185                 lowerCaseButtons,
 186                 i);
 187
 188             buttonPanel.add(button, index);
 189           }
 190       }
 191
 192
 193       if(caseSensitive)
 194       {
 195         buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));
 196         buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));
 197         buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));
 198       }
 199
 200       buttonPanel.validate();
 201       validate();
 202     }
 203
 204
 205     /**
 206      * DOCUMENT ME!
 207      *
 208      * @param evt DOCUMENT ME!
 209      */
 210     public void stateChanged(ChangeEvent evt)
 211     {
 212         if (selectedButtons != null)
 213         {
 214           JButton button=null;
 215           for(int i=0; i<selectedButtons.size(); i++)
 216           {
 217             button = (JButton)selectedButtons.elementAt(i);
 218             button.setBackground(colorChooser.getColor());
 219             button.setForeground( button.getBackground().brighter().brighter().brighter());
 220           }
 221           if(button==lcaseColour)
 222           {
 223             for(int i=0; i<lowerCaseButtons.size(); i++)
 224             {
 225               button = (JButton)lowerCaseButtons.elementAt(i);
 226               button.setBackground(colorChooser.getColor());
 227               button.setForeground( button.getBackground().brighter().brighter().brighter());
 228             }
 229           }
 230         }
 231     }
 232
 233     /**
 234      * DOCUMENT ME!
 235      *
 236      * @param e DOCUMENT ME!
 237      */
 238     public void colourButtonPressed(MouseEvent e)
 239     {
 240       if(selectedButtons == null)
 241         selectedButtons = new Vector();
 242
 243       JButton pressed = (JButton) e.getSource();
 244
 245       if(e.isShiftDown())
 246       {
 247         JButton start, end = (JButton) e.getSource();
 248         if(selectedButtons.size()>0)
 249           start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);
 250         else
 251           start = (JButton) e.getSource();
 252
 253         int startIndex=0, endIndex=0;
 254         for(int b=0; b<buttonPanel.getComponentCount(); b++)
 255         {
 256           if(buttonPanel.getComponent(b)==start)
 257             startIndex = b;
 258           if(buttonPanel.getComponent(b)==end)
 259             endIndex = b;
 260         }
 261
 262         if(startIndex > endIndex)
 263         {
 264           int temp = startIndex;
 265           startIndex = endIndex;
 266           endIndex = temp;
 267         }
 268
 269         for(int b=startIndex; b<=endIndex; b++)
 270         {
 271           JButton button = (JButton)buttonPanel.getComponent(b);
 272           if(!selectedButtons.contains(button))
 273           {
 274             button.setForeground(button.getBackground().brighter().brighter());
 275             selectedButtons.add(button);
 276           }
 277         }
 278       }
 279       else if(!e.isControlDown())
 280       {
 281         for(int b=0; b<selectedButtons.size(); b++)
 282         {
 283           JButton button = (JButton)selectedButtons.elementAt(b);
 284           button.setForeground(button.getBackground().darker().darker());
 285         }
 286         selectedButtons.clear();
 287         pressed.setForeground( pressed.getBackground().brighter().brighter());
 288         selectedButtons.addElement(pressed);
 289
 290       }
 291       else if(e.isControlDown())
 292       {
 293         if(selectedButtons.contains(pressed))
 294         {
 295           pressed.setForeground(pressed.getBackground().darker().darker());
 296           selectedButtons.remove(pressed);
 297         }
 298         else
 299         {
 300           pressed.setForeground( pressed.getBackground().brighter().brighter());
 301           selectedButtons.addElement(pressed);
 302         }
 303       }
 304
 305       if(selectedButtons.size()>0)
 306       colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());
 307     }
 308
 309     /**
 310      * DOCUMENT ME!
 311      *
 312      * @param label DOCUMENT ME!
 313      * @param aa DOCUMENT ME!
 314      */
 315     JButton makeButton(String label,
 316                        String aa,
 317                        Vector caseSensitiveButtons,
 318                        int buttonIndex)
 319     {
 320         final JButton button;
 321         Color col;
 322
 323         if(buttonIndex<caseSensitiveButtons.size())
 324         {
 325           button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);
 326           col = button.getBackground();
 327         }
 328         else
 329         {
 330           button = new JButton();
 331           button.addMouseListener(new java.awt.event.MouseAdapter()
 332           {
 333             public void mouseClicked(MouseEvent e)
 334             {
 335               colourButtonPressed(e);
 336             }
 337           });
 338
 339           caseSensitiveButtons.addElement(button);
 340
 341           col = Color.white;
 342
 343           try
 344           {
 345             col = oldColourScheme.findColour(aa, -1);
 346           }
 347           catch (Exception ex)
 348           {    }
 349         }
 350
 351         if(caseSensitive.isSelected())
 352           button.setMargin(new java.awt.Insets(2,2,2,2));
 353         else
 354           button.setMargin(new java.awt.Insets(2,14,2,14));
 355
 356         button.setBackground(col);
 357         button.setText(label);
 358         button.setForeground(col.darker().darker().darker());
 359         button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));
 360
 361         return button;
 362     }
 363
 364     /**
 365      * DOCUMENT ME!
 366      *
 367      * @param e DOCUMENT ME!
 368      */
 369     protected void okButton_actionPerformed(ActionEvent e)
 370     {
 371         applyButton_actionPerformed(null);
 372
 373         try
 374         {
 375             frame.setClosed(true);
 376         }
 377         catch (Exception ex)
 378         {
 379         }
 380     }
 381
 382     /**
 383      * DOCUMENT ME!
 384      *
 385      * @param e DOCUMENT ME!
 386      */
 387     protected void applyButton_actionPerformed(ActionEvent e)
 388     {
 389         UserColourScheme ucs = getSchemeFromButtons();
 390         ucs.setName(schemeName.getText());
 391
 392         if (seqGroup != null)
 393         {
 394             seqGroup.cs = ucs;
 395             ap.repaint();
 396         }
 397         else if(ap!=null)
 398         {
 399             ap.alignFrame.changeColour(ucs);
 400         }
 401         else if(pdbcanvas!=null)
 402         {
 403           pdbcanvas.pdb.setColours(ucs);
 404           pdbcanvas.updateSeqColours();
 405         }
 406     }
 407
 408     UserColourScheme getSchemeFromButtons()
 409     {
 410
 411       Color[] newColours = new Color[24];
 412
 413       for (int i = 0; i < 24; i++)
 414       {
 415         JButton button = (JButton) upperCaseButtons.elementAt(i);
 416         newColours[i] = button.getBackground();
 417       }
 418
 419       UserColourScheme ucs = new UserColourScheme(newColours);
 420
 421
 422       if(caseSensitive.isSelected())
 423       {
 424         newColours = new Color[23];
 425         for (int i = 0; i < 23; i++)
 426         {
 427           JButton button = (JButton) lowerCaseButtons.elementAt(i);
 428           newColours[i] = button.getBackground();
 429         }
 430         ucs.setLowerCaseColours(newColours);
 431       }
 432
 433       if(ap!=null)
 434         ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 435
 436
 437       return ucs;
 438     }
 439
 440
 441
 442     /**
 443      * DOCUMENT ME!
 444      *
 445      * @param e DOCUMENT ME!
 446      */
 447     protected void loadbutton_actionPerformed(ActionEvent e)
 448     {
 449       upperCaseButtons = new Vector();
 450       lowerCaseButtons = new Vector();
 451
 452         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 453                     "LAST_DIRECTORY"), new String[] { "jc" },
 454                 new String[] { "Jalview User Colours" }, "Jalview User Colours");
 455         chooser.setFileView(new jalview.io.JalviewFileView());
 456         chooser.setDialogTitle("Load colour scheme");
 457         chooser.setToolTipText("Load");
 458
 459         int value = chooser.showOpenDialog(this);
 460
 461         if (value == JalviewFileChooser.APPROVE_OPTION)
 462         {
 463             File choice = chooser.getSelectedFile();
 464             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
 465             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",
 466                 choice.getPath());
 467             if (defaultColours.indexOf(choice.getPath()) == -1)
 468               defaultColours = defaultColours.concat("|").concat(choice.getPath());
 469
 470             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 471
 472
 473             UserColourScheme ucs = loadColours(choice.getAbsolutePath());
 474             Color[] colors = ucs.getColours();
 475             schemeName.setText(ucs.getName());
 476
 477             if(ucs.getLowerCaseColours()!=null)
 478             {
 479               caseSensitive.setSelected(true);
 480               lcaseColour.setEnabled(true);
 481               resetButtonPanel(true);
 482               for (int i = 0; i < lowerCaseButtons.size(); i++)
 483               {
 484                 JButton button = (JButton) lowerCaseButtons.elementAt(i);
 485                 button.setBackground(ucs.getLowerCaseColours()[i]);
 486               }
 487
 488             }
 489             else
 490             {
 491               caseSensitive.setSelected(false);
 492               lcaseColour.setEnabled(false);
 493               resetButtonPanel(false);
 494             }
 495
 496             for (int i = 0; i < upperCaseButtons.size(); i++)
 497             {
 498                 JButton button = (JButton) upperCaseButtons.elementAt(i);
 499                 button.setBackground(colors[i]);
 500             }
 501
 502         }
 503     }
 504
 505     /**
 506      * DOCUMENT ME!
 507      *
 508      * @return DOCUMENT ME!
 509      */
 510     public static UserColourScheme loadDefaultColours()
 511     {
 512         UserColourScheme ret = null;
 513
 514         String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
 515         if ( colours != null )
 516         {
 517           if(colours.indexOf("|")>-1)
 518             colours = colours.substring(0, colours.indexOf("|"));
 519
 520           ret = loadColours(colours);
 521         }
 522
 523         if(ret == null)
 524         {
 525           Color[] newColours = new Color[24];
 526           for (int i = 0; i < 24; i++)
 527           {
 528             newColours[i] = Color.white;
 529           }
 530           ret =  new UserColourScheme(newColours);
 531         }
 532
 533         return ret;
 534     }
 535
 536     /**
 537      * DOCUMENT ME!
 538      *
 539      * @param file DOCUMENT ME!
 540      *
 541      * @return DOCUMENT ME!
 542      */
 543     static UserColourScheme loadColours(String file)
 544     {
 545          UserColourScheme ucs = null;
 546          Color[]  newColours = null;
 547         try
 548         {
 549             InputStreamReader in = new InputStreamReader(new FileInputStream(
 550                         file), "UTF-8");
 551
 552               jalview.schemabinding.version2.JalviewUserColours jucs
 553                   = new jalview.schemabinding.version2.JalviewUserColours();
 554
 555               org.exolab.castor.xml.Unmarshaller unmar
 556                   = new org.exolab.castor.xml.Unmarshaller(jucs);
 557               jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );
 558
 559               newColours = new Color[24];
 560
 561               Color [] lowerCase = null;
 562               boolean caseSensitive = false;
 563
 564
 565             String name;
 566             int index;
 567             for (int i = 0; i < jucs.getColourCount(); i++)
 568             {
 569               name =  jucs.getColour(i).getName();
 570               if(ResidueProperties.aa3Hash.containsKey(name))
 571               {
 572                 index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();
 573               }
 574               else
 575               {
 576                 index = ((Integer)ResidueProperties.aaHash.get(name)).intValue();
 577               }
 578               if(index == -1)
 579                 continue;
 580
 581               if(name.toLowerCase().equals(name))
 582               {
 583                 if(lowerCase==null)
 584                    lowerCase = new Color[23];
 585                 caseSensitive = true;
 586                 lowerCase[index] = new Color(Integer.parseInt(
 587                   jucs.getColour(i).getRGB(), 16));
 588               }
 589               else
 590               {
 591                 newColours[index] = new Color(Integer.parseInt(
 592                     jucs.getColour(i).getRGB(), 16));
 593               }
 594             }
 595
 596             if (newColours != null)
 597             {
 598               ucs = new UserColourScheme(newColours);
 599               ucs.setName( jucs.getSchemeName() );
 600               if(caseSensitive)
 601               {
 602                 ucs.setLowerCaseColours(lowerCase);
 603               }
 604             }
 605
 606         }
 607         catch (Exception ex)
 608         {
 609             //Could be Archive Jalview format
 610             try{
 611               InputStreamReader in = new InputStreamReader(new FileInputStream(
 612                   file), "UTF-8");
 613
 614               jalview.binding.JalviewUserColours jucs
 615                   = new jalview.binding.JalviewUserColours();
 616
 617               jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
 618
 619               newColours = new Color[jucs.getColourCount()];
 620
 621               for (int i = 0; i < 24; i++)
 622               {
 623                 newColours[i] = new Color(Integer.parseInt(
 624                     jucs.getColour(i).getRGB(), 16));
 625               }
 626               if (newColours != null)
 627               {
 628                 ucs = new UserColourScheme(newColours);
 629                 ucs.setName(jucs.getSchemeName());
 630               }
 631             }catch(Exception ex2)
 632             { ex2.printStackTrace(); }
 633
 634             if(newColours==null)
 635               System.out.println("Error loading User ColourFile\n"+ex);
 636         }
 637
 638        return ucs;
 639     }
 640
 641     /**
 642      * DOCUMENT ME!
 643      *
 644      * @param e DOCUMENT ME!
 645      */
 646     protected void savebutton_actionPerformed(ActionEvent e)
 647     {
 648       if(schemeName.getText().trim().length()<1)
 649       {
 650         JOptionPane.showInternalMessageDialog(Desktop.desktop,
 651                                               "User colour scheme must have a name!",
 652                                               "No name for colour scheme",
 653                                               JOptionPane.WARNING_MESSAGE);
 654         return;
 655       }
 656
 657       if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )
 658       {
 659         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."
 660             +"\nContinue saving colour scheme as "+schemeName.getText()+"?",
 661            "Duplicate scheme name", JOptionPane.YES_NO_OPTION);
 662         if(reply != JOptionPane.YES_OPTION)
 663           return;
 664
 665          userColourSchemes.remove(schemeName.getText());
 666       }
 667         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
 668                     "LAST_DIRECTORY"), new String[] { "jc" },
 669                 new String[] { "Jalview User Colours" }, "Jalview User Colours");
 670
 671         chooser.setFileView(new jalview.io.JalviewFileView());
 672         chooser.setDialogTitle("Save colour scheme");
 673         chooser.setToolTipText("Save");
 674
 675         int value = chooser.showSaveDialog(this);
 676
 677         if (value == JalviewFileChooser.APPROVE_OPTION)
 678         {
 679             String choice = chooser.getSelectedFile().getPath();
 680             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);
 681             if(defaultColours.indexOf(choice)==-1)
 682             {
 683               if(defaultColours.length()>0)
 684                 defaultColours = defaultColours.concat("|");
 685               defaultColours = defaultColours.concat(choice);
 686             }
 687
 688             userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());
 689
 690             ap.alignFrame.updateUserColourMenu();
 691
 692             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 693
 694             jalview.schemabinding.version2.JalviewUserColours ucs
 695                 = new jalview.schemabinding.version2.JalviewUserColours();
 696
 697             ucs.setSchemeName(schemeName.getText());
 698             try
 699             {
 700                 PrintWriter out = new PrintWriter(new OutputStreamWriter(
 701                             new FileOutputStream(choice), "UTF-8"));
 702
 703                 for (int i = 0; i < buttonPanel.getComponentCount(); i++)
 704                 {
 705                     JButton button = (JButton) buttonPanel.getComponent(i);
 706                     jalview.schemabinding.version2.Colour col
 707                         = new jalview.schemabinding.version2.Colour();
 708                     col.setName(button.getText());
 709                     col.setRGB(jalview.util.Format.getHexString(
 710                             button.getBackground()));
 711                     ucs.addColour(col);
 712                 }
 713
 714                 ucs.marshal(out);
 715                 out.close();
 716             }
 717             catch (Exception ex)
 718             {
 719                 ex.printStackTrace();
 720             }
 721         }
 722     }
 723
 724     /**
 725      * DOCUMENT ME!
 726      *
 727      * @param e DOCUMENT ME!
 728      */
 729     protected void cancelButton_actionPerformed(ActionEvent e)
 730     {
 731       if (ap != null)
 732       {
 733         if (seqGroup != null)
 734         {
 735           seqGroup.cs = oldColourScheme;
 736         }
 737         else if (ap != null)
 738         {
 739           ap.av.setGlobalColourScheme(oldColourScheme);
 740         }
 741         ap.repaint();
 742       }
 743
 744       if(pdbcanvas!=null)
 745       {
 746         pdbcanvas.pdb.setColours(oldColourScheme);
 747       }
 748
 749         try
 750         {
 751             frame.setClosed(true);
 752         }
 753         catch (Exception ex)
 754         {
 755         }
 756     }
 757
 758
 759     static Hashtable userColourSchemes;
 760
 761     public static Hashtable getUserColourSchemes()
 762     {
 763       return userColourSchemes;
 764     }
 765
 766     public static void initUserColourSchemes(String files)
 767     {
 768       userColourSchemes = new Hashtable();
 769
 770       if(files==null || files.length()==0)
 771         return;
 772
 773
 774       // In case colours can't be loaded, we'll remove them
 775       // from the default list here.
 776       StringBuffer coloursFound = new StringBuffer();
 777       StringTokenizer st = new StringTokenizer(files, "|");
 778       while (st.hasMoreElements())
 779       {
 780         String file = st.nextToken();
 781         try
 782         {
 783           UserColourScheme ucs = loadColours(file);
 784           if (ucs != null)
 785           {
 786             if (coloursFound.length() > 0)
 787               coloursFound.append("|");
 788             coloursFound.append(file);
 789             userColourSchemes.put(ucs.getName(), ucs);
 790           }
 791         }
 792         catch (Exception ex)
 793         {
 794           System.out.println("Error loading User ColourFile\n" + ex);
 795         }
 796       }
 797       if (!files.equals(coloursFound.toString()))
 798       {
 799         if (coloursFound.toString().length() > 1)
 800           jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
 801                                         coloursFound.toString());
 802         else
 803           jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
 804       }
 805     }
 806
 807     public static void removeColourFromDefaults(String target)
 808     {
 809       // The only way to find colours by name is to load them in
 810       // In case colours can't be loaded, we'll remove them
 811       // from the default list here.
 812
 813       userColourSchemes = new Hashtable();
 814
 815       StringBuffer coloursFound = new StringBuffer();
 816       StringTokenizer st = new StringTokenizer(
 817            jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
 818
 819       while (st.hasMoreElements())
 820       {
 821         String file = st.nextToken();
 822         try
 823         {
 824           UserColourScheme ucs = loadColours(file);
 825           if (ucs != null && !ucs.getName().equals(target))
 826           {
 827             if (coloursFound.length() > 0)
 828               coloursFound.append("|");
 829             coloursFound.append(file);
 830             userColourSchemes.put(ucs.getName(), ucs);
 831           }
 832         }
 833         catch (Exception ex)
 834         {
 835           System.out.println("Error loading User ColourFile\n" + ex);
 836         }
 837       }
 838
 839       if (coloursFound.toString().length() > 1)
 840         jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());
 841       else
 842         jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");
 843
 844     }
 845
 846     public void caseSensitive_actionPerformed(ActionEvent e)
 847     {
 848       resetButtonPanel(caseSensitive.isSelected());
 849       lcaseColour.setEnabled(caseSensitive.isSelected());
 850     }
 851
 852     public void lcaseColour_actionPerformed(ActionEvent e)
 853     {
 854       if(selectedButtons==null)
 855         selectedButtons = new Vector();
 856       else
 857         selectedButtons.clear();
 858       selectedButtons.add(lcaseColour);
 859     }
 860
 861 }