src/jalview/gui/UserDefinedColours.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 \r
  23 import jalview.io.*;\r
  24 \r
  25 import jalview.jbgui.*;\r
  26 \r
  27 import jalview.schemes.*;\r
  28 \r
  29 import java.awt.*;\r
  30 import java.awt.event.*;\r
  31 \r
  32 import java.io.*;\r
  33 \r
  34 import java.util.*;\r
  35 \r
  36 import javax.swing.*;\r
  37 import javax.swing.event.*;\r
  38 \r
  39 \r
  40 \r
  41 /**\r
  42  * DOCUMENT ME!\r
  43  *\r
  44  * @author $author$\r
  45  * @version $Revision$\r
  46  */\r
  47 public class UserDefinedColours extends GUserDefinedColours\r
  48     implements ChangeListener\r
  49 {\r
  50     AlignmentPanel ap;\r
  51     SequenceGroup seqGroup;\r
  52     Vector selectedButtons;\r
  53     ColourSchemeI oldColourScheme;\r
  54     JInternalFrame frame;\r
  55     MCview.PDBCanvas pdbcanvas;\r
  56     Vector upperCaseButtons;\r
  57     Vector lowerCaseButtons;\r
  58 \r
  59 \r
  60     /**\r
  61      * Creates a new UserDefinedColours object.\r
  62      *\r
  63      * @param ap DOCUMENT ME!\r
  64      * @param sg DOCUMENT ME!\r
  65      */\r
  66     public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
  67     {\r
  68         super();\r
  69 \r
  70         //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
  71         casePanel.setVisible(false);\r
  72 \r
  73 \r
  74         lcaseColour.setEnabled(false);\r
  75 \r
  76         this.ap = ap;\r
  77         seqGroup = sg;\r
  78 \r
  79         if (seqGroup != null)\r
  80             oldColourScheme = seqGroup.cs;\r
  81         else\r
  82             oldColourScheme = ap.av.getGlobalColourScheme();\r
  83 \r
  84         if (oldColourScheme instanceof UserColourScheme)\r
  85         {\r
  86           schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
  87           if(( (UserColourScheme) oldColourScheme).getLowerCaseColours()!=null)\r
  88           {\r
  89             caseSensitive.setSelected(true);\r
  90             lcaseColour.setEnabled(true);\r
  91             resetButtonPanel(true);\r
  92           }\r
  93           else\r
  94             resetButtonPanel(false);\r
  95         }\r
  96         else\r
  97            resetButtonPanel(false);\r
  98 \r
  99         showFrame();\r
 100     }\r
 101 \r
 102     public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
 103     {\r
 104         super();\r
 105         pdbcanvas = pdb;\r
 106 \r
 107         colorChooser.getSelectionModel().addChangeListener(this);\r
 108 \r
 109         oldColourScheme = oldcs;\r
 110 \r
 111         if (oldColourScheme instanceof UserColourScheme)\r
 112         {\r
 113               schemeName.setText( ( (UserColourScheme) oldColourScheme).getName());\r
 114         }\r
 115 \r
 116         resetButtonPanel(false);\r
 117 \r
 118         showFrame();\r
 119 \r
 120     }\r
 121 \r
 122     void showFrame()\r
 123     {\r
 124       colorChooser.getSelectionModel().addChangeListener(this);\r
 125       frame = new JInternalFrame();\r
 126       frame.setContentPane(this);\r
 127       Desktop.addInternalFrame(frame, "User Defined Colours", 720, 370, true);\r
 128 \r
 129       if (seqGroup != null)\r
 130             frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");\r
 131 \r
 132       if (System.getProperty("os.name").startsWith("Mac"))\r
 133       {\r
 134         frame.setSize(760, 370);\r
 135       }\r
 136     }\r
 137 \r
 138     void resetButtonPanel(boolean caseSensitive)\r
 139     {\r
 140       //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
 141       caseSensitive = false;\r
 142 \r
 143       buttonPanel.removeAll();\r
 144 \r
 145 \r
 146       if(upperCaseButtons==null)\r
 147         upperCaseButtons = new Vector();\r
 148 \r
 149       JButton button;\r
 150       String label;\r
 151       for (int i = 0; i < 20; i++)\r
 152       {\r
 153         if(caseSensitive)\r
 154           label = ResidueProperties.aa[i];\r
 155         else\r
 156           label = ResidueProperties.aa2Triplet.get\r
 157               (ResidueProperties.aa[i]).toString();\r
 158 \r
 159         button = makeButton(label,\r
 160                               ResidueProperties.aa[i],\r
 161                               upperCaseButtons, i);\r
 162 \r
 163         buttonPanel.add(button);\r
 164       }\r
 165 \r
 166         buttonPanel.add(makeButton("B", "B", upperCaseButtons, 20));\r
 167         buttonPanel.add(makeButton("Z", "Z", upperCaseButtons, 21));\r
 168         buttonPanel.add(makeButton("X", "X", upperCaseButtons, 22));\r
 169         buttonPanel.add(makeButton("Gap", "-", upperCaseButtons, 23));\r
 170 \r
 171       if(!caseSensitive)\r
 172       {\r
 173         gridLayout.setRows(6);\r
 174         gridLayout.setColumns(4);\r
 175       }\r
 176       else\r
 177       {\r
 178         gridLayout.setRows(7);\r
 179         int cols = 7;\r
 180         gridLayout.setColumns(cols+1);\r
 181 \r
 182         if(lowerCaseButtons==null)\r
 183           lowerCaseButtons = new Vector();\r
 184 \r
 185 \r
 186           for (int i = 0; i < 20; i++)\r
 187           {\r
 188             int row = i / cols + 1;\r
 189             int index = (row * cols) + i;\r
 190             button = makeButton(\r
 191                 ResidueProperties.aa[i].toLowerCase(),\r
 192                 ResidueProperties.aa[i].toLowerCase(),\r
 193                 lowerCaseButtons,\r
 194                 i);\r
 195 \r
 196             buttonPanel.add(button, index);\r
 197           }\r
 198       }\r
 199 \r
 200 \r
 201       if(caseSensitive)\r
 202       {\r
 203         buttonPanel.add(makeButton("b", "b", lowerCaseButtons, 20));\r
 204         buttonPanel.add(makeButton("z", "z", lowerCaseButtons, 21));\r
 205         buttonPanel.add(makeButton("x", "x", lowerCaseButtons, 22));\r
 206       }\r
 207 \r
 208       buttonPanel.validate();\r
 209       validate();\r
 210     }\r
 211 \r
 212 \r
 213     /**\r
 214      * DOCUMENT ME!\r
 215      *\r
 216      * @param evt DOCUMENT ME!\r
 217      */\r
 218     public void stateChanged(ChangeEvent evt)\r
 219     {\r
 220         if (selectedButtons != null)\r
 221         {\r
 222           JButton button=null;\r
 223           for(int i=0; i<selectedButtons.size(); i++)\r
 224           {\r
 225             button = (JButton)selectedButtons.elementAt(i);\r
 226             button.setBackground(colorChooser.getColor());\r
 227             button.setForeground( button.getBackground().brighter().brighter().brighter());\r
 228           }\r
 229           if(button==lcaseColour)\r
 230           {\r
 231             for(int i=0; i<lowerCaseButtons.size(); i++)\r
 232             {\r
 233               button = (JButton)lowerCaseButtons.elementAt(i);\r
 234               button.setBackground(colorChooser.getColor());\r
 235               button.setForeground( button.getBackground().brighter().brighter().brighter());\r
 236             }\r
 237           }\r
 238         }\r
 239     }\r
 240 \r
 241     /**\r
 242      * DOCUMENT ME!\r
 243      *\r
 244      * @param e DOCUMENT ME!\r
 245      */\r
 246     public void colourButtonPressed(MouseEvent e)\r
 247     {\r
 248       if(selectedButtons == null)\r
 249         selectedButtons = new Vector();\r
 250 \r
 251       JButton pressed = (JButton) e.getSource();\r
 252 \r
 253       if(e.isShiftDown())\r
 254       {\r
 255         JButton start, end = (JButton) e.getSource();\r
 256         if(selectedButtons.size()>0)\r
 257           start = (JButton)selectedButtons.elementAt(selectedButtons.size()-1);\r
 258         else\r
 259           start = (JButton) e.getSource();\r
 260 \r
 261         int startIndex=0, endIndex=0;\r
 262         for(int b=0; b<buttonPanel.getComponentCount(); b++)\r
 263         {\r
 264           if(buttonPanel.getComponent(b)==start)\r
 265             startIndex = b;\r
 266           if(buttonPanel.getComponent(b)==end)\r
 267             endIndex = b;\r
 268         }\r
 269 \r
 270         if(startIndex > endIndex)\r
 271         {\r
 272           int temp = startIndex;\r
 273           startIndex = endIndex;\r
 274           endIndex = temp;\r
 275         }\r
 276 \r
 277         for(int b=startIndex; b<=endIndex; b++)\r
 278         {\r
 279           JButton button = (JButton)buttonPanel.getComponent(b);\r
 280           if(!selectedButtons.contains(button))\r
 281           {\r
 282             button.setForeground(button.getBackground().brighter().brighter());\r
 283             selectedButtons.add(button);\r
 284           }\r
 285         }\r
 286       }\r
 287       else if(!e.isControlDown())\r
 288       {\r
 289         for(int b=0; b<selectedButtons.size(); b++)\r
 290         {\r
 291           JButton button = (JButton)selectedButtons.elementAt(b);\r
 292           button.setForeground(button.getBackground().darker().darker());\r
 293         }\r
 294         selectedButtons.clear();\r
 295         pressed.setForeground( pressed.getBackground().brighter().brighter());\r
 296         selectedButtons.addElement(pressed);\r
 297 \r
 298       }\r
 299       else if(e.isControlDown())\r
 300       {\r
 301         if(selectedButtons.contains(pressed))\r
 302         {\r
 303           pressed.setForeground(pressed.getBackground().darker().darker());\r
 304           selectedButtons.remove(pressed);\r
 305         }\r
 306         else\r
 307         {\r
 308           pressed.setForeground( pressed.getBackground().brighter().brighter());\r
 309           selectedButtons.addElement(pressed);\r
 310         }\r
 311       }\r
 312 \r
 313       if(selectedButtons.size()>0)\r
 314       colorChooser.setColor( ((JButton)selectedButtons.elementAt(0)).getBackground());\r
 315     }\r
 316 \r
 317     /**\r
 318      * DOCUMENT ME!\r
 319      *\r
 320      * @param label DOCUMENT ME!\r
 321      * @param aa DOCUMENT ME!\r
 322      */\r
 323     JButton makeButton(String label,\r
 324                        String aa,\r
 325                        Vector caseSensitiveButtons,\r
 326                        int buttonIndex)\r
 327     {\r
 328         final JButton button;\r
 329         Color col;\r
 330 \r
 331         if(buttonIndex<caseSensitiveButtons.size())\r
 332         {\r
 333           button = (JButton) caseSensitiveButtons.elementAt(buttonIndex);\r
 334           col = button.getBackground();\r
 335         }\r
 336         else\r
 337         {\r
 338           button = new JButton();\r
 339           button.addMouseListener(new java.awt.event.MouseAdapter()\r
 340           {\r
 341             public void mouseClicked(MouseEvent e)\r
 342             {\r
 343               colourButtonPressed(e);\r
 344             }\r
 345           });\r
 346 \r
 347           caseSensitiveButtons.addElement(button);\r
 348 \r
 349           col = Color.white;\r
 350 \r
 351           try\r
 352           {\r
 353             col = oldColourScheme.findColour(aa, -1);\r
 354           }\r
 355           catch (Exception ex)\r
 356           {    }\r
 357         }\r
 358 \r
 359       /* //AW - LOWER CASE DISABLED IN 2.1.01 bug fix release\r
 360         if(caseSensitive.isSelected())\r
 361           button.setMargin(new java.awt.Insets(2,2,2,2));\r
 362         else\r
 363          button.setMargin(new java.awt.Insets(2,14,2,14));\r
 364       */\r
 365 \r
 366         button.setBackground(col);\r
 367         button.setText(label);\r
 368         button.setForeground(col.darker().darker().darker());\r
 369         button.setFont(new java.awt.Font("Verdana", Font.BOLD, 10));\r
 370 \r
 371         return button;\r
 372     }\r
 373 \r
 374     /**\r
 375      * DOCUMENT ME!\r
 376      *\r
 377      * @param e DOCUMENT ME!\r
 378      */\r
 379     protected void okButton_actionPerformed(ActionEvent e)\r
 380     {\r
 381         applyButton_actionPerformed(null);\r
 382 \r
 383         try\r
 384         {\r
 385             frame.setClosed(true);\r
 386         }\r
 387         catch (Exception ex)\r
 388         {\r
 389         }\r
 390     }\r
 391 \r
 392     /**\r
 393      * DOCUMENT ME!\r
 394      *\r
 395      * @param e DOCUMENT ME!\r
 396      */\r
 397     protected void applyButton_actionPerformed(ActionEvent e)\r
 398     {\r
 399         UserColourScheme ucs = getSchemeFromButtons();\r
 400         ucs.setName(schemeName.getText());\r
 401 \r
 402         if (seqGroup != null)\r
 403         {\r
 404             seqGroup.cs = ucs;\r
 405             ap.repaint();\r
 406         }\r
 407         else if(ap!=null)\r
 408         {\r
 409             ap.alignFrame.changeColour(ucs);\r
 410         }\r
 411         else if(pdbcanvas!=null)\r
 412         {\r
 413           pdbcanvas.pdb.setColours(ucs);\r
 414           pdbcanvas.updateSeqColours();\r
 415         }\r
 416     }\r
 417 \r
 418     UserColourScheme getSchemeFromButtons()\r
 419     {\r
 420 \r
 421       Color[] newColours = new Color[24];\r
 422 \r
 423       for (int i = 0; i < 24; i++)\r
 424       {\r
 425         JButton button = (JButton) upperCaseButtons.elementAt(i);\r
 426         newColours[i] = button.getBackground();\r
 427       }\r
 428 \r
 429       UserColourScheme ucs = new UserColourScheme(newColours);\r
 430 \r
 431 \r
 432       if(caseSensitive.isSelected())\r
 433       {\r
 434         newColours = new Color[23];\r
 435         for (int i = 0; i < 23; i++)\r
 436         {\r
 437           JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
 438           newColours[i] = button.getBackground();\r
 439         }\r
 440         ucs.setLowerCaseColours(newColours);\r
 441       }\r
 442 \r
 443       if(ap!=null)\r
 444         ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 445 \r
 446 \r
 447       return ucs;\r
 448     }\r
 449 \r
 450 \r
 451 \r
 452     /**\r
 453      * DOCUMENT ME!\r
 454      *\r
 455      * @param e DOCUMENT ME!\r
 456      */\r
 457     protected void loadbutton_actionPerformed(ActionEvent e)\r
 458     {\r
 459       upperCaseButtons = new Vector();\r
 460       lowerCaseButtons = new Vector();\r
 461 \r
 462         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 463                     "LAST_DIRECTORY"), new String[] { "jc" },\r
 464                 new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
 465         chooser.setFileView(new jalview.io.JalviewFileView());\r
 466         chooser.setDialogTitle("Load colour scheme");\r
 467         chooser.setToolTipText("Load");\r
 468 \r
 469         int value = chooser.showOpenDialog(this);\r
 470 \r
 471         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 472         {\r
 473             File choice = chooser.getSelectedFile();\r
 474             jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
 475             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS",\r
 476                 choice.getPath());\r
 477             if (defaultColours.indexOf(choice.getPath()) == -1)\r
 478               defaultColours = defaultColours.concat("|").concat(choice.getPath());\r
 479 \r
 480             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
 481 \r
 482 \r
 483             UserColourScheme ucs = loadColours(choice.getAbsolutePath());\r
 484             Color[] colors = ucs.getColours();\r
 485             schemeName.setText(ucs.getName());\r
 486 \r
 487             if(ucs.getLowerCaseColours()!=null)\r
 488             {\r
 489               caseSensitive.setSelected(true);\r
 490               lcaseColour.setEnabled(true);\r
 491               resetButtonPanel(true);\r
 492               for (int i = 0; i < lowerCaseButtons.size(); i++)\r
 493               {\r
 494                 JButton button = (JButton) lowerCaseButtons.elementAt(i);\r
 495                 button.setBackground(ucs.getLowerCaseColours()[i]);\r
 496               }\r
 497 \r
 498             }\r
 499             else\r
 500             {\r
 501               caseSensitive.setSelected(false);\r
 502               lcaseColour.setEnabled(false);\r
 503               resetButtonPanel(false);\r
 504             }\r
 505 \r
 506             for (int i = 0; i < upperCaseButtons.size(); i++)\r
 507             {\r
 508                 JButton button = (JButton) upperCaseButtons.elementAt(i);\r
 509                 button.setBackground(colors[i]);\r
 510             }\r
 511 \r
 512         }\r
 513     }\r
 514 \r
 515     /**\r
 516      * DOCUMENT ME!\r
 517      *\r
 518      * @return DOCUMENT ME!\r
 519      */\r
 520     public static UserColourScheme loadDefaultColours()\r
 521     {\r
 522         UserColourScheme ret = null;\r
 523 \r
 524         String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");\r
 525         if ( colours != null )\r
 526         {\r
 527           if(colours.indexOf("|")>-1)\r
 528             colours = colours.substring(0, colours.indexOf("|"));\r
 529 \r
 530           ret = loadColours(colours);\r
 531         }\r
 532 \r
 533         if(ret == null)\r
 534         {\r
 535           Color[] newColours = new Color[24];\r
 536           for (int i = 0; i < 24; i++)\r
 537           {\r
 538             newColours[i] = Color.white;\r
 539           }\r
 540           ret =  new UserColourScheme(newColours);\r
 541         }\r
 542 \r
 543         return ret;\r
 544     }\r
 545 \r
 546     /**\r
 547      * DOCUMENT ME!\r
 548      *\r
 549      * @param file DOCUMENT ME!\r
 550      *\r
 551      * @return DOCUMENT ME!\r
 552      */\r
 553     static UserColourScheme loadColours(String file)\r
 554     {\r
 555          UserColourScheme ucs = null;\r
 556          Color[]  newColours = null;\r
 557         try\r
 558         {\r
 559             InputStreamReader in = new InputStreamReader(new FileInputStream(\r
 560                         file), "UTF-8");\r
 561 \r
 562               jalview.schemabinding.version2.JalviewUserColours jucs\r
 563                   = new jalview.schemabinding.version2.JalviewUserColours();\r
 564 \r
 565               org.exolab.castor.xml.Unmarshaller unmar\r
 566                   = new org.exolab.castor.xml.Unmarshaller(jucs);\r
 567               jucs = (jalview.schemabinding.version2.JalviewUserColours) unmar.unmarshal( in );\r
 568 \r
 569               newColours = new Color[24];\r
 570 \r
 571               Color [] lowerCase = null;\r
 572               boolean caseSensitive = false;\r
 573 \r
 574 \r
 575             String name;\r
 576             int index;\r
 577             for (int i = 0; i < jucs.getColourCount(); i++)\r
 578             {\r
 579               name =  jucs.getColour(i).getName();\r
 580               if(ResidueProperties.aa3Hash.containsKey(name))\r
 581               {\r
 582                 index = ((Integer)ResidueProperties.aa3Hash.get(name)).intValue();\r
 583               }\r
 584               else\r
 585               {\r
 586                 index = ((Integer)ResidueProperties.aaHash.get(name)).intValue();\r
 587               }\r
 588               if(index == -1)\r
 589                 continue;\r
 590 \r
 591               if(name.toLowerCase().equals(name))\r
 592               {\r
 593                 if(lowerCase==null)\r
 594                    lowerCase = new Color[23];\r
 595                 caseSensitive = true;\r
 596                 lowerCase[index] = new Color(Integer.parseInt(\r
 597                   jucs.getColour(i).getRGB(), 16));\r
 598               }\r
 599               else\r
 600               {\r
 601                 newColours[index] = new Color(Integer.parseInt(\r
 602                     jucs.getColour(i).getRGB(), 16));\r
 603               }\r
 604             }\r
 605 \r
 606             if (newColours != null)\r
 607             {\r
 608               ucs = new UserColourScheme(newColours);\r
 609               ucs.setName( jucs.getSchemeName() );\r
 610               if(caseSensitive)\r
 611               {\r
 612                 ucs.setLowerCaseColours(lowerCase);\r
 613               }\r
 614             }\r
 615 \r
 616         }\r
 617         catch (Exception ex)\r
 618         {\r
 619             //Could be Archive Jalview format\r
 620             try{\r
 621               InputStreamReader in = new InputStreamReader(new FileInputStream(\r
 622                   file), "UTF-8");\r
 623 \r
 624               jalview.binding.JalviewUserColours jucs\r
 625                   = new jalview.binding.JalviewUserColours();\r
 626 \r
 627               jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
 628 \r
 629               newColours = new Color[jucs.getColourCount()];\r
 630 \r
 631               for (int i = 0; i < 24; i++)\r
 632               {\r
 633                 newColours[i] = new Color(Integer.parseInt(\r
 634                     jucs.getColour(i).getRGB(), 16));\r
 635               }\r
 636               if (newColours != null)\r
 637               {\r
 638                 ucs = new UserColourScheme(newColours);\r
 639                 ucs.setName(jucs.getSchemeName());\r
 640               }\r
 641             }catch(Exception ex2)\r
 642             { ex2.printStackTrace(); }\r
 643 \r
 644             if(newColours==null)\r
 645               System.out.println("Error loading User ColourFile\n"+ex);\r
 646         }\r
 647 \r
 648        return ucs;\r
 649     }\r
 650 \r
 651     /**\r
 652      * DOCUMENT ME!\r
 653      *\r
 654      * @param e DOCUMENT ME!\r
 655      */\r
 656     protected void savebutton_actionPerformed(ActionEvent e)\r
 657     {\r
 658       if(schemeName.getText().trim().length()<1)\r
 659       {\r
 660         JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 661                                               "User colour scheme must have a name!",\r
 662                                               "No name for colour scheme",\r
 663                                               JOptionPane.WARNING_MESSAGE);\r
 664         return;\r
 665       }\r
 666 \r
 667       if(userColourSchemes!=null && userColourSchemes.containsKey(schemeName.getText()) )\r
 668       {\r
 669         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, "Colour scheme "+schemeName.getText()+ " exists."\r
 670             +"\nContinue saving colour scheme as "+schemeName.getText()+"?",\r
 671            "Duplicate scheme name", JOptionPane.YES_NO_OPTION);\r
 672         if(reply != JOptionPane.YES_OPTION)\r
 673           return;\r
 674 \r
 675          userColourSchemes.remove(schemeName.getText());\r
 676       }\r
 677         JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
 678                     "LAST_DIRECTORY"), new String[] { "jc" },\r
 679                 new String[] { "Jalview User Colours" }, "Jalview User Colours");\r
 680 \r
 681         chooser.setFileView(new jalview.io.JalviewFileView());\r
 682         chooser.setDialogTitle("Save colour scheme");\r
 683         chooser.setToolTipText("Save");\r
 684 \r
 685         int value = chooser.showSaveDialog(this);\r
 686 \r
 687         if (value == JalviewFileChooser.APPROVE_OPTION)\r
 688         {\r
 689             String choice = chooser.getSelectedFile().getPath();\r
 690             String defaultColours = jalview.bin.Cache.getDefault("USER_DEFINED_COLOURS", choice);\r
 691             if(defaultColours.indexOf(choice)==-1)\r
 692             {\r
 693               if(defaultColours.length()>0)\r
 694                 defaultColours = defaultColours.concat("|");\r
 695               defaultColours = defaultColours.concat(choice);\r
 696             }\r
 697 \r
 698             userColourSchemes.put(schemeName.getText(), getSchemeFromButtons());\r
 699 \r
 700             ap.alignFrame.updateUserColourMenu();\r
 701 \r
 702             jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);\r
 703 \r
 704             jalview.schemabinding.version2.JalviewUserColours ucs\r
 705                 = new jalview.schemabinding.version2.JalviewUserColours();\r
 706 \r
 707             ucs.setSchemeName(schemeName.getText());\r
 708             try\r
 709             {\r
 710                 PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
 711                             new FileOutputStream(choice), "UTF-8"));\r
 712 \r
 713                 for (int i = 0; i < buttonPanel.getComponentCount(); i++)\r
 714                 {\r
 715                     JButton button = (JButton) buttonPanel.getComponent(i);\r
 716                     jalview.schemabinding.version2.Colour col\r
 717                         = new jalview.schemabinding.version2.Colour();\r
 718                     col.setName(button.getText());\r
 719                     col.setRGB(jalview.util.Format.getHexString(\r
 720                             button.getBackground()));\r
 721                     ucs.addColour(col);\r
 722                 }\r
 723 \r
 724                 ucs.marshal(out);\r
 725                 out.close();\r
 726             }\r
 727             catch (Exception ex)\r
 728             {\r
 729                 ex.printStackTrace();\r
 730             }\r
 731         }\r
 732     }\r
 733 \r
 734     /**\r
 735      * DOCUMENT ME!\r
 736      *\r
 737      * @param e DOCUMENT ME!\r
 738      */\r
 739     protected void cancelButton_actionPerformed(ActionEvent e)\r
 740     {\r
 741       if (ap != null)\r
 742       {\r
 743         if (seqGroup != null)\r
 744         {\r
 745           seqGroup.cs = oldColourScheme;\r
 746         }\r
 747         else if (ap != null)\r
 748         {\r
 749           ap.av.setGlobalColourScheme(oldColourScheme);\r
 750         }\r
 751         ap.repaint();\r
 752       }\r
 753 \r
 754       if(pdbcanvas!=null)\r
 755       {\r
 756         pdbcanvas.pdb.setColours(oldColourScheme);\r
 757       }\r
 758 \r
 759         try\r
 760         {\r
 761             frame.setClosed(true);\r
 762         }\r
 763         catch (Exception ex)\r
 764         {\r
 765         }\r
 766     }\r
 767 \r
 768 \r
 769     static Hashtable userColourSchemes;\r
 770 \r
 771     public static Hashtable getUserColourSchemes()\r
 772     {\r
 773       return userColourSchemes;\r
 774     }\r
 775 \r
 776     public static void initUserColourSchemes(String files)\r
 777     {\r
 778       userColourSchemes = new Hashtable();\r
 779 \r
 780       if(files==null || files.length()==0)\r
 781         return;\r
 782 \r
 783 \r
 784       // In case colours can't be loaded, we'll remove them\r
 785       // from the default list here.\r
 786       StringBuffer coloursFound = new StringBuffer();\r
 787       StringTokenizer st = new StringTokenizer(files, "|");\r
 788       while (st.hasMoreElements())\r
 789       {\r
 790         String file = st.nextToken();\r
 791         try\r
 792         {\r
 793           UserColourScheme ucs = loadColours(file);\r
 794           if (ucs != null)\r
 795           {\r
 796             if (coloursFound.length() > 0)\r
 797               coloursFound.append("|");\r
 798             coloursFound.append(file);\r
 799             userColourSchemes.put(ucs.getName(), ucs);\r
 800           }\r
 801         }\r
 802         catch (Exception ex)\r
 803         {\r
 804           System.out.println("Error loading User ColourFile\n" + ex);\r
 805         }\r
 806       }\r
 807       if (!files.equals(coloursFound.toString()))\r
 808       {\r
 809         if (coloursFound.toString().length() > 1)\r
 810           jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",\r
 811                                         coloursFound.toString());\r
 812         else\r
 813           jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
 814       }\r
 815     }\r
 816 \r
 817     public static void removeColourFromDefaults(String target)\r
 818     {\r
 819       // The only way to find colours by name is to load them in\r
 820       // In case colours can't be loaded, we'll remove them\r
 821       // from the default list here.\r
 822 \r
 823       userColourSchemes = new Hashtable();\r
 824 \r
 825       StringBuffer coloursFound = new StringBuffer();\r
 826       StringTokenizer st = new StringTokenizer(\r
 827            jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");\r
 828 \r
 829       while (st.hasMoreElements())\r
 830       {\r
 831         String file = st.nextToken();\r
 832         try\r
 833         {\r
 834           UserColourScheme ucs = loadColours(file);\r
 835           if (ucs != null && !ucs.getName().equals(target))\r
 836           {\r
 837             if (coloursFound.length() > 0)\r
 838               coloursFound.append("|");\r
 839             coloursFound.append(file);\r
 840             userColourSchemes.put(ucs.getName(), ucs);\r
 841           }\r
 842         }\r
 843         catch (Exception ex)\r
 844         {\r
 845           System.out.println("Error loading User ColourFile\n" + ex);\r
 846         }\r
 847       }\r
 848 \r
 849       if (coloursFound.toString().length() > 1)\r
 850         jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", coloursFound.toString());\r
 851       else\r
 852         jalview.bin.Cache.applicationProperties.remove("USER_DEFINED_COLOURS");\r
 853 \r
 854     }\r
 855 \r
 856     public void caseSensitive_actionPerformed(ActionEvent e)\r
 857     {\r
 858       resetButtonPanel(caseSensitive.isSelected());\r
 859       lcaseColour.setEnabled(caseSensitive.isSelected());\r
 860     }\r
 861 \r
 862     public void lcaseColour_actionPerformed(ActionEvent e)\r
 863     {\r
 864       if(selectedButtons==null)\r
 865         selectedButtons = new Vector();\r
 866       else\r
 867         selectedButtons.clear();\r
 868       selectedButtons.add(lcaseColour);\r
 869     }\r
 870 \r
 871 }\r