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