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