src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 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 java.util.*;\r
  22 \r
  23 import java.awt.*;\r
  24 import java.awt.event.*;\r
  25 import javax.swing.*;\r
  26 \r
  27 import MCview.*;\r
  28 import jalview.analysis.*;\r
  29 import jalview.commands.*;\r
  30 import jalview.datamodel.*;\r
  31 import jalview.io.*;\r
  32 import jalview.schemes.*;\r
  33 \r
  34 /**\r
  35  * DOCUMENT ME!\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class PopupMenu\r
  41     extends JPopupMenu\r
  42 {\r
  43   JMenu groupMenu = new JMenu();\r
  44   JMenuItem groupName = new JMenuItem();\r
  45   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  46   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  47   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  48   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  49       JRadioButtonMenuItem();\r
  50   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  51   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  52   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  53   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  54   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  55   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  58   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  59   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  60   AlignmentPanel ap;\r
  61   JMenu sequenceMenu = new JMenu();\r
  62   JMenuItem sequenceName = new JMenuItem();\r
  63   Sequence sequence;\r
  64   JMenuItem unGroupMenuItem = new JMenuItem();\r
  65   JMenuItem outline = new JMenuItem();\r
  66   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  67   JMenu colourMenu = new JMenu();\r
  68   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  69   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  70   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  71   JMenu editMenu = new JMenu();\r
  72   JMenuItem cut = new JMenuItem();\r
  73   JMenuItem copy = new JMenuItem();\r
  74   JMenuItem upperCase = new JMenuItem();\r
  75   JMenuItem lowerCase = new JMenuItem();\r
  76   JMenuItem toggle = new JMenuItem();\r
  77   JMenu pdbMenu = new JMenu();\r
  78   JMenuItem pdbFromFile = new JMenuItem();\r
  79   JMenuItem enterPDB = new JMenuItem();\r
  80   JMenuItem discoverPDB = new JMenuItem();\r
  81   JMenu outputMenu = new JMenu();\r
  82   JMenuItem sequenceFeature = new JMenuItem();\r
  83   JMenuItem textColour = new JMenuItem();\r
  84   JMenu jMenu1 = new JMenu();\r
  85   JMenu structureMenu = new JMenu();\r
  86   JMenu viewStructureMenu = new JMenu();\r
  87  // JMenu colStructureMenu = new JMenu();\r
  88   JMenuItem editSequence = new JMenuItem();\r
  89  // JMenuItem annotationMenuItem = new JMenuItem();\r
  90 \r
  91   /**\r
  92    * Creates a new PopupMenu object.\r
  93    *\r
  94    * @param ap DOCUMENT ME!\r
  95    * @param seq DOCUMENT ME!\r
  96    */\r
  97   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  98   {\r
  99     ///////////////////////////////////////////////////////////\r
 100     // If this is activated from the sequence panel, the user may want to\r
 101     // edit or annotate a particular residue. Therefore display the residue menu\r
 102     //\r
 103     // If from the IDPanel, we must display the sequence menu\r
 104     //////////////////////////////////////////////////////////\r
 105     this.ap = ap;\r
 106     sequence = seq;\r
 107 \r
 108     ButtonGroup colours = new ButtonGroup();\r
 109     colours.add(noColourmenuItem);\r
 110     colours.add(clustalColour);\r
 111     colours.add(zappoColour);\r
 112     colours.add(taylorColour);\r
 113     colours.add(hydrophobicityColour);\r
 114     colours.add(helixColour);\r
 115     colours.add(strandColour);\r
 116     colours.add(turnColour);\r
 117     colours.add(buriedColour);\r
 118     colours.add(abovePIDColour);\r
 119     colours.add(userDefinedColour);\r
 120     colours.add(PIDColour);\r
 121     colours.add(BLOSUM62Colour);\r
 122 \r
 123     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 124     {\r
 125       JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
 126                                      i]);\r
 127 \r
 128       item.addActionListener(new java.awt.event.ActionListener()\r
 129       {\r
 130         public void actionPerformed(ActionEvent e)\r
 131         {\r
 132           outputText_actionPerformed(e);\r
 133         }\r
 134       });\r
 135 \r
 136       outputMenu.add(item);\r
 137     }\r
 138 \r
 139     try\r
 140     {\r
 141       jbInit();\r
 142     }\r
 143     catch (Exception e)\r
 144     {\r
 145       e.printStackTrace();\r
 146     }\r
 147 \r
 148     if (seq != null)\r
 149     {\r
 150       sequenceMenu.setText(sequence.getName());\r
 151 \r
 152       JMenuItem menuItem;\r
 153       if (seq.getDatasetSequence().getPDBId() != null\r
 154           && seq.getDatasetSequence().getPDBId().size()>0)\r
 155       {\r
 156         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 157             elements();\r
 158 \r
 159         while (e.hasMoreElements())\r
 160         {\r
 161           final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 162 \r
 163           menuItem = new JMenuItem();\r
 164           menuItem.setText(pdb.getId());\r
 165           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 166           {\r
 167             public void actionPerformed(ActionEvent e)\r
 168             {\r
 169               Vector seqs = new Vector();\r
 170               for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
 171               {\r
 172                 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
 173                 if(pdbs==null)\r
 174                   continue;\r
 175 \r
 176                 for(int p=0; p<pdbs.size(); p++)\r
 177                 {\r
 178                   PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
 179                   if(p1.getId().equals(pdb.getId()))\r
 180                   {\r
 181                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
 182                         seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
 183 \r
 184                       continue;\r
 185                   }\r
 186                 }\r
 187               }\r
 188 \r
 189               SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
 190               seqs.toArray(seqs2);\r
 191 \r
 192               new AppJmol(pdb, seqs2, null, ap);\r
 193               //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
 194             }\r
 195           });\r
 196           viewStructureMenu.add(menuItem);\r
 197 \r
 198        /*   menuItem = new JMenuItem();\r
 199           menuItem.setText(pdb.getId());\r
 200           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 201           {\r
 202             public void actionPerformed(ActionEvent e)\r
 203             {\r
 204               colourByStructure(pdb.getId());\r
 205             }\r
 206           });\r
 207           colStructureMenu.add(menuItem);*/\r
 208         }\r
 209       }\r
 210       else\r
 211       {\r
 212         structureMenu.remove(viewStructureMenu);\r
 213        // structureMenu.remove(colStructureMenu);\r
 214       }\r
 215 \r
 216       menuItem = new JMenuItem("Hide Sequences");\r
 217       menuItem.addActionListener(new java.awt.event.ActionListener()\r
 218       {\r
 219         public void actionPerformed(ActionEvent e)\r
 220         {\r
 221           hideSequences(false);\r
 222         }\r
 223       });\r
 224       add(menuItem);\r
 225 \r
 226       if (ap.av.getSelectionGroup() != null\r
 227           && ap.av.getSelectionGroup().getSize() > 1)\r
 228       {\r
 229         menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 230         menuItem.addActionListener(new java.awt.event.ActionListener()\r
 231         {\r
 232           public void actionPerformed(ActionEvent e)\r
 233           {\r
 234             hideSequences(true);\r
 235           }\r
 236         });\r
 237         sequenceMenu.add(menuItem);\r
 238       }\r
 239 \r
 240       if (ap.av.hasHiddenRows)\r
 241       {\r
 242         final int index = ap.av.alignment.findIndex(seq);\r
 243 \r
 244         if (ap.av.adjustForHiddenSeqs(index) -\r
 245             ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 246         {\r
 247           menuItem = new JMenuItem("Reveal Sequences");\r
 248           menuItem.addActionListener(new ActionListener()\r
 249           {\r
 250             public void actionPerformed(ActionEvent e)\r
 251             {\r
 252               ap.av.showSequence(index);\r
 253               if (ap.overviewPanel != null)\r
 254               {\r
 255                 ap.overviewPanel.updateOverviewImage();\r
 256               }\r
 257             }\r
 258           });\r
 259           add(menuItem);\r
 260         }\r
 261 \r
 262         menuItem = new JMenuItem("Reveal All");\r
 263         menuItem.addActionListener(new ActionListener()\r
 264         {\r
 265           public void actionPerformed(ActionEvent e)\r
 266           {\r
 267             ap.av.showAllHiddenSeqs();\r
 268             if (ap.overviewPanel != null)\r
 269             {\r
 270               ap.overviewPanel.updateOverviewImage();\r
 271             }\r
 272           }\r
 273         });\r
 274 \r
 275         add(menuItem);\r
 276       }\r
 277 \r
 278     }\r
 279 \r
 280     SequenceGroup sg = ap.av.getSelectionGroup();\r
 281 \r
 282     if (sg != null)\r
 283     {\r
 284       groupName.setText(sg.getName());\r
 285 \r
 286       if (sg.cs instanceof ZappoColourScheme)\r
 287       {\r
 288         zappoColour.setSelected(true);\r
 289       }\r
 290       else if (sg.cs instanceof TaylorColourScheme)\r
 291       {\r
 292         taylorColour.setSelected(true);\r
 293       }\r
 294       else if (sg.cs instanceof PIDColourScheme)\r
 295       {\r
 296         PIDColour.setSelected(true);\r
 297       }\r
 298       else if (sg.cs instanceof Blosum62ColourScheme)\r
 299       {\r
 300         BLOSUM62Colour.setSelected(true);\r
 301       }\r
 302       else if (sg.cs instanceof UserColourScheme)\r
 303       {\r
 304         userDefinedColour.setSelected(true);\r
 305       }\r
 306       else if (sg.cs instanceof HydrophobicColourScheme)\r
 307       {\r
 308         hydrophobicityColour.setSelected(true);\r
 309       }\r
 310       else if (sg.cs instanceof HelixColourScheme)\r
 311       {\r
 312         helixColour.setSelected(true);\r
 313       }\r
 314       else if (sg.cs instanceof StrandColourScheme)\r
 315       {\r
 316         strandColour.setSelected(true);\r
 317       }\r
 318       else if (sg.cs instanceof TurnColourScheme)\r
 319       {\r
 320         turnColour.setSelected(true);\r
 321       }\r
 322       else if (sg.cs instanceof BuriedColourScheme)\r
 323       {\r
 324         buriedColour.setSelected(true);\r
 325       }\r
 326       else if (sg.cs instanceof ClustalxColourScheme)\r
 327       {\r
 328         clustalColour.setSelected(true);\r
 329       }\r
 330       else\r
 331       {\r
 332         noColourmenuItem.setSelected(true);\r
 333       }\r
 334 \r
 335       if (sg.cs != null && sg.cs.conservationApplied())\r
 336       {\r
 337         conservationMenuItem.setSelected(true);\r
 338       }\r
 339 \r
 340       showText.setSelected(sg.getDisplayText());\r
 341       showColourText.setSelected(sg.getColourText());\r
 342       showBoxes.setSelected(sg.getDisplayBoxes());\r
 343     }\r
 344     else\r
 345     {\r
 346       groupMenu.setVisible(false);\r
 347       editMenu.setVisible(false);\r
 348     }\r
 349 \r
 350     if (!ap.av.alignment.getGroups().contains(sg))\r
 351     {\r
 352       unGroupMenuItem.setVisible(false);\r
 353     }\r
 354 \r
 355     if (seq == null)\r
 356     {\r
 357       sequenceMenu.setVisible(false);\r
 358       structureMenu.setVisible(false);\r
 359     }\r
 360 \r
 361     if (links != null && links.size() > 0)\r
 362     {\r
 363       JMenu linkMenu = new JMenu("Link");\r
 364       JMenuItem item;\r
 365       for (int i = 0; i < links.size(); i++)\r
 366       {\r
 367         String link = links.elementAt(i).toString();\r
 368         final String label = link.substring(0, link.indexOf("|"));\r
 369         item = new JMenuItem(label);\r
 370         final String url;\r
 371 \r
 372         if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 373         {\r
 374           String id = seq.getName();\r
 375           if (id.indexOf("|") > -1)\r
 376           {\r
 377             id = id.substring(id.lastIndexOf("|") + 1);\r
 378           }\r
 379 \r
 380           url = link.substring(link.indexOf("|") + 1,\r
 381                                link.indexOf("$SEQUENCE_ID$"))\r
 382               + id +\r
 383               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 384         }\r
 385         else\r
 386         {\r
 387           url = link.substring(link.lastIndexOf("|") + 1);\r
 388         }\r
 389 \r
 390         item.addActionListener(new java.awt.event.ActionListener()\r
 391         {\r
 392           public void actionPerformed(ActionEvent e)\r
 393           {\r
 394             showLink(url);\r
 395           }\r
 396         });\r
 397 \r
 398         linkMenu.add(item);\r
 399       }\r
 400       if (sequence != null)\r
 401       {\r
 402         sequenceMenu.add(linkMenu);\r
 403       }\r
 404       else\r
 405       {\r
 406         add(linkMenu);\r
 407       }\r
 408     }\r
 409   }\r
 410 \r
 411   /**\r
 412    * DOCUMENT ME!\r
 413    *\r
 414    * @throws Exception DOCUMENT ME!\r
 415    */\r
 416   private void jbInit()\r
 417       throws Exception\r
 418   {\r
 419     groupMenu.setText("Group");\r
 420     groupMenu.setText("Selection");\r
 421     groupName.setText("Name");\r
 422     groupName.addActionListener(new java.awt.event.ActionListener()\r
 423     {\r
 424       public void actionPerformed(ActionEvent e)\r
 425       {\r
 426         groupName_actionPerformed();\r
 427       }\r
 428     });\r
 429     sequenceMenu.setText("Sequence");\r
 430     sequenceName.setText("Edit Name/Description");\r
 431     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 432     {\r
 433       public void actionPerformed(ActionEvent e)\r
 434       {\r
 435         sequenceName_actionPerformed();\r
 436       }\r
 437     });\r
 438     PIDColour.setFocusPainted(false);\r
 439     unGroupMenuItem.setText("Remove Group");\r
 440     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 441     {\r
 442       public void actionPerformed(ActionEvent e)\r
 443       {\r
 444         unGroupMenuItem_actionPerformed();\r
 445       }\r
 446     });\r
 447 \r
 448     outline.setText("Border colour");\r
 449     outline.addActionListener(new java.awt.event.ActionListener()\r
 450     {\r
 451       public void actionPerformed(ActionEvent e)\r
 452       {\r
 453         outline_actionPerformed();\r
 454       }\r
 455     });\r
 456     nucleotideMenuItem.setText("Nucleotide");\r
 457     nucleotideMenuItem.addActionListener(new ActionListener()\r
 458     {\r
 459       public void actionPerformed(ActionEvent e)\r
 460       {\r
 461         nucleotideMenuItem_actionPerformed();\r
 462       }\r
 463     });\r
 464     colourMenu.setText("Group Colour");\r
 465     showBoxes.setText("Boxes");\r
 466     showBoxes.setState(true);\r
 467     showBoxes.addActionListener(new ActionListener()\r
 468     {\r
 469       public void actionPerformed(ActionEvent e)\r
 470       {\r
 471         showBoxes_actionPerformed();\r
 472       }\r
 473     });\r
 474     showText.setText("Text");\r
 475     showText.setState(true);\r
 476     showText.addActionListener(new ActionListener()\r
 477     {\r
 478       public void actionPerformed(ActionEvent e)\r
 479       {\r
 480         showText_actionPerformed();\r
 481       }\r
 482     });\r
 483     showColourText.setText("Colour Text");\r
 484     showColourText.addActionListener(new ActionListener()\r
 485     {\r
 486       public void actionPerformed(ActionEvent e)\r
 487       {\r
 488         showColourText_actionPerformed();\r
 489       }\r
 490     });\r
 491     editMenu.setText("Edit");\r
 492     cut.setText("Cut");\r
 493     cut.addActionListener(new ActionListener()\r
 494     {\r
 495       public void actionPerformed(ActionEvent e)\r
 496       {\r
 497         cut_actionPerformed();\r
 498       }\r
 499     });\r
 500     upperCase.setText("To Upper Case");\r
 501     upperCase.addActionListener(new ActionListener()\r
 502     {\r
 503       public void actionPerformed(ActionEvent e)\r
 504       {\r
 505         changeCase(e);\r
 506       }\r
 507     });\r
 508     copy.setText("Copy");\r
 509     copy.addActionListener(new ActionListener()\r
 510     {\r
 511       public void actionPerformed(ActionEvent e)\r
 512       {\r
 513         copy_actionPerformed();\r
 514       }\r
 515     });\r
 516     lowerCase.setText("To Lower Case");\r
 517     lowerCase.addActionListener(new ActionListener()\r
 518     {\r
 519       public void actionPerformed(ActionEvent e)\r
 520       {\r
 521         changeCase(e);\r
 522       }\r
 523     });\r
 524     toggle.setText("Toggle Case");\r
 525     toggle.addActionListener(new ActionListener()\r
 526     {\r
 527       public void actionPerformed(ActionEvent e)\r
 528       {\r
 529         changeCase(e);\r
 530       }\r
 531     });\r
 532     pdbMenu.setText("Associate Structure with Sequence");\r
 533     pdbFromFile.setText("From File");\r
 534     pdbFromFile.addActionListener(new ActionListener()\r
 535     {\r
 536       public void actionPerformed(ActionEvent e)\r
 537       {\r
 538         pdbFromFile_actionPerformed();\r
 539       }\r
 540     });\r
 541     enterPDB.setText("Enter PDB Id");\r
 542     enterPDB.addActionListener(new ActionListener()\r
 543     {\r
 544       public void actionPerformed(ActionEvent e)\r
 545       {\r
 546         enterPDB_actionPerformed();\r
 547       }\r
 548     });\r
 549     discoverPDB.setText("Discover PDB ids");\r
 550     discoverPDB.addActionListener(new ActionListener()\r
 551     {\r
 552       public void actionPerformed(ActionEvent e)\r
 553       {\r
 554         discoverPDB_actionPerformed();\r
 555       }\r
 556     });\r
 557     outputMenu.setText("Output to Textbox...");\r
 558     sequenceFeature.setText("Create Sequence Feature");\r
 559     sequenceFeature.addActionListener(new ActionListener()\r
 560     {\r
 561       public void actionPerformed(ActionEvent e)\r
 562       {\r
 563         sequenceFeature_actionPerformed();\r
 564       }\r
 565     });\r
 566     textColour.setText("Text Colour");\r
 567     textColour.addActionListener(new ActionListener()\r
 568     {\r
 569       public void actionPerformed(ActionEvent e)\r
 570       {\r
 571         textColour_actionPerformed();\r
 572       }\r
 573     });\r
 574     jMenu1.setText("Group");\r
 575     structureMenu.setText("Structure");\r
 576     viewStructureMenu.setText("View Structure");\r
 577   //  colStructureMenu.setText("Colour By Structure");\r
 578     editSequence.setText("Edit Sequence...");\r
 579     editSequence.addActionListener(new ActionListener()\r
 580     {\r
 581       public void actionPerformed(ActionEvent actionEvent)\r
 582       {\r
 583         editSequence_actionPerformed(actionEvent);\r
 584       }\r
 585     });\r
 586    /* annotationMenuItem.setText("By Annotation");\r
 587     annotationMenuItem.addActionListener(new ActionListener()\r
 588     {\r
 589       public void actionPerformed(ActionEvent actionEvent)\r
 590       {\r
 591         annotationMenuItem_actionPerformed(actionEvent);\r
 592       }\r
 593     });*/\r
 594 \r
 595     add(groupMenu);\r
 596 \r
 597     add(sequenceMenu);\r
 598     this.add(structureMenu);\r
 599     groupMenu.add(editMenu);\r
 600     groupMenu.add(outputMenu);\r
 601     groupMenu.add(sequenceFeature);\r
 602     groupMenu.add(jMenu1);\r
 603     sequenceMenu.add(sequenceName);\r
 604     colourMenu.add(textColour);\r
 605     colourMenu.add(noColourmenuItem);\r
 606     colourMenu.add(clustalColour);\r
 607     colourMenu.add(BLOSUM62Colour);\r
 608     colourMenu.add(PIDColour);\r
 609     colourMenu.add(zappoColour);\r
 610     colourMenu.add(taylorColour);\r
 611     colourMenu.add(hydrophobicityColour);\r
 612     colourMenu.add(helixColour);\r
 613     colourMenu.add(strandColour);\r
 614     colourMenu.add(turnColour);\r
 615     colourMenu.add(buriedColour);\r
 616     colourMenu.add(nucleotideMenuItem);\r
 617     colourMenu.add(userDefinedColour);\r
 618 \r
 619     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
 620     {\r
 621       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 622           getUserColourSchemes().keys();\r
 623 \r
 624       while (userColours.hasMoreElements())\r
 625       {\r
 626         JMenuItem item = new JMenuItem(userColours.\r
 627                                        nextElement().toString());\r
 628         item.addActionListener(new ActionListener()\r
 629         {\r
 630           public void actionPerformed(ActionEvent evt)\r
 631           {\r
 632             userDefinedColour_actionPerformed(evt);\r
 633           }\r
 634         });\r
 635         colourMenu.add(item);\r
 636       }\r
 637     }\r
 638 \r
 639     colourMenu.addSeparator();\r
 640     colourMenu.add(abovePIDColour);\r
 641     colourMenu.add(conservationMenuItem);\r
 642     //colourMenu.add(annotationMenuItem);\r
 643     editMenu.add(copy);\r
 644     editMenu.add(cut);\r
 645     editMenu.add(editSequence);\r
 646     editMenu.add(upperCase);\r
 647     editMenu.add(lowerCase);\r
 648     editMenu.add(toggle);\r
 649     pdbMenu.add(pdbFromFile);\r
 650     pdbMenu.add(enterPDB);\r
 651     pdbMenu.add(discoverPDB);\r
 652     jMenu1.add(groupName);\r
 653     jMenu1.add(unGroupMenuItem);\r
 654     jMenu1.add(colourMenu);\r
 655     jMenu1.add(showBoxes);\r
 656     jMenu1.add(showText);\r
 657     jMenu1.add(showColourText);\r
 658     jMenu1.add(outline);\r
 659     structureMenu.add(pdbMenu);\r
 660     structureMenu.add(viewStructureMenu);\r
 661    // structureMenu.add(colStructureMenu);\r
 662     noColourmenuItem.setText("None");\r
 663     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 664     {\r
 665       public void actionPerformed(ActionEvent e)\r
 666       {\r
 667         noColourmenuItem_actionPerformed();\r
 668       }\r
 669     });\r
 670 \r
 671     clustalColour.setText("Clustalx colours");\r
 672     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 673     {\r
 674       public void actionPerformed(ActionEvent e)\r
 675       {\r
 676         clustalColour_actionPerformed();\r
 677       }\r
 678     });\r
 679     zappoColour.setText("Zappo");\r
 680     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 681     {\r
 682       public void actionPerformed(ActionEvent e)\r
 683       {\r
 684         zappoColour_actionPerformed();\r
 685       }\r
 686     });\r
 687     taylorColour.setText("Taylor");\r
 688     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 689     {\r
 690       public void actionPerformed(ActionEvent e)\r
 691       {\r
 692         taylorColour_actionPerformed();\r
 693       }\r
 694     });\r
 695     hydrophobicityColour.setText("Hydrophobicity");\r
 696     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 697     {\r
 698       public void actionPerformed(ActionEvent e)\r
 699       {\r
 700         hydrophobicityColour_actionPerformed();\r
 701       }\r
 702     });\r
 703     helixColour.setText("Helix propensity");\r
 704     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 705     {\r
 706       public void actionPerformed(ActionEvent e)\r
 707       {\r
 708         helixColour_actionPerformed();\r
 709       }\r
 710     });\r
 711     strandColour.setText("Strand propensity");\r
 712     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 713     {\r
 714       public void actionPerformed(ActionEvent e)\r
 715       {\r
 716         strandColour_actionPerformed();\r
 717       }\r
 718     });\r
 719     turnColour.setText("Turn propensity");\r
 720     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 721     {\r
 722       public void actionPerformed(ActionEvent e)\r
 723       {\r
 724         turnColour_actionPerformed();\r
 725       }\r
 726     });\r
 727     buriedColour.setText("Buried Index");\r
 728     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 729     {\r
 730       public void actionPerformed(ActionEvent e)\r
 731       {\r
 732         buriedColour_actionPerformed();\r
 733       }\r
 734     });\r
 735     abovePIDColour.setText("Above % Identity");\r
 736     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 737     {\r
 738       public void actionPerformed(ActionEvent e)\r
 739       {\r
 740         abovePIDColour_actionPerformed();\r
 741       }\r
 742     });\r
 743     userDefinedColour.setText("User Defined...");\r
 744     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 745     {\r
 746       public void actionPerformed(ActionEvent e)\r
 747       {\r
 748         userDefinedColour_actionPerformed(e);\r
 749       }\r
 750     });\r
 751     PIDColour.setText("Percentage Identity");\r
 752     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 753     {\r
 754       public void actionPerformed(ActionEvent e)\r
 755       {\r
 756         PIDColour_actionPerformed();\r
 757       }\r
 758     });\r
 759     BLOSUM62Colour.setText("BLOSUM62");\r
 760     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 761     {\r
 762       public void actionPerformed(ActionEvent e)\r
 763       {\r
 764         BLOSUM62Colour_actionPerformed();\r
 765       }\r
 766     });\r
 767     conservationMenuItem.setText("Conservation");\r
 768     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 769     {\r
 770       public void actionPerformed(ActionEvent e)\r
 771       {\r
 772         conservationMenuItem_actionPerformed();\r
 773       }\r
 774     });\r
 775   }\r
 776 \r
 777   /**\r
 778    * DOCUMENT ME!\r
 779    */\r
 780   void refresh()\r
 781   {\r
 782     ap.paintAlignment(true);\r
 783 \r
 784     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 785   }\r
 786 \r
 787   /**\r
 788    * DOCUMENT ME!\r
 789    *\r
 790    * @param e DOCUMENT ME!\r
 791    */\r
 792   protected void clustalColour_actionPerformed()\r
 793   {\r
 794     SequenceGroup sg = getGroup();\r
 795     sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
 796                                      ap.av.alignment.getWidth());\r
 797     refresh();\r
 798   }\r
 799 \r
 800   /**\r
 801    * DOCUMENT ME!\r
 802    *\r
 803    * @param e DOCUMENT ME!\r
 804    */\r
 805   protected void zappoColour_actionPerformed()\r
 806   {\r
 807     getGroup().cs = new ZappoColourScheme();\r
 808     refresh();\r
 809   }\r
 810 \r
 811   /**\r
 812    * DOCUMENT ME!\r
 813    *\r
 814    * @param e DOCUMENT ME!\r
 815    */\r
 816   protected void taylorColour_actionPerformed()\r
 817   {\r
 818     getGroup().cs = new TaylorColourScheme();\r
 819     refresh();\r
 820   }\r
 821 \r
 822   /**\r
 823    * DOCUMENT ME!\r
 824    *\r
 825    * @param e DOCUMENT ME!\r
 826    */\r
 827   protected void hydrophobicityColour_actionPerformed()\r
 828   {\r
 829     getGroup().cs = new HydrophobicColourScheme();\r
 830     refresh();\r
 831   }\r
 832 \r
 833   /**\r
 834    * DOCUMENT ME!\r
 835    *\r
 836    * @param e DOCUMENT ME!\r
 837    */\r
 838   protected void helixColour_actionPerformed()\r
 839   {\r
 840     getGroup().cs = new HelixColourScheme();\r
 841     refresh();\r
 842   }\r
 843 \r
 844   /**\r
 845    * DOCUMENT ME!\r
 846    *\r
 847    * @param e DOCUMENT ME!\r
 848    */\r
 849   protected void strandColour_actionPerformed()\r
 850   {\r
 851     getGroup().cs = new StrandColourScheme();\r
 852     refresh();\r
 853   }\r
 854 \r
 855   /**\r
 856    * DOCUMENT ME!\r
 857    *\r
 858    * @param e DOCUMENT ME!\r
 859    */\r
 860   protected void turnColour_actionPerformed()\r
 861   {\r
 862     getGroup().cs = new TurnColourScheme();\r
 863     refresh();\r
 864   }\r
 865 \r
 866   /**\r
 867    * DOCUMENT ME!\r
 868    *\r
 869    * @param e DOCUMENT ME!\r
 870    */\r
 871   protected void buriedColour_actionPerformed()\r
 872   {\r
 873     getGroup().cs = new BuriedColourScheme();\r
 874     refresh();\r
 875   }\r
 876 \r
 877   /**\r
 878    * DOCUMENT ME!\r
 879    *\r
 880    * @param e DOCUMENT ME!\r
 881    */\r
 882   public void nucleotideMenuItem_actionPerformed()\r
 883   {\r
 884     getGroup().cs = new NucleotideColourScheme();\r
 885     refresh();\r
 886   }\r
 887 \r
 888   /**\r
 889    * DOCUMENT ME!\r
 890    *\r
 891    * @param e DOCUMENT ME!\r
 892    */\r
 893   protected void abovePIDColour_actionPerformed()\r
 894   {\r
 895     SequenceGroup sg = getGroup();\r
 896     if (sg.cs == null)\r
 897     {\r
 898       return;\r
 899     }\r
 900 \r
 901     if (abovePIDColour.isSelected())\r
 902     {\r
 903       sg.cs.setConsensus(AAFrequency.calculate(\r
 904           sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
 905           sg.getEndRes() + 1));\r
 906 \r
 907       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 908           getGroup().getName());\r
 909 \r
 910       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 911 \r
 912       SliderPanel.showPIDSlider();\r
 913     }\r
 914     else // remove PIDColouring\r
 915     {\r
 916       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 917     }\r
 918 \r
 919     refresh();\r
 920   }\r
 921 \r
 922   /**\r
 923    * DOCUMENT ME!\r
 924    *\r
 925    * @param e DOCUMENT ME!\r
 926    */\r
 927   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 928   {\r
 929     SequenceGroup sg = getGroup();\r
 930 \r
 931     if (e.getActionCommand().equals("User Defined..."))\r
 932     {\r
 933       new UserDefinedColours(ap, sg);\r
 934     }\r
 935     else\r
 936     {\r
 937       UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 938           getUserColourSchemes().get(e.getActionCommand());\r
 939 \r
 940       sg.cs = udc;\r
 941     }\r
 942     refresh();\r
 943   }\r
 944 \r
 945   /**\r
 946    * DOCUMENT ME!\r
 947    *\r
 948    * @param e DOCUMENT ME!\r
 949    */\r
 950   protected void PIDColour_actionPerformed()\r
 951   {\r
 952     SequenceGroup sg = getGroup();\r
 953     sg.cs = new PIDColourScheme();\r
 954     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
 955         hiddenRepSequences),\r
 956                                              sg.getStartRes(),\r
 957                                              sg.getEndRes() + 1));\r
 958     refresh();\r
 959   }\r
 960 \r
 961   /**\r
 962    * DOCUMENT ME!\r
 963    *\r
 964    * @param e DOCUMENT ME!\r
 965    */\r
 966   protected void BLOSUM62Colour_actionPerformed()\r
 967   {\r
 968     SequenceGroup sg = getGroup();\r
 969 \r
 970     sg.cs = new Blosum62ColourScheme();\r
 971 \r
 972     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
 973         hiddenRepSequences),\r
 974                                              sg.getStartRes(),\r
 975                                              sg.getEndRes() + 1));\r
 976 \r
 977     refresh();\r
 978   }\r
 979 \r
 980   /**\r
 981    * DOCUMENT ME!\r
 982    *\r
 983    * @param e DOCUMENT ME!\r
 984    */\r
 985   protected void noColourmenuItem_actionPerformed()\r
 986   {\r
 987     getGroup().cs = null;\r
 988     refresh();\r
 989   }\r
 990 \r
 991   /**\r
 992    * DOCUMENT ME!\r
 993    *\r
 994    * @param e DOCUMENT ME!\r
 995    */\r
 996   protected void conservationMenuItem_actionPerformed()\r
 997   {\r
 998     SequenceGroup sg = getGroup();\r
 999     if (sg.cs == null)\r
1000     {\r
1001       return;\r
1002     }\r
1003 \r
1004     if (conservationMenuItem.isSelected())\r
1005     {\r
1006       Conservation c = new Conservation("Group",\r
1007                                         ResidueProperties.propHash, 3,\r
1008                                         sg.getSequences(ap.av.\r
1009           hiddenRepSequences),\r
1010                                         sg.getStartRes(),\r
1011                                         sg.getEndRes() + 1);\r
1012 \r
1013       c.calculate();\r
1014       c.verdict(false, ap.av.ConsPercGaps);\r
1015 \r
1016       sg.cs.setConservation(c);\r
1017 \r
1018       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
1019       SliderPanel.showConservationSlider();\r
1020     }\r
1021     else // remove ConservationColouring\r
1022     {\r
1023       sg.cs.setConservation(null);\r
1024     }\r
1025 \r
1026     refresh();\r
1027   }\r
1028 \r
1029   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
1030   {\r
1031     SequenceGroup sg = getGroup();\r
1032     if (sg == null)\r
1033     {\r
1034       return;\r
1035     }\r
1036 \r
1037     AnnotationColourGradient acg = new AnnotationColourGradient(\r
1038         sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);\r
1039 \r
1040     acg.predefinedColours = true;\r
1041     sg.cs = acg;\r
1042 \r
1043     refresh();\r
1044   }\r
1045 \r
1046   /**\r
1047    * DOCUMENT ME!\r
1048    *\r
1049    * @param e DOCUMENT ME!\r
1050    */\r
1051   protected void groupName_actionPerformed()\r
1052   {\r
1053 \r
1054     SequenceGroup sg = getGroup();\r
1055     EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
1056                                                sg.getDescription(),\r
1057                                                "       Group Name ",\r
1058                                                "Group Description ",\r
1059                                                "Edit Group Name/Description");\r
1060 \r
1061     if (!dialog.accept)\r
1062     {\r
1063       return;\r
1064     }\r
1065 \r
1066     sg.setName(dialog.getName());\r
1067     sg.setDescription(dialog.getDescription());\r
1068   }\r
1069 \r
1070   /**\r
1071    * DOCUMENT ME!\r
1072    *\r
1073    * @return DOCUMENT ME!\r
1074    */\r
1075   SequenceGroup getGroup()\r
1076   {\r
1077     SequenceGroup sg = ap.av.getSelectionGroup();\r
1078     // this method won't add a new group if it already exists\r
1079     if (sg != null)\r
1080     {\r
1081       ap.av.alignment.addGroup(sg);\r
1082     }\r
1083 \r
1084     return sg;\r
1085   }\r
1086 \r
1087   /**\r
1088    * DOCUMENT ME!\r
1089    *\r
1090    * @param e DOCUMENT ME!\r
1091    */\r
1092   void sequenceName_actionPerformed()\r
1093   {\r
1094     EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
1095                                                sequence.getDescription(),\r
1096                                                "       Sequence Name ",\r
1097                                                "Sequence Description ",\r
1098                                                "Edit Sequence Name/Description");\r
1099 \r
1100     if (!dialog.accept)\r
1101     {\r
1102       return;\r
1103     }\r
1104 \r
1105     if (dialog.getName() != null)\r
1106     {\r
1107       if (dialog.getName().indexOf(" ") > -1)\r
1108       {\r
1109         JOptionPane.showMessageDialog(ap,\r
1110                                       "Spaces have been converted to \"_\"",\r
1111                                       "No spaces allowed in Sequence Name",\r
1112                                       JOptionPane.WARNING_MESSAGE);\r
1113       }\r
1114 \r
1115       sequence.setName(dialog.getName().replace(' ', '_'));\r
1116       ap.paintAlignment(false);\r
1117     }\r
1118 \r
1119     sequence.setDescription(dialog.getDescription());\r
1120 \r
1121     ap.av.firePropertyChange("alignment", null,\r
1122                              ap.av.getAlignment().getSequences());\r
1123 \r
1124   }\r
1125 \r
1126   /**\r
1127    * DOCUMENT ME!\r
1128    *\r
1129    * @param e DOCUMENT ME!\r
1130    */\r
1131   void unGroupMenuItem_actionPerformed()\r
1132   {\r
1133     SequenceGroup sg = ap.av.getSelectionGroup();\r
1134     ap.av.alignment.deleteGroup(sg);\r
1135     ap.av.setSelectionGroup(null);\r
1136     refresh();\r
1137   }\r
1138 \r
1139   /**\r
1140    * DOCUMENT ME!\r
1141    *\r
1142    * @param e DOCUMENT ME!\r
1143    */\r
1144   protected void outline_actionPerformed()\r
1145   {\r
1146     SequenceGroup sg = getGroup();\r
1147     Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1148                                          Color.BLUE);\r
1149 \r
1150     if (col != null)\r
1151     {\r
1152       sg.setOutlineColour(col);\r
1153     }\r
1154 \r
1155     refresh();\r
1156   }\r
1157 \r
1158   /**\r
1159    * DOCUMENT ME!\r
1160    *\r
1161    * @param e DOCUMENT ME!\r
1162    */\r
1163   public void showBoxes_actionPerformed()\r
1164   {\r
1165     getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1166     refresh();\r
1167   }\r
1168 \r
1169   /**\r
1170    * DOCUMENT ME!\r
1171    *\r
1172    * @param e DOCUMENT ME!\r
1173    */\r
1174   public void showText_actionPerformed()\r
1175   {\r
1176     getGroup().setDisplayText(showText.isSelected());\r
1177     refresh();\r
1178   }\r
1179 \r
1180   /**\r
1181    * DOCUMENT ME!\r
1182    *\r
1183    * @param e DOCUMENT ME!\r
1184    */\r
1185   public void showColourText_actionPerformed()\r
1186   {\r
1187     getGroup().setColourText(showColourText.isSelected());\r
1188     refresh();\r
1189   }\r
1190 \r
1191   public void showLink(String url)\r
1192   {\r
1193     try\r
1194     {\r
1195       jalview.util.BrowserLauncher.openURL(url);\r
1196     }\r
1197     catch (Exception ex)\r
1198     {\r
1199       JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1200                                             "Unixers: Couldn't find default web browser."\r
1201                                             +\r
1202           "\nAdd the full path to your browser in Preferences.",\r
1203                                             "Web browser not found",\r
1204                                             JOptionPane.WARNING_MESSAGE);\r
1205 \r
1206       ex.printStackTrace();\r
1207     }\r
1208   }\r
1209 \r
1210   void hideSequences(boolean representGroup)\r
1211   {\r
1212     SequenceGroup sg = ap.av.getSelectionGroup();\r
1213     if (sg == null || sg.getSize() < 1)\r
1214     {\r
1215       ap.av.hideSequence(new SequenceI[]\r
1216                          {sequence});\r
1217       return;\r
1218     }\r
1219 \r
1220     ap.av.setSelectionGroup(null);\r
1221 \r
1222     if (representGroup)\r
1223     {\r
1224       ap.av.hideRepSequences(sequence, sg);\r
1225 \r
1226       return;\r
1227     }\r
1228 \r
1229     int gsize = sg.getSize();\r
1230     SequenceI[] hseqs;\r
1231 \r
1232     hseqs = new SequenceI[gsize];\r
1233 \r
1234     int index = 0;\r
1235     for (int i = 0; i < gsize; i++)\r
1236     {\r
1237       hseqs[index++] = sg.getSequenceAt(i);\r
1238     }\r
1239 \r
1240     ap.av.hideSequence(hseqs);\r
1241   }\r
1242 \r
1243   public void copy_actionPerformed()\r
1244   {\r
1245     ap.alignFrame.copy_actionPerformed(null);\r
1246   }\r
1247 \r
1248   public void cut_actionPerformed()\r
1249   {\r
1250     ap.alignFrame.cut_actionPerformed(null);\r
1251   }\r
1252 \r
1253   void changeCase(ActionEvent e)\r
1254   {\r
1255     Object source = e.getSource();\r
1256     SequenceGroup sg = ap.av.getSelectionGroup();\r
1257 \r
1258     if (sg != null)\r
1259     {\r
1260       int[][] startEnd = ap.av.getVisibleRegionBoundaries(\r
1261           sg.getStartRes(), sg.getEndRes() + 1);\r
1262 \r
1263       String description;\r
1264       int caseChange;\r
1265 \r
1266       if (source == toggle)\r
1267       {\r
1268         description = "Toggle Case";\r
1269         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1270       }\r
1271       else if (source == upperCase)\r
1272       {\r
1273         description = "To Upper Case";\r
1274         caseChange = ChangeCaseCommand.TO_UPPER;\r
1275       }\r
1276       else\r
1277       {\r
1278         description = "To Lower Case";\r
1279         caseChange = ChangeCaseCommand.TO_LOWER;\r
1280       }\r
1281 \r
1282       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1283           description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
1284           startEnd, caseChange\r
1285           );\r
1286 \r
1287       ap.alignFrame.addHistoryItem(caseCommand);\r
1288 \r
1289       ap.av.firePropertyChange("alignment", null,\r
1290                                ap.av.getAlignment().getSequences());\r
1291 \r
1292     }\r
1293   }\r
1294 \r
1295   public void outputText_actionPerformed(ActionEvent e)\r
1296   {\r
1297     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1298     cap.setForInput(null);\r
1299     Desktop.addInternalFrame(cap,\r
1300                              "Alignment output - " + e.getActionCommand(), 600,\r
1301                              500);\r
1302 \r
1303     String[] omitHidden = null;\r
1304 \r
1305     if (ap.av.hasHiddenColumns)\r
1306     {\r
1307       System.out.println("PROMPT USER HERE");\r
1308       omitHidden = ap.av.getViewAsString(true);\r
1309     }\r
1310 \r
1311     cap.setText(new FormatAdapter().formatSequences(\r
1312         e.getActionCommand(),\r
1313         ap.av.getSelectionAsNewSequence(),\r
1314         omitHidden));\r
1315   }\r
1316 \r
1317   public void pdbFromFile_actionPerformed()\r
1318   {\r
1319     jalview.io.JalviewFileChooser chooser\r
1320         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1321                                             getProperty(\r
1322                                                 "LAST_DIRECTORY"));\r
1323     chooser.setFileView(new jalview.io.JalviewFileView());\r
1324     chooser.setDialogTitle("Select a PDB file");\r
1325     chooser.setToolTipText("Load a PDB file");\r
1326 \r
1327     int value = chooser.showOpenDialog(null);\r
1328 \r
1329     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1330     {\r
1331       PDBEntry entry = new PDBEntry();\r
1332       String choice = chooser.getSelectedFile().getPath();\r
1333       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1334       try\r
1335       {\r
1336         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1337             jalview.io.AppletFormatAdapter.FILE);\r
1338 \r
1339         if (pdbfile.id == null)\r
1340         {\r
1341           String reply = JOptionPane.showInternalInputDialog(\r
1342               Desktop.desktop,\r
1343               "Couldn't find a PDB id in the file supplied."\r
1344               + "Please enter an Id to identify this structure.",\r
1345               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1346           if (reply == null)\r
1347           {\r
1348             return;\r
1349           }\r
1350 \r
1351           entry.setId(reply);\r
1352         }\r
1353         else\r
1354         {\r
1355           entry.setId(pdbfile.id);\r
1356         }\r
1357       }\r
1358       catch (java.io.IOException ex)\r
1359       {\r
1360         ex.printStackTrace();\r
1361       }\r
1362 \r
1363       entry.setFile(choice);\r
1364       sequence.getDatasetSequence().addPDBId(entry);\r
1365     }\r
1366 \r
1367   }\r
1368 \r
1369   public void enterPDB_actionPerformed()\r
1370   {\r
1371     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1372         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1373 \r
1374     if (id != null && id.length() > 0)\r
1375     {\r
1376       PDBEntry entry = new PDBEntry();\r
1377       entry.setId(id.toUpperCase());\r
1378       sequence.getDatasetSequence()\r
1379           .addPDBId(entry);\r
1380     }\r
1381   }\r
1382 \r
1383   public void discoverPDB_actionPerformed()\r
1384   {\r
1385     SequenceI[] sequences =\r
1386          ap.av.selectionGroup == null ?\r
1387            new Sequence[]{sequence}\r
1388          : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);\r
1389 \r
1390     new jalview.io.DBRefFetcher(sequences,\r
1391         ap.alignFrame).fetchDBRefs(false);\r
1392   }\r
1393 \r
1394   public void sequenceFeature_actionPerformed()\r
1395   {\r
1396     SequenceGroup sg = ap.av.getSelectionGroup();\r
1397     if (sg == null)\r
1398     {\r
1399       return;\r
1400     }\r
1401 \r
1402     int gSize = sg.getSize();\r
1403     SequenceI[] seqs = new SequenceI[gSize];\r
1404     SequenceFeature[] features = new SequenceFeature[gSize];\r
1405 \r
1406     for (int i = 0; i < gSize; i++)\r
1407     {\r
1408       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1409       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1410       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1411       features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
1412     }\r
1413 \r
1414     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1415         .amendFeatures(seqs, features, true, ap))\r
1416     {\r
1417       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1418       ap.av.setShowSequenceFeatures(true);\r
1419       ap.highlightSearchResults(null);\r
1420     }\r
1421   }\r
1422 \r
1423   public void textColour_actionPerformed()\r
1424   {\r
1425     SequenceGroup sg = getGroup();\r
1426     if (sg != null)\r
1427     {\r
1428       new TextColourChooser().chooseColour(ap, sg);\r
1429     }\r
1430   }\r
1431 \r
1432   public void colourByStructure(String pdbid)\r
1433   {\r
1434     Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
1435         .colourSequenceFromStructure(sequence, pdbid);\r
1436 \r
1437     AlignmentAnnotation an = new AlignmentAnnotation(\r
1438       "Structure", "Coloured by "+pdbid, anots);\r
1439 \r
1440     ap.av.alignment.addAnnotation(an);\r
1441     an.createSequenceMapping(sequence, 0, true);\r
1442     //an.adjustForAlignment();\r
1443     ap.av.alignment.setAnnotationIndex(an,0);\r
1444 \r
1445     ap.adjustAnnotationHeight();\r
1446 \r
1447     sequence.addAlignmentAnnotation(an);\r
1448 \r
1449     }\r
1450 \r
1451   public void editSequence_actionPerformed(ActionEvent actionEvent)\r
1452   {\r
1453       SequenceGroup sg = ap.av.getSelectionGroup();\r
1454 \r
1455       if(sg!=null)\r
1456       {\r
1457         if (sequence == null)\r
1458           sequence = (Sequence) sg.getSequenceAt(0);\r
1459 \r
1460         EditNameDialog dialog = new EditNameDialog(\r
1461             sequence.getSequenceAsString(\r
1462                 sg.getStartRes(),\r
1463                 sg.getEndRes() + 1),\r
1464             null,\r
1465             "Edit Sequence ",\r
1466             null,\r
1467             "Edit Sequence");\r
1468 \r
1469         if (dialog.accept)\r
1470         {\r
1471           EditCommand editCommand = new EditCommand(\r
1472               "Edit Sequences", EditCommand.REPLACE,\r
1473               dialog.getName().replace(' ', ap.av.getGapCharacter()),\r
1474               sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
1475               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment\r
1476               );\r
1477 \r
1478           ap.alignFrame.addHistoryItem(editCommand);\r
1479 \r
1480           ap.av.firePropertyChange("alignment", null,\r
1481                                    ap.av.getAlignment().getSequences());\r
1482         }\r
1483       }\r
1484   }\r
1485 \r
1486 \r
1487 }\r