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