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