src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import java.util.*;\r
  22 \r
  23 import java.awt.*;\r
  24 import java.awt.event.*;\r
  25 import javax.swing.*;\r
  26 \r
  27 import MCview.*;\r
  28 import jalview.analysis.*;\r
  29 import jalview.commands.*;\r
  30 import jalview.datamodel.*;\r
  31 import jalview.io.*;\r
  32 import jalview.schemes.*;\r
  33 \r
  34 /**\r
  35  * DOCUMENT ME!\r
  36  *\r
  37  * @author $author$\r
  38  * @version $Revision$\r
  39  */\r
  40 public class PopupMenu\r
  41     extends JPopupMenu\r
  42 {\r
  43   JMenu groupMenu = new JMenu();\r
  44   JMenuItem groupName = new JMenuItem();\r
  45   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  46   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  47   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  48   protected JRadioButtonMenuItem hydrophobicityColour = new\r
  49       JRadioButtonMenuItem();\r
  50   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  51   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  52   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  53   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  54   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  55   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  56   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  57   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  58   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  59   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  60   AlignmentPanel ap;\r
  61   JMenu sequenceMenu = new JMenu();\r
  62   JMenuItem sequenceName = new JMenuItem();\r
  63   Sequence sequence;\r
  64   JMenuItem unGroupMenuItem = new JMenuItem();\r
  65   JMenuItem outline = new JMenuItem();\r
  66   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  67   JMenu colourMenu = new JMenu();\r
  68   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
  69   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
  70   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
  71   JMenu editMenu = new JMenu();\r
  72   JMenuItem cut = new JMenuItem();\r
  73   JMenuItem copy = new JMenuItem();\r
  74   JMenuItem upperCase = new JMenuItem();\r
  75   JMenuItem lowerCase = new JMenuItem();\r
  76   JMenuItem toggle = new JMenuItem();\r
  77   JMenu pdbMenu = new JMenu();\r
  78   JMenuItem pdbFromFile = new JMenuItem();\r
  79   JMenuItem enterPDB = new JMenuItem();\r
  80   JMenuItem discoverPDB = new JMenuItem();\r
  81   JMenu outputMenu = new JMenu();\r
  82   JMenuItem sequenceFeature = new JMenuItem();\r
  83   JMenuItem textColour = new JMenuItem();\r
  84   JMenu jMenu1 = new JMenu();\r
  85   JMenu structureMenu = new JMenu();\r
  86   JMenu viewStructureMenu = new JMenu();\r
  87  // JMenu colStructureMenu = new JMenu();\r
  88   JMenuItem editSequence = new JMenuItem();\r
  89  // JMenuItem annotationMenuItem = new JMenuItem();\r
  90 \r
  91   /**\r
  92    * Creates a new PopupMenu object.\r
  93    *\r
  94    * @param ap DOCUMENT ME!\r
  95    * @param seq DOCUMENT ME!\r
  96    */\r
  97   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
  98   {\r
  99     ///////////////////////////////////////////////////////////\r
 100     // If this is activated from the sequence panel, the user may want to\r
 101     // edit or annotate a particular residue. Therefore display the residue menu\r
 102     //\r
 103     // If from the IDPanel, we must display the sequence menu\r
 104     //////////////////////////////////////////////////////////\r
 105     this.ap = ap;\r
 106     sequence = seq;\r
 107 \r
 108     ButtonGroup colours = new ButtonGroup();\r
 109     colours.add(noColourmenuItem);\r
 110     colours.add(clustalColour);\r
 111     colours.add(zappoColour);\r
 112     colours.add(taylorColour);\r
 113     colours.add(hydrophobicityColour);\r
 114     colours.add(helixColour);\r
 115     colours.add(strandColour);\r
 116     colours.add(turnColour);\r
 117     colours.add(buriedColour);\r
 118     colours.add(abovePIDColour);\r
 119     colours.add(userDefinedColour);\r
 120     colours.add(PIDColour);\r
 121     colours.add(BLOSUM62Colour);\r
 122 \r
 123     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 124     {\r
 125       JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[\r
 126                                      i]);\r
 127 \r
 128       item.addActionListener(new java.awt.event.ActionListener()\r
 129       {\r
 130         public void actionPerformed(ActionEvent e)\r
 131         {\r
 132           outputText_actionPerformed(e);\r
 133         }\r
 134       });\r
 135 \r
 136       outputMenu.add(item);\r
 137     }\r
 138 \r
 139     try\r
 140     {\r
 141       jbInit();\r
 142     }\r
 143     catch (Exception e)\r
 144     {\r
 145       e.printStackTrace();\r
 146     }\r
 147 \r
 148     if (seq != null)\r
 149     {\r
 150       sequenceMenu.setText(sequence.getName());\r
 151 \r
 152       JMenuItem menuItem;\r
 153       if (seq.getDatasetSequence().getPDBId() != null\r
 154           && seq.getDatasetSequence().getPDBId().size()>0)\r
 155       {\r
 156         java.util.Enumeration e = seq.getDatasetSequence().getPDBId().\r
 157             elements();\r
 158 \r
 159         while (e.hasMoreElements())\r
 160         {\r
 161           final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 162 \r
 163           menuItem = new JMenuItem();\r
 164           menuItem.setText(pdb.getId());\r
 165           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 166           {\r
 167             public void actionPerformed(ActionEvent e)\r
 168             {\r
 169               Vector seqs = new Vector();\r
 170               for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
 171               {\r
 172                 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();\r
 173                 if(pdbs==null)\r
 174                   continue;\r
 175 \r
 176                 for(int p=0; p<pdbs.size(); p++)\r
 177                 {\r
 178                   PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);\r
 179                   if(p1.getId().equals(pdb.getId()))\r
 180                   {\r
 181                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))\r
 182                         seqs.addElement(ap.av.alignment.getSequenceAt(i));\r
 183 \r
 184                       continue;\r
 185                   }\r
 186                 }\r
 187               }\r
 188 \r
 189               SequenceI [] seqs2 = new SequenceI[seqs.size()];\r
 190               seqs.toArray(seqs2);\r
 191 \r
 192               new AppJmol(pdb, seqs2, null, ap);\r
 193             }\r
 194           });\r
 195           viewStructureMenu.add(menuItem);\r
 196 \r
 197        /*   menuItem = new JMenuItem();\r
 198           menuItem.setText(pdb.getId());\r
 199           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 200           {\r
 201             public void actionPerformed(ActionEvent e)\r
 202             {\r
 203               colourByStructure(pdb.getId());\r
 204             }\r
 205           });\r
 206           colStructureMenu.add(menuItem);*/\r
 207         }\r
 208       }\r
 209       else\r
 210       {\r
 211         structureMenu.remove(viewStructureMenu);\r
 212        // structureMenu.remove(colStructureMenu);\r
 213       }\r
 214 \r
 215       menuItem = new JMenuItem("Hide Sequences");\r
 216       menuItem.addActionListener(new java.awt.event.ActionListener()\r
 217       {\r
 218         public void actionPerformed(ActionEvent e)\r
 219         {\r
 220           hideSequences(false);\r
 221         }\r
 222       });\r
 223       add(menuItem);\r
 224 \r
 225       if (ap.av.getSelectionGroup() != null\r
 226           && ap.av.getSelectionGroup().getSize() > 1)\r
 227       {\r
 228         menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
 229         menuItem.addActionListener(new java.awt.event.ActionListener()\r
 230         {\r
 231           public void actionPerformed(ActionEvent e)\r
 232           {\r
 233             hideSequences(true);\r
 234           }\r
 235         });\r
 236         sequenceMenu.add(menuItem);\r
 237       }\r
 238 \r
 239       if (ap.av.hasHiddenRows)\r
 240       {\r
 241         final int index = ap.av.alignment.findIndex(seq);\r
 242 \r
 243         if (ap.av.adjustForHiddenSeqs(index) -\r
 244             ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 245         {\r
 246           menuItem = new JMenuItem("Reveal Sequences");\r
 247           menuItem.addActionListener(new ActionListener()\r
 248           {\r
 249             public void actionPerformed(ActionEvent e)\r
 250             {\r
 251               ap.av.showSequence(index);\r
 252               if (ap.overviewPanel != null)\r
 253               {\r
 254                 ap.overviewPanel.updateOverviewImage();\r
 255               }\r
 256             }\r
 257           });\r
 258           add(menuItem);\r
 259         }\r
 260 \r
 261         menuItem = new JMenuItem("Reveal All");\r
 262         menuItem.addActionListener(new ActionListener()\r
 263         {\r
 264           public void actionPerformed(ActionEvent e)\r
 265           {\r
 266             ap.av.showAllHiddenSeqs();\r
 267             if (ap.overviewPanel != null)\r
 268             {\r
 269               ap.overviewPanel.updateOverviewImage();\r
 270             }\r
 271           }\r
 272         });\r
 273 \r
 274         add(menuItem);\r
 275       }\r
 276 \r
 277     }\r
 278 \r
 279     SequenceGroup sg = ap.av.getSelectionGroup();\r
 280 \r
 281     if (sg != null)\r
 282     {\r
 283       groupName.setText(sg.getName());\r
 284 \r
 285       if (sg.cs instanceof ZappoColourScheme)\r
 286       {\r
 287         zappoColour.setSelected(true);\r
 288       }\r
 289       else if (sg.cs instanceof TaylorColourScheme)\r
 290       {\r
 291         taylorColour.setSelected(true);\r
 292       }\r
 293       else if (sg.cs instanceof PIDColourScheme)\r
 294       {\r
 295         PIDColour.setSelected(true);\r
 296       }\r
 297       else if (sg.cs instanceof Blosum62ColourScheme)\r
 298       {\r
 299         BLOSUM62Colour.setSelected(true);\r
 300       }\r
 301       else if (sg.cs instanceof UserColourScheme)\r
 302       {\r
 303         userDefinedColour.setSelected(true);\r
 304       }\r
 305       else if (sg.cs instanceof HydrophobicColourScheme)\r
 306       {\r
 307         hydrophobicityColour.setSelected(true);\r
 308       }\r
 309       else if (sg.cs instanceof HelixColourScheme)\r
 310       {\r
 311         helixColour.setSelected(true);\r
 312       }\r
 313       else if (sg.cs instanceof StrandColourScheme)\r
 314       {\r
 315         strandColour.setSelected(true);\r
 316       }\r
 317       else if (sg.cs instanceof TurnColourScheme)\r
 318       {\r
 319         turnColour.setSelected(true);\r
 320       }\r
 321       else if (sg.cs instanceof BuriedColourScheme)\r
 322       {\r
 323         buriedColour.setSelected(true);\r
 324       }\r
 325       else if (sg.cs instanceof ClustalxColourScheme)\r
 326       {\r
 327         clustalColour.setSelected(true);\r
 328       }\r
 329       else\r
 330       {\r
 331         noColourmenuItem.setSelected(true);\r
 332       }\r
 333 \r
 334       if (sg.cs != null && sg.cs.conservationApplied())\r
 335       {\r
 336         conservationMenuItem.setSelected(true);\r
 337       }\r
 338 \r
 339       showText.setSelected(sg.getDisplayText());\r
 340       showColourText.setSelected(sg.getColourText());\r
 341       showBoxes.setSelected(sg.getDisplayBoxes());\r
 342     }\r
 343     else\r
 344     {\r
 345       groupMenu.setVisible(false);\r
 346       editMenu.setVisible(false);\r
 347     }\r
 348 \r
 349     if (!ap.av.alignment.getGroups().contains(sg))\r
 350     {\r
 351       unGroupMenuItem.setVisible(false);\r
 352     }\r
 353 \r
 354     if (seq == null)\r
 355     {\r
 356       sequenceMenu.setVisible(false);\r
 357       structureMenu.setVisible(false);\r
 358     }\r
 359 \r
 360     if (links != null && links.size() > 0)\r
 361     {\r
 362       JMenu linkMenu = new JMenu("Link");\r
 363       JMenuItem item;\r
 364       for (int i = 0; i < links.size(); i++)\r
 365       {\r
 366         String link = links.elementAt(i).toString();\r
 367         final String label = link.substring(0, link.indexOf("|"));\r
 368         item = new JMenuItem(label);\r
 369         final String url;\r
 370 \r
 371         if (link.indexOf("$SEQUENCE_ID$") > -1)\r
 372         {\r
 373           String id = seq.getName();\r
 374           if (id.indexOf("|") > -1)\r
 375           {\r
 376             id = id.substring(id.lastIndexOf("|") + 1);\r
 377           }\r
 378 \r
 379           url = link.substring(link.indexOf("|") + 1,\r
 380                                link.indexOf("$SEQUENCE_ID$"))\r
 381               + id +\r
 382               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
 383         }\r
 384         else\r
 385         {\r
 386           url = link.substring(link.lastIndexOf("|") + 1);\r
 387         }\r
 388 \r
 389         item.addActionListener(new java.awt.event.ActionListener()\r
 390         {\r
 391           public void actionPerformed(ActionEvent e)\r
 392           {\r
 393             showLink(url);\r
 394           }\r
 395         });\r
 396 \r
 397         linkMenu.add(item);\r
 398       }\r
 399       if (sequence != null)\r
 400       {\r
 401         sequenceMenu.add(linkMenu);\r
 402       }\r
 403       else\r
 404       {\r
 405         add(linkMenu);\r
 406       }\r
 407     }\r
 408   }\r
 409 \r
 410   /**\r
 411    * DOCUMENT ME!\r
 412    *\r
 413    * @throws Exception DOCUMENT ME!\r
 414    */\r
 415   private void jbInit()\r
 416       throws Exception\r
 417   {\r
 418     groupMenu.setText("Group");\r
 419     groupMenu.setText("Selection");\r
 420     groupName.setText("Name");\r
 421     groupName.addActionListener(new java.awt.event.ActionListener()\r
 422     {\r
 423       public void actionPerformed(ActionEvent e)\r
 424       {\r
 425         groupName_actionPerformed();\r
 426       }\r
 427     });\r
 428     sequenceMenu.setText("Sequence");\r
 429     sequenceName.setText("Edit Name/Description");\r
 430     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 431     {\r
 432       public void actionPerformed(ActionEvent e)\r
 433       {\r
 434         sequenceName_actionPerformed();\r
 435       }\r
 436     });\r
 437     PIDColour.setFocusPainted(false);\r
 438     unGroupMenuItem.setText("Remove Group");\r
 439     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 440     {\r
 441       public void actionPerformed(ActionEvent e)\r
 442       {\r
 443         unGroupMenuItem_actionPerformed();\r
 444       }\r
 445     });\r
 446 \r
 447     outline.setText("Border colour");\r
 448     outline.addActionListener(new java.awt.event.ActionListener()\r
 449     {\r
 450       public void actionPerformed(ActionEvent e)\r
 451       {\r
 452         outline_actionPerformed();\r
 453       }\r
 454     });\r
 455     nucleotideMenuItem.setText("Nucleotide");\r
 456     nucleotideMenuItem.addActionListener(new ActionListener()\r
 457     {\r
 458       public void actionPerformed(ActionEvent e)\r
 459       {\r
 460         nucleotideMenuItem_actionPerformed();\r
 461       }\r
 462     });\r
 463     colourMenu.setText("Group Colour");\r
 464     showBoxes.setText("Boxes");\r
 465     showBoxes.setState(true);\r
 466     showBoxes.addActionListener(new ActionListener()\r
 467     {\r
 468       public void actionPerformed(ActionEvent e)\r
 469       {\r
 470         showBoxes_actionPerformed();\r
 471       }\r
 472     });\r
 473     showText.setText("Text");\r
 474     showText.setState(true);\r
 475     showText.addActionListener(new ActionListener()\r
 476     {\r
 477       public void actionPerformed(ActionEvent e)\r
 478       {\r
 479         showText_actionPerformed();\r
 480       }\r
 481     });\r
 482     showColourText.setText("Colour Text");\r
 483     showColourText.addActionListener(new ActionListener()\r
 484     {\r
 485       public void actionPerformed(ActionEvent e)\r
 486       {\r
 487         showColourText_actionPerformed();\r
 488       }\r
 489     });\r
 490     editMenu.setText("Edit");\r
 491     cut.setText("Cut");\r
 492     cut.addActionListener(new ActionListener()\r
 493     {\r
 494       public void actionPerformed(ActionEvent e)\r
 495       {\r
 496         cut_actionPerformed();\r
 497       }\r
 498     });\r
 499     upperCase.setText("To Upper Case");\r
 500     upperCase.addActionListener(new ActionListener()\r
 501     {\r
 502       public void actionPerformed(ActionEvent e)\r
 503       {\r
 504         changeCase(e);\r
 505       }\r
 506     });\r
 507     copy.setText("Copy");\r
 508     copy.addActionListener(new ActionListener()\r
 509     {\r
 510       public void actionPerformed(ActionEvent e)\r
 511       {\r
 512         copy_actionPerformed();\r
 513       }\r
 514     });\r
 515     lowerCase.setText("To Lower Case");\r
 516     lowerCase.addActionListener(new ActionListener()\r
 517     {\r
 518       public void actionPerformed(ActionEvent e)\r
 519       {\r
 520         changeCase(e);\r
 521       }\r
 522     });\r
 523     toggle.setText("Toggle Case");\r
 524     toggle.addActionListener(new ActionListener()\r
 525     {\r
 526       public void actionPerformed(ActionEvent e)\r
 527       {\r
 528         changeCase(e);\r
 529       }\r
 530     });\r
 531     pdbMenu.setText("Associate Structure with Sequence");\r
 532     pdbFromFile.setText("From File");\r
 533     pdbFromFile.addActionListener(new ActionListener()\r
 534     {\r
 535       public void actionPerformed(ActionEvent e)\r
 536       {\r
 537         pdbFromFile_actionPerformed();\r
 538       }\r
 539     });\r
 540     enterPDB.setText("Enter PDB Id");\r
 541     enterPDB.addActionListener(new ActionListener()\r
 542     {\r
 543       public void actionPerformed(ActionEvent e)\r
 544       {\r
 545         enterPDB_actionPerformed();\r
 546       }\r
 547     });\r
 548     discoverPDB.setText("Discover PDB ids");\r
 549     discoverPDB.addActionListener(new ActionListener()\r
 550     {\r
 551       public void actionPerformed(ActionEvent e)\r
 552       {\r
 553         discoverPDB_actionPerformed();\r
 554       }\r
 555     });\r
 556     outputMenu.setText("Output to Textbox...");\r
 557     sequenceFeature.setText("Create Sequence Feature");\r
 558     sequenceFeature.addActionListener(new ActionListener()\r
 559     {\r
 560       public void actionPerformed(ActionEvent e)\r
 561       {\r
 562         sequenceFeature_actionPerformed();\r
 563       }\r
 564     });\r
 565     textColour.setText("Text Colour");\r
 566     textColour.addActionListener(new ActionListener()\r
 567     {\r
 568       public void actionPerformed(ActionEvent e)\r
 569       {\r
 570         textColour_actionPerformed();\r
 571       }\r
 572     });\r
 573     jMenu1.setText("Group");\r
 574     structureMenu.setText("Structure");\r
 575     viewStructureMenu.setText("View Structure");\r
 576   //  colStructureMenu.setText("Colour By Structure");\r
 577     editSequence.setText("Edit Sequence...");\r
 578     editSequence.addActionListener(new ActionListener()\r
 579     {\r
 580       public void actionPerformed(ActionEvent actionEvent)\r
 581       {\r
 582         editSequence_actionPerformed(actionEvent);\r
 583       }\r
 584     });\r
 585    /* annotationMenuItem.setText("By Annotation");\r
 586     annotationMenuItem.addActionListener(new ActionListener()\r
 587     {\r
 588       public void actionPerformed(ActionEvent actionEvent)\r
 589       {\r
 590         annotationMenuItem_actionPerformed(actionEvent);\r
 591       }\r
 592     });*/\r
 593 \r
 594     add(groupMenu);\r
 595 \r
 596     add(sequenceMenu);\r
 597     this.add(structureMenu);\r
 598     groupMenu.add(editMenu);\r
 599     groupMenu.add(outputMenu);\r
 600     groupMenu.add(sequenceFeature);\r
 601     groupMenu.add(jMenu1);\r
 602     sequenceMenu.add(sequenceName);\r
 603     colourMenu.add(textColour);\r
 604     colourMenu.add(noColourmenuItem);\r
 605     colourMenu.add(clustalColour);\r
 606     colourMenu.add(BLOSUM62Colour);\r
 607     colourMenu.add(PIDColour);\r
 608     colourMenu.add(zappoColour);\r
 609     colourMenu.add(taylorColour);\r
 610     colourMenu.add(hydrophobicityColour);\r
 611     colourMenu.add(helixColour);\r
 612     colourMenu.add(strandColour);\r
 613     colourMenu.add(turnColour);\r
 614     colourMenu.add(buriedColour);\r
 615     colourMenu.add(nucleotideMenuItem);\r
 616     colourMenu.add(userDefinedColour);\r
 617 \r
 618     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
 619     {\r
 620       java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
 621           getUserColourSchemes().keys();\r
 622 \r
 623       while (userColours.hasMoreElements())\r
 624       {\r
 625         JMenuItem item = new JMenuItem(userColours.\r
 626                                        nextElement().toString());\r
 627         item.addActionListener(new ActionListener()\r
 628         {\r
 629           public void actionPerformed(ActionEvent evt)\r
 630           {\r
 631             userDefinedColour_actionPerformed(evt);\r
 632           }\r
 633         });\r
 634         colourMenu.add(item);\r
 635       }\r
 636     }\r
 637 \r
 638     colourMenu.addSeparator();\r
 639     colourMenu.add(abovePIDColour);\r
 640     colourMenu.add(conservationMenuItem);\r
 641     //colourMenu.add(annotationMenuItem);\r
 642     editMenu.add(copy);\r
 643     editMenu.add(cut);\r
 644     editMenu.add(editSequence);\r
 645     editMenu.add(upperCase);\r
 646     editMenu.add(lowerCase);\r
 647     editMenu.add(toggle);\r
 648     pdbMenu.add(pdbFromFile);\r
 649     pdbMenu.add(enterPDB);\r
 650     pdbMenu.add(discoverPDB);\r
 651     jMenu1.add(groupName);\r
 652     jMenu1.add(unGroupMenuItem);\r
 653     jMenu1.add(colourMenu);\r
 654     jMenu1.add(showBoxes);\r
 655     jMenu1.add(showText);\r
 656     jMenu1.add(showColourText);\r
 657     jMenu1.add(outline);\r
 658     structureMenu.add(pdbMenu);\r
 659     structureMenu.add(viewStructureMenu);\r
 660    // structureMenu.add(colStructureMenu);\r
 661     noColourmenuItem.setText("None");\r
 662     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
 663     {\r
 664       public void actionPerformed(ActionEvent e)\r
 665       {\r
 666         noColourmenuItem_actionPerformed();\r
 667       }\r
 668     });\r
 669 \r
 670     clustalColour.setText("Clustalx colours");\r
 671     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
 672     {\r
 673       public void actionPerformed(ActionEvent e)\r
 674       {\r
 675         clustalColour_actionPerformed();\r
 676       }\r
 677     });\r
 678     zappoColour.setText("Zappo");\r
 679     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
 680     {\r
 681       public void actionPerformed(ActionEvent e)\r
 682       {\r
 683         zappoColour_actionPerformed();\r
 684       }\r
 685     });\r
 686     taylorColour.setText("Taylor");\r
 687     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
 688     {\r
 689       public void actionPerformed(ActionEvent e)\r
 690       {\r
 691         taylorColour_actionPerformed();\r
 692       }\r
 693     });\r
 694     hydrophobicityColour.setText("Hydrophobicity");\r
 695     hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
 696     {\r
 697       public void actionPerformed(ActionEvent e)\r
 698       {\r
 699         hydrophobicityColour_actionPerformed();\r
 700       }\r
 701     });\r
 702     helixColour.setText("Helix propensity");\r
 703     helixColour.addActionListener(new java.awt.event.ActionListener()\r
 704     {\r
 705       public void actionPerformed(ActionEvent e)\r
 706       {\r
 707         helixColour_actionPerformed();\r
 708       }\r
 709     });\r
 710     strandColour.setText("Strand propensity");\r
 711     strandColour.addActionListener(new java.awt.event.ActionListener()\r
 712     {\r
 713       public void actionPerformed(ActionEvent e)\r
 714       {\r
 715         strandColour_actionPerformed();\r
 716       }\r
 717     });\r
 718     turnColour.setText("Turn propensity");\r
 719     turnColour.addActionListener(new java.awt.event.ActionListener()\r
 720     {\r
 721       public void actionPerformed(ActionEvent e)\r
 722       {\r
 723         turnColour_actionPerformed();\r
 724       }\r
 725     });\r
 726     buriedColour.setText("Buried Index");\r
 727     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
 728     {\r
 729       public void actionPerformed(ActionEvent e)\r
 730       {\r
 731         buriedColour_actionPerformed();\r
 732       }\r
 733     });\r
 734     abovePIDColour.setText("Above % Identity");\r
 735     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
 736     {\r
 737       public void actionPerformed(ActionEvent e)\r
 738       {\r
 739         abovePIDColour_actionPerformed();\r
 740       }\r
 741     });\r
 742     userDefinedColour.setText("User Defined...");\r
 743     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
 744     {\r
 745       public void actionPerformed(ActionEvent e)\r
 746       {\r
 747         userDefinedColour_actionPerformed(e);\r
 748       }\r
 749     });\r
 750     PIDColour.setText("Percentage Identity");\r
 751     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
 752     {\r
 753       public void actionPerformed(ActionEvent e)\r
 754       {\r
 755         PIDColour_actionPerformed();\r
 756       }\r
 757     });\r
 758     BLOSUM62Colour.setText("BLOSUM62");\r
 759     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
 760     {\r
 761       public void actionPerformed(ActionEvent e)\r
 762       {\r
 763         BLOSUM62Colour_actionPerformed();\r
 764       }\r
 765     });\r
 766     conservationMenuItem.setText("Conservation");\r
 767     conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 768     {\r
 769       public void actionPerformed(ActionEvent e)\r
 770       {\r
 771         conservationMenuItem_actionPerformed();\r
 772       }\r
 773     });\r
 774   }\r
 775 \r
 776   /**\r
 777    * DOCUMENT ME!\r
 778    */\r
 779   void refresh()\r
 780   {\r
 781     ap.paintAlignment(true);\r
 782 \r
 783     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
 784   }\r
 785 \r
 786   /**\r
 787    * DOCUMENT ME!\r
 788    *\r
 789    * @param e DOCUMENT ME!\r
 790    */\r
 791   protected void clustalColour_actionPerformed()\r
 792   {\r
 793     SequenceGroup sg = getGroup();\r
 794     sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
 795                                      ap.av.alignment.getWidth());\r
 796     refresh();\r
 797   }\r
 798 \r
 799   /**\r
 800    * DOCUMENT ME!\r
 801    *\r
 802    * @param e DOCUMENT ME!\r
 803    */\r
 804   protected void zappoColour_actionPerformed()\r
 805   {\r
 806     getGroup().cs = new ZappoColourScheme();\r
 807     refresh();\r
 808   }\r
 809 \r
 810   /**\r
 811    * DOCUMENT ME!\r
 812    *\r
 813    * @param e DOCUMENT ME!\r
 814    */\r
 815   protected void taylorColour_actionPerformed()\r
 816   {\r
 817     getGroup().cs = new TaylorColourScheme();\r
 818     refresh();\r
 819   }\r
 820 \r
 821   /**\r
 822    * DOCUMENT ME!\r
 823    *\r
 824    * @param e DOCUMENT ME!\r
 825    */\r
 826   protected void hydrophobicityColour_actionPerformed()\r
 827   {\r
 828     getGroup().cs = new HydrophobicColourScheme();\r
 829     refresh();\r
 830   }\r
 831 \r
 832   /**\r
 833    * DOCUMENT ME!\r
 834    *\r
 835    * @param e DOCUMENT ME!\r
 836    */\r
 837   protected void helixColour_actionPerformed()\r
 838   {\r
 839     getGroup().cs = new HelixColourScheme();\r
 840     refresh();\r
 841   }\r
 842 \r
 843   /**\r
 844    * DOCUMENT ME!\r
 845    *\r
 846    * @param e DOCUMENT ME!\r
 847    */\r
 848   protected void strandColour_actionPerformed()\r
 849   {\r
 850     getGroup().cs = new StrandColourScheme();\r
 851     refresh();\r
 852   }\r
 853 \r
 854   /**\r
 855    * DOCUMENT ME!\r
 856    *\r
 857    * @param e DOCUMENT ME!\r
 858    */\r
 859   protected void turnColour_actionPerformed()\r
 860   {\r
 861     getGroup().cs = new TurnColourScheme();\r
 862     refresh();\r
 863   }\r
 864 \r
 865   /**\r
 866    * DOCUMENT ME!\r
 867    *\r
 868    * @param e DOCUMENT ME!\r
 869    */\r
 870   protected void buriedColour_actionPerformed()\r
 871   {\r
 872     getGroup().cs = new BuriedColourScheme();\r
 873     refresh();\r
 874   }\r
 875 \r
 876   /**\r
 877    * DOCUMENT ME!\r
 878    *\r
 879    * @param e DOCUMENT ME!\r
 880    */\r
 881   public void nucleotideMenuItem_actionPerformed()\r
 882   {\r
 883     getGroup().cs = new NucleotideColourScheme();\r
 884     refresh();\r
 885   }\r
 886 \r
 887   /**\r
 888    * DOCUMENT ME!\r
 889    *\r
 890    * @param e DOCUMENT ME!\r
 891    */\r
 892   protected void abovePIDColour_actionPerformed()\r
 893   {\r
 894     SequenceGroup sg = getGroup();\r
 895     if (sg.cs == null)\r
 896     {\r
 897       return;\r
 898     }\r
 899 \r
 900     if (abovePIDColour.isSelected())\r
 901     {\r
 902       sg.cs.setConsensus(AAFrequency.calculate(\r
 903           sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),\r
 904           sg.getEndRes() + 1));\r
 905 \r
 906       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
 907           getGroup().getName());\r
 908 \r
 909       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
 910 \r
 911       SliderPanel.showPIDSlider();\r
 912     }\r
 913     else // remove PIDColouring\r
 914     {\r
 915       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 916     }\r
 917 \r
 918     refresh();\r
 919   }\r
 920 \r
 921   /**\r
 922    * DOCUMENT ME!\r
 923    *\r
 924    * @param e DOCUMENT ME!\r
 925    */\r
 926   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
 927   {\r
 928     SequenceGroup sg = getGroup();\r
 929 \r
 930     if (e.getActionCommand().equals("User Defined..."))\r
 931     {\r
 932       new UserDefinedColours(ap, sg);\r
 933     }\r
 934     else\r
 935     {\r
 936       UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
 937           getUserColourSchemes().get(e.getActionCommand());\r
 938 \r
 939       sg.cs = udc;\r
 940     }\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 PIDColour_actionPerformed()\r
 950   {\r
 951     SequenceGroup sg = getGroup();\r
 952     sg.cs = new PIDColourScheme();\r
 953     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
 954         hiddenRepSequences),\r
 955                                              sg.getStartRes(),\r
 956                                              sg.getEndRes() + 1));\r
 957     refresh();\r
 958   }\r
 959 \r
 960   /**\r
 961    * DOCUMENT ME!\r
 962    *\r
 963    * @param e DOCUMENT ME!\r
 964    */\r
 965   protected void BLOSUM62Colour_actionPerformed()\r
 966   {\r
 967     SequenceGroup sg = getGroup();\r
 968 \r
 969     sg.cs = new Blosum62ColourScheme();\r
 970 \r
 971     sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
 972         hiddenRepSequences),\r
 973                                              sg.getStartRes(),\r
 974                                              sg.getEndRes() + 1));\r
 975 \r
 976     refresh();\r
 977   }\r
 978 \r
 979   /**\r
 980    * DOCUMENT ME!\r
 981    *\r
 982    * @param e DOCUMENT ME!\r
 983    */\r
 984   protected void noColourmenuItem_actionPerformed()\r
 985   {\r
 986     getGroup().cs = null;\r
 987     refresh();\r
 988   }\r
 989 \r
 990   /**\r
 991    * DOCUMENT ME!\r
 992    *\r
 993    * @param e DOCUMENT ME!\r
 994    */\r
 995   protected void conservationMenuItem_actionPerformed()\r
 996   {\r
 997     SequenceGroup sg = getGroup();\r
 998     if (sg.cs == null)\r
 999     {\r
1000       return;\r
1001     }\r
1002 \r
1003     if (conservationMenuItem.isSelected())\r
1004     {\r
1005       Conservation c = new Conservation("Group",\r
1006                                         ResidueProperties.propHash, 3,\r
1007                                         sg.getSequences(ap.av.\r
1008           hiddenRepSequences),\r
1009                                         sg.getStartRes(),\r
1010                                         sg.getEndRes() + 1);\r
1011 \r
1012       c.calculate();\r
1013       c.verdict(false, ap.av.ConsPercGaps);\r
1014 \r
1015       sg.cs.setConservation(c);\r
1016 \r
1017       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
1018       SliderPanel.showConservationSlider();\r
1019     }\r
1020     else // remove ConservationColouring\r
1021     {\r
1022       sg.cs.setConservation(null);\r
1023     }\r
1024 \r
1025     refresh();\r
1026   }\r
1027 \r
1028   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
1029   {\r
1030     SequenceGroup sg = getGroup();\r
1031     if (sg == null)\r
1032     {\r
1033       return;\r
1034     }\r
1035 \r
1036     AnnotationColourGradient acg = new AnnotationColourGradient(\r
1037         sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);\r
1038 \r
1039     acg.predefinedColours = true;\r
1040     sg.cs = acg;\r
1041 \r
1042     refresh();\r
1043   }\r
1044 \r
1045   /**\r
1046    * DOCUMENT ME!\r
1047    *\r
1048    * @param e DOCUMENT ME!\r
1049    */\r
1050   protected void groupName_actionPerformed()\r
1051   {\r
1052 \r
1053     SequenceGroup sg = getGroup();\r
1054     EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
1055                                                sg.getDescription(),\r
1056                                                "       Group Name ",\r
1057                                                "Group Description ",\r
1058                                                "Edit Group Name/Description");\r
1059 \r
1060     if (!dialog.accept)\r
1061     {\r
1062       return;\r
1063     }\r
1064 \r
1065     sg.setName(dialog.getName());\r
1066     sg.setDescription(dialog.getDescription());\r
1067   }\r
1068 \r
1069   /**\r
1070    * DOCUMENT ME!\r
1071    *\r
1072    * @return DOCUMENT ME!\r
1073    */\r
1074   SequenceGroup getGroup()\r
1075   {\r
1076     SequenceGroup sg = ap.av.getSelectionGroup();\r
1077     // this method won't add a new group if it already exists\r
1078     if (sg != null)\r
1079     {\r
1080       ap.av.alignment.addGroup(sg);\r
1081     }\r
1082 \r
1083     return sg;\r
1084   }\r
1085 \r
1086   /**\r
1087    * DOCUMENT ME!\r
1088    *\r
1089    * @param e DOCUMENT ME!\r
1090    */\r
1091   void sequenceName_actionPerformed()\r
1092   {\r
1093     EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
1094                                                sequence.getDescription(),\r
1095                                                "       Sequence Name ",\r
1096                                                "Sequence Description ",\r
1097                                                "Edit Sequence Name/Description");\r
1098 \r
1099     if (!dialog.accept)\r
1100     {\r
1101       return;\r
1102     }\r
1103 \r
1104     if (dialog.getName() != null)\r
1105     {\r
1106       if (dialog.getName().indexOf(" ") > -1)\r
1107       {\r
1108         JOptionPane.showMessageDialog(ap,\r
1109                                       "Spaces have been converted to \"_\"",\r
1110                                       "No spaces allowed in Sequence Name",\r
1111                                       JOptionPane.WARNING_MESSAGE);\r
1112       }\r
1113 \r
1114       sequence.setName(dialog.getName().replace(' ', '_'));\r
1115       ap.paintAlignment(false);\r
1116     }\r
1117 \r
1118     sequence.setDescription(dialog.getDescription());\r
1119 \r
1120     ap.av.firePropertyChange("alignment", null,\r
1121                              ap.av.getAlignment().getSequences());\r
1122 \r
1123   }\r
1124 \r
1125   /**\r
1126    * DOCUMENT ME!\r
1127    *\r
1128    * @param e DOCUMENT ME!\r
1129    */\r
1130   void unGroupMenuItem_actionPerformed()\r
1131   {\r
1132     SequenceGroup sg = ap.av.getSelectionGroup();\r
1133     ap.av.alignment.deleteGroup(sg);\r
1134     ap.av.setSelectionGroup(null);\r
1135     refresh();\r
1136   }\r
1137 \r
1138   /**\r
1139    * DOCUMENT ME!\r
1140    *\r
1141    * @param e DOCUMENT ME!\r
1142    */\r
1143   protected void outline_actionPerformed()\r
1144   {\r
1145     SequenceGroup sg = getGroup();\r
1146     Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
1147                                          Color.BLUE);\r
1148 \r
1149     if (col != null)\r
1150     {\r
1151       sg.setOutlineColour(col);\r
1152     }\r
1153 \r
1154     refresh();\r
1155   }\r
1156 \r
1157   /**\r
1158    * DOCUMENT ME!\r
1159    *\r
1160    * @param e DOCUMENT ME!\r
1161    */\r
1162   public void showBoxes_actionPerformed()\r
1163   {\r
1164     getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1165     refresh();\r
1166   }\r
1167 \r
1168   /**\r
1169    * DOCUMENT ME!\r
1170    *\r
1171    * @param e DOCUMENT ME!\r
1172    */\r
1173   public void showText_actionPerformed()\r
1174   {\r
1175     getGroup().setDisplayText(showText.isSelected());\r
1176     refresh();\r
1177   }\r
1178 \r
1179   /**\r
1180    * DOCUMENT ME!\r
1181    *\r
1182    * @param e DOCUMENT ME!\r
1183    */\r
1184   public void showColourText_actionPerformed()\r
1185   {\r
1186     getGroup().setColourText(showColourText.isSelected());\r
1187     refresh();\r
1188   }\r
1189 \r
1190   public void showLink(String url)\r
1191   {\r
1192     try\r
1193     {\r
1194       jalview.util.BrowserLauncher.openURL(url);\r
1195     }\r
1196     catch (Exception ex)\r
1197     {\r
1198       JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
1199                                             "Unixers: Couldn't find default web browser."\r
1200                                             +\r
1201           "\nAdd the full path to your browser in Preferences.",\r
1202                                             "Web browser not found",\r
1203                                             JOptionPane.WARNING_MESSAGE);\r
1204 \r
1205       ex.printStackTrace();\r
1206     }\r
1207   }\r
1208 \r
1209   void hideSequences(boolean representGroup)\r
1210   {\r
1211     SequenceGroup sg = ap.av.getSelectionGroup();\r
1212     if (sg == null || sg.getSize() < 1)\r
1213     {\r
1214       ap.av.hideSequence(new SequenceI[]\r
1215                          {sequence});\r
1216       return;\r
1217     }\r
1218 \r
1219     ap.av.setSelectionGroup(null);\r
1220 \r
1221     if (representGroup)\r
1222     {\r
1223       ap.av.hideRepSequences(sequence, sg);\r
1224 \r
1225       return;\r
1226     }\r
1227 \r
1228     int gsize = sg.getSize();\r
1229     SequenceI[] hseqs;\r
1230 \r
1231     hseqs = new SequenceI[gsize];\r
1232 \r
1233     int index = 0;\r
1234     for (int i = 0; i < gsize; i++)\r
1235     {\r
1236       hseqs[index++] = sg.getSequenceAt(i);\r
1237     }\r
1238 \r
1239     ap.av.hideSequence(hseqs);\r
1240   }\r
1241 \r
1242   public void copy_actionPerformed()\r
1243   {\r
1244     ap.alignFrame.copy_actionPerformed(null);\r
1245   }\r
1246 \r
1247   public void cut_actionPerformed()\r
1248   {\r
1249     ap.alignFrame.cut_actionPerformed(null);\r
1250   }\r
1251 \r
1252   void changeCase(ActionEvent e)\r
1253   {\r
1254     Object source = e.getSource();\r
1255     SequenceGroup sg = ap.av.getSelectionGroup();\r
1256 \r
1257     if (sg != null)\r
1258     {\r
1259       int[][] startEnd = ap.av.getVisibleRegionBoundaries(\r
1260           sg.getStartRes(), sg.getEndRes() + 1);\r
1261 \r
1262       String description;\r
1263       int caseChange;\r
1264 \r
1265       if (source == toggle)\r
1266       {\r
1267         description = "Toggle Case";\r
1268         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1269       }\r
1270       else if (source == upperCase)\r
1271       {\r
1272         description = "To Upper Case";\r
1273         caseChange = ChangeCaseCommand.TO_UPPER;\r
1274       }\r
1275       else\r
1276       {\r
1277         description = "To Lower Case";\r
1278         caseChange = ChangeCaseCommand.TO_LOWER;\r
1279       }\r
1280 \r
1281       ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
1282           description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
1283           startEnd, caseChange\r
1284           );\r
1285 \r
1286       ap.alignFrame.addHistoryItem(caseCommand);\r
1287 \r
1288       ap.av.firePropertyChange("alignment", null,\r
1289                                ap.av.getAlignment().getSequences());\r
1290 \r
1291     }\r
1292   }\r
1293 \r
1294   public void outputText_actionPerformed(ActionEvent e)\r
1295   {\r
1296     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1297     cap.setForInput(null);\r
1298     Desktop.addInternalFrame(cap,\r
1299                              "Alignment output - " + e.getActionCommand(), 600,\r
1300                              500);\r
1301 \r
1302     String[] omitHidden = null;\r
1303 \r
1304     if (ap.av.hasHiddenColumns)\r
1305     {\r
1306       System.out.println("PROMPT USER HERE");\r
1307       omitHidden = ap.av.getViewAsString(true);\r
1308     }\r
1309 \r
1310     cap.setText(new FormatAdapter().formatSequences(\r
1311         e.getActionCommand(),\r
1312         ap.av.getSelectionAsNewSequence(),\r
1313         omitHidden));\r
1314   }\r
1315 \r
1316   public void pdbFromFile_actionPerformed()\r
1317   {\r
1318     jalview.io.JalviewFileChooser chooser\r
1319         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
1320                                             getProperty(\r
1321                                                 "LAST_DIRECTORY"));\r
1322     chooser.setFileView(new jalview.io.JalviewFileView());\r
1323     chooser.setDialogTitle("Select a PDB file");\r
1324     chooser.setToolTipText("Load a PDB file");\r
1325 \r
1326     int value = chooser.showOpenDialog(null);\r
1327 \r
1328     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1329     {\r
1330       PDBEntry entry = new PDBEntry();\r
1331       String choice = chooser.getSelectedFile().getPath();\r
1332       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1333       try\r
1334       {\r
1335         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,\r
1336             jalview.io.AppletFormatAdapter.FILE);\r
1337 \r
1338         if (pdbfile.id == null)\r
1339         {\r
1340           String reply = JOptionPane.showInternalInputDialog(\r
1341               Desktop.desktop,\r
1342               "Couldn't find a PDB id in the file supplied."\r
1343               + "Please enter an Id to identify this structure.",\r
1344               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);\r
1345           if (reply == null)\r
1346           {\r
1347             return;\r
1348           }\r
1349 \r
1350           entry.setId(reply);\r
1351         }\r
1352         else\r
1353         {\r
1354           entry.setId(pdbfile.id);\r
1355         }\r
1356       }\r
1357       catch (java.io.IOException ex)\r
1358       {\r
1359         ex.printStackTrace();\r
1360       }\r
1361 \r
1362       entry.setFile(choice);\r
1363       sequence.getDatasetSequence().addPDBId(entry);\r
1364     }\r
1365 \r
1366   }\r
1367 \r
1368   public void enterPDB_actionPerformed()\r
1369   {\r
1370     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1371         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
1372 \r
1373     if (id != null && id.length() > 0)\r
1374     {\r
1375       PDBEntry entry = new PDBEntry();\r
1376       entry.setId(id.toUpperCase());\r
1377       sequence.getDatasetSequence()\r
1378           .addPDBId(entry);\r
1379     }\r
1380   }\r
1381 \r
1382   public void discoverPDB_actionPerformed()\r
1383   {\r
1384     SequenceI[] sequences =\r
1385          ap.av.selectionGroup == null ?\r
1386            new Sequence[]{sequence}\r
1387          : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);\r
1388 \r
1389     new jalview.io.DBRefFetcher(sequences,\r
1390         ap.alignFrame).fetchDBRefs(false);\r
1391   }\r
1392 \r
1393   public void sequenceFeature_actionPerformed()\r
1394   {\r
1395     SequenceGroup sg = ap.av.getSelectionGroup();\r
1396     if (sg == null)\r
1397     {\r
1398       return;\r
1399     }\r
1400 \r
1401     int gSize = sg.getSize();\r
1402     SequenceI[] seqs = new SequenceI[gSize];\r
1403     SequenceFeature[] features = new SequenceFeature[gSize];\r
1404 \r
1405     for (int i = 0; i < gSize; i++)\r
1406     {\r
1407       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
1408       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1409       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1410       features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");\r
1411     }\r
1412 \r
1413     if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
1414         .amendFeatures(seqs, features, true, ap))\r
1415     {\r
1416       ap.alignFrame.showSeqFeatures.setSelected(true);\r
1417       ap.av.setShowSequenceFeatures(true);\r
1418       ap.highlightSearchResults(null);\r
1419     }\r
1420   }\r
1421 \r
1422   public void textColour_actionPerformed()\r
1423   {\r
1424     SequenceGroup sg = getGroup();\r
1425     if (sg != null)\r
1426     {\r
1427       new TextColourChooser().chooseColour(ap, sg);\r
1428     }\r
1429   }\r
1430 \r
1431   public void colourByStructure(String pdbid)\r
1432   {\r
1433     Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
1434         .colourSequenceFromStructure(sequence, pdbid);\r
1435 \r
1436     AlignmentAnnotation an = new AlignmentAnnotation(\r
1437       "Structure", "Coloured by "+pdbid, anots);\r
1438 \r
1439     ap.av.alignment.addAnnotation(an);\r
1440     an.createSequenceMapping(sequence, 0, true);\r
1441     //an.adjustForAlignment();\r
1442     ap.av.alignment.setAnnotationIndex(an,0);\r
1443 \r
1444     ap.adjustAnnotationHeight();\r
1445 \r
1446     sequence.addAlignmentAnnotation(an);\r
1447 \r
1448     }\r
1449 \r
1450   public void editSequence_actionPerformed(ActionEvent actionEvent)\r
1451   {\r
1452       SequenceGroup sg = ap.av.getSelectionGroup();\r
1453 \r
1454       if(sg!=null)\r
1455       {\r
1456         if (sequence == null)\r
1457           sequence = (Sequence) sg.getSequenceAt(0);\r
1458 \r
1459         EditNameDialog dialog = new EditNameDialog(\r
1460             sequence.getSequenceAsString(\r
1461                 sg.getStartRes(),\r
1462                 sg.getEndRes() + 1),\r
1463             null,\r
1464             "Edit Sequence ",\r
1465             null,\r
1466             "Edit Sequence");\r
1467 \r
1468         if (dialog.accept)\r
1469         {\r
1470           EditCommand editCommand = new EditCommand(\r
1471               "Edit Sequences", EditCommand.REPLACE,\r
1472               dialog.getName().replace(' ', ap.av.getGapCharacter()),\r
1473               sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
1474               sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment\r
1475               );\r
1476 \r
1477           ap.alignFrame.addHistoryItem(editCommand);\r
1478 \r
1479           ap.av.firePropertyChange("alignment", null,\r
1480                                    ap.av.getAlignment().getSequences());\r
1481         }\r
1482       }\r
1483   }\r
1484 \r
1485 \r
1486 }\r