src/jalview/gui/PopupMenu.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
   4  * \r
   5  * This file is part of Jalview.\r
   6  * \r
   7  * Jalview is free software: you can redistribute it and/or\r
   8  * modify it under the terms of the GNU General Public License \r
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  10  *  \r
  11  * Jalview is distributed in the hope that it will be useful, but \r
  12  * WITHOUT ANY WARRANTY; without even the implied warranty \r
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  14  * PURPOSE.  See the GNU General Public License for more details.\r
  15  * \r
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  17  */\r
  18 package jalview.gui;\r
  19 \r
  20 import java.util.*;\r
  21 \r
  22 import java.awt.*;\r
  23 import java.awt.event.*;\r
  24 \r
  25 import javax.swing.*;\r
  26 \r
  27 import jalview.analysis.*;\r
  28 import jalview.commands.*;\r
  29 import jalview.datamodel.*;\r
  30 import jalview.io.*;\r
  31 import jalview.schemes.*;\r
  32 import jalview.util.GroupUrlLink;\r
  33 import jalview.util.GroupUrlLink.UrlStringTooLongException;\r
  34 import jalview.util.MessageManager;\r
  35 import jalview.util.UrlLink;\r
  36 \r
  37 /**\r
  38  * DOCUMENT ME!\r
  39  * \r
  40  * @author $author$\r
  41  * @version $Revision: 1.118 $\r
  42  */\r
  43 public class PopupMenu extends JPopupMenu\r
  44 {\r
  45   JMenu groupMenu = new JMenu();\r
  46 \r
  47   JMenuItem groupName = new JMenuItem();\r
  48 \r
  49   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
  50 \r
  51   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
  52 \r
  53   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
  54 \r
  55   protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
  56 \r
  57   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
  58 \r
  59   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
  60 \r
  61   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
  62 \r
  63   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
  64 \r
  65   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
  66 \r
  67   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
  68 \r
  69   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
  70 \r
  71   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
  72 \r
  73   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();\r
  74 \r
  75   // protected JRadioButtonMenuItem covariationColour = new\r
  76   // JRadioButtonMenuItem();\r
  77 \r
  78   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
  79 \r
  80   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
  81 \r
  82   AlignmentPanel ap;\r
  83 \r
  84   JMenu sequenceMenu = new JMenu();\r
  85 \r
  86   JMenuItem sequenceName = new JMenuItem();\r
  87 \r
  88   JMenuItem sequenceDetails = new JMenuItem();\r
  89 \r
  90   JMenuItem sequenceSelDetails = new JMenuItem();\r
  91 \r
  92   SequenceI sequence;\r
  93   JMenuItem createGroupMenuItem = new JMenuItem();\r
  94   JMenuItem unGroupMenuItem = new JMenuItem();\r
  95 \r
  96   JMenuItem outline = new JMenuItem();\r
  97 \r
  98   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
  99 \r
 100   JMenu colourMenu = new JMenu();\r
 101 \r
 102   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
 103 \r
 104   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
 105 \r
 106   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
 107 \r
 108   JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();\r
 109 \r
 110   JMenu editMenu = new JMenu();\r
 111 \r
 112   JMenuItem cut = new JMenuItem();\r
 113 \r
 114   JMenuItem copy = new JMenuItem();\r
 115 \r
 116   JMenuItem upperCase = new JMenuItem();\r
 117 \r
 118   JMenuItem lowerCase = new JMenuItem();\r
 119 \r
 120   JMenuItem toggle = new JMenuItem();\r
 121 \r
 122   JMenu pdbMenu = new JMenu();\r
 123 \r
 124   JMenuItem pdbFromFile = new JMenuItem();\r
 125 \r
 126   JMenuItem enterPDB = new JMenuItem();\r
 127 \r
 128   JMenuItem discoverPDB = new JMenuItem();\r
 129 \r
 130   JMenu outputMenu = new JMenu();\r
 131 \r
 132   JMenuItem sequenceFeature = new JMenuItem();\r
 133 \r
 134   JMenuItem textColour = new JMenuItem();\r
 135 \r
 136   JMenu jMenu1 = new JMenu();\r
 137 \r
 138   JMenu structureMenu = new JMenu();\r
 139 \r
 140   JMenu viewStructureMenu = new JMenu();\r
 141 \r
 142   // JMenu colStructureMenu = new JMenu();\r
 143   JMenuItem editSequence = new JMenuItem();\r
 144 \r
 145   // JMenuItem annotationMenuItem = new JMenuItem();\r
 146 \r
 147   JMenu groupLinksMenu;\r
 148 \r
 149   /**\r
 150    * Creates a new PopupMenu object.\r
 151    * \r
 152    * @param ap\r
 153    *          DOCUMENT ME!\r
 154    * @param seq\r
 155    *          DOCUMENT ME!\r
 156    */\r
 157   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)\r
 158   {\r
 159     this(ap, seq, links, null);\r
 160   }\r
 161 \r
 162   /**\r
 163    * \r
 164    * @param ap\r
 165    * @param seq\r
 166    * @param links\r
 167    * @param groupLinks\r
 168    */\r
 169   public PopupMenu(final AlignmentPanel ap, final SequenceI seq,\r
 170           Vector links, Vector groupLinks)\r
 171   {\r
 172     // /////////////////////////////////////////////////////////\r
 173     // If this is activated from the sequence panel, the user may want to\r
 174     // edit or annotate a particular residue. Therefore display the residue menu\r
 175     //\r
 176     // If from the IDPanel, we must display the sequence menu\r
 177     // ////////////////////////////////////////////////////////\r
 178     this.ap = ap;\r
 179     sequence = seq;\r
 180 \r
 181     ButtonGroup colours = new ButtonGroup();\r
 182     colours.add(noColourmenuItem);\r
 183     colours.add(clustalColour);\r
 184     colours.add(zappoColour);\r
 185     colours.add(taylorColour);\r
 186     colours.add(hydrophobicityColour);\r
 187     colours.add(helixColour);\r
 188     colours.add(strandColour);\r
 189     colours.add(turnColour);\r
 190     colours.add(buriedColour);\r
 191     colours.add(abovePIDColour);\r
 192     colours.add(userDefinedColour);\r
 193     colours.add(PIDColour);\r
 194     colours.add(BLOSUM62Colour);\r
 195     colours.add(purinePyrimidineColour);\r
 196     // colours.add(covariationColour);\r
 197 \r
 198     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)\r
 199     {\r
 200       JMenuItem item = new JMenuItem(\r
 201               jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);\r
 202 \r
 203       item.addActionListener(new java.awt.event.ActionListener()\r
 204       {\r
 205         public void actionPerformed(ActionEvent e)\r
 206         {\r
 207           outputText_actionPerformed(e);\r
 208         }\r
 209       });\r
 210 \r
 211       outputMenu.add(item);\r
 212     }\r
 213 \r
 214     try\r
 215     {\r
 216       jbInit();\r
 217     } catch (Exception e)\r
 218     {\r
 219       e.printStackTrace();\r
 220     }\r
 221 \r
 222     JMenuItem menuItem;\r
 223     if (seq != null)\r
 224     {\r
 225       sequenceMenu.setText(sequence.getName());\r
 226 \r
 227       if (seq.getDatasetSequence().getPDBId() != null\r
 228               && seq.getDatasetSequence().getPDBId().size() > 0)\r
 229       {\r
 230         java.util.Enumeration e = seq.getDatasetSequence().getPDBId()\r
 231                 .elements();\r
 232 \r
 233         while (e.hasMoreElements())\r
 234         {\r
 235           final PDBEntry pdb = (PDBEntry) e.nextElement();\r
 236 \r
 237           menuItem = new JMenuItem();\r
 238           menuItem.setText(pdb.getId());\r
 239           menuItem.addActionListener(new java.awt.event.ActionListener()\r
 240           {\r
 241             public void actionPerformed(ActionEvent e)\r
 242             {\r
 243               // TODO re JAL-860: optionally open dialog or provide a menu entry\r
 244               // allowing user to open just one structure per sequence\r
 245               new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]\r
 246               { pdb })[0], null, ap);\r
 247               // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);\r
 248             }\r
 249 \r
 250           });\r
 251           viewStructureMenu.add(menuItem);\r
 252 \r
 253           /*\r
 254            * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());\r
 255            * menuItem.addActionListener(new java.awt.event.ActionListener() {\r
 256            * public void actionPerformed(ActionEvent e) {\r
 257            * colourByStructure(pdb.getId()); } });\r
 258            * colStructureMenu.add(menuItem);\r
 259            */\r
 260         }\r
 261       }\r
 262       else\r
 263       {\r
 264         if (ap.av.getAlignment().isNucleotide() == false)\r
 265         {\r
 266           structureMenu.remove(viewStructureMenu);\r
 267         }\r
 268         // structureMenu.remove(colStructureMenu);\r
 269       }\r
 270 \r
 271       if (ap.av.getAlignment().isNucleotide() == true)\r
 272       {\r
 273         AlignmentAnnotation[] aa = ap.av.getAlignment()\r
 274                 .getAlignmentAnnotation();\r
 275         for (int i = 0; i < aa.length; i++)\r
 276         {\r
 277           if (aa[i].getRNAStruc() != null)\r
 278           {\r
 279             final String rnastruc = aa[i].getRNAStruc();\r
 280             final String structureLine = aa[i].label;\r
 281             menuItem = new JMenuItem();\r
 282             menuItem.setText(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{structureLine}));\r
 283             menuItem.addActionListener(new java.awt.event.ActionListener()\r
 284             {\r
 285               public void actionPerformed(ActionEvent e)\r
 286               {\r
 287                 new AppVarna(structureLine, seq, seq.getSequenceAsString(),\r
 288                         rnastruc, seq.getName(), ap);\r
 289               }\r
 290             });\r
 291             viewStructureMenu.add(menuItem);\r
 292           }\r
 293         }\r
 294 \r
 295         // SequenceFeatures[] test = seq.getSequenceFeatures();\r
 296 \r
 297         if (seq.getAnnotation() != null)\r
 298         {\r
 299           AlignmentAnnotation seqAnno[] = seq.getAnnotation();\r
 300           for (int i = 0; i < seqAnno.length; i++)\r
 301           {\r
 302             if (seqAnno[i].getRNAStruc() != null)\r
 303             {\r
 304               final String rnastruc = seqAnno[i].getRNAStruc();\r
 305 \r
 306               // TODO: make rnastrucF a bit more nice\r
 307               menuItem = new JMenuItem();\r
 308               menuItem.setText(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{seq.getName()}));\r
 309               menuItem.addActionListener(new java.awt.event.ActionListener()\r
 310               {\r
 311                 public void actionPerformed(ActionEvent e)\r
 312                 {\r
 313                   // TODO: VARNA does'nt print gaps in the sequence\r
 314                   new AppVarna(seq.getName() + " structure", seq, seq\r
 315                           .getSequenceAsString(), rnastruc, seq.getName(),\r
 316                           ap);\r
 317                 }\r
 318               });\r
 319               viewStructureMenu.add(menuItem);\r
 320             }\r
 321           }\r
 322         }\r
 323 \r
 324       }\r
 325 \r
 326       menuItem = new JMenuItem(MessageManager.getString("action.hide_sequences"));\r
 327       menuItem.addActionListener(new java.awt.event.ActionListener()\r
 328       {\r
 329         public void actionPerformed(ActionEvent e)\r
 330         {\r
 331           hideSequences(false);\r
 332         }\r
 333       });\r
 334       add(menuItem);\r
 335 \r
 336       if (ap.av.getSelectionGroup() != null\r
 337               && ap.av.getSelectionGroup().getSize() > 1)\r
 338       {\r
 339         menuItem = new JMenuItem(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));\r
 340         menuItem.addActionListener(new java.awt.event.ActionListener()\r
 341         {\r
 342           public void actionPerformed(ActionEvent e)\r
 343           {\r
 344             hideSequences(true);\r
 345           }\r
 346         });\r
 347         sequenceMenu.add(menuItem);\r
 348       }\r
 349 \r
 350       if (ap.av.hasHiddenRows())\r
 351       {\r
 352         final int index = ap.av.getAlignment().findIndex(seq);\r
 353 \r
 354         if (ap.av.adjustForHiddenSeqs(index)\r
 355                 - ap.av.adjustForHiddenSeqs(index - 1) > 1)\r
 356         {\r
 357           menuItem = new JMenuItem(MessageManager.getString("action.reveal_sequences"));\r
 358           menuItem.addActionListener(new ActionListener()\r
 359           {\r
 360             public void actionPerformed(ActionEvent e)\r
 361             {\r
 362               ap.av.showSequence(index);\r
 363               if (ap.overviewPanel != null)\r
 364               {\r
 365                 ap.overviewPanel.updateOverviewImage();\r
 366               }\r
 367             }\r
 368           });\r
 369           add(menuItem);\r
 370         }\r
 371       }\r
 372     }\r
 373     // for the case when no sequences are even visible\r
 374     if (ap.av.hasHiddenRows())\r
 375     {\r
 376       {\r
 377         menuItem = new JMenuItem(MessageManager.getString("action.reveal_all"));\r
 378         menuItem.addActionListener(new ActionListener()\r
 379         {\r
 380           public void actionPerformed(ActionEvent e)\r
 381           {\r
 382             ap.av.showAllHiddenSeqs();\r
 383             if (ap.overviewPanel != null)\r
 384             {\r
 385               ap.overviewPanel.updateOverviewImage();\r
 386             }\r
 387           }\r
 388         });\r
 389 \r
 390         add(menuItem);\r
 391       }\r
 392 \r
 393     }\r
 394 \r
 395     SequenceGroup sg = ap.av.getSelectionGroup();\r
 396     boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;\r
 397 \r
 398     if (sg != null && sg.getSize() > 0)\r
 399     {      \r
 400       groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));\r
 401       groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));\r
 402 \r
 403       if (sg.cs instanceof ZappoColourScheme)\r
 404       {\r
 405         zappoColour.setSelected(true);\r
 406       }\r
 407       else if (sg.cs instanceof TaylorColourScheme)\r
 408       {\r
 409         taylorColour.setSelected(true);\r
 410       }\r
 411       else if (sg.cs instanceof PIDColourScheme)\r
 412       {\r
 413         PIDColour.setSelected(true);\r
 414       }\r
 415       else if (sg.cs instanceof Blosum62ColourScheme)\r
 416       {\r
 417         BLOSUM62Colour.setSelected(true);\r
 418       }\r
 419       else if (sg.cs instanceof UserColourScheme)\r
 420       {\r
 421         userDefinedColour.setSelected(true);\r
 422       }\r
 423       else if (sg.cs instanceof HydrophobicColourScheme)\r
 424       {\r
 425         hydrophobicityColour.setSelected(true);\r
 426       }\r
 427       else if (sg.cs instanceof HelixColourScheme)\r
 428       {\r
 429         helixColour.setSelected(true);\r
 430       }\r
 431       else if (sg.cs instanceof StrandColourScheme)\r
 432       {\r
 433         strandColour.setSelected(true);\r
 434       }\r
 435       else if (sg.cs instanceof TurnColourScheme)\r
 436       {\r
 437         turnColour.setSelected(true);\r
 438       }\r
 439       else if (sg.cs instanceof BuriedColourScheme)\r
 440       {\r
 441         buriedColour.setSelected(true);\r
 442       }\r
 443       else if (sg.cs instanceof ClustalxColourScheme)\r
 444       {\r
 445         clustalColour.setSelected(true);\r
 446       }\r
 447       else if (sg.cs instanceof PurinePyrimidineColourScheme)\r
 448       {\r
 449         purinePyrimidineColour.setSelected(true);\r
 450       }\r
 451       /*\r
 452        * else if (sg.cs instanceof CovariationColourScheme) {\r
 453        * covariationColour.setSelected(true); }\r
 454        */\r
 455       else\r
 456       {\r
 457         noColourmenuItem.setSelected(true);\r
 458       }\r
 459 \r
 460       if (sg.cs != null && sg.cs.conservationApplied())\r
 461       {\r
 462         conservationMenuItem.setSelected(true);\r
 463       }\r
 464       displayNonconserved.setSelected(sg.getShowNonconserved());\r
 465       showText.setSelected(sg.getDisplayText());\r
 466       showColourText.setSelected(sg.getColourText());\r
 467       showBoxes.setSelected(sg.getDisplayBoxes());\r
 468       // add any groupURLs to the groupURL submenu and make it visible\r
 469       if (groupLinks != null && groupLinks.size() > 0)\r
 470       {\r
 471         buildGroupURLMenu(sg, groupLinks);\r
 472       }\r
 473       // Add a 'show all structures' for the current selection\r
 474       Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();\r
 475       SequenceI sqass = null;\r
 476       for (SequenceI sq : ap.av.getSequenceSelection())\r
 477       {\r
 478         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()\r
 479                 .getPDBId();\r
 480         if (pes != null)\r
 481         {\r
 482           for (PDBEntry pe : pes)\r
 483           {\r
 484             pdbe.put(pe.getId(), pe);\r
 485             if (sqass == null)\r
 486             {\r
 487               sqass = sq;\r
 488             }\r
 489           }\r
 490         }\r
 491       }\r
 492       if (pdbe.size() > 0)\r
 493       {\r
 494         final PDBEntry[] pe = pdbe.values().toArray(\r
 495                 new PDBEntry[pdbe.size()]);\r
 496         final JMenuItem gpdbview;\r
 497         if (pdbe.size() == 1)\r
 498         {\r
 499           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));\r
 500         }\r
 501         else\r
 502         {\r
 503           structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));\r
 504         }\r
 505         gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));\r
 506         gpdbview.addActionListener(new ActionListener()\r
 507         {\r
 508 \r
 509           @Override\r
 510           public void actionPerformed(ActionEvent e)\r
 511           {\r
 512             new AppJmol(ap, pe, ap.av.collateForPDB(pe));\r
 513           }\r
 514         });\r
 515       }\r
 516     }\r
 517     else\r
 518     {\r
 519       groupMenu.setVisible(false);\r
 520       editMenu.setVisible(false);\r
 521     }\r
 522 \r
 523     if (!isDefinedGroup)\r
 524     {\r
 525       createGroupMenuItem.setVisible(true);\r
 526       unGroupMenuItem.setVisible(false);\r
 527       jMenu1.setText(MessageManager.getString("action.edit_new_group"));\r
 528     } else {\r
 529       createGroupMenuItem.setVisible(false);\r
 530       unGroupMenuItem.setVisible(true);\r
 531       jMenu1.setText(MessageManager.getString("action.edit_group"));\r
 532     }\r
 533 \r
 534     if (seq == null)\r
 535     {\r
 536       sequenceMenu.setVisible(false);\r
 537       structureMenu.setVisible(false);\r
 538     }\r
 539 \r
 540     if (links != null && links.size() > 0)\r
 541     {\r
 542 \r
 543       JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));\r
 544       Vector linkset = new Vector();\r
 545       for (int i = 0; i < links.size(); i++)\r
 546       {\r
 547         String link = links.elementAt(i).toString();\r
 548         UrlLink urlLink = null;\r
 549         try\r
 550         {\r
 551           urlLink = new UrlLink(link);\r
 552         } catch (Exception foo)\r
 553         {\r
 554           jalview.bin.Cache.log.error("Exception for URLLink '" + link\r
 555                   + "'", foo);\r
 556           continue;\r
 557         }\r
 558         ;\r
 559         if (!urlLink.isValid())\r
 560         {\r
 561           jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
 562           continue;\r
 563         }\r
 564         final String label = urlLink.getLabel();\r
 565         if (seq != null && urlLink.isDynamic())\r
 566         {\r
 567 \r
 568           // collect matching db-refs\r
 569           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(\r
 570                   seq.getDBRef(), new String[]\r
 571                   { urlLink.getTarget() });\r
 572           // collect id string too\r
 573           String id = seq.getName();\r
 574           String descr = seq.getDescription();\r
 575           if (descr != null && descr.length() < 1)\r
 576           {\r
 577             descr = null;\r
 578           }\r
 579 \r
 580           if (dbr != null)\r
 581           {\r
 582             for (int r = 0; r < dbr.length; r++)\r
 583             {\r
 584               if (id != null && dbr[r].getAccessionId().equals(id))\r
 585               {\r
 586                 // suppress duplicate link creation for the bare sequence ID\r
 587                 // string with this link\r
 588                 id = null;\r
 589               }\r
 590               // create Bare ID link for this RUL\r
 591               String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),\r
 592                       true);\r
 593               if (urls != null)\r
 594               {\r
 595                 for (int u = 0; u < urls.length; u += 2)\r
 596                 {\r
 597                   if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
 598                   {\r
 599                     linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
 600                     addshowLink(linkMenu, label + "|" + urls[u],\r
 601                             urls[u + 1]);\r
 602                   }\r
 603                 }\r
 604               }\r
 605             }\r
 606           }\r
 607           if (id != null)\r
 608           {\r
 609             // create Bare ID link for this RUL\r
 610             String[] urls = urlLink.makeUrls(id, true);\r
 611             if (urls != null)\r
 612             {\r
 613               for (int u = 0; u < urls.length; u += 2)\r
 614               {\r
 615                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
 616                 {\r
 617                   linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
 618                   addshowLink(linkMenu, label, urls[u + 1]);\r
 619                 }\r
 620               }\r
 621             }\r
 622           }\r
 623           // Create urls from description but only for URL links which are regex\r
 624           // links\r
 625           if (descr != null && urlLink.getRegexReplace() != null)\r
 626           {\r
 627             // create link for this URL from description where regex matches\r
 628             String[] urls = urlLink.makeUrls(descr, true);\r
 629             if (urls != null)\r
 630             {\r
 631               for (int u = 0; u < urls.length; u += 2)\r
 632               {\r
 633                 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))\r
 634                 {\r
 635                   linkset.addElement(urls[u] + "|" + urls[u + 1]);\r
 636                   addshowLink(linkMenu, label, urls[u + 1]);\r
 637                 }\r
 638               }\r
 639             }\r
 640           }\r
 641         }\r
 642         else\r
 643         {\r
 644           if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))\r
 645           {\r
 646             linkset.addElement(label + "|" + urlLink.getUrl_prefix());\r
 647             // Add a non-dynamic link\r
 648             addshowLink(linkMenu, label, urlLink.getUrl_prefix());\r
 649           }\r
 650         }\r
 651       }\r
 652       if (sequence != null)\r
 653       {\r
 654         sequenceMenu.add(linkMenu);\r
 655       }\r
 656       else\r
 657       {\r
 658         add(linkMenu);\r
 659       }\r
 660     }\r
 661   }\r
 662 \r
 663   private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)\r
 664   {\r
 665 \r
 666     // TODO: usability: thread off the generation of group url content so root\r
 667     // menu appears asap\r
 668     // sequence only URLs\r
 669     // ID/regex match URLs\r
 670     groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 671     JMenu[] linkMenus = new JMenu[]\r
 672     { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),\r
 673         new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be\r
 674                                           // created.\r
 675     SequenceI[] seqs = ap.av.getSelectionAsNewSequence();\r
 676     String[][] idandseqs = GroupUrlLink.formStrings(seqs);\r
 677     Hashtable commonDbrefs = new Hashtable();\r
 678     for (int sq = 0; sq < seqs.length; sq++)\r
 679     {\r
 680 \r
 681       int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]\r
 682               .findPosition(sg.getEndRes());\r
 683       // just collect ids from dataset sequence\r
 684       // TODO: check if IDs collected from selecton group intersects with the\r
 685       // current selection, too\r
 686       SequenceI sqi = seqs[sq];\r
 687       while (sqi.getDatasetSequence() != null)\r
 688       {\r
 689         sqi = sqi.getDatasetSequence();\r
 690       }\r
 691       DBRefEntry[] dbr = sqi.getDBRef();\r
 692       if (dbr != null && dbr.length > 0)\r
 693       {\r
 694         for (int d = 0; d < dbr.length; d++)\r
 695         {\r
 696           String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();\r
 697           Object[] sarray = (Object[]) commonDbrefs.get(src);\r
 698           if (sarray == null)\r
 699           {\r
 700             sarray = new Object[2];\r
 701             sarray[0] = new int[]\r
 702             { 0 };\r
 703             sarray[1] = new String[seqs.length];\r
 704 \r
 705             commonDbrefs.put(src, sarray);\r
 706           }\r
 707 \r
 708           if (((String[]) sarray[1])[sq] == null)\r
 709           {\r
 710             if (!dbr[d].hasMap()\r
 711                     || (dbr[d].getMap().locateMappedRange(start, end) != null))\r
 712             {\r
 713               ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();\r
 714               ((int[]) sarray[0])[0]++;\r
 715             }\r
 716           }\r
 717         }\r
 718       }\r
 719     }\r
 720     // now create group links for all distinct ID/sequence sets.\r
 721     boolean addMenu = false; // indicates if there are any group links to give\r
 722                              // to user\r
 723     for (int i = 0; i < groupLinks.size(); i++)\r
 724     {\r
 725       String link = groupLinks.elementAt(i).toString();\r
 726       GroupUrlLink urlLink = null;\r
 727       try\r
 728       {\r
 729         urlLink = new GroupUrlLink(link);\r
 730       } catch (Exception foo)\r
 731       {\r
 732         jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link\r
 733                 + "'", foo);\r
 734         continue;\r
 735       }\r
 736       ;\r
 737       if (!urlLink.isValid())\r
 738       {\r
 739         jalview.bin.Cache.log.error(urlLink.getInvalidMessage());\r
 740         continue;\r
 741       }\r
 742       final String label = urlLink.getLabel();\r
 743       boolean usingNames = false;\r
 744       // Now see which parts of the group apply for this URL\r
 745       String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());\r
 746       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());\r
 747       String[] seqstr, ids; // input to makeUrl\r
 748       if (idset != null)\r
 749       {\r
 750         int numinput = ((int[]) idset[0])[0];\r
 751         String[] allids = ((String[]) idset[1]);\r
 752         seqstr = new String[numinput];\r
 753         ids = new String[numinput];\r
 754         for (int sq = 0, idcount = 0; sq < seqs.length; sq++)\r
 755         {\r
 756           if (allids[sq] != null)\r
 757           {\r
 758             ids[idcount] = allids[sq];\r
 759             seqstr[idcount++] = idandseqs[1][sq];\r
 760           }\r
 761         }\r
 762       }\r
 763       else\r
 764       {\r
 765         // just use the id/seq set\r
 766         seqstr = idandseqs[1];\r
 767         ids = idandseqs[0];\r
 768         usingNames = true;\r
 769       }\r
 770       // and try and make the groupURL!\r
 771 \r
 772       Object[] urlset = null;\r
 773       try\r
 774       {\r
 775         urlset = urlLink.makeUrlStubs(ids, seqstr,\r
 776                 "FromJalview" + System.currentTimeMillis(), false);\r
 777       } catch (UrlStringTooLongException e)\r
 778       {\r
 779       }\r
 780       if (urlset != null)\r
 781       {\r
 782         int type = urlLink.getGroupURLType() & 3;\r
 783         // System.out.println(urlLink.getGroupURLType()\r
 784         // +" "+((String[])urlset[3])[0]);\r
 785         // first two bits ofurlLink type bitfield are sequenceids and sequences\r
 786         // TODO: FUTURE: ensure the groupURL menu structure can be generalised\r
 787         addshowLink(linkMenus[type], label\r
 788                 + (((type & 1) == 1) ? ("("\r
 789                         + (usingNames ? "Names" : ltarget) + ")") : ""),\r
 790                 urlLink, urlset);\r
 791         addMenu = true;\r
 792       }\r
 793     }\r
 794     if (addMenu)\r
 795     {\r
 796       groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));\r
 797       for (int m = 0; m < linkMenus.length; m++)\r
 798       {\r
 799         if (linkMenus[m] != null\r
 800                 && linkMenus[m].getMenuComponentCount() > 0)\r
 801         {\r
 802           groupLinksMenu.add(linkMenus[m]);\r
 803         }\r
 804       }\r
 805 \r
 806       groupMenu.add(groupLinksMenu);\r
 807     }\r
 808   }\r
 809 \r
 810   /**\r
 811    * add a show URL menu item to the given linkMenu\r
 812    * \r
 813    * @param linkMenu\r
 814    * @param label\r
 815    *          - menu label string\r
 816    * @param url\r
 817    *          - url to open\r
 818    */\r
 819   private void addshowLink(JMenu linkMenu, String label, final String url)\r
 820   {\r
 821     JMenuItem item = new JMenuItem(label);\r
 822     item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));\r
 823     item.addActionListener(new java.awt.event.ActionListener()\r
 824     {\r
 825       public void actionPerformed(ActionEvent e)\r
 826       {\r
 827         new Thread(new Runnable()\r
 828         {\r
 829 \r
 830           public void run()\r
 831           {\r
 832             showLink(url);\r
 833           }\r
 834 \r
 835         }).start();\r
 836       }\r
 837     });\r
 838 \r
 839     linkMenu.add(item);\r
 840   }\r
 841 \r
 842   /**\r
 843    * add a late bound groupURL item to the given linkMenu\r
 844    * \r
 845    * @param linkMenu\r
 846    * @param label\r
 847    *          - menu label string\r
 848    * @param urlgenerator\r
 849    *          GroupURLLink used to generate URL\r
 850    * @param urlstub\r
 851    *          Object array returned from the makeUrlStubs function.\r
 852    */\r
 853   private void addshowLink(JMenu linkMenu, String label,\r
 854           final GroupUrlLink urlgenerator, final Object[] urlstub)\r
 855   {\r
 856     JMenuItem item = new JMenuItem(label);\r
 857     item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));\r
 858     // TODO: put in info about what is being sent.\r
 859     item.addActionListener(new java.awt.event.ActionListener()\r
 860     {\r
 861       public void actionPerformed(ActionEvent e)\r
 862       {\r
 863         new Thread(new Runnable()\r
 864         {\r
 865 \r
 866           public void run()\r
 867           {\r
 868             try\r
 869             {\r
 870               showLink(urlgenerator.constructFrom(urlstub));\r
 871             } catch (UrlStringTooLongException e)\r
 872             {\r
 873             }\r
 874           }\r
 875 \r
 876         }).start();\r
 877       }\r
 878     });\r
 879 \r
 880     linkMenu.add(item);\r
 881   }\r
 882 \r
 883   /**\r
 884    * DOCUMENT ME!\r
 885    * \r
 886    * @throws Exception\r
 887    *           DOCUMENT ME!\r
 888    */\r
 889   private void jbInit() throws Exception\r
 890   {\r
 891     groupMenu.setText(MessageManager.getString("label.group"));\r
 892     groupMenu.setText(MessageManager.getString("label.selection"));\r
 893     groupName.setText(MessageManager.getString("label.name"));\r
 894     groupName.addActionListener(new java.awt.event.ActionListener()\r
 895     {\r
 896       public void actionPerformed(ActionEvent e)\r
 897       {\r
 898         groupName_actionPerformed();\r
 899       }\r
 900     });\r
 901     sequenceMenu.setText(MessageManager.getString("label.sequence"));\r
 902     sequenceName.setText(MessageManager.getString("label.edit_name_description"));\r
 903     sequenceName.addActionListener(new java.awt.event.ActionListener()\r
 904     {\r
 905       public void actionPerformed(ActionEvent e)\r
 906       {\r
 907         sequenceName_actionPerformed();\r
 908       }\r
 909     });\r
 910     sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 911     sequenceDetails.addActionListener(new java.awt.event.ActionListener()\r
 912     {\r
 913       public void actionPerformed(ActionEvent e)\r
 914       {\r
 915         sequenceDetails_actionPerformed();\r
 916       }\r
 917     });\r
 918     sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");\r
 919     sequenceSelDetails\r
 920             .addActionListener(new java.awt.event.ActionListener()\r
 921             {\r
 922               public void actionPerformed(ActionEvent e)\r
 923               {\r
 924                 sequenceSelectionDetails_actionPerformed();\r
 925               }\r
 926             });\r
 927     PIDColour.setFocusPainted(false);\r
 928     unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));\r
 929     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 930     {\r
 931       public void actionPerformed(ActionEvent e)\r
 932       {\r
 933         unGroupMenuItem_actionPerformed();\r
 934       }\r
 935     });\r
 936     createGroupMenuItem.setText(MessageManager.getString("action.create_group"));\r
 937     createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
 938     {\r
 939       public void actionPerformed(ActionEvent e)\r
 940       {\r
 941         createGroupMenuItem_actionPerformed();\r
 942       }\r
 943     });\r
 944 \r
 945     outline.setText(MessageManager.getString("action.border_colour"));\r
 946     outline.addActionListener(new java.awt.event.ActionListener()\r
 947     {\r
 948       public void actionPerformed(ActionEvent e)\r
 949       {\r
 950         outline_actionPerformed();\r
 951       }\r
 952     });\r
 953     nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));\r
 954     nucleotideMenuItem.addActionListener(new ActionListener()\r
 955     {\r
 956       public void actionPerformed(ActionEvent e)\r
 957       {\r
 958         nucleotideMenuItem_actionPerformed();\r
 959       }\r
 960     });\r
 961     colourMenu.setText(MessageManager.getString("label.group_colour"));\r
 962     showBoxes.setText(MessageManager.getString("action.boxes"));\r
 963     showBoxes.setState(true);\r
 964     showBoxes.addActionListener(new ActionListener()\r
 965     {\r
 966       public void actionPerformed(ActionEvent e)\r
 967       {\r
 968         showBoxes_actionPerformed();\r
 969       }\r
 970     });\r
 971     showText.setText(MessageManager.getString("action.text"));\r
 972     showText.setState(true);\r
 973     showText.addActionListener(new ActionListener()\r
 974     {\r
 975       public void actionPerformed(ActionEvent e)\r
 976       {\r
 977         showText_actionPerformed();\r
 978       }\r
 979     });\r
 980     showColourText.setText(MessageManager.getString("label.colour_text"));\r
 981     showColourText.addActionListener(new ActionListener()\r
 982     {\r
 983       public void actionPerformed(ActionEvent e)\r
 984       {\r
 985         showColourText_actionPerformed();\r
 986       }\r
 987     });\r
 988     displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));\r
 989     displayNonconserved.setState(true);\r
 990     displayNonconserved.addActionListener(new ActionListener()\r
 991     {\r
 992       public void actionPerformed(ActionEvent e)\r
 993       {\r
 994         showNonconserved_actionPerformed();\r
 995       }\r
 996     });\r
 997     editMenu.setText(MessageManager.getString("action.edit"));\r
 998     cut.setText(MessageManager.getString("action.cut"));\r
 999     cut.addActionListener(new ActionListener()\r
1000     {\r
1001       public void actionPerformed(ActionEvent e)\r
1002       {\r
1003         cut_actionPerformed();\r
1004       }\r
1005     });\r
1006     upperCase.setText(MessageManager.getString("label.to_upper_case"));\r
1007     upperCase.addActionListener(new ActionListener()\r
1008     {\r
1009       public void actionPerformed(ActionEvent e)\r
1010       {\r
1011         changeCase(e);\r
1012       }\r
1013     });\r
1014     copy.setText(MessageManager.getString("action.copy"));\r
1015     copy.addActionListener(new ActionListener()\r
1016     {\r
1017       public void actionPerformed(ActionEvent e)\r
1018       {\r
1019         copy_actionPerformed();\r
1020       }\r
1021     });\r
1022     lowerCase.setText(MessageManager.getString("label.to_lower_case"));\r
1023     lowerCase.addActionListener(new ActionListener()\r
1024     {\r
1025       public void actionPerformed(ActionEvent e)\r
1026       {\r
1027         changeCase(e);\r
1028       }\r
1029     });\r
1030     toggle.setText(MessageManager.getString("label.toggle_case"));\r
1031     toggle.addActionListener(new ActionListener()\r
1032     {\r
1033       public void actionPerformed(ActionEvent e)\r
1034       {\r
1035         changeCase(e);\r
1036       }\r
1037     });\r
1038     pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));\r
1039     pdbFromFile.setText(MessageManager.getString("label.from_file"));\r
1040     pdbFromFile.addActionListener(new ActionListener()\r
1041     {\r
1042       public void actionPerformed(ActionEvent e)\r
1043       {\r
1044         pdbFromFile_actionPerformed();\r
1045       }\r
1046     });\r
1047     enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));\r
1048     enterPDB.addActionListener(new ActionListener()\r
1049     {\r
1050       public void actionPerformed(ActionEvent e)\r
1051       {\r
1052         enterPDB_actionPerformed();\r
1053       }\r
1054     });\r
1055     discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));\r
1056     discoverPDB.addActionListener(new ActionListener()\r
1057     {\r
1058       public void actionPerformed(ActionEvent e)\r
1059       {\r
1060         discoverPDB_actionPerformed();\r
1061       }\r
1062     });\r
1063     outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");\r
1064     sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));\r
1065     sequenceFeature.addActionListener(new ActionListener()\r
1066     {\r
1067       public void actionPerformed(ActionEvent e)\r
1068       {\r
1069         sequenceFeature_actionPerformed();\r
1070       }\r
1071     });\r
1072     textColour.setText(MessageManager.getString("label.text_colour"));\r
1073     textColour.addActionListener(new ActionListener()\r
1074     {\r
1075       public void actionPerformed(ActionEvent e)\r
1076       {\r
1077         textColour_actionPerformed();\r
1078       }\r
1079     });\r
1080     jMenu1.setText(MessageManager.getString("label.group"));\r
1081     structureMenu.setText(MessageManager.getString("label.structure"));\r
1082     viewStructureMenu.setText(MessageManager.getString("label.view_structure"));\r
1083     // colStructureMenu.setText("Colour By Structure");\r
1084     editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");\r
1085     editSequence.addActionListener(new ActionListener()\r
1086     {\r
1087       public void actionPerformed(ActionEvent actionEvent)\r
1088       {\r
1089         editSequence_actionPerformed(actionEvent);\r
1090       }\r
1091     });\r
1092 \r
1093     /*\r
1094      * annotationMenuItem.setText("By Annotation");\r
1095      * annotationMenuItem.addActionListener(new ActionListener() { public void\r
1096      * actionPerformed(ActionEvent actionEvent) {\r
1097      * annotationMenuItem_actionPerformed(actionEvent); } });\r
1098      */\r
1099     groupMenu.add(sequenceSelDetails);\r
1100     add(groupMenu);\r
1101     add(sequenceMenu);\r
1102     this.add(structureMenu);\r
1103     groupMenu.add(editMenu);\r
1104     groupMenu.add(outputMenu);\r
1105     groupMenu.add(sequenceFeature);\r
1106     groupMenu.add(createGroupMenuItem);\r
1107     groupMenu.add(unGroupMenuItem);\r
1108     groupMenu.add(jMenu1);\r
1109     sequenceMenu.add(sequenceName);\r
1110     sequenceMenu.add(sequenceDetails);\r
1111     colourMenu.add(textColour);\r
1112     colourMenu.add(noColourmenuItem);\r
1113     colourMenu.add(clustalColour);\r
1114     colourMenu.add(BLOSUM62Colour);\r
1115     colourMenu.add(PIDColour);\r
1116     colourMenu.add(zappoColour);\r
1117     colourMenu.add(taylorColour);\r
1118     colourMenu.add(hydrophobicityColour);\r
1119     colourMenu.add(helixColour);\r
1120     colourMenu.add(strandColour);\r
1121     colourMenu.add(turnColour);\r
1122     colourMenu.add(buriedColour);\r
1123     colourMenu.add(nucleotideMenuItem);\r
1124     if (ap.getAlignment().isNucleotide())\r
1125     {\r
1126       colourMenu.add(purinePyrimidineColour);\r
1127     }\r
1128     // colourMenu.add(covariationColour);\r
1129     colourMenu.add(userDefinedColour);\r
1130 \r
1131     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
1132     {\r
1133       java.util.Enumeration userColours = jalview.gui.UserDefinedColours\r
1134               .getUserColourSchemes().keys();\r
1135 \r
1136       while (userColours.hasMoreElements())\r
1137       {\r
1138         JMenuItem item = new JMenuItem(userColours.nextElement().toString());\r
1139         item.addActionListener(new ActionListener()\r
1140         {\r
1141           public void actionPerformed(ActionEvent evt)\r
1142           {\r
1143             userDefinedColour_actionPerformed(evt);\r
1144           }\r
1145         });\r
1146         colourMenu.add(item);\r
1147       }\r
1148     }\r
1149 \r
1150     colourMenu.addSeparator();\r
1151     colourMenu.add(abovePIDColour);\r
1152     colourMenu.add(conservationMenuItem);\r
1153     // colourMenu.add(annotationMenuItem);\r
1154     editMenu.add(copy);\r
1155     editMenu.add(cut);\r
1156     editMenu.add(editSequence);\r
1157     editMenu.add(upperCase);\r
1158     editMenu.add(lowerCase);\r
1159     editMenu.add(toggle);\r
1160     pdbMenu.add(pdbFromFile);\r
1161     pdbMenu.add(enterPDB);\r
1162     pdbMenu.add(discoverPDB);\r
1163     jMenu1.add(groupName);\r
1164     jMenu1.add(colourMenu);\r
1165     jMenu1.add(showBoxes);\r
1166     jMenu1.add(showText);\r
1167     jMenu1.add(showColourText);\r
1168     jMenu1.add(outline);\r
1169     jMenu1.add(displayNonconserved);\r
1170     structureMenu.add(pdbMenu);\r
1171     structureMenu.add(viewStructureMenu);\r
1172     // structureMenu.add(colStructureMenu);\r
1173     noColourmenuItem.setText(MessageManager.getString("label.none"));\r
1174     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
1175     {\r
1176       public void actionPerformed(ActionEvent e)\r
1177       {\r
1178         noColourmenuItem_actionPerformed();\r
1179       }\r
1180     });\r
1181 \r
1182     clustalColour.setText(MessageManager.getString("label.clustalx_colours"));\r
1183     clustalColour.addActionListener(new java.awt.event.ActionListener()\r
1184     {\r
1185       public void actionPerformed(ActionEvent e)\r
1186       {\r
1187         clustalColour_actionPerformed();\r
1188       }\r
1189     });\r
1190     zappoColour.setText(MessageManager.getString("label.zappo"));\r
1191     zappoColour.addActionListener(new java.awt.event.ActionListener()\r
1192     {\r
1193       public void actionPerformed(ActionEvent e)\r
1194       {\r
1195         zappoColour_actionPerformed();\r
1196       }\r
1197     });\r
1198     taylorColour.setText(MessageManager.getString("label.taylor"));\r
1199     taylorColour.addActionListener(new java.awt.event.ActionListener()\r
1200     {\r
1201       public void actionPerformed(ActionEvent e)\r
1202       {\r
1203         taylorColour_actionPerformed();\r
1204       }\r
1205     });\r
1206     hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));\r
1207     hydrophobicityColour\r
1208             .addActionListener(new java.awt.event.ActionListener()\r
1209             {\r
1210               public void actionPerformed(ActionEvent e)\r
1211               {\r
1212                 hydrophobicityColour_actionPerformed();\r
1213               }\r
1214             });\r
1215     helixColour.setText(MessageManager.getString("label.helix_propensity"));\r
1216     helixColour.addActionListener(new java.awt.event.ActionListener()\r
1217     {\r
1218       public void actionPerformed(ActionEvent e)\r
1219       {\r
1220         helixColour_actionPerformed();\r
1221       }\r
1222     });\r
1223     strandColour.setText(MessageManager.getString("label.strand_propensity"));\r
1224     strandColour.addActionListener(new java.awt.event.ActionListener()\r
1225     {\r
1226       public void actionPerformed(ActionEvent e)\r
1227       {\r
1228         strandColour_actionPerformed();\r
1229       }\r
1230     });\r
1231     turnColour.setText(MessageManager.getString("label.turn_propensity"));\r
1232     turnColour.addActionListener(new java.awt.event.ActionListener()\r
1233     {\r
1234       public void actionPerformed(ActionEvent e)\r
1235       {\r
1236         turnColour_actionPerformed();\r
1237       }\r
1238     });\r
1239     buriedColour.setText(MessageManager.getString("label.buried_index"));\r
1240     buriedColour.addActionListener(new java.awt.event.ActionListener()\r
1241     {\r
1242       public void actionPerformed(ActionEvent e)\r
1243       {\r
1244         buriedColour_actionPerformed();\r
1245       }\r
1246     });\r
1247     abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));\r
1248     abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
1249     {\r
1250       public void actionPerformed(ActionEvent e)\r
1251       {\r
1252         abovePIDColour_actionPerformed();\r
1253       }\r
1254     });\r
1255     userDefinedColour.setText(MessageManager.getString("action.user_defined"));\r
1256     userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
1257     {\r
1258       public void actionPerformed(ActionEvent e)\r
1259       {\r
1260         userDefinedColour_actionPerformed(e);\r
1261       }\r
1262     });\r
1263     PIDColour.setText(MessageManager.getString("label.percentage_identity"));\r
1264     PIDColour.addActionListener(new java.awt.event.ActionListener()\r
1265     {\r
1266       public void actionPerformed(ActionEvent e)\r
1267       {\r
1268         PIDColour_actionPerformed();\r
1269       }\r
1270     });\r
1271     BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));\r
1272     BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
1273     {\r
1274       public void actionPerformed(ActionEvent e)\r
1275       {\r
1276         BLOSUM62Colour_actionPerformed();\r
1277       }\r
1278     });\r
1279     purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));\r
1280     purinePyrimidineColour\r
1281             .addActionListener(new java.awt.event.ActionListener()\r
1282             {\r
1283               public void actionPerformed(ActionEvent e)\r
1284               {\r
1285                 purinePyrimidineColour_actionPerformed();\r
1286               }\r
1287             });\r
1288     /*\r
1289      * covariationColour.addActionListener(new java.awt.event.ActionListener() {\r
1290      * public void actionPerformed(ActionEvent e) {\r
1291      * covariationColour_actionPerformed(); } });\r
1292      */\r
1293 \r
1294     conservationMenuItem.setText(MessageManager.getString("label.conservation"));\r
1295     conservationMenuItem\r
1296             .addActionListener(new java.awt.event.ActionListener()\r
1297             {\r
1298               public void actionPerformed(ActionEvent e)\r
1299               {\r
1300                 conservationMenuItem_actionPerformed();\r
1301               }\r
1302             });\r
1303   }\r
1304 \r
1305   protected void sequenceSelectionDetails_actionPerformed()\r
1306   {\r
1307     createSequenceDetailsReport(ap.av.getSequenceSelection());\r
1308   }\r
1309 \r
1310   protected void sequenceDetails_actionPerformed()\r
1311   {\r
1312     createSequenceDetailsReport(new SequenceI[]\r
1313     { sequence });\r
1314   }\r
1315 \r
1316   public void createSequenceDetailsReport(SequenceI[] sequences)\r
1317   {\r
1318     CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();\r
1319     StringBuffer contents = new StringBuffer();\r
1320     for (SequenceI seq : sequences)\r
1321     {           \r
1322       contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})\r
1323               + "</h2></p><p>");\r
1324       new SequenceAnnotationReport(null)\r
1325               .createSequenceAnnotationReport(\r
1326                       contents,\r
1327                       seq,\r
1328                       true,\r
1329                       true,\r
1330                       false,\r
1331                       (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax\r
1332                               : null);\r
1333       contents.append("</p>");\r
1334     }\r
1335     cap.setText("<html>" + contents.toString() + "</html>");\r
1336 \r
1337     Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))\r
1338                 ,500, 400);\r
1339 \r
1340   }\r
1341 \r
1342   protected void showNonconserved_actionPerformed()\r
1343   {\r
1344     getGroup().setShowNonconserved(displayNonconserved.isSelected());\r
1345     refresh();\r
1346   }\r
1347 \r
1348   /**\r
1349    * call to refresh view after settings change\r
1350    */\r
1351   void refresh()\r
1352   {\r
1353     ap.updateAnnotation();\r
1354     ap.paintAlignment(true);\r
1355 \r
1356     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
1357   }\r
1358 \r
1359   /**\r
1360    * DOCUMENT ME!\r
1361    * \r
1362    * @param e\r
1363    *          DOCUMENT ME!\r
1364    */\r
1365   protected void clustalColour_actionPerformed()\r
1366   {\r
1367     SequenceGroup sg = getGroup();\r
1368     sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());\r
1369     refresh();\r
1370   }\r
1371 \r
1372   /**\r
1373    * DOCUMENT ME!\r
1374    * \r
1375    * @param e\r
1376    *          DOCUMENT ME!\r
1377    */\r
1378   protected void zappoColour_actionPerformed()\r
1379   {\r
1380     getGroup().cs = new ZappoColourScheme();\r
1381     refresh();\r
1382   }\r
1383 \r
1384   /**\r
1385    * DOCUMENT ME!\r
1386    * \r
1387    * @param e\r
1388    *          DOCUMENT ME!\r
1389    */\r
1390   protected void taylorColour_actionPerformed()\r
1391   {\r
1392     getGroup().cs = new TaylorColourScheme();\r
1393     refresh();\r
1394   }\r
1395 \r
1396   /**\r
1397    * DOCUMENT ME!\r
1398    * \r
1399    * @param e\r
1400    *          DOCUMENT ME!\r
1401    */\r
1402   protected void hydrophobicityColour_actionPerformed()\r
1403   {\r
1404     getGroup().cs = new HydrophobicColourScheme();\r
1405     refresh();\r
1406   }\r
1407 \r
1408   /**\r
1409    * DOCUMENT ME!\r
1410    * \r
1411    * @param e\r
1412    *          DOCUMENT ME!\r
1413    */\r
1414   protected void helixColour_actionPerformed()\r
1415   {\r
1416     getGroup().cs = new HelixColourScheme();\r
1417     refresh();\r
1418   }\r
1419 \r
1420   /**\r
1421    * DOCUMENT ME!\r
1422    * \r
1423    * @param e\r
1424    *          DOCUMENT ME!\r
1425    */\r
1426   protected void strandColour_actionPerformed()\r
1427   {\r
1428     getGroup().cs = new StrandColourScheme();\r
1429     refresh();\r
1430   }\r
1431 \r
1432   /**\r
1433    * DOCUMENT ME!\r
1434    * \r
1435    * @param e\r
1436    *          DOCUMENT ME!\r
1437    */\r
1438   protected void turnColour_actionPerformed()\r
1439   {\r
1440     getGroup().cs = new TurnColourScheme();\r
1441     refresh();\r
1442   }\r
1443 \r
1444   /**\r
1445    * DOCUMENT ME!\r
1446    * \r
1447    * @param e\r
1448    *          DOCUMENT ME!\r
1449    */\r
1450   protected void buriedColour_actionPerformed()\r
1451   {\r
1452     getGroup().cs = new BuriedColourScheme();\r
1453     refresh();\r
1454   }\r
1455 \r
1456   /**\r
1457    * DOCUMENT ME!\r
1458    * \r
1459    * @param e\r
1460    *          DOCUMENT ME!\r
1461    */\r
1462   public void nucleotideMenuItem_actionPerformed()\r
1463   {\r
1464     getGroup().cs = new NucleotideColourScheme();\r
1465     refresh();\r
1466   }\r
1467 \r
1468   protected void purinePyrimidineColour_actionPerformed()\r
1469   {\r
1470     getGroup().cs = new PurinePyrimidineColourScheme();\r
1471     refresh();\r
1472   }\r
1473 \r
1474   /*\r
1475    * protected void covariationColour_actionPerformed() { getGroup().cs = new\r
1476    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }\r
1477    */\r
1478   /**\r
1479    * DOCUMENT ME!\r
1480    * \r
1481    * @param e\r
1482    *          DOCUMENT ME!\r
1483    */\r
1484   protected void abovePIDColour_actionPerformed()\r
1485   {\r
1486     SequenceGroup sg = getGroup();\r
1487     if (sg.cs == null)\r
1488     {\r
1489       return;\r
1490     }\r
1491 \r
1492     if (abovePIDColour.isSelected())\r
1493     {\r
1494       sg.cs.setConsensus(AAFrequency.calculate(\r
1495               sg.getSequences(ap.av.getHiddenRepSequences()),\r
1496               sg.getStartRes(), sg.getEndRes() + 1));\r
1497 \r
1498       int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()\r
1499               .getName());\r
1500 \r
1501       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
1502 \r
1503       SliderPanel.showPIDSlider();\r
1504     }\r
1505     else\r
1506     // remove PIDColouring\r
1507     {\r
1508       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
1509     }\r
1510 \r
1511     refresh();\r
1512   }\r
1513 \r
1514   /**\r
1515    * DOCUMENT ME!\r
1516    * \r
1517    * @param e\r
1518    *          DOCUMENT ME!\r
1519    */\r
1520   protected void userDefinedColour_actionPerformed(ActionEvent e)\r
1521   {\r
1522     SequenceGroup sg = getGroup();\r
1523 \r
1524     if (e.getSource().equals(userDefinedColour))\r
1525     {\r
1526       new UserDefinedColours(ap, sg);\r
1527     }\r
1528     else\r
1529     {\r
1530       UserColourScheme udc = (UserColourScheme) UserDefinedColours\r
1531               .getUserColourSchemes().get(e.getActionCommand());\r
1532 \r
1533       sg.cs = udc;\r
1534     }\r
1535     refresh();\r
1536   }\r
1537 \r
1538   /**\r
1539    * DOCUMENT ME!\r
1540    * \r
1541    * @param e\r
1542    *          DOCUMENT ME!\r
1543    */\r
1544   protected void PIDColour_actionPerformed()\r
1545   {\r
1546     SequenceGroup sg = getGroup();\r
1547     sg.cs = new PIDColourScheme();\r
1548     sg.cs.setConsensus(AAFrequency.calculate(\r
1549             sg.getSequences(ap.av.getHiddenRepSequences()),\r
1550             sg.getStartRes(), sg.getEndRes() + 1));\r
1551     refresh();\r
1552   }\r
1553 \r
1554   /**\r
1555    * DOCUMENT ME!\r
1556    * \r
1557    * @param e\r
1558    *          DOCUMENT ME!\r
1559    */\r
1560   protected void BLOSUM62Colour_actionPerformed()\r
1561   {\r
1562     SequenceGroup sg = getGroup();\r
1563 \r
1564     sg.cs = new Blosum62ColourScheme();\r
1565 \r
1566     sg.cs.setConsensus(AAFrequency.calculate(\r
1567             sg.getSequences(ap.av.getHiddenRepSequences()),\r
1568             sg.getStartRes(), sg.getEndRes() + 1));\r
1569 \r
1570     refresh();\r
1571   }\r
1572 \r
1573   /**\r
1574    * DOCUMENT ME!\r
1575    * \r
1576    * @param e\r
1577    *          DOCUMENT ME!\r
1578    */\r
1579   protected void noColourmenuItem_actionPerformed()\r
1580   {\r
1581     getGroup().cs = null;\r
1582     refresh();\r
1583   }\r
1584 \r
1585   /**\r
1586    * DOCUMENT ME!\r
1587    * \r
1588    * @param e\r
1589    *          DOCUMENT ME!\r
1590    */\r
1591   protected void conservationMenuItem_actionPerformed()\r
1592   {\r
1593     SequenceGroup sg = getGroup();\r
1594     if (sg.cs == null)\r
1595     {\r
1596       return;\r
1597     }\r
1598 \r
1599     if (conservationMenuItem.isSelected())\r
1600     {\r
1601       Conservation c = new Conservation(MessageManager.getString("label.group"),\r
1602               ResidueProperties.propHash, 3, sg.getSequences(ap.av\r
1603                       .getHiddenRepSequences()), sg.getStartRes(),\r
1604               sg.getEndRes() + 1);\r
1605 \r
1606       c.calculate();\r
1607       c.verdict(false, ap.av.getConsPercGaps());\r
1608 \r
1609       sg.cs.setConservation(c);\r
1610 \r
1611       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
1612       SliderPanel.showConservationSlider();\r
1613     }\r
1614     else\r
1615     // remove ConservationColouring\r
1616     {\r
1617       sg.cs.setConservation(null);\r
1618     }\r
1619 \r
1620     refresh();\r
1621   }\r
1622 \r
1623   public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)\r
1624   {\r
1625     SequenceGroup sg = getGroup();\r
1626     if (sg == null)\r
1627     {\r
1628       return;\r
1629     }\r
1630 \r
1631     AnnotationColourGradient acg = new AnnotationColourGradient(\r
1632             sequence.getAnnotation()[0], null,\r
1633             AnnotationColourGradient.NO_THRESHOLD);\r
1634 \r
1635     acg.setPredefinedColours(true);\r
1636     sg.cs = acg;\r
1637 \r
1638     refresh();\r
1639   }\r
1640 \r
1641   /**\r
1642    * DOCUMENT ME!\r
1643    * \r
1644    * @param e\r
1645    *          DOCUMENT ME!\r
1646    */\r
1647   protected void groupName_actionPerformed()\r
1648   {\r
1649 \r
1650     SequenceGroup sg = getGroup();\r
1651     EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
1652             sg.getDescription(), "       " + MessageManager.getString("label.group_name") + " ",\r
1653             MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),\r
1654             ap.alignFrame);\r
1655 \r
1656     if (!dialog.accept)\r
1657     {\r
1658       return;\r
1659     }\r
1660 \r
1661     sg.setName(dialog.getName());\r
1662     sg.setDescription(dialog.getDescription());\r
1663     refresh();\r
1664   }\r
1665 \r
1666   /**\r
1667    * Get selection group - adding it to the alignment if necessary.\r
1668    * \r
1669    * @return sequence group to operate on\r
1670    */\r
1671   SequenceGroup getGroup()\r
1672   {\r
1673     SequenceGroup sg = ap.av.getSelectionGroup();\r
1674     // this method won't add a new group if it already exists\r
1675     if (sg != null)\r
1676     {\r
1677       ap.av.getAlignment().addGroup(sg);\r
1678     }\r
1679 \r
1680     return sg;\r
1681   }\r
1682 \r
1683   /**\r
1684    * DOCUMENT ME!\r
1685    * \r
1686    * @param e\r
1687    *          DOCUMENT ME!\r
1688    */\r
1689   void sequenceName_actionPerformed()\r
1690   {\r
1691     EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
1692             sequence.getDescription(), "       " + MessageManager.getString("label.sequence_name") + " ",\r
1693             MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),\r
1694             ap.alignFrame);\r
1695 \r
1696     if (!dialog.accept)\r
1697     {\r
1698       return;\r
1699     }\r
1700 \r
1701     if (dialog.getName() != null)\r
1702     {\r
1703       if (dialog.getName().indexOf(" ") > -1)\r
1704       {\r
1705         JOptionPane.showMessageDialog(ap,\r
1706                 MessageManager.getString("label.spaces_converted_to_backslashes"),\r
1707                 MessageManager.getString("label.no_spaces_allowed_sequence_name"),\r
1708                 JOptionPane.WARNING_MESSAGE);\r
1709       }\r
1710 \r
1711       sequence.setName(dialog.getName().replace(' ', '_'));\r
1712       ap.paintAlignment(false);\r
1713     }\r
1714 \r
1715     sequence.setDescription(dialog.getDescription());\r
1716 \r
1717     ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
1718             .getSequences());\r
1719 \r
1720   }\r
1721 \r
1722   /**\r
1723    * DOCUMENT ME!\r
1724    * \r
1725    * @param e\r
1726    *          DOCUMENT ME!\r
1727    */\r
1728   void unGroupMenuItem_actionPerformed()\r
1729   {\r
1730     SequenceGroup sg = ap.av.getSelectionGroup();\r
1731     ap.av.getAlignment().deleteGroup(sg);\r
1732     ap.av.setSelectionGroup(null);\r
1733     refresh();\r
1734   }\r
1735   void createGroupMenuItem_actionPerformed()\r
1736   {\r
1737     getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this\r
1738     refresh();\r
1739   }\r
1740 \r
1741   /**\r
1742    * DOCUMENT ME!\r
1743    * \r
1744    * @param e\r
1745    *          DOCUMENT ME!\r
1746    */\r
1747   protected void outline_actionPerformed()\r
1748   {\r
1749     SequenceGroup sg = getGroup();\r
1750     Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),\r
1751             Color.BLUE);\r
1752 \r
1753     if (col != null)\r
1754     {\r
1755       sg.setOutlineColour(col);\r
1756     }\r
1757 \r
1758     refresh();\r
1759   }\r
1760 \r
1761   /**\r
1762    * DOCUMENT ME!\r
1763    * \r
1764    * @param e\r
1765    *          DOCUMENT ME!\r
1766    */\r
1767   public void showBoxes_actionPerformed()\r
1768   {\r
1769     getGroup().setDisplayBoxes(showBoxes.isSelected());\r
1770     refresh();\r
1771   }\r
1772 \r
1773   /**\r
1774    * DOCUMENT ME!\r
1775    * \r
1776    * @param e\r
1777    *          DOCUMENT ME!\r
1778    */\r
1779   public void showText_actionPerformed()\r
1780   {\r
1781     getGroup().setDisplayText(showText.isSelected());\r
1782     refresh();\r
1783   }\r
1784 \r
1785   /**\r
1786    * DOCUMENT ME!\r
1787    * \r
1788    * @param e\r
1789    *          DOCUMENT ME!\r
1790    */\r
1791   public void showColourText_actionPerformed()\r
1792   {\r
1793     getGroup().setColourText(showColourText.isSelected());\r
1794     refresh();\r
1795   }\r
1796 \r
1797   public void showLink(String url)\r
1798   {\r
1799     try\r
1800     {\r
1801       jalview.util.BrowserLauncher.openURL(url);\r
1802     } catch (Exception ex)\r
1803     {\r
1804       JOptionPane\r
1805               .showInternalMessageDialog(\r
1806                       Desktop.desktop,\r
1807                       MessageManager.getString("label.web_browser_not_found_unix"),\r
1808                       MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);\r
1809 \r
1810       ex.printStackTrace();\r
1811     }\r
1812   }\r
1813 \r
1814   void hideSequences(boolean representGroup)\r
1815   {\r
1816     SequenceGroup sg = ap.av.getSelectionGroup();\r
1817     if (sg == null || sg.getSize() < 1)\r
1818     {\r
1819       ap.av.hideSequence(new SequenceI[]\r
1820       { sequence });\r
1821       return;\r
1822     }\r
1823 \r
1824     ap.av.setSelectionGroup(null);\r
1825 \r
1826     if (representGroup)\r
1827     {\r
1828       ap.av.hideRepSequences(sequence, sg);\r
1829 \r
1830       return;\r
1831     }\r
1832 \r
1833     int gsize = sg.getSize();\r
1834     SequenceI[] hseqs;\r
1835 \r
1836     hseqs = new SequenceI[gsize];\r
1837 \r
1838     int index = 0;\r
1839     for (int i = 0; i < gsize; i++)\r
1840     {\r
1841       hseqs[index++] = sg.getSequenceAt(i);\r
1842     }\r
1843 \r
1844     ap.av.hideSequence(hseqs);\r
1845     // refresh(); TODO: ? needed ?\r
1846     ap.av.sendSelection();\r
1847   }\r
1848 \r
1849   public void copy_actionPerformed()\r
1850   {\r
1851     ap.alignFrame.copy_actionPerformed(null);\r
1852   }\r
1853 \r
1854   public void cut_actionPerformed()\r
1855   {\r
1856     ap.alignFrame.cut_actionPerformed(null);\r
1857   }\r
1858 \r
1859   void changeCase(ActionEvent e)\r
1860   {\r
1861     Object source = e.getSource();\r
1862     SequenceGroup sg = ap.av.getSelectionGroup();\r
1863 \r
1864     if (sg != null)\r
1865     {\r
1866       int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),\r
1867               sg.getEndRes() + 1);\r
1868 \r
1869       String description;\r
1870       int caseChange;\r
1871 \r
1872       if (source == toggle)\r
1873       {\r
1874         description = MessageManager.getString("label.toggle_case");\r
1875         caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
1876       }\r
1877       else if (source == upperCase)\r
1878       {\r
1879         description = MessageManager.getString("label.to_upper_case");\r
1880         caseChange = ChangeCaseCommand.TO_UPPER;\r
1881       }\r
1882       else\r
1883       {\r
1884         description = MessageManager.getString("label.to_lower_case");\r
1885         caseChange = ChangeCaseCommand.TO_LOWER;\r
1886       }\r
1887 \r
1888       ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,\r
1889               sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
1890               startEnd, caseChange);\r
1891 \r
1892       ap.alignFrame.addHistoryItem(caseCommand);\r
1893 \r
1894       ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
1895               .getSequences());\r
1896 \r
1897     }\r
1898   }\r
1899 \r
1900   public void outputText_actionPerformed(ActionEvent e)\r
1901   {\r
1902     CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
1903     cap.setForInput(null);\r
1904     Desktop.addInternalFrame(cap,\r
1905             MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);\r
1906 \r
1907     String[] omitHidden = null;\r
1908 \r
1909     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens\r
1910     // or we simply trust the user wants\r
1911     // wysiwig behaviour\r
1912     SequenceGroup sg = ap.av.getSelectionGroup();\r
1913     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());\r
1914     omitHidden = ap.av.getViewAsString(true);\r
1915     Alignment oal = new Alignment(ap.av.getSequenceSelection());\r
1916     AlignmentAnnotation[] nala = ap.av.getAlignment()\r
1917             .getAlignmentAnnotation();\r
1918     if (nala != null)\r
1919     {\r
1920       for (int i = 0; i < nala.length; i++)\r
1921       {\r
1922         AlignmentAnnotation na = nala[i];\r
1923         oal.addAnnotation(na);\r
1924       }\r
1925     }\r
1926     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
1927             oal, omitHidden, csel, sg));\r
1928     oal = null;\r
1929   }\r
1930 \r
1931   public void pdbFromFile_actionPerformed()\r
1932   {\r
1933     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
1934             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
1935     chooser.setFileView(new jalview.io.JalviewFileView());\r
1936     chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));\r
1937     chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));\r
1938 \r
1939     int value = chooser.showOpenDialog(null);\r
1940 \r
1941     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
1942     {\r
1943       String choice = chooser.getSelectedFile().getPath();\r
1944       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
1945       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,\r
1946               jalview.io.AppletFormatAdapter.FILE, sequence, true);\r
1947     }\r
1948 \r
1949   }\r
1950 \r
1951   public void enterPDB_actionPerformed()\r
1952   {\r
1953     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
1954             MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);\r
1955 \r
1956     if (id != null && id.length() > 0)\r
1957     {\r
1958       PDBEntry entry = new PDBEntry();\r
1959       entry.setId(id.toUpperCase());\r
1960       sequence.getDatasetSequence().addPDBId(entry);\r
1961     }\r
1962   }\r
1963 \r
1964   public void discoverPDB_actionPerformed()\r
1965   {\r
1966 \r
1967     final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]\r
1968     { sequence }\r
1969             : ap.av.getSequenceSelection());\r
1970     Thread discpdb = new Thread(new Runnable()\r
1971     {\r
1972       public void run()\r
1973       {\r
1974 \r
1975         new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)\r
1976                 .fetchDBRefs(false);\r
1977       }\r
1978 \r
1979     });\r
1980     discpdb.start();\r
1981   }\r
1982 \r
1983   public void sequenceFeature_actionPerformed()\r
1984   {\r
1985     SequenceGroup sg = ap.av.getSelectionGroup();\r
1986     if (sg == null)\r
1987     {\r
1988       return;\r
1989     }\r
1990 \r
1991     int rsize = 0, gSize = sg.getSize();\r
1992     SequenceI[] rseqs, seqs = new SequenceI[gSize];\r
1993     SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];\r
1994 \r
1995     for (int i = 0; i < gSize; i++)\r
1996     {\r
1997       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
1998       int end = sg.findEndRes(sg.getSequenceAt(i));\r
1999       if (start <= end)\r
2000       {\r
2001         seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();\r
2002         features[rsize] = new SequenceFeature(null, null, null, start, end,\r
2003                 "Jalview");\r
2004         rsize++;\r
2005       }\r
2006     }\r
2007     rseqs = new SequenceI[rsize];\r
2008     tfeatures = new SequenceFeature[rsize];\r
2009     System.arraycopy(seqs, 0, rseqs, 0, rsize);\r
2010     System.arraycopy(features, 0, tfeatures, 0, rsize);\r
2011     features = tfeatures;\r
2012     seqs = rseqs;\r
2013     if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
2014             features, true, ap))\r
2015     {\r
2016       ap.alignFrame.setShowSeqFeatures(true);\r
2017       ap.highlightSearchResults(null);\r
2018     }\r
2019   }\r
2020 \r
2021   public void textColour_actionPerformed()\r
2022   {\r
2023     SequenceGroup sg = getGroup();\r
2024     if (sg != null)\r
2025     {\r
2026       new TextColourChooser().chooseColour(ap, sg);\r
2027     }\r
2028   }\r
2029 \r
2030   public void colourByStructure(String pdbid)\r
2031   {\r
2032     Annotation[] anots = ap.av.getStructureSelectionManager()\r
2033             .colourSequenceFromStructure(sequence, pdbid);\r
2034 \r
2035     AlignmentAnnotation an = new AlignmentAnnotation("Structure",\r
2036             "Coloured by " + pdbid, anots);\r
2037 \r
2038     ap.av.getAlignment().addAnnotation(an);\r
2039     an.createSequenceMapping(sequence, 0, true);\r
2040     // an.adjustForAlignment();\r
2041     ap.av.getAlignment().setAnnotationIndex(an, 0);\r
2042 \r
2043     ap.adjustAnnotationHeight();\r
2044 \r
2045     sequence.addAlignmentAnnotation(an);\r
2046 \r
2047   }\r
2048 \r
2049   public void editSequence_actionPerformed(ActionEvent actionEvent)\r
2050   {\r
2051     SequenceGroup sg = ap.av.getSelectionGroup();\r
2052 \r
2053     if (sg != null)\r
2054     {\r
2055       if (sequence == null)\r
2056         sequence = (Sequence) sg.getSequenceAt(0);\r
2057 \r
2058       EditNameDialog dialog = new EditNameDialog(\r
2059               sequence.getSequenceAsString(sg.getStartRes(),\r
2060                       sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,\r
2061                       MessageManager.getString("label.edit_sequence"), ap.alignFrame);\r
2062 \r
2063       if (dialog.accept)\r
2064       {\r
2065         EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),\r
2066                 EditCommand.REPLACE, dialog.getName().replace(' ',\r
2067                         ap.av.getGapCharacter()),\r
2068                 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),\r
2069                 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());\r
2070 \r
2071         ap.alignFrame.addHistoryItem(editCommand);\r
2072 \r
2073         ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()\r
2074                 .getSequences());\r
2075       }\r
2076     }\r
2077   }\r
2078 \r
2079 }\r