help/html/releases.html

   1 <html>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   4  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 --!>
  19 <head>
  20 <title>Release History</title>
  21 </head>
  22 <body>
  23 <p><strong>Release History</strong></p>
  24 <table border="1">
  25         <tr>
  26                 <td width="60" nowrap>
  27                 <div align="center"><em><strong>Release</strong></em></div>
  28                 </td>
  29                 <td>
  30                 <div align="center"><em><strong>New Features</strong></em></div>
  31                 </td>
  32                 <td>
  33                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
  34                 </td>
  35         </tr>
  36         <tr>
  37
  38                 <td>
  39                 <div align="center"><strong>2.5</strong><br>
  40                 <em>30th April 2010</em></div>
  41                 </td>
  42                 <td>
  43                 <ul>
  44                         <li>URL links generated from description line for
  45                         regular-expression based URL links (applet and application)
  46                         <li>Non-positional feature URL links are shown in link menu</li>
  47                         <li>Linked viewing of nucleic acid sequences and structures</li>
  48                         <li>Automatic Scrolling option in View menu to display the
  49                         currently highlighted region of an alignment.</li>
  50                         <li>Order an alignment by sequence length, or using the average score or total feature count for each sequence.</li>
  51                         <li>Shading features by score or associated description</li>
  52                         <li>Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).</li>
  53                         <li>New hide/show options including Shift+Control+H to hide everything but the currently selected region.</li>
  54                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
  55                 </ul>
  56                 <em>Vamsas Capabilities</em>
  57                 <ul>
  58                         <li>Improved VAMSAS synchronization (jalview archive used to
  59                         preserve views, structures, and tree display settings)</li>
  60                         <li>Import of vamsas documents from disk or URL via command line</li>
  61                         <li>Sharing of selected regions between views and with other
  62                         VAMSAS applications (Experimental feature!)</li>
  63                         <li>Updated API to VAMSAS version 0.2</li>
  64                 </ul>
  65                 <em>Application</em>
  66                 <ul>
  67                         <li>Fetch DB References capabilities and UI expanded to support
  68                         retrieval from DAS sequence sources</li>
  69                         <li>Local DAS Sequence sources can be added via the command line
  70                         or via the Add local source dialog box.</li>
  71                         <li>DAS Dbref and DbxRef feature types are parsed as database
  72                         references and protein_name is parsed as description line (BioSapiens terms).</li>
  73                         <li>Enable or disable non-positional feature and database
  74                         references in sequence ID tooltip from View menu in application.</li>
  75         <!--                    <li>New hidden columns and rows and representatives capabilities
  76                         in annotations file (in progress - not yet fully implemented)</li> -->
  77                         <li>Group-associated consensus, sequence logos and conservation plots</li>
  78                         <li>Symbol distributions for each column can be exported and
  79                         visualized as sequence logos</li>
  80                         <li>Optionally scale multi-character column labels to fit within each column of annotation row<!-- todo for applet --></li>
  81                         <li>Optional automatic sort of associated alignment view when a
  82                         new tree is opened.</li>
  83                         <li>Jalview Java Console</li>
  84                         <li>New preference items for sequence ID tooltip and consensus annotation</li>
  85                         <li>Client to submit sequences and IDs to <a href="webServices/index.html#envision2">Envision2</a> Workflows</li>
  86                 </ul>
  87                 <em>Applet</em>
  88                 <ul>
  89                         <li>Middle button resizes annotation row height</li>
  90                         <li>New Parameters
  91                         <ul>
  92                          <li>sortByTree (true/false) - automatically sort the associated alignment view by the tree when a new tree is opened.</li>
  93                          <li>showTreeBootstraps (true/false) - show or hide branch bootstraps (default is to show them if available)</li>
  94                          <li>showTreeDistances (true/false) - show or hide branch lengths (default is to show them if available)</li>
  95                          <li>showUnlinkedTreeNodes (true/false) - indicate if unassociated nodes should be highlighted in the tree view</li>
  96                          <li>heightScale and widthScale (1.0 or more) - increase the height or width of a cell in the alignment grid relative to the current font size.</li>
  97                         </ul>
  98                         </li>
  99                         <li>Non-positional features displayed in sequence ID tooltip</li>
 100                 <li></li>
 101                 </ul>
 102                 <em>Other</em>
 103                 <ul>
 104                         <li>Features format: graduated colour definitions and
 105                         specification of feature scores</li>
 106                         <li>Alignment Annotations format: new keywords for group associated annotation (GROUP_REF) and annotation row display properties (ROW_PROPERTIES)</li>
 107                         <li>XML formats extended to support graduated feature colourschemes, group associated annotation, and profile visualization settings.</li>
 108                 </td>
 109                 <td>
 110                 <ul>
 111                         <li>Source field in GFF files parsed as feature source rather
 112                         than description</li>
 113                         <li>Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).</li>
 114                         <li>URL links generated for all feature links (bugfix)</li>
 115                         <li>Added URL embedding instructions to features file
 116                         documentation.</li>
 117                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 118                         peptide product</li>
 119                         <li>Match case switch in find dialog box works for both sequence
 120                         ID and sequence string and query strings do not have to be in upper
 121                         case to match case-insensitively.</li>
 122                         <li>AMSA files only contain first column of multi-character column annotation labels</li>
 123                         <li>Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)</li>
 124                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 125                         <li>Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.</li>
 126                         <li>Applet:
 127                         <ul>
 128                                 <li></li>
 129                         </ul>
 130                         </li>
 131                         <li>Application:
 132                         <ul>
 133                                 <li>Better handling of exceptions during sequence retrieval</li>
 134                                 <li>Dasobert generated non-positional feature URL link text
 135                                 excludes the start_end suffix (application)</li>
 136                                 <li>PDB files retrieved from URLs are cached properly</li>
 137                                 <li>Sequence description lines properly shared via VAMSAS</li>
 138                                 <li>Sequence fetcher fetches multiple records for all data
 139                                 sources</li>
 140                                 <li>Ensured that command line das feature retrieval completes
 141                                 before alignment figures are generated.</li>
 142                                 <li>Reduced time taken when opening file browser for first time.</li>
 143                                 <li>isAligned check prior to calculating tree, PCA or submitting an MSA to JNet now excludes hidden sequences.</li>
 144                         </ul>
 145                         </li>
 146                 </ul>
 147                 </td>
 148
 149         </tr>
 150         <tr>
 151                 <td>
 152                 <div align="center"><strong>2.4.0.b2</strong><br>
 153                 28/10/2009</div>
 154                 </td>
 155                 <td>
 156                 <ul>
 157                         <li>Experimental support for google analytics usage tracking.</li>
 158                         <li>Jalview privacy settings (user preferences and docs).</li>
 159                 </ul>
 160                 </td>
 161                 <td>
 162                 <ul>
 163                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 164                         <li>Exception when feature created from selection beyond length
 165                         of sequence.</li>
 166                         <li>Allow synthetic PDB files to be imported gracefully</li>
 167                         <li>Sequence associated annotation rows associate with all
 168                         sequences with a given id</li>
 169                         <li>Find function matches case-insensitively for sequence ID
 170                         string searches</li>
 171                         <li>Non-standard characters do not cause pairwise alignment to
 172                         fail with exception</li>
 173                 </ul>
 174                 <em>Application Issues</em>
 175                 <ul>
 176                         <li>Sequences are now validated against EMBL database</li>
 177                         <li>Sequence fetcher fetches multiple records for all data
 178                         sources</li>
 179                 </ul>
 180                 <em>InstallAnywhere Issues</em>
 181                 <ul>
 182                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 183                         installAnywhere mechanism)</li>
 184                         <li>Command line launching of JARs from InstallAnywhere version
 185                         (java class versioning error fixed)</li>
 186                 </ul>
 187                 </td>
 188         </tr>
 189         <tr>
 190                 <td>
 191
 192                 <div align="center"><strong>2.4</strong><br>
 193                 27/8/2008</div>
 194                 </td>
 195                 <td><em>User Interface</em>
 196                 <ul>
 197                         <li>Linked highlighting of codon and amino acid from translation
 198                         and protein products</li>
 199                         <li>Linked highlighting of structure associated with residue
 200                         mapping to codon position</li>
 201                         <li>Sequence Fetcher provides example accession numbers and
 202                         'clear' button</li>
 203                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 204                         <li>Extract score function to parse whitespace separated numeric
 205                         data in description line</li>
 206                         <li>Column labels in alignment annotation can be centred.</li>
 207                         <li>Tooltip for sequence associated annotation give name of
 208                         sequence</li>
 209                 </ul>
 210                 <em>Web Services and URL fetching</em>
 211                 <ul>
 212                         <li>JPred3 web service</li>
 213                         <li>Prototype sequence search client (no public services
 214                         available yet)</li>
 215                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 216                         <li>URL Links created for matching database cross references as
 217                         well as sequence ID</li>
 218                         <li>URL Links can be created using regular-expressions</li>
 219                 </ul>
 220                 <em>Sequence Database Connectivity</em>
 221                 <ul>
 222                         <li>Retrieval of cross-referenced sequences from other databases
 223                         </li>
 224                         <li>Generalised database reference retrieval and validation to
 225                         all fetchable databases</li>
 226                         <li>Fetch sequences from DAS sources supporting the sequence
 227                         command</li>
 228                 </ul>
 229                 <em>Import and Export</em>
 230                 <li>export annotation rows as CSV for spreadsheet import</li>
 231                 <li>Jalview projects record alignment dataset associations, EMBL
 232                 products, and cDNA sequence mappings</li>
 233                 <li>Sequence Group colour can be specified in Annotation File</li>
 234                 <li>Ad-hoc colouring of group in Annotation File using RGB
 235                 triplet as name of colourscheme</li>
 236                 </ul>
 237                 <em>VAMSAS Client capabilities (Experimental)</em>
 238                 <ul>
 239                         <li>treenode binding for VAMSAS tree exchange</li>
 240                         <li>local editing and update of sequences in VAMSAS alignments
 241                         (experimental)</li>
 242                         <li>Create new or select existing session to join</li>
 243                         <li>load and save of vamsas documents</li>
 244                 </ul>
 245                 <em>Application command line</em>
 246                 <ul>
 247                         <li>-tree parameter to open trees (introduced for passing from
 248                         applet)</li>
 249                         <li>-fetchfrom command line argument to specify nicknames of DAS
 250                         servers to query for alignment features</li>
 251                         <li>-dasserver command line argument to add new servers that are
 252                         also automatically queried for features</li>
 253                         <li>-groovy command line argument executes a given groovy script
 254                         after all input data has been loaded and parsed</li>
 255                 </ul>
 256                 <em>Applet-Application data exchange</em>
 257                 <ul>
 258                         <li>Trees passed as applet parameters can be passed to
 259                         application (when using &quot;View in full application&quot;)</li>
 260                 </ul>
 261                 <em>Applet Parameters</em>
 262                 <ul>
 263                         <li>feature group display control parameter</li>
 264                         <li>debug parameter</li>
 265                         <li>showbutton parameter</li>
 266                 </ul>
 267                 <em>Applet API methods</em>
 268                 <ul>
 269                         <li>newView public method</li>
 270                         <li>Window (current view) specific get/set public methods</li>
 271                         <li>Feature display control methods</li>
 272                         <li>get list of currently selected sequences</li>
 273                 </ul>
 274                 <em>New Jalview distribution features</em>
 275                 <ul>
 276                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 277                         <li>RELEASE file gives build properties for the latest Jalview
 278                         release.</li>
 279                         <li>Java 1.1 Applet build made easier and donotobfuscate
 280                         property controls execution of obfuscator</li>
 281                         <li>Build target for generating source distribution</li>
 282                         <li>Debug flag for javacc</li>
 283                         <li>.jalview_properties file is documented (slightly) in
 284                         jalview.bin.Cache</li>
 285                         <li>Continuous Build Integration for stable and development
 286                         version of Application, Applet and source distribution</li>
 287                 </ul>
 288
 289                 </td>
 290                 <td>
 291                 <ul>
 292                         <li>selected region output includes visible annotations (for
 293                         certain formats)</li>
 294                         <li>edit label/displaychar contains existing label/char for
 295                         editing</li>
 296                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 297                         <li>shorter peptide product names from EMBL records</li>
 298                         <li>Newick string generator makes compact representations</li>
 299                         <li>bootstrap values parsed correctly for tree files with
 300                         comments</li>
 301                         <li>pathological filechooser bug avoided by not allowing
 302                         filenames containing a ':'</li>
 303                         <li>Fixed exception when parsing GFF files containing global
 304                         sequence features</li>
 305                         <li>Alignment datasets are finalized only when number of
 306                         references from alignment sequences goes to zero</li>
 307                         <li>Close of tree branch colour box without colour selection
 308                         causes cascading exceptions</li>
 309                         <li>occasional negative imgwidth exceptions</li>
 310                         <li>better reporting of non-fatal warnings to user when file
 311                         parsing fails.</li>
 312                         <li>Save works when Jalview project is default format</li>
 313                         <li>Save as dialog opened if current alignment format is not a
 314                         valid output format</li>
 315                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 316                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 317                         <li>error messages passed up and output when data read fails</li>
 318                         <li>edit undo recovers previous dataset sequence when sequence
 319                         is edited</li>
 320                         <li>allow PDB files without pdb ID HEADER lines (like those
 321                         generated by MODELLER) to be read in properly</li>
 322                         <li>allow reading of JPred concise files as a normal filetype</li>
 323                         <li>Stockholm annotation parsing and alignment properties import
 324                         fixed for PFAM records</li>
 325                         <li>Structure view windows have correct name in Desktop window
 326                         list</li>
 327                         <li>annotation consisting of sequence associated scores can be
 328                         read and written correctly to annotation file</li>
 329                         <li>Aligned cDNA translation to aligned peptide works correctly
 330                         </li>
 331                         <li>Fixed display of hidden sequence markers and non-italic font
 332                         for representatives in Applet</li>
 333                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 334                         <li>Newly shown features appear at top of stack (in Applet)</li>
 335                         <li>Annotations added via parameter not drawn properly due to
 336                         null pointer exceptions</li>
 337                         <li>Secondary structure lines are drawn starting from first
 338                         column of alignment</li>
 339                         <li>Uniprot XML import updated for new schema release in July
 340                         2008</li>
 341                         <li>Sequence feature to sequence ID match for Features file is
 342                         case-insensitive</li>
 343                         <li>Sequence features read from Features file appended to all
 344                         sequences with matching IDs</li>
 345                         <li>PDB structure coloured correctly for associated views
 346                         containing a sub-sequence</li>
 347                         <li>PDB files can be retrieved by applet from Jar files</li>
 348                         <li>feature and annotation file applet parameters referring to
 349                         different directories are retrieved correctly</li>
 350                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 351                         <li>Fixed application hang whilst waiting for splash-screen
 352                         version check to complete</li>
 353                         <li>Applet properly URLencodes input parameter values when
 354                         passing them to the launchApp service</li>
 355                         <li>display name and local features preserved in results
 356                         retrieved from web service</li>
 357                         <li>Visual delay indication for sequence retrieval and sequence
 358                         fetcher initialisation</li>
 359                         <li>updated Application to use DAS 1.53e version of dasobert DAS
 360                         client</li>
 361                         <li>Re-instated Full AMSA support and .amsa file association</li>
 362                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
 363                         sequences</li>
 364                 </ul>
 365                 </td>
 366         </tr>
 367         <tr>
 368                 <td>
 369                 <div align="center"><strong>2.3</strong><br>
 370                 9/5/07</div>
 371                 </td>
 372                 <td>
 373                 <ul>
 374                         <li>Jmol 11.0.2 integration</li>
 375                         <li>PDB views stored in Jalview XML files</li>
 376                         <li>Slide sequences</li>
 377                         <li>Edit sequence in place</li>
 378                         <li>EMBL CDS features</li>
 379                         <li>DAS Feature mapping</li>
 380                         <li>Feature ordering</li>
 381                         <li>Alignment Properties</li>
 382                         <li>Annotation Scores</li>
 383                         <li>Sort by scores</li>
 384                         <li>Feature/annotation editing in applet</li>
 385                 </ul>
 386                 </td>
 387                 <td>
 388                 <ul>
 389                         <li>Headless state operation in 2.2.1</li>
 390                         <li>Incorrect and unstable DNA pairwise alignment</li>
 391                         <li>Cut and paste of sequences with annotation</li>
 392                         <li>Feature group display state in XML</li>
 393                         <li>Feature ordering in XML</li>
 394                         <li>blc file iteration selection using filename # suffix</li>
 395                         <li>Stockholm alignment properties</li>
 396                         <li>Stockhom alignment secondary structure annotation</li>
 397                         <li>2.2.1 applet had no feature transparency</li>
 398                         <li>Number pad keys can be used in cursor mode</li>
 399                         <li>Structure Viewer mirror image resolved</li>
 400                 </ul>
 401                 </td>
 402
 403         </tr>
 404         <tr>
 405                 <td>
 406                 <div align="center"><strong>2.2.1</strong><br>
 407                 12/2/07</div>
 408                 </td>
 409                 <td>
 410                 <ul>
 411                         <li>Non standard characters can be read and displayed
 412                         <li>Annotations/Features can be imported/exported to the applet
 413                         via textbox
 414                         <li>Applet allows editing of sequence/annotation/group name
 415                         &amp; description
 416                         <li>Preference setting to display sequence name in italics
 417                         <li>Annotation file format extended to allow Sequence_groups to
 418                         be defined
 419                         <li>Default opening of alignment overview panel can be specified
 420                         in preferences
 421                         <li>PDB residue numbering annotation added to associated
 422                         sequences
 423                 </ul>
 424                 </td>
 425                 <td>
 426                 <ul>
 427                         <li>Applet crash under certain Linux OS with Java 1.6 installed
 428                         <li>Annotation file export / import bugs fixed
 429                         <li>PNG / EPS image output bugs fixed
 430                 </ul>
 431                 </td>
 432         </tr>
 433         <tr>
 434                 <td>
 435                 <div align="center"><strong>2.2</strong><br>
 436                 27/11/06</div>
 437                 </td>
 438                 <td>
 439                 <ul>
 440                         <li>Multiple views on alignment
 441                         <li>Sequence feature editing
 442                         <li>&quot;Reload&quot; alignment
 443                         <li>&quot;Save&quot; to current filename
 444                         <li>Background dependent text colour
 445                         <li>Right align sequence ids
 446                         <li>User-defined lower case residue colours
 447                         <li>Format Menu
 448                         <li>Select Menu
 449                         <li>Menu item accelerator keys
 450                         <li>Control-V pastes to current alignment
 451                         <li>Cancel button for DAS Feature Fetching
 452                         <li>PCA and PDB Viewers zoom via mouse roller
 453                         <li>User-defined sub-tree colours and sub-tree selection
 454                         <li>'New Window' button on the 'Output to Text box'
 455                 </ul>
 456                 </td>
 457                 <td>
 458                 <ul>
 459                         <li>New memory efficient Undo/Redo System
 460                         <li>Optimised symbol lookups and conservation/consensus
 461                         calculations
 462                         <li>Region Conservation/Consensus recalculated after edits
 463                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
 464                         alignment)
 465                         <li>Slowed DAS Feature Fetching for increased robustness.
 466                         <li>Made angle brackets in ASCII feature descriptions display
 467                         correctly
 468                         <li>Re-instated Zoom function for PCA
 469                         <li>Sequence descriptions conserved in web service analysis
 470                         results
 471                         <li>Uniprot ID discoverer uses any word separated by &#8739;
 472                         <li>WsDbFetch query/result association resolved
 473                         <li>Tree leaf to sequence mapping improved
 474                         <li>Smooth fonts switch moved to FontChooser dialog box.
 475                 </ul>
 476                 </td>
 477         </tr>
 478         <tr>
 479                 <td>
 480                 <div align="center"><strong>2.1.1</strong><br>
 481                 12/9/06</div>
 482                 </td>
 483                 <td>
 484                 <ul>
 485                         <li>Copy consensus sequence to clipboard</li>
 486                 </ul>
 487                 </td>
 488                 <td>
 489                 <ul>
 490                         <li>Image output - rightmost residues are rendered if sequence
 491                         id panel has been resized</li>
 492                         <li>Image output - all offscreen group boundaries are rendered</li>
 493                         <li>Annotation files with sequence references - all elements in
 494                         file are relative to sequence position</li>
 495                         <li>Mac Applet users can use Alt key for group editing</li>
 496                 </ul>
 497                 </td>
 498         </tr>
 499         <tr>
 500                 <td>
 501                 <div align="center"><strong>2.1</strong><br>
 502                 22/8/06</div>
 503                 </td>
 504                 <td>
 505                 <ul>
 506                         <li>MAFFT Multiple Alignment in default Web Service list</li>
 507                         <li>DAS Feature fetching</li>
 508                         <li>Hide sequences and columns</li>
 509                         <li>Export Annotations and Features</li>
 510                         <li>GFF file reading / writing</li>
 511                         <li>Associate structures with sequences from local PDB files</li>
 512                         <li>Add sequences to exisiting alignment</li>
 513                         <li>Recently opened files / URL lists</li>
 514                         <li>Applet can launch the full application</li>
 515                         <li>Applet has transparency for features (Java 1.2 required)</li>
 516                         <li>Applet has user defined colours parameter</li>
 517                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
 518                 </ul>
 519                 </td>
 520                 <td>
 521                 <ul>
 522                         <li>Redundancy Panel reinstalled in the Applet</li>
 523                         <li>Monospaced font - EPS / rescaling bug fixed</li>
 524                         <li>Annotation files with sequence references bug fixed</li>
 525                 </ul>
 526                 </td>
 527         </tr>
 528         <tr>
 529                 <td>
 530                 <div align="center"><strong>2.08.1</strong><br>
 531                 2/5/06</div>
 532                 </td>
 533                 <td>
 534                 <ul>
 535                         <li>Change case of selected region from Popup menu</li>
 536                         <li>Choose to match case when searching</li>
 537                         <li>Middle mouse button and mouse movement can compress / expand
 538                         the visible width and height of the alignment</li>
 539                 </ul>
 540                 </td>
 541                 <td>
 542                 <ul>
 543                         <li>Annotation Panel displays complete JNet results</li>
 544                 </ul>
 545                 </td>
 546         </tr>
 547         <tr>
 548                 <td>
 549                 <div align="center"><strong>2.08b</strong><br>
 550                 18/4/06</div>
 551                 </td>
 552                 <td>&nbsp;</td>
 553                 <td>
 554                 <ul>
 555                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
 556                         <li>Righthand label on wrapped alignments shows correct value</li>
 557                 </ul>
 558                 </td>
 559         </tr>
 560         <tr>
 561                 <td>
 562                 <div align="center"><strong>2.08</strong><br>
 563                 10/4/06</div>
 564                 </td>
 565                 <td>
 566                 <ul>
 567                         <li>Editing can be locked to the selection area</li>
 568                         <li>Keyboard editing</li>
 569                         <li>Create sequence features from searches</li>
 570                         <li>Precalculated annotations can be loaded onto alignments</li>
 571                         <li>Features file allows grouping of features</li>
 572                         <li>Annotation Colouring scheme added</li>
 573                         <li>Smooth fonts off by default - Faster rendering</li>
 574                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
 575                 </ul>
 576                 </td>
 577                 <td>
 578                 <ul>
 579                         <li>Drag &amp; Drop fixed on Linux</li>
 580                         <li>Jalview Archive file faster to load/save, sequence
 581                         descriptions saved.</li>
 582                 </ul>
 583                 </td>
 584         </tr>
 585         <tr>
 586                 <td>
 587                 <div align="center"><strong>2.07</strong><br>
 588                 12/12/05</div>
 589                 </td>
 590                 <td>
 591                 <ul>
 592                         <li>PDB Structure Viewer enhanced</li>
 593                         <li>Sequence Feature retrieval and display enhanced</li>
 594                         <li>Choose to output sequence start-end after sequence name for
 595                         file output</li>
 596                         <li>Sequence Fetcher WSDBFetch@EBI</li>
 597                         <li>Applet can read feature files, PDB files and can be used for
 598                         HTML form input</li>
 599                 </ul>
 600                 </td>
 601                 <td>
 602                 <ul>
 603                         <li>HTML output writes groups and features</li>
 604                         <li>Group editing is Control and mouse click</li>
 605                         <li>File IO bugs</li>
 606                 </ul>
 607                 </td>
 608         </tr>
 609         <tr>
 610                 <td>
 611                 <div align="center"><strong>2.06</strong><br>
 612                 28/9/05</div>
 613                 </td>
 614                 <td>
 615                 <ul>
 616                         <li>View annotations in wrapped mode</li>
 617                         <li>More options for PCA viewer</li>
 618                 </ul>
 619                 </td>
 620                 <td>
 621                 <ul>
 622                         <li>GUI bugs resolved</li>
 623                         <li>Runs with -nodisplay from command line</li>
 624                 </ul>
 625                 </td>
 626         </tr>
 627         <tr>
 628                 <td height="63">
 629                 <div align="center"><strong>2.05b</strong><br>
 630                 15/9/05</div>
 631                 </td>
 632                 <td>
 633                 <ul>
 634                         <li>Choose EPS export as lineart or text</li>
 635                         <li>Jar files are executable</li>
 636                         <li>Can read in Uracil - maps to unknown residue</li>
 637                 </ul>
 638                 </td>
 639                 <td>
 640                 <ul>
 641                         <li>Known OutOfMemory errors give warning message</li>
 642                         <li>Overview window calculated more efficiently</li>
 643                         <li>Several GUI bugs resolved</li>
 644                 </ul>
 645                 </td>
 646         </tr>
 647         <tr>
 648                 <td>
 649                 <div align="center"><strong>2.05</strong><br>
 650                 30/8/05</div>
 651                 </td>
 652                 <td>
 653                 <ul>
 654                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
 655                 </ul>
 656                 </td>
 657                 <td>
 658                 <ul>
 659                         <li>Several GUI bugs resolved</li>
 660                 </ul>
 661                 </td>
 662         </tr>
 663         <tr>
 664                 <td>
 665                 <div align="center"><strong>2.04</strong><br>
 666                 24/8/05</div>
 667                 </td>
 668                 <td>
 669                 <ul>
 670                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
 671                 </ul>
 672                 </td>
 673                 <td>
 674                 <ul>
 675                         <li>Improved JPred client reliability</li>
 676                         <li>Improved loading of Jalview files</li>
 677                 </ul>
 678                 </td>
 679         </tr>
 680         <tr>
 681                 <td>
 682                 <div align="center"><strong>2.03</strong><br>
 683                 18/8/05</div>
 684                 </td>
 685                 <td>
 686                 <ul>
 687                         <li>Set Proxy server name and port in preferences</li>
 688                         <li>Multiple URL links from sequence ids</li>
 689                         <li>User Defined Colours can have a scheme name and added to
 690                         Colour Menu</li>
 691                         <li>Choose to ignore gaps in consensus calculation</li>
 692                         <li>Unix users can set default web browser</li>
 693                         <li>Runs without GUI for batch processing</li>
 694                         <li>Dynamically generated Web Service Menus</li>
 695                 </ul>
 696                 </td>
 697                 <td>
 698                 <ul>
 699                         <li>InstallAnywhere download for Sparc Solaris</li>
 700                 </ul>
 701                 </td>
 702         </tr>
 703         <tr>
 704                 <td>
 705                 <div align="center"><strong>2.02</strong><br>
 706                 18/7/05</div>
 707                 </td>
 708                 <td>&nbsp;</td>
 709                 <td>
 710                 <ul>
 711                         <li>Copy &amp; Paste order of sequences maintains alignment
 712                         order.</li>
 713                 </ul>
 714                 </td>
 715         </tr>
 716         <tr>
 717                 <td>
 718                 <div align="center"><strong>2.01</strong><br>
 719                 12/7/05</div>
 720                 </td>
 721                 <td>
 722                 <ul>
 723                         <li>Use delete key for deleting selection.</li>
 724                         <li>Use Mouse wheel to scroll sequences.</li>
 725                         <li>Help file updated to describe how to add alignment
 726                         annotations.</li>
 727                         <li>Version and build date written to build properties file.</li>
 728                         <li>InstallAnywhere installation will check for updates at
 729                         launch of Jalview.</li>
 730                 </ul>
 731                 </td>
 732                 <td>
 733                 <ul>
 734                         <li>Delete gaps bug fixed.</li>
 735                         <li>FileChooser sorts columns.</li>
 736                         <li>Can remove groups one by one.</li>
 737                         <li>Filechooser icons installed.</li>
 738                         <li>Finder ignores return character when searching. Return key
 739                         will initiate a search.<br>
 740                         </li>
 741                 </ul>
 742                 </td>
 743         </tr>
 744         <tr>
 745                 <td>
 746                 <div align="center"><strong>2.0</strong><br>
 747                 20/6/05</div>
 748                 </td>
 749                 <td>
 750                 <ul>
 751                         <li>New codebase</li>
 752                 </ul>
 753                 </td>
 754                 <td>&nbsp;</td>
 755         </tr>
 756 </table>
 757 <p>&nbsp;</p>
 758 </body>
 759 </html>