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  *
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   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  *
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  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                 <td>
  38                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
  39                 <em>X/7/2010</em></div>
  40                 </td>
  41                 <td>
  42                 <ul>
  43                         <li>Changed minimum Java version required for Jalview<br>
  44                         When used with Jmol, JalviewLite needs at least Java 1.5<br>
  45                         The application needs at least 1.6.</li>
  46                         <li>Updated embedded Jmol to series 12.XX<br><strong>See note about use of applet with Jmol</strong></li>
  47
  48                 </ul>
  49                 <em>Applet</em>
  50                 <ul>
  51                         <li></li>
  52                 </ul>
  53                 <em>Application</em>
  54                 <ul>
  55                         <li>Jalview 2 Web Services</li>
  56                         <li>Web Services configuration tab in preferences</li>
  57                 </ul>
  58                 </td>
  59                 <td></td>
  60         </tr>
  61         <tr>
  62                 <td>
  63                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
  64                 <em>14/6/2010</em></div>
  65                 </td>
  66                 <td></td>
  67                 <td>
  68                 <ul>
  69                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
  70                         </li>
  71                         <li>clustalx colourscheme colours Ds preferentially when both
  72                         D+E are present in over 50% of the column</li>
  73                         <li>nucleic acid structures retrieved from PDB do not import
  74                         correctly</li>
  75                         <li>More columns get selected than were clicked on when a number
  76                         of columns are hidden</li>
  77                         <li>annotation label popup menu not providing correct
  78                         add/hide/show options when rows are hidden or none are present</li>
  79                         <li>Stockholm format shown in list of readable formats, and
  80                         parser copes better with alignments from RFAM.</li>
  81                         <li>CSV output of consensus only includes the percentage of all
  82                         symbols if sequence logo display is enabled</li>
  83
  84                 </ul>
  85                 <em>Applet</em>
  86                 <ul>
  87                         <li>annotation panel disappears when annotation is
  88                         hidden/removed</li>
  89                 </ul>
  90                 <em>Application</em>
  91                 <ul>
  92                         <li>Alignment view not redrawn properly when new alignment
  93                         opened where annotation panel is visible but no annotations are
  94                         present on alignment</li>
  95                         <li>pasted region containing hidden columns is incorrectly
  96                         displayed in new alignment window</li>
  97                         <li>Jalview slow to complete operations when stdout is flooded
  98                         (fix is to close the Jalview console)</li>
  99                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 100                         selected Rregions menu item.</li>
 101                         <li>inconsistent group submenu and Format submenu entry 'Un' or
 102                         'Non'conserved</li>
 103                         <li>Sequence feature settings are being shared by multiple
 104                         distinct alignments</li>
 105                         <li>group annotation not recreated when tree partition is
 106                         changed</li>
 107                         <li>double click on group annotation to select sequences does
 108                         not propagate to associated trees</li>
 109                         <li>Mac OSX specific issues:
 110                         <ul>
 111                                 <li>exception raised when mouse clicked on desktop window
 112                                 background</li>
 113                                 <li>Desktop menu placed on menu bar and application name set
 114                                 correctly</li>
 115                                 <li>sequence feature settings not wide enough for the save
 116                                 feature colourscheme button</li>
 117                         </ul>
 118                         </li>
 119                 </ul>
 120                 </td>
 121         </tr>
 122         <tr>
 123
 124                 <td>
 125                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 126                 <em>30/4/2010</em></div>
 127                 </td>
 128                 <td><em>New Capabilities</em>
 129                 <ul>
 130                         <li>URL links generated from description line for
 131                         regular-expression based URL links (applet and application)
 132                         <li>Non-positional feature URL links are shown in link menu</li>
 133                         <li>Linked viewing of nucleic acid sequences and structures</li>
 134                         <li>Automatic Scrolling option in View menu to display the
 135                         currently highlighted region of an alignment.</li>
 136                         <li>Order an alignment by sequence length, or using the average
 137                         score or total feature count for each sequence.</li>
 138                         <li>Shading features by score or associated description</li>
 139                         <li>Subdivide alignment and groups based on identity of selected
 140                         subsequence (Make Groups from Selection).</li>
 141                         <li>New hide/show options including Shift+Control+H to hide
 142                         everything but the currently selected region.</li>
 143                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 144                 </ul>
 145                 <em>Application</em>
 146                 <ul>
 147                         <li>Fetch DB References capabilities and UI expanded to support
 148                         retrieval from DAS sequence sources</li>
 149                         <li>Local DAS Sequence sources can be added via the command line
 150                         or via the Add local source dialog box.</li>
 151                         <li>DAS Dbref and DbxRef feature types are parsed as database
 152                         references and protein_name is parsed as description line (BioSapiens
 153                         terms).</li>
 154                         <li>Enable or disable non-positional feature and database
 155                         references in sequence ID tooltip from View menu in application.</li>
 156                         <!--                    <li>New hidden columns and rows and representatives capabilities
 157                         in annotations file (in progress - not yet fully implemented)</li> -->
 158                         <li>Group-associated consensus, sequence logos and conservation
 159                         plots</li>
 160                         <li>Symbol distributions for each column can be exported and
 161                         visualized as sequence logos</li>
 162                         <li>Optionally scale multi-character column labels to fit within
 163                         each column of annotation row<!-- todo for applet --></li>
 164                         <li>Optional automatic sort of associated alignment view when a
 165                         new tree is opened.</li>
 166                         <li>Jalview Java Console</li>
 167                         <li>Better placement of desktop window when moving between
 168                         different screens.</li>
 169                         <li>New preference items for sequence ID tooltip and consensus
 170                         annotation</li>
 171                         <li>Client to submit sequences and IDs to <a
 172                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 173                         <li><em>Vamsas Capabilities</em>
 174                         <ul>
 175                                 <li>Improved VAMSAS synchronization (jalview archive used to
 176                                 preserve views, structures, and tree display settings)</li>
 177                                 <li>Import of vamsas documents from disk or URL via command
 178                                 line</li>
 179                                 <li>Sharing of selected regions between views and with other
 180                                 VAMSAS applications (Experimental feature!)</li>
 181                                 <li>Updated API to VAMSAS version 0.2</li>
 182                         </ul>
 183                         </li>
 184                 </ul>
 185                 <em>Applet</em>
 186                 <ul>
 187                         <li>Middle button resizes annotation row height</li>
 188                         <li>New Parameters
 189                         <ul>
 190                                 <li>sortByTree (true/false) - automatically sort the associated
 191                                 alignment view by the tree when a new tree is opened.</li>
 192                                 <li>showTreeBootstraps (true/false) - show or hide branch
 193                                 bootstraps (default is to show them if available)</li>
 194                                 <li>showTreeDistances (true/false) - show or hide branch
 195                                 lengths (default is to show them if available)</li>
 196                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
 197                                 unassociated nodes should be highlighted in the tree view</li>
 198                                 <li>heightScale and widthScale (1.0 or more) - increase the
 199                                 height or width of a cell in the alignment grid relative to the
 200                                 current font size.</li>
 201                         </ul>
 202                         </li>
 203                         <li>Non-positional features displayed in sequence ID tooltip</li>
 204                 </ul>
 205                 <em>Other</em>
 206                 <ul>
 207                         <li>Features format: graduated colour definitions and
 208                         specification of feature scores</li>
 209                         <li>Alignment Annotations format: new keywords for group
 210                         associated annotation (GROUP_REF) and annotation row display
 211                         properties (ROW_PROPERTIES)</li>
 212                         <li>XML formats extended to support graduated feature
 213                         colourschemes, group associated annotation, and profile visualization
 214                         settings.</li>
 215                 </td>
 216                 <td>
 217                 <ul>
 218                         <li>Source field in GFF files parsed as feature source rather
 219                         than description</li>
 220                         <li>Non-positional features are now included in sequence feature
 221                         and gff files (controlled via non-positional feature visibility in
 222                         tooltip).</li>
 223                         <li>URL links generated for all feature links (bugfix)</li>
 224                         <li>Added URL embedding instructions to features file
 225                         documentation.</li>
 226                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 227                         peptide product</li>
 228                         <li>Match case switch in find dialog box works for both sequence
 229                         ID and sequence string and query strings do not have to be in upper
 230                         case to match case-insensitively.</li>
 231                         <li>AMSA files only contain first column of multi-character
 232                         column annotation labels</li>
 233                         <li>Jalview Annotation File generation/parsing consistent with
 234                         documentation (e.g. Stockholm annotation can be exported and
 235                         re-imported)</li>
 236                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 237                         <li>Find incrementally searches ID string matches as well as
 238                         subsequence matches, and correctly reports total number of both.</li>
 239                         <li>Application:
 240                         <ul>
 241                                 <li>Better handling of exceptions during sequence retrieval</li>
 242                                 <li>Dasobert generated non-positional feature URL link text
 243                                 excludes the start_end suffix</li>
 244                                 <li>DAS feature and source retrieval buttons disabled when
 245                                 fetch or registry operations in progress.</li>
 246                                 <li>PDB files retrieved from URLs are cached properly</li>
 247                                 <li>Sequence description lines properly shared via VAMSAS</li>
 248                                 <li>Sequence fetcher fetches multiple records for all data
 249                                 sources</li>
 250                                 <li>Ensured that command line das feature retrieval completes
 251                                 before alignment figures are generated.</li>
 252                                 <li>Reduced time taken when opening file browser for first
 253                                 time.</li>
 254                                 <li>isAligned check prior to calculating tree, PCA or
 255                                 submitting an MSA to JNet now excludes hidden sequences.</li>
 256                                 <li>User defined group colours properly recovered from Jalview
 257                                 projects.</li>
 258                         </ul>
 259                         </li>
 260                 </ul>
 261                 </td>
 262
 263         </tr>
 264         <tr>
 265                 <td>
 266                 <div align="center"><strong>2.4.0.b2</strong><br>
 267                 28/10/2009</div>
 268                 </td>
 269                 <td>
 270                 <ul>
 271                         <li>Experimental support for google analytics usage tracking.</li>
 272                         <li>Jalview privacy settings (user preferences and docs).</li>
 273                 </ul>
 274                 </td>
 275                 <td>
 276                 <ul>
 277                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 278                         <li>Exception when feature created from selection beyond length
 279                         of sequence.</li>
 280                         <li>Allow synthetic PDB files to be imported gracefully</li>
 281                         <li>Sequence associated annotation rows associate with all
 282                         sequences with a given id</li>
 283                         <li>Find function matches case-insensitively for sequence ID
 284                         string searches</li>
 285                         <li>Non-standard characters do not cause pairwise alignment to
 286                         fail with exception</li>
 287                 </ul>
 288                 <em>Application Issues</em>
 289                 <ul>
 290                         <li>Sequences are now validated against EMBL database</li>
 291                         <li>Sequence fetcher fetches multiple records for all data
 292                         sources</li>
 293                 </ul>
 294                 <em>InstallAnywhere Issues</em>
 295                 <ul>
 296                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 297                         installAnywhere mechanism)</li>
 298                         <li>Command line launching of JARs from InstallAnywhere version
 299                         (java class versioning error fixed)</li>
 300                 </ul>
 301                 </td>
 302         </tr>
 303         <tr>
 304                 <td>
 305
 306                 <div align="center"><strong>2.4</strong><br>
 307                 27/8/2008</div>
 308                 </td>
 309                 <td><em>User Interface</em>
 310                 <ul>
 311                         <li>Linked highlighting of codon and amino acid from translation
 312                         and protein products</li>
 313                         <li>Linked highlighting of structure associated with residue
 314                         mapping to codon position</li>
 315                         <li>Sequence Fetcher provides example accession numbers and
 316                         'clear' button</li>
 317                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 318                         <li>Extract score function to parse whitespace separated numeric
 319                         data in description line</li>
 320                         <li>Column labels in alignment annotation can be centred.</li>
 321                         <li>Tooltip for sequence associated annotation give name of
 322                         sequence</li>
 323                 </ul>
 324                 <em>Web Services and URL fetching</em>
 325                 <ul>
 326                         <li>JPred3 web service</li>
 327                         <li>Prototype sequence search client (no public services
 328                         available yet)</li>
 329                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 330                         <li>URL Links created for matching database cross references as
 331                         well as sequence ID</li>
 332                         <li>URL Links can be created using regular-expressions</li>
 333                 </ul>
 334                 <em>Sequence Database Connectivity</em>
 335                 <ul>
 336                         <li>Retrieval of cross-referenced sequences from other databases
 337                         </li>
 338                         <li>Generalised database reference retrieval and validation to
 339                         all fetchable databases</li>
 340                         <li>Fetch sequences from DAS sources supporting the sequence
 341                         command</li>
 342                 </ul>
 343                 <em>Import and Export</em>
 344                 <li>export annotation rows as CSV for spreadsheet import</li>
 345                 <li>Jalview projects record alignment dataset associations, EMBL
 346                 products, and cDNA sequence mappings</li>
 347                 <li>Sequence Group colour can be specified in Annotation File</li>
 348                 <li>Ad-hoc colouring of group in Annotation File using RGB
 349                 triplet as name of colourscheme</li>
 350                 </ul>
 351                 <em>VAMSAS Client capabilities (Experimental)</em>
 352                 <ul>
 353                         <li>treenode binding for VAMSAS tree exchange</li>
 354                         <li>local editing and update of sequences in VAMSAS alignments
 355                         (experimental)</li>
 356                         <li>Create new or select existing session to join</li>
 357                         <li>load and save of vamsas documents</li>
 358                 </ul>
 359                 <em>Application command line</em>
 360                 <ul>
 361                         <li>-tree parameter to open trees (introduced for passing from
 362                         applet)</li>
 363                         <li>-fetchfrom command line argument to specify nicknames of DAS
 364                         servers to query for alignment features</li>
 365                         <li>-dasserver command line argument to add new servers that are
 366                         also automatically queried for features</li>
 367                         <li>-groovy command line argument executes a given groovy script
 368                         after all input data has been loaded and parsed</li>
 369                 </ul>
 370                 <em>Applet-Application data exchange</em>
 371                 <ul>
 372                         <li>Trees passed as applet parameters can be passed to
 373                         application (when using &quot;View in full application&quot;)</li>
 374                 </ul>
 375                 <em>Applet Parameters</em>
 376                 <ul>
 377                         <li>feature group display control parameter</li>
 378                         <li>debug parameter</li>
 379                         <li>showbutton parameter</li>
 380                 </ul>
 381                 <em>Applet API methods</em>
 382                 <ul>
 383                         <li>newView public method</li>
 384                         <li>Window (current view) specific get/set public methods</li>
 385                         <li>Feature display control methods</li>
 386                         <li>get list of currently selected sequences</li>
 387                 </ul>
 388                 <em>New Jalview distribution features</em>
 389                 <ul>
 390                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 391                         <li>RELEASE file gives build properties for the latest Jalview
 392                         release.</li>
 393                         <li>Java 1.1 Applet build made easier and donotobfuscate
 394                         property controls execution of obfuscator</li>
 395                         <li>Build target for generating source distribution</li>
 396                         <li>Debug flag for javacc</li>
 397                         <li>.jalview_properties file is documented (slightly) in
 398                         jalview.bin.Cache</li>
 399                         <li>Continuous Build Integration for stable and development
 400                         version of Application, Applet and source distribution</li>
 401                 </ul>
 402
 403                 </td>
 404                 <td>
 405                 <ul>
 406                         <li>selected region output includes visible annotations (for
 407                         certain formats)</li>
 408                         <li>edit label/displaychar contains existing label/char for
 409                         editing</li>
 410                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 411                         <li>shorter peptide product names from EMBL records</li>
 412                         <li>Newick string generator makes compact representations</li>
 413                         <li>bootstrap values parsed correctly for tree files with
 414                         comments</li>
 415                         <li>pathological filechooser bug avoided by not allowing
 416                         filenames containing a ':'</li>
 417                         <li>Fixed exception when parsing GFF files containing global
 418                         sequence features</li>
 419                         <li>Alignment datasets are finalized only when number of
 420                         references from alignment sequences goes to zero</li>
 421                         <li>Close of tree branch colour box without colour selection
 422                         causes cascading exceptions</li>
 423                         <li>occasional negative imgwidth exceptions</li>
 424                         <li>better reporting of non-fatal warnings to user when file
 425                         parsing fails.</li>
 426                         <li>Save works when Jalview project is default format</li>
 427                         <li>Save as dialog opened if current alignment format is not a
 428                         valid output format</li>
 429                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 430                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 431                         <li>error messages passed up and output when data read fails</li>
 432                         <li>edit undo recovers previous dataset sequence when sequence
 433                         is edited</li>
 434                         <li>allow PDB files without pdb ID HEADER lines (like those
 435                         generated by MODELLER) to be read in properly</li>
 436                         <li>allow reading of JPred concise files as a normal filetype</li>
 437                         <li>Stockholm annotation parsing and alignment properties import
 438                         fixed for PFAM records</li>
 439                         <li>Structure view windows have correct name in Desktop window
 440                         list</li>
 441                         <li>annotation consisting of sequence associated scores can be
 442                         read and written correctly to annotation file</li>
 443                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
 444                         <li>Fixed display of hidden sequence markers and non-italic font
 445                         for representatives in Applet</li>
 446                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 447                         <li>Newly shown features appear at top of stack (in Applet)</li>
 448                         <li>Annotations added via parameter not drawn properly due to
 449                         null pointer exceptions</li>
 450                         <li>Secondary structure lines are drawn starting from first
 451                         column of alignment</li>
 452                         <li>Uniprot XML import updated for new schema release in July
 453                         2008</li>
 454                         <li>Sequence feature to sequence ID match for Features file is
 455                         case-insensitive</li>
 456                         <li>Sequence features read from Features file appended to all
 457                         sequences with matching IDs</li>
 458                         <li>PDB structure coloured correctly for associated views
 459                         containing a sub-sequence</li>
 460                         <li>PDB files can be retrieved by applet from Jar files</li>
 461                         <li>feature and annotation file applet parameters referring to
 462                         different directories are retrieved correctly</li>
 463                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 464                         <li>Fixed application hang whilst waiting for splash-screen
 465                         version check to complete</li>
 466                         <li>Applet properly URLencodes input parameter values when
 467                         passing them to the launchApp service</li>
 468                         <li>display name and local features preserved in results
 469                         retrieved from web service</li>
 470                         <li>Visual delay indication for sequence retrieval and sequence
 471                         fetcher initialisation</li>
 472                         <li>updated Application to use DAS 1.53e version of dasobert DAS
 473                         client</li>
 474                         <li>Re-instated Full AMSA support and .amsa file association</li>
 475                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
 476                         sequences</li>
 477                 </ul>
 478                 </td>
 479         </tr>
 480         <tr>
 481                 <td>
 482                 <div align="center"><strong>2.3</strong><br>
 483                 9/5/07</div>
 484                 </td>
 485                 <td>
 486                 <ul>
 487                         <li>Jmol 11.0.2 integration</li>
 488                         <li>PDB views stored in Jalview XML files</li>
 489                         <li>Slide sequences</li>
 490                         <li>Edit sequence in place</li>
 491                         <li>EMBL CDS features</li>
 492                         <li>DAS Feature mapping</li>
 493                         <li>Feature ordering</li>
 494                         <li>Alignment Properties</li>
 495                         <li>Annotation Scores</li>
 496                         <li>Sort by scores</li>
 497                         <li>Feature/annotation editing in applet</li>
 498                 </ul>
 499                 </td>
 500                 <td>
 501                 <ul>
 502                         <li>Headless state operation in 2.2.1</li>
 503                         <li>Incorrect and unstable DNA pairwise alignment</li>
 504                         <li>Cut and paste of sequences with annotation</li>
 505                         <li>Feature group display state in XML</li>
 506                         <li>Feature ordering in XML</li>
 507                         <li>blc file iteration selection using filename # suffix</li>
 508                         <li>Stockholm alignment properties</li>
 509                         <li>Stockhom alignment secondary structure annotation</li>
 510                         <li>2.2.1 applet had no feature transparency</li>
 511                         <li>Number pad keys can be used in cursor mode</li>
 512                         <li>Structure Viewer mirror image resolved</li>
 513                 </ul>
 514                 </td>
 515
 516         </tr>
 517         <tr>
 518                 <td>
 519                 <div align="center"><strong>2.2.1</strong><br>
 520                 12/2/07</div>
 521                 </td>
 522                 <td>
 523                 <ul>
 524                         <li>Non standard characters can be read and displayed
 525                         <li>Annotations/Features can be imported/exported to the applet
 526                         via textbox
 527                         <li>Applet allows editing of sequence/annotation/group name
 528                         &amp; description
 529                         <li>Preference setting to display sequence name in italics
 530                         <li>Annotation file format extended to allow Sequence_groups to
 531                         be defined
 532                         <li>Default opening of alignment overview panel can be specified
 533                         in preferences
 534                         <li>PDB residue numbering annotation added to associated
 535                         sequences
 536                 </ul>
 537                 </td>
 538                 <td>
 539                 <ul>
 540                         <li>Applet crash under certain Linux OS with Java 1.6 installed
 541                         <li>Annotation file export / import bugs fixed
 542                         <li>PNG / EPS image output bugs fixed
 543                 </ul>
 544                 </td>
 545         </tr>
 546         <tr>
 547                 <td>
 548                 <div align="center"><strong>2.2</strong><br>
 549                 27/11/06</div>
 550                 </td>
 551                 <td>
 552                 <ul>
 553                         <li>Multiple views on alignment
 554                         <li>Sequence feature editing
 555                         <li>&quot;Reload&quot; alignment
 556                         <li>&quot;Save&quot; to current filename
 557                         <li>Background dependent text colour
 558                         <li>Right align sequence ids
 559                         <li>User-defined lower case residue colours
 560                         <li>Format Menu
 561                         <li>Select Menu
 562                         <li>Menu item accelerator keys
 563                         <li>Control-V pastes to current alignment
 564                         <li>Cancel button for DAS Feature Fetching
 565                         <li>PCA and PDB Viewers zoom via mouse roller
 566                         <li>User-defined sub-tree colours and sub-tree selection
 567                         <li>'New Window' button on the 'Output to Text box'
 568                 </ul>
 569                 </td>
 570                 <td>
 571                 <ul>
 572                         <li>New memory efficient Undo/Redo System
 573                         <li>Optimised symbol lookups and conservation/consensus
 574                         calculations
 575                         <li>Region Conservation/Consensus recalculated after edits
 576                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
 577                         alignment)
 578                         <li>Slowed DAS Feature Fetching for increased robustness.
 579                         <li>Made angle brackets in ASCII feature descriptions display
 580                         correctly
 581                         <li>Re-instated Zoom function for PCA
 582                         <li>Sequence descriptions conserved in web service analysis
 583                         results
 584                         <li>Uniprot ID discoverer uses any word separated by &#8739;
 585                         <li>WsDbFetch query/result association resolved
 586                         <li>Tree leaf to sequence mapping improved
 587                         <li>Smooth fonts switch moved to FontChooser dialog box.
 588                 </ul>
 589                 </td>
 590         </tr>
 591         <tr>
 592                 <td>
 593                 <div align="center"><strong>2.1.1</strong><br>
 594                 12/9/06</div>
 595                 </td>
 596                 <td>
 597                 <ul>
 598                         <li>Copy consensus sequence to clipboard</li>
 599                 </ul>
 600                 </td>
 601                 <td>
 602                 <ul>
 603                         <li>Image output - rightmost residues are rendered if sequence
 604                         id panel has been resized</li>
 605                         <li>Image output - all offscreen group boundaries are rendered</li>
 606                         <li>Annotation files with sequence references - all elements in
 607                         file are relative to sequence position</li>
 608                         <li>Mac Applet users can use Alt key for group editing</li>
 609                 </ul>
 610                 </td>
 611         </tr>
 612         <tr>
 613                 <td>
 614                 <div align="center"><strong>2.1</strong><br>
 615                 22/8/06</div>
 616                 </td>
 617                 <td>
 618                 <ul>
 619                         <li>MAFFT Multiple Alignment in default Web Service list</li>
 620                         <li>DAS Feature fetching</li>
 621                         <li>Hide sequences and columns</li>
 622                         <li>Export Annotations and Features</li>
 623                         <li>GFF file reading / writing</li>
 624                         <li>Associate structures with sequences from local PDB files</li>
 625                         <li>Add sequences to exisiting alignment</li>
 626                         <li>Recently opened files / URL lists</li>
 627                         <li>Applet can launch the full application</li>
 628                         <li>Applet has transparency for features (Java 1.2 required)</li>
 629                         <li>Applet has user defined colours parameter</li>
 630                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
 631                 </ul>
 632                 </td>
 633                 <td>
 634                 <ul>
 635                         <li>Redundancy Panel reinstalled in the Applet</li>
 636                         <li>Monospaced font - EPS / rescaling bug fixed</li>
 637                         <li>Annotation files with sequence references bug fixed</li>
 638                 </ul>
 639                 </td>
 640         </tr>
 641         <tr>
 642                 <td>
 643                 <div align="center"><strong>2.08.1</strong><br>
 644                 2/5/06</div>
 645                 </td>
 646                 <td>
 647                 <ul>
 648                         <li>Change case of selected region from Popup menu</li>
 649                         <li>Choose to match case when searching</li>
 650                         <li>Middle mouse button and mouse movement can compress / expand
 651                         the visible width and height of the alignment</li>
 652                 </ul>
 653                 </td>
 654                 <td>
 655                 <ul>
 656                         <li>Annotation Panel displays complete JNet results</li>
 657                 </ul>
 658                 </td>
 659         </tr>
 660         <tr>
 661                 <td>
 662                 <div align="center"><strong>2.08b</strong><br>
 663                 18/4/06</div>
 664                 </td>
 665                 <td>&nbsp;</td>
 666                 <td>
 667                 <ul>
 668                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
 669                         <li>Righthand label on wrapped alignments shows correct value</li>
 670                 </ul>
 671                 </td>
 672         </tr>
 673         <tr>
 674                 <td>
 675                 <div align="center"><strong>2.08</strong><br>
 676                 10/4/06</div>
 677                 </td>
 678                 <td>
 679                 <ul>
 680                         <li>Editing can be locked to the selection area</li>
 681                         <li>Keyboard editing</li>
 682                         <li>Create sequence features from searches</li>
 683                         <li>Precalculated annotations can be loaded onto alignments</li>
 684                         <li>Features file allows grouping of features</li>
 685                         <li>Annotation Colouring scheme added</li>
 686                         <li>Smooth fonts off by default - Faster rendering</li>
 687                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
 688                 </ul>
 689                 </td>
 690                 <td>
 691                 <ul>
 692                         <li>Drag &amp; Drop fixed on Linux</li>
 693                         <li>Jalview Archive file faster to load/save, sequence
 694                         descriptions saved.</li>
 695                 </ul>
 696                 </td>
 697         </tr>
 698         <tr>
 699                 <td>
 700                 <div align="center"><strong>2.07</strong><br>
 701                 12/12/05</div>
 702                 </td>
 703                 <td>
 704                 <ul>
 705                         <li>PDB Structure Viewer enhanced</li>
 706                         <li>Sequence Feature retrieval and display enhanced</li>
 707                         <li>Choose to output sequence start-end after sequence name for
 708                         file output</li>
 709                         <li>Sequence Fetcher WSDBFetch@EBI</li>
 710                         <li>Applet can read feature files, PDB files and can be used for
 711                         HTML form input</li>
 712                 </ul>
 713                 </td>
 714                 <td>
 715                 <ul>
 716                         <li>HTML output writes groups and features</li>
 717                         <li>Group editing is Control and mouse click</li>
 718                         <li>File IO bugs</li>
 719                 </ul>
 720                 </td>
 721         </tr>
 722         <tr>
 723                 <td>
 724                 <div align="center"><strong>2.06</strong><br>
 725                 28/9/05</div>
 726                 </td>
 727                 <td>
 728                 <ul>
 729                         <li>View annotations in wrapped mode</li>
 730                         <li>More options for PCA viewer</li>
 731                 </ul>
 732                 </td>
 733                 <td>
 734                 <ul>
 735                         <li>GUI bugs resolved</li>
 736                         <li>Runs with -nodisplay from command line</li>
 737                 </ul>
 738                 </td>
 739         </tr>
 740         <tr>
 741                 <td height="63">
 742                 <div align="center"><strong>2.05b</strong><br>
 743                 15/9/05</div>
 744                 </td>
 745                 <td>
 746                 <ul>
 747                         <li>Choose EPS export as lineart or text</li>
 748                         <li>Jar files are executable</li>
 749                         <li>Can read in Uracil - maps to unknown residue</li>
 750                 </ul>
 751                 </td>
 752                 <td>
 753                 <ul>
 754                         <li>Known OutOfMemory errors give warning message</li>
 755                         <li>Overview window calculated more efficiently</li>
 756                         <li>Several GUI bugs resolved</li>
 757                 </ul>
 758                 </td>
 759         </tr>
 760         <tr>
 761                 <td>
 762                 <div align="center"><strong>2.05</strong><br>
 763                 30/8/05</div>
 764                 </td>
 765                 <td>
 766                 <ul>
 767                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
 768                 </ul>
 769                 </td>
 770                 <td>
 771                 <ul>
 772                         <li>Several GUI bugs resolved</li>
 773                 </ul>
 774                 </td>
 775         </tr>
 776         <tr>
 777                 <td>
 778                 <div align="center"><strong>2.04</strong><br>
 779                 24/8/05</div>
 780                 </td>
 781                 <td>
 782                 <ul>
 783                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
 784                 </ul>
 785                 </td>
 786                 <td>
 787                 <ul>
 788                         <li>Improved JPred client reliability</li>
 789                         <li>Improved loading of Jalview files</li>
 790                 </ul>
 791                 </td>
 792         </tr>
 793         <tr>
 794                 <td>
 795                 <div align="center"><strong>2.03</strong><br>
 796                 18/8/05</div>
 797                 </td>
 798                 <td>
 799                 <ul>
 800                         <li>Set Proxy server name and port in preferences</li>
 801                         <li>Multiple URL links from sequence ids</li>
 802                         <li>User Defined Colours can have a scheme name and added to
 803                         Colour Menu</li>
 804                         <li>Choose to ignore gaps in consensus calculation</li>
 805                         <li>Unix users can set default web browser</li>
 806                         <li>Runs without GUI for batch processing</li>
 807                         <li>Dynamically generated Web Service Menus</li>
 808                 </ul>
 809                 </td>
 810                 <td>
 811                 <ul>
 812                         <li>InstallAnywhere download for Sparc Solaris</li>
 813                 </ul>
 814                 </td>
 815         </tr>
 816         <tr>
 817                 <td>
 818                 <div align="center"><strong>2.02</strong><br>
 819                 18/7/05</div>
 820                 </td>
 821                 <td>&nbsp;</td>
 822                 <td>
 823                 <ul>
 824                         <li>Copy &amp; Paste order of sequences maintains alignment
 825                         order.</li>
 826                 </ul>
 827                 </td>
 828         </tr>
 829         <tr>
 830                 <td>
 831                 <div align="center"><strong>2.01</strong><br>
 832                 12/7/05</div>
 833                 </td>
 834                 <td>
 835                 <ul>
 836                         <li>Use delete key for deleting selection.</li>
 837                         <li>Use Mouse wheel to scroll sequences.</li>
 838                         <li>Help file updated to describe how to add alignment
 839                         annotations.</li>
 840                         <li>Version and build date written to build properties file.</li>
 841                         <li>InstallAnywhere installation will check for updates at
 842                         launch of Jalview.</li>
 843                 </ul>
 844                 </td>
 845                 <td>
 846                 <ul>
 847                         <li>Delete gaps bug fixed.</li>
 848                         <li>FileChooser sorts columns.</li>
 849                         <li>Can remove groups one by one.</li>
 850                         <li>Filechooser icons installed.</li>
 851                         <li>Finder ignores return character when searching. Return key
 852                         will initiate a search.<br>
 853                         </li>
 854                 </ul>
 855                 </td>
 856         </tr>
 857         <tr>
 858                 <td>
 859                 <div align="center"><strong>2.0</strong><br>
 860                 20/6/05</div>
 861                 </td>
 862                 <td>
 863                 <ul>
 864                         <li>New codebase</li>
 865                 </ul>
 866                 </td>
 867                 <td>&nbsp;</td>
 868         </tr>
 869 </table>
 870 <p>&nbsp;</p>
 871 </body>
 872 </html>