help/html/releases.html

   1 #-------------------------------------------------------------------------------
   2 # Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
   3 # Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
   4 #
   5 # This file is part of Jalview.
   6 #
   7 # Jalview is free software: you can redistribute it and/or
   8 # modify it under the terms of the GNU General Public License
   9 # as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  10 #
  11 # Jalview is distributed in the hope that it will be useful, but
  12 # WITHOUT ANY WARRANTY; without even the implied warranty
  13 # of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14 # PURPOSE.  See the GNU General Public License for more details.
  15 #
  16 # You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17 #-------------------------------------------------------------------------------
  18 <html>
  19 <!--
  20  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
  21  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  22  *
  23  * This file is part of Jalview.
  24  *
  25  * Jalview is free software: you can redistribute it and/or
  26  * modify it under the terms of the GNU General Public License
  27  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  28  *
  29  * Jalview is distributed in the hope that it will be useful, but
  30  * WITHOUT ANY WARRANTY; without even the implied warranty
  31  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  32  * PURPOSE.  See the GNU General Public License for more details.
  33  *
  34  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  35 -->
  36 <head>
  37 <title>Release History</title>
  38 </head>
  39 <body>
  40 <p><strong>Release History</strong></p>
  41 <table border="1">
  42         <tr>
  43                 <td width="60" nowrap>
  44                 <div align="center"><em><strong>Release</strong></em></div>
  45                 </td>
  46                 <td>
  47                 <div align="center"><em><strong>New Features</strong></em></div>
  48                 </td>
  49                 <td>
  50                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
  51                 </td>
  52         </tr>
  53         <tr>
  54                 <td>
  55                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
  56                 <em>14/6/2010</em></div>
  57                 </td>
  58                 <td></td>
  59                 <td>
  60                 <ul>
  61                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
  62                         </li>
  63                         <li>clustalx colourscheme colours Ds preferentially when both
  64                         D+E are present in over 50% of the column</li>
  65                         <li>nucleic acid structures retrieved from PDB do not import
  66                         correctly</li>
  67                         <li>More columns get selected than were clicked on when a number
  68                         of columns are hidden</li>
  69                         <li>annotation label popup menu not providing correct
  70                         add/hide/show options when rows are hidden or none are present</li>
  71                         <li>Stockholm format shown in list of readable formats.</li>
  72                 </ul>
  73                 <em>Applet</em>
  74                 <ul>
  75                         <li>annotation panel disappears when annotation is
  76                         hidden/removed</li>
  77                 </ul>
  78                 <em>Application</em>
  79                 <ul>
  80                         <li>Alignment view not redrawn properly when new alignment
  81                         opened where annotation panel is visible but no annotations are
  82                         present on alignment</li>
  83                         <li>pasted region containing hidden columns is incorrectly
  84                         displayed in new alignment window</li>
  85                         <li>Jalview slow to complete operations when stdout is flooded
  86                         (fix is to close the Jalview console)</li>
  87                         <li>CSV output of consensus only includes the percentage of all
  88                         symbols if sequence logo display is enabled</li>
  89                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
  90                         selected Rregions menu item.</li>
  91                         <li>inconsistent group submenu and Format submenu entry 'Un' or
  92                         'Non'conserved</li>
  93                         <li>Sequence feature settings are being shared by multiple
  94                         distinct alignments</li>
  95                         <li>group annotation not recreated when tree partition is
  96                         changed</li>
  97                         <li>double click on group annotation to select sequences does
  98                         not propagate to associated trees</li>
  99                         <li>Mac OSX specific issues:
 100                         <ul>
 101                                 <li>exception raised when mouse clicked on desktop window
 102                                 background</li>
 103                                 <li>Desktop menu placed on menu bar and application name set
 104                                 correctly</li>
 105                                 <li>sequence feature settings not wide enough for the save
 106                                 feature colourscheme button</li>
 107                         </ul>
 108                         </li>
 109                 </ul>
 110                 </td>
 111         </tr>
 112         <tr>
 113
 114                 <td>
 115                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 116                 <em>30/4/2010</em></div>
 117                 </td>
 118                 <td><em>New Capabilities</em>
 119                 <ul>
 120                         <li>URL links generated from description line for
 121                         regular-expression based URL links (applet and application)
 122                         <li>Non-positional feature URL links are shown in link menu</li>
 123                         <li>Linked viewing of nucleic acid sequences and structures</li>
 124                         <li>Automatic Scrolling option in View menu to display the
 125                         currently highlighted region of an alignment.</li>
 126                         <li>Order an alignment by sequence length, or using the average
 127                         score or total feature count for each sequence.</li>
 128                         <li>Shading features by score or associated description</li>
 129                         <li>Subdivide alignment and groups based on identity of selected
 130                         subsequence (Make Groups from Selection).</li>
 131                         <li>New hide/show options including Shift+Control+H to hide
 132                         everything but the currently selected region.</li>
 133                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 134                 </ul>
 135                 <em>Application</em>
 136                 <ul>
 137                         <li>Fetch DB References capabilities and UI expanded to support
 138                         retrieval from DAS sequence sources</li>
 139                         <li>Local DAS Sequence sources can be added via the command line
 140                         or via the Add local source dialog box.</li>
 141                         <li>DAS Dbref and DbxRef feature types are parsed as database
 142                         references and protein_name is parsed as description line (BioSapiens
 143                         terms).</li>
 144                         <li>Enable or disable non-positional feature and database
 145                         references in sequence ID tooltip from View menu in application.</li>
 146                         <!--                    <li>New hidden columns and rows and representatives capabilities
 147                         in annotations file (in progress - not yet fully implemented)</li> -->
 148                         <li>Group-associated consensus, sequence logos and conservation
 149                         plots</li>
 150                         <li>Symbol distributions for each column can be exported and
 151                         visualized as sequence logos</li>
 152                         <li>Optionally scale multi-character column labels to fit within
 153                         each column of annotation row<!-- todo for applet --></li>
 154                         <li>Optional automatic sort of associated alignment view when a
 155                         new tree is opened.</li>
 156                         <li>Jalview Java Console</li>
 157                         <li>Better placement of desktop window when moving between
 158                         different screens.</li>
 159                         <li>New preference items for sequence ID tooltip and consensus
 160                         annotation</li>
 161                         <li>Client to submit sequences and IDs to <a
 162                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 163                         <li><em>Vamsas Capabilities</em>
 164                         <ul>
 165                                 <li>Improved VAMSAS synchronization (jalview archive used to
 166                                 preserve views, structures, and tree display settings)</li>
 167                                 <li>Import of vamsas documents from disk or URL via command
 168                                 line</li>
 169                                 <li>Sharing of selected regions between views and with other
 170                                 VAMSAS applications (Experimental feature!)</li>
 171                                 <li>Updated API to VAMSAS version 0.2</li>
 172                         </ul>
 173                         </li>
 174                 </ul>
 175                 <em>Applet</em>
 176                 <ul>
 177                         <li>Middle button resizes annotation row height</li>
 178                         <li>New Parameters
 179                         <ul>
 180                                 <li>sortByTree (true/false) - automatically sort the associated
 181                                 alignment view by the tree when a new tree is opened.</li>
 182                                 <li>showTreeBootstraps (true/false) - show or hide branch
 183                                 bootstraps (default is to show them if available)</li>
 184                                 <li>showTreeDistances (true/false) - show or hide branch
 185                                 lengths (default is to show them if available)</li>
 186                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
 187                                 unassociated nodes should be highlighted in the tree view</li>
 188                                 <li>heightScale and widthScale (1.0 or more) - increase the
 189                                 height or width of a cell in the alignment grid relative to the
 190                                 current font size.</li>
 191                         </ul>
 192                         </li>
 193                         <li>Non-positional features displayed in sequence ID tooltip</li>
 194                 </ul>
 195                 <em>Other</em>
 196                 <ul>
 197                         <li>Features format: graduated colour definitions and
 198                         specification of feature scores</li>
 199                         <li>Alignment Annotations format: new keywords for group
 200                         associated annotation (GROUP_REF) and annotation row display
 201                         properties (ROW_PROPERTIES)</li>
 202                         <li>XML formats extended to support graduated feature
 203                         colourschemes, group associated annotation, and profile visualization
 204                         settings.</li>
 205                 </td>
 206                 <td>
 207                 <ul>
 208                         <li>Source field in GFF files parsed as feature source rather
 209                         than description</li>
 210                         <li>Non-positional features are now included in sequence feature
 211                         and gff files (controlled via non-positional feature visibility in
 212                         tooltip).</li>
 213                         <li>URL links generated for all feature links (bugfix)</li>
 214                         <li>Added URL embedding instructions to features file
 215                         documentation.</li>
 216                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 217                         peptide product</li>
 218                         <li>Match case switch in find dialog box works for both sequence
 219                         ID and sequence string and query strings do not have to be in upper
 220                         case to match case-insensitively.</li>
 221                         <li>AMSA files only contain first column of multi-character
 222                         column annotation labels</li>
 223                         <li>Jalview Annotation File generation/parsing consistent with
 224                         documentation (e.g. Stockholm annotation can be exported and
 225                         re-imported)</li>
 226                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 227                         <li>Find incrementally searches ID string matches as well as
 228                         subsequence matches, and correctly reports total number of both.</li>
 229                         <li>Application:
 230                         <ul>
 231                                 <li>Better handling of exceptions during sequence retrieval</li>
 232                                 <li>Dasobert generated non-positional feature URL link text
 233                                 excludes the start_end suffix</li>
 234                                 <li>DAS feature and source retrieval buttons disabled when
 235                                 fetch or registry operations in progress.</li>
 236                                 <li>PDB files retrieved from URLs are cached properly</li>
 237                                 <li>Sequence description lines properly shared via VAMSAS</li>
 238                                 <li>Sequence fetcher fetches multiple records for all data
 239                                 sources</li>
 240                                 <li>Ensured that command line das feature retrieval completes
 241                                 before alignment figures are generated.</li>
 242                                 <li>Reduced time taken when opening file browser for first
 243                                 time.</li>
 244                                 <li>isAligned check prior to calculating tree, PCA or
 245                                 submitting an MSA to JNet now excludes hidden sequences.</li>
 246                                 <li>User defined group colours properly recovered from Jalview
 247                                 projects.</li>
 248                         </ul>
 249                         </li>
 250                 </ul>
 251                 </td>
 252
 253         </tr>
 254         <tr>
 255                 <td>
 256                 <div align="center"><strong>2.4.0.b2</strong><br>
 257                 28/10/2009</div>
 258                 </td>
 259                 <td>
 260                 <ul>
 261                         <li>Experimental support for google analytics usage tracking.</li>
 262                         <li>Jalview privacy settings (user preferences and docs).</li>
 263                 </ul>
 264                 </td>
 265                 <td>
 266                 <ul>
 267                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 268                         <li>Exception when feature created from selection beyond length
 269                         of sequence.</li>
 270                         <li>Allow synthetic PDB files to be imported gracefully</li>
 271                         <li>Sequence associated annotation rows associate with all
 272                         sequences with a given id</li>
 273                         <li>Find function matches case-insensitively for sequence ID
 274                         string searches</li>
 275                         <li>Non-standard characters do not cause pairwise alignment to
 276                         fail with exception</li>
 277                 </ul>
 278                 <em>Application Issues</em>
 279                 <ul>
 280                         <li>Sequences are now validated against EMBL database</li>
 281                         <li>Sequence fetcher fetches multiple records for all data
 282                         sources</li>
 283                 </ul>
 284                 <em>InstallAnywhere Issues</em>
 285                 <ul>
 286                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 287                         installAnywhere mechanism)</li>
 288                         <li>Command line launching of JARs from InstallAnywhere version
 289                         (java class versioning error fixed)</li>
 290                 </ul>
 291                 </td>
 292         </tr>
 293         <tr>
 294                 <td>
 295
 296                 <div align="center"><strong>2.4</strong><br>
 297                 27/8/2008</div>
 298                 </td>
 299                 <td><em>User Interface</em>
 300                 <ul>
 301                         <li>Linked highlighting of codon and amino acid from translation
 302                         and protein products</li>
 303                         <li>Linked highlighting of structure associated with residue
 304                         mapping to codon position</li>
 305                         <li>Sequence Fetcher provides example accession numbers and
 306                         'clear' button</li>
 307                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 308                         <li>Extract score function to parse whitespace separated numeric
 309                         data in description line</li>
 310                         <li>Column labels in alignment annotation can be centred.</li>
 311                         <li>Tooltip for sequence associated annotation give name of
 312                         sequence</li>
 313                 </ul>
 314                 <em>Web Services and URL fetching</em>
 315                 <ul>
 316                         <li>JPred3 web service</li>
 317                         <li>Prototype sequence search client (no public services
 318                         available yet)</li>
 319                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 320                         <li>URL Links created for matching database cross references as
 321                         well as sequence ID</li>
 322                         <li>URL Links can be created using regular-expressions</li>
 323                 </ul>
 324                 <em>Sequence Database Connectivity</em>
 325                 <ul>
 326                         <li>Retrieval of cross-referenced sequences from other databases
 327                         </li>
 328                         <li>Generalised database reference retrieval and validation to
 329                         all fetchable databases</li>
 330                         <li>Fetch sequences from DAS sources supporting the sequence
 331                         command</li>
 332                 </ul>
 333                 <em>Import and Export</em>
 334                 <li>export annotation rows as CSV for spreadsheet import</li>
 335                 <li>Jalview projects record alignment dataset associations, EMBL
 336                 products, and cDNA sequence mappings</li>
 337                 <li>Sequence Group colour can be specified in Annotation File</li>
 338                 <li>Ad-hoc colouring of group in Annotation File using RGB
 339                 triplet as name of colourscheme</li>
 340                 </ul>
 341                 <em>VAMSAS Client capabilities (Experimental)</em>
 342                 <ul>
 343                         <li>treenode binding for VAMSAS tree exchange</li>
 344                         <li>local editing and update of sequences in VAMSAS alignments
 345                         (experimental)</li>
 346                         <li>Create new or select existing session to join</li>
 347                         <li>load and save of vamsas documents</li>
 348                 </ul>
 349                 <em>Application command line</em>
 350                 <ul>
 351                         <li>-tree parameter to open trees (introduced for passing from
 352                         applet)</li>
 353                         <li>-fetchfrom command line argument to specify nicknames of DAS
 354                         servers to query for alignment features</li>
 355                         <li>-dasserver command line argument to add new servers that are
 356                         also automatically queried for features</li>
 357                         <li>-groovy command line argument executes a given groovy script
 358                         after all input data has been loaded and parsed</li>
 359                 </ul>
 360                 <em>Applet-Application data exchange</em>
 361                 <ul>
 362                         <li>Trees passed as applet parameters can be passed to
 363                         application (when using &quot;View in full application&quot;)</li>
 364                 </ul>
 365                 <em>Applet Parameters</em>
 366                 <ul>
 367                         <li>feature group display control parameter</li>
 368                         <li>debug parameter</li>
 369                         <li>showbutton parameter</li>
 370                 </ul>
 371                 <em>Applet API methods</em>
 372                 <ul>
 373                         <li>newView public method</li>
 374                         <li>Window (current view) specific get/set public methods</li>
 375                         <li>Feature display control methods</li>
 376                         <li>get list of currently selected sequences</li>
 377                 </ul>
 378                 <em>New Jalview distribution features</em>
 379                 <ul>
 380                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 381                         <li>RELEASE file gives build properties for the latest Jalview
 382                         release.</li>
 383                         <li>Java 1.1 Applet build made easier and donotobfuscate
 384                         property controls execution of obfuscator</li>
 385                         <li>Build target for generating source distribution</li>
 386                         <li>Debug flag for javacc</li>
 387                         <li>.jalview_properties file is documented (slightly) in
 388                         jalview.bin.Cache</li>
 389                         <li>Continuous Build Integration for stable and development
 390                         version of Application, Applet and source distribution</li>
 391                 </ul>
 392
 393                 </td>
 394                 <td>
 395                 <ul>
 396                         <li>selected region output includes visible annotations (for
 397                         certain formats)</li>
 398                         <li>edit label/displaychar contains existing label/char for
 399                         editing</li>
 400                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 401                         <li>shorter peptide product names from EMBL records</li>
 402                         <li>Newick string generator makes compact representations</li>
 403                         <li>bootstrap values parsed correctly for tree files with
 404                         comments</li>
 405                         <li>pathological filechooser bug avoided by not allowing
 406                         filenames containing a ':'</li>
 407                         <li>Fixed exception when parsing GFF files containing global
 408                         sequence features</li>
 409                         <li>Alignment datasets are finalized only when number of
 410                         references from alignment sequences goes to zero</li>
 411                         <li>Close of tree branch colour box without colour selection
 412                         causes cascading exceptions</li>
 413                         <li>occasional negative imgwidth exceptions</li>
 414                         <li>better reporting of non-fatal warnings to user when file
 415                         parsing fails.</li>
 416                         <li>Save works when Jalview project is default format</li>
 417                         <li>Save as dialog opened if current alignment format is not a
 418                         valid output format</li>
 419                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 420                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 421                         <li>error messages passed up and output when data read fails</li>
 422                         <li>edit undo recovers previous dataset sequence when sequence
 423                         is edited</li>
 424                         <li>allow PDB files without pdb ID HEADER lines (like those
 425                         generated by MODELLER) to be read in properly</li>
 426                         <li>allow reading of JPred concise files as a normal filetype</li>
 427                         <li>Stockholm annotation parsing and alignment properties import
 428                         fixed for PFAM records</li>
 429                         <li>Structure view windows have correct name in Desktop window
 430                         list</li>
 431                         <li>annotation consisting of sequence associated scores can be
 432                         read and written correctly to annotation file</li>
 433                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
 434                         <li>Fixed display of hidden sequence markers and non-italic font
 435                         for representatives in Applet</li>
 436                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 437                         <li>Newly shown features appear at top of stack (in Applet)</li>
 438                         <li>Annotations added via parameter not drawn properly due to
 439                         null pointer exceptions</li>
 440                         <li>Secondary structure lines are drawn starting from first
 441                         column of alignment</li>
 442                         <li>Uniprot XML import updated for new schema release in July
 443                         2008</li>
 444                         <li>Sequence feature to sequence ID match for Features file is
 445                         case-insensitive</li>
 446                         <li>Sequence features read from Features file appended to all
 447                         sequences with matching IDs</li>
 448                         <li>PDB structure coloured correctly for associated views
 449                         containing a sub-sequence</li>
 450                         <li>PDB files can be retrieved by applet from Jar files</li>
 451                         <li>feature and annotation file applet parameters referring to
 452                         different directories are retrieved correctly</li>
 453                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 454                         <li>Fixed application hang whilst waiting for splash-screen
 455                         version check to complete</li>
 456                         <li>Applet properly URLencodes input parameter values when
 457                         passing them to the launchApp service</li>
 458                         <li>display name and local features preserved in results
 459                         retrieved from web service</li>
 460                         <li>Visual delay indication for sequence retrieval and sequence
 461                         fetcher initialisation</li>
 462                         <li>updated Application to use DAS 1.53e version of dasobert DAS
 463                         client</li>
 464                         <li>Re-instated Full AMSA support and .amsa file association</li>
 465                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
 466                         sequences</li>
 467                 </ul>
 468                 </td>
 469         </tr>
 470         <tr>
 471                 <td>
 472                 <div align="center"><strong>2.3</strong><br>
 473                 9/5/07</div>
 474                 </td>
 475                 <td>
 476                 <ul>
 477                         <li>Jmol 11.0.2 integration</li>
 478                         <li>PDB views stored in Jalview XML files</li>
 479                         <li>Slide sequences</li>
 480                         <li>Edit sequence in place</li>
 481                         <li>EMBL CDS features</li>
 482                         <li>DAS Feature mapping</li>
 483                         <li>Feature ordering</li>
 484                         <li>Alignment Properties</li>
 485                         <li>Annotation Scores</li>
 486                         <li>Sort by scores</li>
 487                         <li>Feature/annotation editing in applet</li>
 488                 </ul>
 489                 </td>
 490                 <td>
 491                 <ul>
 492                         <li>Headless state operation in 2.2.1</li>
 493                         <li>Incorrect and unstable DNA pairwise alignment</li>
 494                         <li>Cut and paste of sequences with annotation</li>
 495                         <li>Feature group display state in XML</li>
 496                         <li>Feature ordering in XML</li>
 497                         <li>blc file iteration selection using filename # suffix</li>
 498                         <li>Stockholm alignment properties</li>
 499                         <li>Stockhom alignment secondary structure annotation</li>
 500                         <li>2.2.1 applet had no feature transparency</li>
 501                         <li>Number pad keys can be used in cursor mode</li>
 502                         <li>Structure Viewer mirror image resolved</li>
 503                 </ul>
 504                 </td>
 505
 506         </tr>
 507         <tr>
 508                 <td>
 509                 <div align="center"><strong>2.2.1</strong><br>
 510                 12/2/07</div>
 511                 </td>
 512                 <td>
 513                 <ul>
 514                         <li>Non standard characters can be read and displayed
 515                         <li>Annotations/Features can be imported/exported to the applet
 516                         via textbox
 517                         <li>Applet allows editing of sequence/annotation/group name
 518                         &amp; description
 519                         <li>Preference setting to display sequence name in italics
 520                         <li>Annotation file format extended to allow Sequence_groups to
 521                         be defined
 522                         <li>Default opening of alignment overview panel can be specified
 523                         in preferences
 524                         <li>PDB residue numbering annotation added to associated
 525                         sequences
 526                 </ul>
 527                 </td>
 528                 <td>
 529                 <ul>
 530                         <li>Applet crash under certain Linux OS with Java 1.6 installed
 531                         <li>Annotation file export / import bugs fixed
 532                         <li>PNG / EPS image output bugs fixed
 533                 </ul>
 534                 </td>
 535         </tr>
 536         <tr>
 537                 <td>
 538                 <div align="center"><strong>2.2</strong><br>
 539                 27/11/06</div>
 540                 </td>
 541                 <td>
 542                 <ul>
 543                         <li>Multiple views on alignment
 544                         <li>Sequence feature editing
 545                         <li>&quot;Reload&quot; alignment
 546                         <li>&quot;Save&quot; to current filename
 547                         <li>Background dependent text colour
 548                         <li>Right align sequence ids
 549                         <li>User-defined lower case residue colours
 550                         <li>Format Menu
 551                         <li>Select Menu
 552                         <li>Menu item accelerator keys
 553                         <li>Control-V pastes to current alignment
 554                         <li>Cancel button for DAS Feature Fetching
 555                         <li>PCA and PDB Viewers zoom via mouse roller
 556                         <li>User-defined sub-tree colours and sub-tree selection
 557                         <li>'New Window' button on the 'Output to Text box'
 558                 </ul>
 559                 </td>
 560                 <td>
 561                 <ul>
 562                         <li>New memory efficient Undo/Redo System
 563                         <li>Optimised symbol lookups and conservation/consensus
 564                         calculations
 565                         <li>Region Conservation/Consensus recalculated after edits
 566                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
 567                         alignment)
 568                         <li>Slowed DAS Feature Fetching for increased robustness.
 569                         <li>Made angle brackets in ASCII feature descriptions display
 570                         correctly
 571                         <li>Re-instated Zoom function for PCA
 572                         <li>Sequence descriptions conserved in web service analysis
 573                         results
 574                         <li>Uniprot ID discoverer uses any word separated by &#8739;
 575                         <li>WsDbFetch query/result association resolved
 576                         <li>Tree leaf to sequence mapping improved
 577                         <li>Smooth fonts switch moved to FontChooser dialog box.
 578                 </ul>
 579                 </td>
 580         </tr>
 581         <tr>
 582                 <td>
 583                 <div align="center"><strong>2.1.1</strong><br>
 584                 12/9/06</div>
 585                 </td>
 586                 <td>
 587                 <ul>
 588                         <li>Copy consensus sequence to clipboard</li>
 589                 </ul>
 590                 </td>
 591                 <td>
 592                 <ul>
 593                         <li>Image output - rightmost residues are rendered if sequence
 594                         id panel has been resized</li>
 595                         <li>Image output - all offscreen group boundaries are rendered</li>
 596                         <li>Annotation files with sequence references - all elements in
 597                         file are relative to sequence position</li>
 598                         <li>Mac Applet users can use Alt key for group editing</li>
 599                 </ul>
 600                 </td>
 601         </tr>
 602         <tr>
 603                 <td>
 604                 <div align="center"><strong>2.1</strong><br>
 605                 22/8/06</div>
 606                 </td>
 607                 <td>
 608                 <ul>
 609                         <li>MAFFT Multiple Alignment in default Web Service list</li>
 610                         <li>DAS Feature fetching</li>
 611                         <li>Hide sequences and columns</li>
 612                         <li>Export Annotations and Features</li>
 613                         <li>GFF file reading / writing</li>
 614                         <li>Associate structures with sequences from local PDB files</li>
 615                         <li>Add sequences to exisiting alignment</li>
 616                         <li>Recently opened files / URL lists</li>
 617                         <li>Applet can launch the full application</li>
 618                         <li>Applet has transparency for features (Java 1.2 required)</li>
 619                         <li>Applet has user defined colours parameter</li>
 620                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
 621                 </ul>
 622                 </td>
 623                 <td>
 624                 <ul>
 625                         <li>Redundancy Panel reinstalled in the Applet</li>
 626                         <li>Monospaced font - EPS / rescaling bug fixed</li>
 627                         <li>Annotation files with sequence references bug fixed</li>
 628                 </ul>
 629                 </td>
 630         </tr>
 631         <tr>
 632                 <td>
 633                 <div align="center"><strong>2.08.1</strong><br>
 634                 2/5/06</div>
 635                 </td>
 636                 <td>
 637                 <ul>
 638                         <li>Change case of selected region from Popup menu</li>
 639                         <li>Choose to match case when searching</li>
 640                         <li>Middle mouse button and mouse movement can compress / expand
 641                         the visible width and height of the alignment</li>
 642                 </ul>
 643                 </td>
 644                 <td>
 645                 <ul>
 646                         <li>Annotation Panel displays complete JNet results</li>
 647                 </ul>
 648                 </td>
 649         </tr>
 650         <tr>
 651                 <td>
 652                 <div align="center"><strong>2.08b</strong><br>
 653                 18/4/06</div>
 654                 </td>
 655                 <td>&nbsp;</td>
 656                 <td>
 657                 <ul>
 658                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
 659                         <li>Righthand label on wrapped alignments shows correct value</li>
 660                 </ul>
 661                 </td>
 662         </tr>
 663         <tr>
 664                 <td>
 665                 <div align="center"><strong>2.08</strong><br>
 666                 10/4/06</div>
 667                 </td>
 668                 <td>
 669                 <ul>
 670                         <li>Editing can be locked to the selection area</li>
 671                         <li>Keyboard editing</li>
 672                         <li>Create sequence features from searches</li>
 673                         <li>Precalculated annotations can be loaded onto alignments</li>
 674                         <li>Features file allows grouping of features</li>
 675                         <li>Annotation Colouring scheme added</li>
 676                         <li>Smooth fonts off by default - Faster rendering</li>
 677                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
 678                 </ul>
 679                 </td>
 680                 <td>
 681                 <ul>
 682                         <li>Drag &amp; Drop fixed on Linux</li>
 683                         <li>Jalview Archive file faster to load/save, sequence
 684                         descriptions saved.</li>
 685                 </ul>
 686                 </td>
 687         </tr>
 688         <tr>
 689                 <td>
 690                 <div align="center"><strong>2.07</strong><br>
 691                 12/12/05</div>
 692                 </td>
 693                 <td>
 694                 <ul>
 695                         <li>PDB Structure Viewer enhanced</li>
 696                         <li>Sequence Feature retrieval and display enhanced</li>
 697                         <li>Choose to output sequence start-end after sequence name for
 698                         file output</li>
 699                         <li>Sequence Fetcher WSDBFetch@EBI</li>
 700                         <li>Applet can read feature files, PDB files and can be used for
 701                         HTML form input</li>
 702                 </ul>
 703                 </td>
 704                 <td>
 705                 <ul>
 706                         <li>HTML output writes groups and features</li>
 707                         <li>Group editing is Control and mouse click</li>
 708                         <li>File IO bugs</li>
 709                 </ul>
 710                 </td>
 711         </tr>
 712         <tr>
 713                 <td>
 714                 <div align="center"><strong>2.06</strong><br>
 715                 28/9/05</div>
 716                 </td>
 717                 <td>
 718                 <ul>
 719                         <li>View annotations in wrapped mode</li>
 720                         <li>More options for PCA viewer</li>
 721                 </ul>
 722                 </td>
 723                 <td>
 724                 <ul>
 725                         <li>GUI bugs resolved</li>
 726                         <li>Runs with -nodisplay from command line</li>
 727                 </ul>
 728                 </td>
 729         </tr>
 730         <tr>
 731                 <td height="63">
 732                 <div align="center"><strong>2.05b</strong><br>
 733                 15/9/05</div>
 734                 </td>
 735                 <td>
 736                 <ul>
 737                         <li>Choose EPS export as lineart or text</li>
 738                         <li>Jar files are executable</li>
 739                         <li>Can read in Uracil - maps to unknown residue</li>
 740                 </ul>
 741                 </td>
 742                 <td>
 743                 <ul>
 744                         <li>Known OutOfMemory errors give warning message</li>
 745                         <li>Overview window calculated more efficiently</li>
 746                         <li>Several GUI bugs resolved</li>
 747                 </ul>
 748                 </td>
 749         </tr>
 750         <tr>
 751                 <td>
 752                 <div align="center"><strong>2.05</strong><br>
 753                 30/8/05</div>
 754                 </td>
 755                 <td>
 756                 <ul>
 757                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
 758                 </ul>
 759                 </td>
 760                 <td>
 761                 <ul>
 762                         <li>Several GUI bugs resolved</li>
 763                 </ul>
 764                 </td>
 765         </tr>
 766         <tr>
 767                 <td>
 768                 <div align="center"><strong>2.04</strong><br>
 769                 24/8/05</div>
 770                 </td>
 771                 <td>
 772                 <ul>
 773                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
 774                 </ul>
 775                 </td>
 776                 <td>
 777                 <ul>
 778                         <li>Improved JPred client reliability</li>
 779                         <li>Improved loading of Jalview files</li>
 780                 </ul>
 781                 </td>
 782         </tr>
 783         <tr>
 784                 <td>
 785                 <div align="center"><strong>2.03</strong><br>
 786                 18/8/05</div>
 787                 </td>
 788                 <td>
 789                 <ul>
 790                         <li>Set Proxy server name and port in preferences</li>
 791                         <li>Multiple URL links from sequence ids</li>
 792                         <li>User Defined Colours can have a scheme name and added to
 793                         Colour Menu</li>
 794                         <li>Choose to ignore gaps in consensus calculation</li>
 795                         <li>Unix users can set default web browser</li>
 796                         <li>Runs without GUI for batch processing</li>
 797                         <li>Dynamically generated Web Service Menus</li>
 798                 </ul>
 799                 </td>
 800                 <td>
 801                 <ul>
 802                         <li>InstallAnywhere download for Sparc Solaris</li>
 803                 </ul>
 804                 </td>
 805         </tr>
 806         <tr>
 807                 <td>
 808                 <div align="center"><strong>2.02</strong><br>
 809                 18/7/05</div>
 810                 </td>
 811                 <td>&nbsp;</td>
 812                 <td>
 813                 <ul>
 814                         <li>Copy &amp; Paste order of sequences maintains alignment
 815                         order.</li>
 816                 </ul>
 817                 </td>
 818         </tr>
 819         <tr>
 820                 <td>
 821                 <div align="center"><strong>2.01</strong><br>
 822                 12/7/05</div>
 823                 </td>
 824                 <td>
 825                 <ul>
 826                         <li>Use delete key for deleting selection.</li>
 827                         <li>Use Mouse wheel to scroll sequences.</li>
 828                         <li>Help file updated to describe how to add alignment
 829                         annotations.</li>
 830                         <li>Version and build date written to build properties file.</li>
 831                         <li>InstallAnywhere installation will check for updates at
 832                         launch of Jalview.</li>
 833                 </ul>
 834                 </td>
 835                 <td>
 836                 <ul>
 837                         <li>Delete gaps bug fixed.</li>
 838                         <li>FileChooser sorts columns.</li>
 839                         <li>Can remove groups one by one.</li>
 840                         <li>Filechooser icons installed.</li>
 841                         <li>Finder ignores return character when searching. Return key
 842                         will initiate a search.<br>
 843                         </li>
 844                 </ul>
 845                 </td>
 846         </tr>
 847         <tr>
 848                 <td>
 849                 <div align="center"><strong>2.0</strong><br>
 850                 20/6/05</div>
 851                 </td>
 852                 <td>
 853                 <ul>
 854                         <li>New codebase</li>
 855                 </ul>
 856                 </td>
 857                 <td>&nbsp;</td>
 858         </tr>
 859 </table>
 860 <p>&nbsp;</p>
 861 </body>
 862 </html>