help/html/releases.html

   1 <html>
   2 <head>
   3 <title>Release History</title>
   4 </head>
   5 <body>
   6 <p><strong>Release History</strong></p>
   7 <table border="1">
   8         <tr>
   9                 <td width="60" nowrap>
  10                 <div align="center"><em><strong>Release</strong></em></div>
  11                 </td>
  12                 <td>
  13                 <div align="center"><em><strong>New Features</strong></em></div>
  14                 </td>
  15                 <td>
  16                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
  17                 </td>
  18         </tr>
  19         <tr>
  20         <td>
  21         <div align="center"><strong>2.4.0.b2</strong><br>
  22                 2/6/2009</div>
  23         </td>
  24         <td>
  25         <ul><li>Experimental support for google analytics usage tracking.</li>
  26         </ul>
  27         </td>
  28         <td>
  29                 <ul><li>Fixed race condition in applet preventing startup in jre1.6.0u12+.</li>
  30                 <li></li>
  31                 </ul>
  32         </td>
  33         </tr>
  34         <tr>
  35             <td>
  36               <div align="center"><strong>2.4 bugfixes</strong><br>
  37                 12/11/2008</div>
  38                 </td>
  39             <td>
  40             </td>
  41             <td>
  42             <ul>
  43                         <li>Sequences are now validated against EMBL database</li>
  44                         <li>Sequence fetcher fetches multiple records for all data sources</li>
  45             </ul>
  46             </td>
  47         </tr>
  48         <tr>
  49                 <td>
  50
  51                 <div align="center"><strong>2.4</strong><br>
  52                 27/8/2008</div>
  53                 </td>
  54                 <td>
  55                         <em>User Interface</em>
  56                         <ul>
  57                         <li>Linked highlighting of codon and amino acid from translation
  58                         and protein products</li>
  59                         <li>Linked highlighting of structure associated with residue mapping to codon position</li>
  60                         <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
  61                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
  62                         <li>Extract score function to parse whitespace separated numeric data in description line</li>
  63                         <li>Column labels in alignment annotation can be centred.</li>
  64                         <li>Tooltip for sequence associated annotation give name of sequence</li>
  65                         </ul>
  66                         <em>Web Services and URL fetching</em>
  67                         <ul>
  68                         <li>JPred3 web service</li>
  69                         <li>Prototype sequence search client (no public services available yet)</li>
  70                         <li>Fetch either seed alignment or full alignment from PFAM</li>
  71                         <li>URL Links created for matching database cross references as well as sequence ID</li>
  72                         <li>URL Links can be created using regular-expressions</li>
  73                         </ul>
  74                 <em>Sequence Database Connectivity</em>
  75                         <ul>
  76                         <li>Retrieval of cross-referenced sequences from other databases
  77                         </li>
  78                         <li>Generalised database reference retrieval and validation to
  79                         all fetchable databases</li>
  80                         <li>Fetch sequences from DAS sources supporting the sequence command</li>
  81                         </ul>
  82                         <em>Import and Export</em>
  83                         <li>export annotation rows as CSV for spreadsheet import</li>
  84                         <li>Jalview projects record alignment dataset associations, EMBL
  85                         products, and cDNA sequence mappings</li>
  86                         <li>Sequence Group colour can be specified in Annotation File</li>
  87                         <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
  88                         </ul>
  89                 <em>VAMSAS Client capabilities (Experimental)</em>
  90                         <ul>
  91                                 <li>treenode binding for VAMSAS tree exchange</li>
  92                                 <li>local editing and update of sequences in VAMSAS alignments
  93                                 (experimental)</li>
  94                                 <li>Create new or select existing session to join</li>
  95                                 <li>load and save of vamsas documents</li>
  96                         </ul>
  97         <em>Application command line</em>
  98                         <ul>
  99                                 <li>-tree parameter to open trees (introduced for passing from
 100                                 applet)</li>
 101                                 <li>-fetchfrom command line argument to specify nicknames of
 102                                 DAS servers to query for alignment features</li>
 103                                 <li>-dasserver command line argument to add new servers that
 104                                 are also automatically queried for features</li>
 105                                 <li>-groovy command line argument executes a given groovy
 106                                 script after all input data has been loaded and parsed</li>
 107                         </ul>
 108         <em>Applet-Application data exchange</em>
 109                 <ul>
 110                 <li>Trees passed as applet parameters can be passed to
 111                         application (when using &quot;View in full application&quot;)</li>
 112                 </ul>
 113         <em>Applet Parameters</em>
 114                         <ul>
 115                                 <li>feature group display control parameter</li>
 116                                 <li>debug parameter</li>
 117                                 <li>showbutton parameter</li>
 118                         </ul>
 119         <em>Applet API methods</em>
 120                         <ul>
 121                                 <li>newView public method</li>
 122                                 <li>Window (current view) specific get/set public methods</li>
 123                                 <li>Feature display control methods</li>
 124                                 <li>get list of currently selected sequences</li>
 125                         </ul>
 126         <em>New Jalview distribution features</em>
 127                 <ul>
 128                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 129                         <li>RELEASE file gives build properties for the latest Jalview
 130                         release.</li>
 131                         <li>Java 1.1 Applet build made easier and donotobfuscate
 132                         property controls execution of obfuscator</li>
 133                         <li>Build target for generating source distribution</li>
 134                         <li>Debug flag for javacc</li>
 135                         <li>.jalview_properties file is documented (slightly) in
 136                         jalview.bin.Cache</li>
 137             <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>
 138                 </ul>
 139
 140                 </td>
 141                 <td>
 142                 <ul>
 143                         <li>selected region output includes visible annotations (for
 144                         certain formats)</li>
 145                         <li>edit label/displaychar contains existing label/char for
 146                         editing</li>
 147                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 148                         <li>shorter peptide product names from EMBL records</li>
 149                         <li>Newick string generator makes compact representations</li>
 150                         <li>bootstrap values parsed correctly for tree files with
 151                         comments</li>
 152                         <li>pathological filechooser bug avoided by not allowing
 153                         filenames containing a ':'</li>
 154                         <li>Fixed exception when parsing GFF files containing global
 155                         sequence features</li>
 156                         <li>Alignment datasets are finalized only when number of
 157                         references from alignment sequences goes to zero</li>
 158                         <li>Close of tree branch colour box without colour selection
 159                         causes cascading exceptions</li>
 160                         <li>occasional negative imgwidth exceptions</li>
 161                         <li>better reporting of non-fatal warnings to user when file
 162                         parsing fails.</li>
 163                         <li>Save works when Jalview project is default format</li>
 164                         <li>Save as dialog opened if current alignment format is not a valid output format</li>
 165                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 166                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 167                         <li>error messages passed up and output when data read fails</li>
 168                         <li>edit undo recovers previous dataset sequence when sequence
 169                         is edited</li>
 170                         <li>allow PDB files without pdb ID HEADER lines (like those
 171                         generated by MODELLER) to be read in properly</li>
 172                         <li>allow reading of JPred concise files as a normal filetype</li>
 173                         <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
 174                         </li>
 175                         <li>Structure view windows have correct name in Desktop window list</li>
 176                         <li>annotation consisting of sequence associated scores can be
 177                         read and written correctly to annotation file</li>
 178                         <li>Aligned cDNA translation to aligned peptide works correctly
 179                         </li>
 180                         <li>Fixed display of hidden sequence markers and non-italic font
 181                         for representatives in Applet</li>
 182                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 183                         <li>Newly shown features appear at top of stack (in Applet)</li>
 184                         <li>Annotations added via parameter not drawn properly due to
 185                         null pointer exceptions</li>
 186                         <li>Secondary structure lines are drawn starting from first
 187                         column of alignment</li>
 188                         <li>Uniprot XML import updated for new schema release in July 2008</li>
 189                         <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
 190                         <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
 191                         <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
 192                         <li>PDB files can be retrieved by applet from Jar files</li>
 193                         <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>
 194                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 195                         <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
 196                         <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
 197                         <li>display name and local features preserved in results retrieved from web service</li>
 198                         <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
 199                         <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
 200                         <li>Re-instated Full AMSA support and .amsa file association</li>
 201                         <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>
 202
 203                 </ul>
 204                 </td>
 205         </tr>
 206         <tr>
 207         <td>
 208                 <div align="center"><strong>2.3</strong><br>
 209                 9/5/07</div>
 210                 </td>
 211                 <td>
 212                 <ul>
 213                         <li>Jmol 11.0.2 integration</li>
 214                         <li>PDB views stored in Jalview XML files</li>
 215                         <li>Slide sequences</li>
 216                         <li>Edit sequence in place</li>
 217                         <li>EMBL CDS features</li>
 218                         <li>DAS Feature mapping</li>
 219                         <li>Feature ordering</li>
 220                         <li>Alignment Properties</li>
 221                         <li>Annotation Scores</li>
 222                         <li>Sort by scores</li>
 223                         <li>Feature/annotation editing in applet</li>
 224                 </ul>
 225                 </td>
 226                 <td>
 227                 <ul>
 228                         <li>Headless state operation in 2.2.1</li>
 229                         <li>Incorrect and unstable DNA pairwise alignment</li>
 230                         <li>Cut and paste of sequences with annotation</li>
 231                         <li>Feature group display state in XML</li>
 232                         <li>Feature ordering in XML</li>
 233                         <li>blc file iteration selection using filename # suffix</li>
 234                         <li>Stockholm alignment properties</li>
 235                         <li>Stockhom alignment secondary structure annotation</li>
 236                         <li>2.2.1 applet had no feature transparency</li>
 237                         <li>Number pad keys can be used in cursor mode</li>
 238                         <li>Structure Viewer mirror image resolved</li>
 239                 </ul>
 240                 </td>
 241
 242         </tr>
 243         <tr>
 244                 <td>
 245                 <div align="center"><strong>2.2.1</strong><br>
 246                 12/2/07</div>
 247                 </td>
 248                 <td>
 249                 <ul>
 250                         <li>Non standard characters can be read and displayed
 251                         <li>Annotations/Features can be imported/exported to the applet
 252                         via textbox
 253                         <li>Applet allows editing of sequence/annotation/group name
 254                         &amp; description
 255                         <li>Preference setting to display sequence name in italics
 256                         <li>Annotation file format extended to allow Sequence_groups to
 257                         be defined
 258                         <li>Default opening of alignment overview panel can be specified
 259                         in preferences
 260                         <li>PDB residue numbering annotation added to associated
 261                         sequences
 262                 </ul>
 263                 </td>
 264                 <td>
 265                 <ul>
 266                         <li>Applet crash under certain Linux OS with Java 1.6 installed
 267                         <li>Annotation file export / import bugs fixed
 268                         <li>PNG / EPS image output bugs fixed
 269                 </ul>
 270                 </td>
 271         </tr>
 272         <tr>
 273                 <td>
 274                 <div align="center"><strong>2.2</strong><br>
 275                 27/11/06</div>
 276                 </td>
 277                 <td>
 278                 <ul>
 279                         <li>Multiple views on alignment
 280                         <li>Sequence feature editing
 281                         <li>&quot;Reload&quot; alignment
 282                         <li>&quot;Save&quot; to current filename
 283                         <li>Background dependent text colour
 284                         <li>Right align sequence ids
 285                         <li>User-defined lower case residue colours
 286                         <li>Format Menu
 287                         <li>Select Menu
 288                         <li>Menu item accelerator keys
 289                         <li>Control-V pastes to current alignment
 290                         <li>Cancel button for DAS Feature Fetching
 291                         <li>PCA and PDB Viewers zoom via mouse roller
 292                         <li>User-defined sub-tree colours and sub-tree selection
 293                         <li>'New Window' button on the 'Output to Text box'
 294                 </ul>
 295                 </td>
 296                 <td>
 297                 <ul>
 298                         <li>New memory efficient Undo/Redo System
 299                         <li>Optimised symbol lookups and conservation/consensus
 300                         calculations
 301                         <li>Region Conservation/Consensus recalculated after edits
 302                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
 303                         alignment)
 304                         <li>Slowed DAS Feature Fetching for increased robustness.
 305                         <li>Made angle brackets in ASCII feature descriptions display
 306                         correctly
 307                         <li>Re-instated Zoom function for PCA
 308                         <li>Sequence descriptions conserved in web service analysis
 309                         results
 310                         <li>Uniprot ID discoverer uses any word separated by &#8739;
 311                         <li>WsDbFetch query/result association resolved
 312                         <li>Tree leaf to sequence mapping improved
 313                         <li>Smooth fonts switch moved to FontChooser dialog box.
 314                 </ul>
 315                 </td>
 316         </tr>
 317         <tr>
 318                 <td>
 319                 <div align="center"><strong>2.1.1</strong><br>
 320                 12/9/06</div>
 321                 </td>
 322                 <td>
 323                 <ul>
 324                         <li>Copy consensus sequence to clipboard</li>
 325                 </ul>
 326                 </td>
 327                 <td>
 328                 <ul>
 329                         <li>Image output - rightmost residues are rendered if sequence
 330                         id panel has been resized</li>
 331                         <li>Image output - all offscreen group boundaries are rendered</li>
 332                         <li>Annotation files with sequence references - all elements in
 333                         file are relative to sequence position</li>
 334                         <li>Mac Applet users can use Alt key for group editing</li>
 335                 </ul>
 336                 </td>
 337         </tr>
 338         <tr>
 339                 <td>
 340                 <div align="center"><strong>2.1</strong><br>
 341                 22/8/06</div>
 342                 </td>
 343                 <td>
 344                 <ul>
 345                         <li>MAFFT Multiple Alignment in default Web Service list</li>
 346                         <li>DAS Feature fetching</li>
 347                         <li>Hide sequences and columns</li>
 348                         <li>Export Annotations and Features</li>
 349                         <li>GFF file reading / writing</li>
 350                         <li>Associate structures with sequences from local PDB files</li>
 351                         <li>Add sequences to exisiting alignment</li>
 352                         <li>Recently opened files / URL lists</li>
 353                         <li>Applet can launch the full application</li>
 354                         <li>Applet has transparency for features (Java 1.2 required)</li>
 355                         <li>Applet has user defined colours parameter</li>
 356                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
 357                 </ul>
 358                 </td>
 359                 <td>
 360                 <ul>
 361                         <li>Redundancy Panel reinstalled in the Applet</li>
 362                         <li>Monospaced font - EPS / rescaling bug fixed</li>
 363                         <li>Annotation files with sequence references bug fixed</li>
 364                 </ul>
 365                 </td>
 366         </tr>
 367         <tr>
 368                 <td>
 369                 <div align="center"><strong>2.08.1</strong><br>
 370                 2/5/06</div>
 371                 </td>
 372                 <td>
 373                 <ul>
 374                         <li>Change case of selected region from Popup menu</li>
 375                         <li>Choose to match case when searching</li>
 376                         <li>Middle mouse button and mouse movement can compress / expand
 377                         the visible width and height of the alignment</li>
 378                 </ul>
 379                 </td>
 380                 <td>
 381                 <ul>
 382                         <li>Annotation Panel displays complete JNet results</li>
 383                 </ul>
 384                 </td>
 385         </tr>
 386         <tr>
 387                 <td>
 388                 <div align="center"><strong>2.08b</strong><br>
 389                 18/4/06</div>
 390                 </td>
 391                 <td>&nbsp;</td>
 392                 <td>
 393                 <ul>
 394                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
 395                         <li>Righthand label on wrapped alignments shows correct value</li>
 396                 </ul>
 397                 </td>
 398         </tr>
 399         <tr>
 400                 <td>
 401                 <div align="center"><strong>2.08</strong><br>
 402                 10/4/06</div>
 403                 </td>
 404                 <td>
 405                 <ul>
 406                         <li>Editing can be locked to the selection area</li>
 407                         <li>Keyboard editing</li>
 408                         <li>Create sequence features from searches</li>
 409                         <li>Precalculated annotations can be loaded onto alignments</li>
 410                         <li>Features file allows grouping of features</li>
 411                         <li>Annotation Colouring scheme added</li>
 412                         <li>Smooth fonts off by default - Faster rendering</li>
 413                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
 414                 </ul>
 415                 </td>
 416                 <td>
 417                 <ul>
 418                         <li>Drag &amp; Drop fixed on Linux</li>
 419                         <li>Jalview Archive file faster to load/save, sequence
 420                         descriptions saved.</li>
 421                 </ul>
 422                 </td>
 423         </tr>
 424         <tr>
 425                 <td>
 426                 <div align="center"><strong>2.07</strong><br>
 427                 12/12/05</div>
 428                 </td>
 429                 <td>
 430                 <ul>
 431                         <li>PDB Structure Viewer enhanced</li>
 432                         <li>Sequence Feature retrieval and display enhanced</li>
 433                         <li>Choose to output sequence start-end after sequence name for
 434                         file output</li>
 435                         <li>Sequence Fetcher WSDBFetch@EBI</li>
 436                         <li>Applet can read feature files, PDB files and can be used for
 437                         HTML form input</li>
 438                 </ul>
 439                 </td>
 440                 <td>
 441                 <ul>
 442                         <li>HTML output writes groups and features</li>
 443                         <li>Group editing is Control and mouse click</li>
 444                         <li>File IO bugs</li>
 445                 </ul>
 446                 </td>
 447         </tr>
 448         <tr>
 449                 <td>
 450                 <div align="center"><strong>2.06</strong><br>
 451                 28/9/05</div>
 452                 </td>
 453                 <td>
 454                 <ul>
 455                         <li>View annotations in wrapped mode</li>
 456                         <li>More options for PCA viewer</li>
 457                 </ul>
 458                 </td>
 459                 <td>
 460                 <ul>
 461                         <li>GUI bugs resolved</li>
 462                         <li>Runs with -nodisplay from command line</li>
 463                 </ul>
 464                 </td>
 465         </tr>
 466         <tr>
 467                 <td height="63">
 468                 <div align="center"><strong>2.05b</strong><br>
 469                 15/9/05</div>
 470                 </td>
 471                 <td>
 472                 <ul>
 473                         <li>Choose EPS export as lineart or text</li>
 474                         <li>Jar files are executable</li>
 475                         <li>Can read in Uracil - maps to unknown residue</li>
 476                 </ul>
 477                 </td>
 478                 <td>
 479                 <ul>
 480                         <li>Known OutOfMemory errors give warning message</li>
 481                         <li>Overview window calculated more efficiently</li>
 482                         <li>Several GUI bugs resolved</li>
 483                 </ul>
 484                 </td>
 485         </tr>
 486         <tr>
 487                 <td>
 488                 <div align="center"><strong>2.05</strong><br>
 489                 30/8/05</div>
 490                 </td>
 491                 <td>
 492                 <ul>
 493                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
 494                 </ul>
 495                 </td>
 496                 <td>
 497                 <ul>
 498                         <li>Several GUI bugs resolved</li>
 499                 </ul>
 500                 </td>
 501         </tr>
 502         <tr>
 503                 <td>
 504                 <div align="center"><strong>2.04</strong><br>
 505                 24/8/05</div>
 506                 </td>
 507                 <td>
 508                 <ul>
 509                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
 510                 </ul>
 511                 </td>
 512                 <td>
 513                 <ul>
 514                         <li>Improved JPred client reliability</li>
 515                         <li>Improved loading of Jalview files</li>
 516                 </ul>
 517                 </td>
 518         </tr>
 519         <tr>
 520                 <td>
 521                 <div align="center"><strong>2.03</strong><br>
 522                 18/8/05</div>
 523                 </td>
 524                 <td>
 525                 <ul>
 526                         <li>Set Proxy server name and port in preferences</li>
 527                         <li>Multiple URL links from sequence ids</li>
 528                         <li>User Defined Colours can have a scheme name and added to
 529                         Colour Menu</li>
 530                         <li>Choose to ignore gaps in consensus calculation</li>
 531                         <li>Unix users can set default web browser</li>
 532                         <li>Runs without GUI for batch processing</li>
 533                         <li>Dynamically generated Web Service Menus</li>
 534                 </ul>
 535                 </td>
 536                 <td>
 537                 <ul>
 538                         <li>InstallAnywhere download for Sparc Solaris</li>
 539                 </ul>
 540                 </td>
 541         </tr>
 542         <tr>
 543                 <td>
 544                 <div align="center"><strong>2.02</strong><br>
 545                 18/7/05</div>
 546                 </td>
 547                 <td>&nbsp;</td>
 548                 <td>
 549                 <ul>
 550                         <li>Copy &amp; Paste order of sequences maintains alignment
 551                         order.</li>
 552                 </ul>
 553                 </td>
 554         </tr>
 555         <tr>
 556                 <td>
 557                 <div align="center"><strong>2.01</strong><br>
 558                 12/7/05</div>
 559                 </td>
 560                 <td>
 561                 <ul>
 562                         <li>Use delete key for deleting selection.</li>
 563                         <li>Use Mouse wheel to scroll sequences.</li>
 564                         <li>Help file updated to describe how to add alignment
 565                         annotations.</li>
 566                         <li>Version and build date written to build properties file.</li>
 567                         <li>InstallAnywhere installation will check for updates at
 568                         launch of Jalview.</li>
 569                 </ul>
 570                 </td>
 571                 <td>
 572                 <ul>
 573                         <li>Delete gaps bug fixed.</li>
 574                         <li>FileChooser sorts columns.</li>
 575                         <li>Can remove groups one by one.</li>
 576                         <li>Filechooser icons installed.</li>
 577                         <li>Finder ignores return character when searching. Return key
 578                         will initiate a search.<br>
 579                         </li>
 580                 </ul>
 581                 </td>
 582         </tr>
 583         <tr>
 584                 <td>
 585                 <div align="center"><strong>2.0</strong><br>
 586                 20/6/05</div>
 587                 </td>
 588                 <td>
 589                 <ul>
 590                         <li>New codebase</li>
 591                 </ul>
 592                 </td>
 593                 <td>&nbsp;</td>
 594         </tr>
 595 </table>
 596 <p>&nbsp;</p>
 597 </body>
 598 </html>