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