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