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
  21                 <td>
  22                 <div align="center"><strong>2.4.1</strong><br>
  23                 <em>Not Yet Released</em></div>
  24                 </td>
  25                 <td>
  26                 <ul>
  27                 <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
  28                 </li>
  29                 <li>URL links generated from description line for regular-expression based URL links (applet and application)
  30                 </li>
  31                 <li>Non-positional features displayed in sequence ID tooltip on applet
  32                 </li>
  33                 <li>Non-positional feature URL links are shown in link menu (applet and application)
  34                 </li>
  35                 <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
  36                 </li>
  37                 <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
  38                 </li>
  39                 <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
  40                 </li>
  41                 <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
  42                 </ul>
  43                 </td>
  44                 <td>
  45                 <ul>
  46                 <li>URL links generated for all feature links (bugfix)</li>
  47                 <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
  48                 <li>Added URL embedding instructions to features file documentation.</li>
  49                 <li>Sequences are now validated against EMBL database (broken in Version 2.4.0)</li>
  50                 <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
  51                 <li>Sequence description lines properly shared via VAMSAS</li>
  52                 <li>Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.</li>
  53                 </ul>
  54                 </td>
  55
  56         </tr>
  57         <tr>
  58                 <td>
  59                 <div align="center"><strong>2.4</strong><br>
  60                 27/8//2008</div>
  61                 </td>
  62                 <td>
  63                         <em>User Interface</em>
  64                         <ul>
  65                         <li>Linked highlighting of codon and amino acid from translation
  66                         and protein products</li>
  67                         <li>Linked highlighting of structure associated with residue mapping to codon position</li>
  68                         <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
  69                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
  70                         <li>Extract score function to parse whitespace separated numeric data in description line</li>
  71                         <li>Column labels in alignment annotation can be centred.</li>
  72                         <li>Tooltip for sequence associated annotation give name of sequence</li>
  73                         </ul>
  74                         <em>Web Services and URL fetching</em>
  75                         <ul>
  76                         <li>JPred3 web service</li>
  77                         <li>Prototype sequence search client (no public services available yet)</li>
  78                         <li>Fetch either seed alignment or full alignment from PFAM</li>
  79                         <li>URL Links created for matching database cross references as well as sequence ID</li>
  80                         <li>URL Links can be created using regular-expressions</li>
  81                         </ul>
  82                 <em>Sequence Database Connectivity</em>
  83                         <ul>
  84                         <li>Retrieval of cross-referenced sequences from other databases
  85                         </li>
  86                         <li>Generalised database reference retrieval and validation to
  87                         all fetchable databases</li>
  88                         <li>Fetch sequences from DAS sources supporting the sequence command</li>
  89                         </ul>
  90                         <em>Import and Export</em>
  91                         <li>export annotation rows as CSV for spreadsheet import</li>
  92                         <li>Jalview projects record alignment dataset associations, EMBL
  93                         products, and cDNA sequence mappings</li>
  94                         <li>Sequence Group colour can be specified in Annotation File</li>
  95                         <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
  96                         </ul>
  97                 <em>VAMSAS Client capabilities (Experimental)</em>
  98                         <ul>
  99                                 <li>treenode binding for VAMSAS tree exchange</li>
 100                                 <li>local editing and update of sequences in VAMSAS alignments
 101                                 (experimental)</li>
 102                                 <li>Create new or select existing session to join</li>
 103                                 <li>load and save of vamsas documents</li>
 104                         </ul>
 105         <em>Application command line</em>
 106                         <ul>
 107                                 <li>-tree parameter to open trees (introduced for passing from
 108                                 applet)</li>
 109                                 <li>-fetchfrom command line argument to specify nicknames of
 110                                 DAS servers to query for alignment features</li>
 111                                 <li>-dasserver command line argument to add new servers that
 112                                 are also automatically queried for features</li>
 113                                 <li>-groovy command line argument executes a given groovy
 114                                 script after all input data has been loaded and parsed</li>
 115                         </ul>
 116         <em>Applet-Application data exchange</em>
 117                 <ul>
 118                 <li>Trees passed as applet parameters can be passed to
 119                         application (when using &quot;View in full application&quot;)</li>
 120                 </ul>
 121         <em>Applet Parameters</em>
 122                         <ul>
 123                                 <li>feature group display control parameter</li>
 124                                 <li>debug parameter</li>
 125                                 <li>showbutton parameter</li>
 126                         </ul>
 127         <em>Applet API methods</em>
 128                         <ul>
 129                                 <li>newView public method</li>
 130                                 <li>Window (current view) specific get/set public methods</li>
 131                                 <li>Feature display control methods</li>
 132                                 <li>get list of currently selected sequences</li>
 133                         </ul>
 134         <em>New Jalview distribution features</em>
 135                 <ul>
 136                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 137                         <li>RELEASE file gives build properties for the latest Jalview
 138                         release.</li>
 139                         <li>Java 1.1 Applet build made easier and donotobfuscate
 140                         property controls execution of obfuscator</li>
 141                         <li>Build target for generating source distribution</li>
 142                         <li>Debug flag for javacc</li>
 143                         <li>.jalview_properties file is documented (slightly) in
 144                         jalview.bin.Cache</li>
 145             <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>
 146                 </ul>
 147
 148                 </td>
 149                 <td>
 150                 <ul>
 151                         <li>selected region output includes visible annotations (for
 152                         certain formats)</li>
 153                         <li>edit label/displaychar contains existing label/char for
 154                         editing</li>
 155                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 156                         <li>shorter peptide product names from EMBL records</li>
 157                         <li>Newick string generator makes compact representations</li>
 158                         <li>bootstrap values parsed correctly for tree files with
 159                         comments</li>
 160                         <li>pathological filechooser bug avoided by not allowing
 161                         filenames containing a ':'</li>
 162                         <li>Fixed exception when parsing GFF files containing global
 163                         sequence features</li>
 164                         <li>Alignment datasets are finalized only when number of
 165                         references from alignment sequences goes to zero</li>
 166                         <li>Close of tree branch colour box without colour selection
 167                         causes cascading exceptions</li>
 168                         <li>occasional negative imgwidth exceptions</li>
 169                         <li>better reporting of non-fatal warnings to user when file
 170                         parsing fails.</li>
 171                         <li>Save works when Jalview project is default format</li>
 172                         <li>Save as dialog opened if current alignment format is not a valid output format</li>
 173                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 174                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 175                         <li>error messages passed up and output when data read fails</li>
 176                         <li>edit undo recovers previous dataset sequence when sequence
 177                         is edited</li>
 178                         <li>allow PDB files without pdb ID HEADER lines (like those
 179                         generated by MODELLER) to be read in properly</li>
 180                         <li>allow reading of JPred concise files as a normal filetype</li>
 181                         <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
 182                         </li>
 183                         <li>Structure view windows have correct name in Desktop window list</li>
 184                         <li>annotation consisting of sequence associated scores can be
 185                         read and written correctly to annotation file</li>
 186                         <li>Aligned cDNA translation to aligned peptide works correctly
 187                         </li>
 188                         <li>Fixed display of hidden sequence markers and non-italic font
 189                         for representatives in Applet</li>
 190                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 191                         <li>Newly shown features appear at top of stack (in Applet)</li>
 192                         <li>Annotations added via parameter not drawn properly due to
 193                         null pointer exceptions</li>
 194                         <li>Secondary structure lines are drawn starting from first
 195                         column of alignment</li>
 196                         <li>Uniprot XML import updated for new schema release in July 2008</li>
 197                         <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
 198                         <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
 199                         <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
 200                         <li>PDB files can be retrieved by applet from Jar files</li>
 201                         <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>
 202                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 203                         <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
 204                         <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
 205                         <li>display name and local features preserved in results retrieved from web service</li>
 206                         <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
 207                         <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
 208                         <li>Re-instated Full AMSA support and .amsa file association</li>
 209                         <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>
 210                 </ul>
 211                 </td>
 212         </tr>
 213         <tr>
 214         <td>
 215                 <div align="center"><strong>2.3</strong><br>
 216                 9/5/07</div>
 217                 </td>
 218                 <td>
 219                 <ul>
 220                         <li>Jmol 11.0.2 integration</li>
 221                         <li>PDB views stored in Jalview XML files</li>
 222                         <li>Slide sequences</li>
 223                         <li>Edit sequence in place</li>
 224                         <li>EMBL CDS features</li>
 225                         <li>DAS Feature mapping</li>
 226                         <li>Feature ordering</li>
 227                         <li>Alignment Properties</li>
 228                         <li>Annotation Scores</li>
 229                         <li>Sort by scores</li>
 230                         <li>Feature/annotation editing in applet</li>
 231                 </ul>
 232                 </td>
 233                 <td>
 234                 <ul>
 235                         <li>Headless state operation in 2.2.1</li>
 236                         <li>Incorrect and unstable DNA pairwise alignment</li>
 237                         <li>Cut and paste of sequences with annotation</li>
 238                         <li>Feature group display state in XML</li>
 239                         <li>Feature ordering in XML</li>
 240                         <li>blc file iteration selection using filename # suffix</li>
 241                         <li>Stockholm alignment properties</li>
 242                         <li>Stockhom alignment secondary structure annotation</li>
 243                         <li>2.2.1 applet had no feature transparency</li>
 244                         <li>Number pad keys can be used in cursor mode</li>
 245                         <li>Structure Viewer mirror image resolved</li>
 246                 </ul>
 247                 </td>
 248
 249         </tr>
 250         <tr>
 251                 <td>
 252                 <div align="center"><strong>2.2.1</strong><br>
 253                 12/2/07</div>
 254                 </td>
 255                 <td>
 256                 <ul>
 257                         <li>Non standard characters can be read and displayed
 258                         <li>Annotations/Features can be imported/exported to the applet
 259                         via textbox
 260                         <li>Applet allows editing of sequence/annotation/group name
 261                         &amp; description
 262                         <li>Preference setting to display sequence name in italics
 263                         <li>Annotation file format extended to allow Sequence_groups to
 264                         be defined
 265                         <li>Default opening of alignment overview panel can be specified
 266                         in preferences
 267                         <li>PDB residue numbering annotation added to associated
 268                         sequences
 269                 </ul>
 270                 </td>
 271                 <td>
 272                 <ul>
 273                         <li>Applet crash under certain Linux OS with Java 1.6 installed
 274                         <li>Annotation file export / import bugs fixed
 275                         <li>PNG / EPS image output bugs fixed
 276                 </ul>
 277                 </td>
 278         </tr>
 279         <tr>
 280                 <td>
 281                 <div align="center"><strong>2.2</strong><br>
 282                 27/11/06</div>
 283                 </td>
 284                 <td>
 285                 <ul>
 286                         <li>Multiple views on alignment
 287                         <li>Sequence feature editing
 288                         <li>&quot;Reload&quot; alignment
 289                         <li>&quot;Save&quot; to current filename
 290                         <li>Background dependent text colour
 291                         <li>Right align sequence ids
 292                         <li>User-defined lower case residue colours
 293                         <li>Format Menu
 294                         <li>Select Menu
 295                         <li>Menu item accelerator keys
 296                         <li>Control-V pastes to current alignment
 297                         <li>Cancel button for DAS Feature Fetching
 298                         <li>PCA and PDB Viewers zoom via mouse roller
 299                         <li>User-defined sub-tree colours and sub-tree selection
 300                         <li>'New Window' button on the 'Output to Text box'
 301                 </ul>
 302                 </td>
 303                 <td>
 304                 <ul>
 305                         <li>New memory efficient Undo/Redo System
 306                         <li>Optimised symbol lookups and conservation/consensus
 307                         calculations
 308                         <li>Region Conservation/Consensus recalculated after edits
 309                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
 310                         alignment)
 311                         <li>Slowed DAS Feature Fetching for increased robustness.
 312                         <li>Made angle brackets in ASCII feature descriptions display
 313                         correctly
 314                         <li>Re-instated Zoom function for PCA
 315                         <li>Sequence descriptions conserved in web service analysis
 316                         results
 317                         <li>Uniprot ID discoverer uses any word separated by &#8739;
 318                         <li>WsDbFetch query/result association resolved
 319                         <li>Tree leaf to sequence mapping improved
 320                         <li>Smooth fonts switch moved to FontChooser dialog box.
 321                 </ul>
 322                 </td>
 323         </tr>
 324         <tr>
 325                 <td>
 326                 <div align="center"><strong>2.1.1</strong><br>
 327                 12/9/06</div>
 328                 </td>
 329                 <td>
 330                 <ul>
 331                         <li>Copy consensus sequence to clipboard</li>
 332                 </ul>
 333                 </td>
 334                 <td>
 335                 <ul>
 336                         <li>Image output - rightmost residues are rendered if sequence
 337                         id panel has been resized</li>
 338                         <li>Image output - all offscreen group boundaries are rendered</li>
 339                         <li>Annotation files with sequence references - all elements in
 340                         file are relative to sequence position</li>
 341                         <li>Mac Applet users can use Alt key for group editing</li>
 342                 </ul>
 343                 </td>
 344         </tr>
 345         <tr>
 346                 <td>
 347                 <div align="center"><strong>2.1</strong><br>
 348                 22/8/06</div>
 349                 </td>
 350                 <td>
 351                 <ul>
 352                         <li>MAFFT Multiple Alignment in default Web Service list</li>
 353                         <li>DAS Feature fetching</li>
 354                         <li>Hide sequences and columns</li>
 355                         <li>Export Annotations and Features</li>
 356                         <li>GFF file reading / writing</li>
 357                         <li>Associate structures with sequences from local PDB files</li>
 358                         <li>Add sequences to exisiting alignment</li>
 359                         <li>Recently opened files / URL lists</li>
 360                         <li>Applet can launch the full application</li>
 361                         <li>Applet has transparency for features (Java 1.2 required)</li>
 362                         <li>Applet has user defined colours parameter</li>
 363                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
 364                 </ul>
 365                 </td>
 366                 <td>
 367                 <ul>
 368                         <li>Redundancy Panel reinstalled in the Applet</li>
 369                         <li>Monospaced font - EPS / rescaling bug fixed</li>
 370                         <li>Annotation files with sequence references bug fixed</li>
 371                 </ul>
 372                 </td>
 373         </tr>
 374         <tr>
 375                 <td>
 376                 <div align="center"><strong>2.08.1</strong><br>
 377                 2/5/06</div>
 378                 </td>
 379                 <td>
 380                 <ul>
 381                         <li>Change case of selected region from Popup menu</li>
 382                         <li>Choose to match case when searching</li>
 383                         <li>Middle mouse button and mouse movement can compress / expand
 384                         the visible width and height of the alignment</li>
 385                 </ul>
 386                 </td>
 387                 <td>
 388                 <ul>
 389                         <li>Annotation Panel displays complete JNet results</li>
 390                 </ul>
 391                 </td>
 392         </tr>
 393         <tr>
 394                 <td>
 395                 <div align="center"><strong>2.08b</strong><br>
 396                 18/4/06</div>
 397                 </td>
 398                 <td>&nbsp;</td>
 399                 <td>
 400                 <ul>
 401                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
 402                         <li>Righthand label on wrapped alignments shows correct value</li>
 403                 </ul>
 404                 </td>
 405         </tr>
 406         <tr>
 407                 <td>
 408                 <div align="center"><strong>2.08</strong><br>
 409                 10/4/06</div>
 410                 </td>
 411                 <td>
 412                 <ul>
 413                         <li>Editing can be locked to the selection area</li>
 414                         <li>Keyboard editing</li>
 415                         <li>Create sequence features from searches</li>
 416                         <li>Precalculated annotations can be loaded onto alignments</li>
 417                         <li>Features file allows grouping of features</li>
 418                         <li>Annotation Colouring scheme added</li>
 419                         <li>Smooth fonts off by default - Faster rendering</li>
 420                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
 421                 </ul>
 422                 </td>
 423                 <td>
 424                 <ul>
 425                         <li>Drag &amp; Drop fixed on Linux</li>
 426                         <li>Jalview Archive file faster to load/save, sequence
 427                         descriptions saved.</li>
 428                 </ul>
 429                 </td>
 430         </tr>
 431         <tr>
 432                 <td>
 433                 <div align="center"><strong>2.07</strong><br>
 434                 12/12/05</div>
 435                 </td>
 436                 <td>
 437                 <ul>
 438                         <li>PDB Structure Viewer enhanced</li>
 439                         <li>Sequence Feature retrieval and display enhanced</li>
 440                         <li>Choose to output sequence start-end after sequence name for
 441                         file output</li>
 442                         <li>Sequence Fetcher WSDBFetch@EBI</li>
 443                         <li>Applet can read feature files, PDB files and can be used for
 444                         HTML form input</li>
 445                 </ul>
 446                 </td>
 447                 <td>
 448                 <ul>
 449                         <li>HTML output writes groups and features</li>
 450                         <li>Group editing is Control and mouse click</li>
 451                         <li>File IO bugs</li>
 452                 </ul>
 453                 </td>
 454         </tr>
 455         <tr>
 456                 <td>
 457                 <div align="center"><strong>2.06</strong><br>
 458                 28/9/05</div>
 459                 </td>
 460                 <td>
 461                 <ul>
 462                         <li>View annotations in wrapped mode</li>
 463                         <li>More options for PCA viewer</li>
 464                 </ul>
 465                 </td>
 466                 <td>
 467                 <ul>
 468                         <li>GUI bugs resolved</li>
 469                         <li>Runs with -nodisplay from command line</li>
 470                 </ul>
 471                 </td>
 472         </tr>
 473         <tr>
 474                 <td height="63">
 475                 <div align="center"><strong>2.05b</strong><br>
 476                 15/9/05</div>
 477                 </td>
 478                 <td>
 479                 <ul>
 480                         <li>Choose EPS export as lineart or text</li>
 481                         <li>Jar files are executable</li>
 482                         <li>Can read in Uracil - maps to unknown residue</li>
 483                 </ul>
 484                 </td>
 485                 <td>
 486                 <ul>
 487                         <li>Known OutOfMemory errors give warning message</li>
 488                         <li>Overview window calculated more efficiently</li>
 489                         <li>Several GUI bugs resolved</li>
 490                 </ul>
 491                 </td>
 492         </tr>
 493         <tr>
 494                 <td>
 495                 <div align="center"><strong>2.05</strong><br>
 496                 30/8/05</div>
 497                 </td>
 498                 <td>
 499                 <ul>
 500                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
 501                 </ul>
 502                 </td>
 503                 <td>
 504                 <ul>
 505                         <li>Several GUI bugs resolved</li>
 506                 </ul>
 507                 </td>
 508         </tr>
 509         <tr>
 510                 <td>
 511                 <div align="center"><strong>2.04</strong><br>
 512                 24/8/05</div>
 513                 </td>
 514                 <td>
 515                 <ul>
 516                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
 517                 </ul>
 518                 </td>
 519                 <td>
 520                 <ul>
 521                         <li>Improved JPred client reliability</li>
 522                         <li>Improved loading of Jalview files</li>
 523                 </ul>
 524                 </td>
 525         </tr>
 526         <tr>
 527                 <td>
 528                 <div align="center"><strong>2.03</strong><br>
 529                 18/8/05</div>
 530                 </td>
 531                 <td>
 532                 <ul>
 533                         <li>Set Proxy server name and port in preferences</li>
 534                         <li>Multiple URL links from sequence ids</li>
 535                         <li>User Defined Colours can have a scheme name and added to
 536                         Colour Menu</li>
 537                         <li>Choose to ignore gaps in consensus calculation</li>
 538                         <li>Unix users can set default web browser</li>
 539                         <li>Runs without GUI for batch processing</li>
 540                         <li>Dynamically generated Web Service Menus</li>
 541                 </ul>
 542                 </td>
 543                 <td>
 544                 <ul>
 545                         <li>InstallAnywhere download for Sparc Solaris</li>
 546                 </ul>
 547                 </td>
 548         </tr>
 549         <tr>
 550                 <td>
 551                 <div align="center"><strong>2.02</strong><br>
 552                 18/7/05</div>
 553                 </td>
 554                 <td>&nbsp;</td>
 555                 <td>
 556                 <ul>
 557                         <li>Copy &amp; Paste order of sequences maintains alignment
 558                         order.</li>
 559                 </ul>
 560                 </td>
 561         </tr>
 562         <tr>
 563                 <td>
 564                 <div align="center"><strong>2.01</strong><br>
 565                 12/7/05</div>
 566                 </td>
 567                 <td>
 568                 <ul>
 569                         <li>Use delete key for deleting selection.</li>
 570                         <li>Use Mouse wheel to scroll sequences.</li>
 571                         <li>Help file updated to describe how to add alignment
 572                         annotations.</li>
 573                         <li>Version and build date written to build properties file.</li>
 574                         <li>InstallAnywhere installation will check for updates at
 575                         launch of Jalview.</li>
 576                 </ul>
 577                 </td>
 578                 <td>
 579                 <ul>
 580                         <li>Delete gaps bug fixed.</li>
 581                         <li>FileChooser sorts columns.</li>
 582                         <li>Can remove groups one by one.</li>
 583                         <li>Filechooser icons installed.</li>
 584                         <li>Finder ignores return character when searching. Return key
 585                         will initiate a search.<br>
 586                         </li>
 587                 </ul>
 588                 </td>
 589         </tr>
 590         <tr>
 591                 <td>
 592                 <div align="center"><strong>2.0</strong><br>
 593                 20/6/05</div>
 594                 </td>
 595                 <td>
 596                 <ul>
 597                         <li>New codebase</li>
 598                 </ul>
 599                 </td>
 600                 <td>&nbsp;</td>
 601         </tr>
 602 </table>
 603 <p>&nbsp;</p>
 604 </body>
 605 </html>