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