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