help/html/releases.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   4  * Copyright (C) 2014 The Jalview Authors
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  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <head>
  21 <title>Release History</title>
  22 </head>
  23 <body>
  24 <p><strong>Release History</strong></p>
  25 <table border="1">
  26         <tr>
  27                 <td width="60" nowrap>
  28                 <div align="center"><em><strong>Release</strong></em></div>
  29                 </td>
  30                 <td>
  31                 <div align="center"><em><strong>New Features</strong></em></div>
  32                 </td>
  33                 <td>
  34                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
  35                 </td>
  36         </tr>
  37         <tr>
  38         <td><div align="center">
  39         <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
  40         </div>
  41         </td>
  42       <td>
  43         <ul>
  44           <li>Trusted certificates for JalviewLite applet and
  45             Jalview Desktop application<br />Certificate was donated by
  46             <a href="https://www.certum.eu">Certum</a> to the Jalview
  47             open source project).
  48           </li>
  49           <li>Jalview SRS links replaced by Uniprot and EBI-search
  50           </li>
  51           <li>Output in Stockholm format</li>
  52           <li>Allow import of data from gzipped files</li>
  53           <li>Export/import group and sequence associated line
  54             graph thresholds</li>
  55           <li>Nucleotide substitution matrix that supports RNA and
  56             ambiguity codes</li>
  57           <li>Allow disorder predictions to be made on the current
  58             selection (or visible selection) in the same way that JPred
  59             works</li>
  60           <li>Groovy scripting for headless jalview operation</li>
  61         </ul> <em>Other improvements</em>
  62         <ul>
  63           <li>Upgrade desktop installer to InstallAnywhere 2013</li>
  64           <li>COMBINE statement uses current SEQUENCE_REF and
  65             GROUP_REF scope to group annotation rows</li>
  66           <li>Support &#39;&#39; style escaping of quotes in Newick
  67             files</li>
  68           <li>Group options for JABAWS service by command line name</li>
  69           <li>Empty tooltip shown for JABA service options with a
  70             link but no description</li>
  71           <li>Select primary source when selecting authority in
  72             database fetcher GUI</li>
  73           <li>Add .mfa to FASTA file extensions recognised by
  74             Jalview</li>
  75           <li>Annotation label tooltip text wrap</li>
  76         </ul>
  77       </td>
  78       <td>
  79         <ul>
  80           <li>Slow scrolling when lots of annotation rows are
  81             displayed</li>
  82           <li>Lots of NPE (and slowness) after creating RNA
  83             secondary structure annotation line</li>
  84           <li>Sequence database accessions not imported when
  85             fetching alignments from Rfam</li>
  86           <li>Incorrect SHMR submission for sequences with
  87             identical IDs</li>
  88           <li>View all structures does not always superpose
  89             structures</li>
  90           <li>Option widgets in service parameters not updated to
  91             reflect user or preset settings</li>
  92           <li>Null pointer exceptions for some services without
  93             presets or adjustable parameters</li>
  94           <li>Discover PDB IDs entry in structure menu doesn&#39;t
  95             discover PDB xRefs</li>
  96           <li>Exception encountered while trying to retrieve
  97             features with DAS</li>
  98           <li>Lowest value in annotation row isn&#39;t coloured
  99             when colour by annotation (per sequence) is coloured</li>
 100           <li>Keyboard mode P jumps to start of gapped region when
 101             residue follows a gap</li>
 102           <li>Jalview appears to hang importing an alignment with
 103             Wrap as default or after enabling Wrap</li>
 104           <li>&#39;Right click to add annotations&#39; message
 105             shown in wrap mode when no annotations present</li>
 106           <li>Disorder predictions fail with NPE if no automatic
 107             annotation already exists on alignment</li>
 108           <li>oninit javascript function should be called after
 109             initialisation completes</li>
 110           <li>Remove redundancy after disorder prediction corrupts
 111             alignment window display</li>
 112           <li>Example annotation file in documentation is invalid</li>
 113           <li>Grouped line graph annotation rows are not exported
 114             to annotation file</li>
 115           <li>Multi-harmony analysis cannot be run when only two
 116             groups created</li>
 117           <li>Cannot create multiple groups of line graphs with
 118             several &#39;combine&#39; statements in annotation file</li>
 119           <li>Pressing return several times causes Number Format
 120             exceptions in keyboard mode</li>
 121           <li>Multi-harmony (SHMMR) method doesn&#39;t submit
 122             correct partitions for input data</li>
 123           <li>Translation from DNA to Amino Acids fails</li>
 124           <li>Jalview fail to load newick tree with quoted label</li>
 125           <li>--headless flag isn&#39;t understood</li>
 126           <li>ClassCastException when generating EPS in headless
 127             mode</li>
 128           <li>Adjusting sequence-associated shading threshold only
 129             changes one row&#39;s threshold</li>
 130           <li>Preferences and Feature settings panel panel
 131             doesn&#39;t open</li>
 132         </ul>
 133       </td>
 134     </tr>
 135   <tr>
 136    <td><div align="center">
 137      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
 138     </div></td>
 139    <td><em>Application</em>
 140     <li>Support for JABAWS 2.0 Services (AACon alignment
 141      conservation, protein disorder and Clustal Omega)</li>
 142     <li>JABAWS server status indicator in Web Services preferences
 143    </li>
 144     <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
 145      Jalview alignment window</li>
 146     <li>Updated Jalview build and deploy framework for OSX mountain
 147      lion, windows 7, and 8</li>
 148     <li>Nucleotide substitution matrix for PCA that supports RNA
 149      and ambiguity codes</li>
 150
 151     <li>Improved sequence database retrieval GUI</li>
 152     <li>Support fetching and database reference look up against
 153      multiple DAS sources (Fetch all from in 'fetch db refs')</li>
 154     <li>Jalview project improvements
 155      <ul>
 156       <li>Store and retrieve the &#39;belowAlignment&#39; flag for
 157        annotation</li>
 158       <li>calcId attribute to group annotation rows on the
 159        alignment</li>
 160       <li>Store AACon calculation settings for a view in Jalview
 161        project</li>
 162
 163      </ul>
 164    </li>
 165     <li>horizontal scrolling gesture support</li>
 166     <li>Visual progress indicator when PCA calculation is running</li>
 167     <li>Simpler JABA web services menus</li>
 168     <li>visual indication that web service results are still being
 169      retrieved from server</li>
 170     <li>Serialise the dialogs that are shown when Jalview starts up
 171      for first time</li>
 172     <li>Jalview user agent string for interacting with HTTP
 173      services</li>
 174     <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
 175      library</li>
 176     <li>Examples directory and Groovy library included in
 177      InstallAnywhere distribution</li>
 178     </ul> <em>Applet</em>
 179     <ul>
 180      <li>RNA alignment and secondary structure annotation
 181       visualization applet example</li>
 182     </ul> <em>General</em>
 183     <ul>
 184      <li>Normalise option for consensus sequence logo</li>
 185      <li>Reset button in PCA window to return dimensions to
 186       defaults</li>
 187      <li>Allow seqspace or Jalview variant of alignment PCA
 188       calculation</li>
 189      <li>PCA with either nucleic acid and protein substitution
 190       matrices
 191      <li>Allow windows containing HTML reports to be exported in
 192       HTML</li>
 193      <li>Interactive display and editing of RNA secondary structure
 194       contacts</li>
 195      <li>RNA Helix Alignment Colouring</li>
 196      <li>RNA base pair logo consensus</li>
 197      <li>Parse sequence associated secondary structure information
 198       in Stockholm files</li>
 199      <li>HTML Export database accessions and annotation information
 200       presented in tooltip for sequences</li>
 201      <li>Import secondary structure from LOCARNA clustalw style RNA
 202       alignment files</li>
 203      <li>import and visualise T-COFFEE quality scores for an
 204       alignment</li>
 205      <li>&#39;colour by annotation&#39; per sequence option to
 206       shade each sequence according to its associated alignment
 207       annotation</li>
 208      <li>New Jalview Logo</li>
 209     </ul> <em>Documentation and Development</em>
 210     <ul>
 211      <li>documentation for score matrices used in Jalview</li>
 212      <li>New Website!</li>
 213     </ul></td>
 214    <td><em>Application</em>
 215     <ul>
 216      <li>PDB, Unprot and EMBL (ENA) databases retrieved via
 217       wsdbfetch REST service</li>
 218      <li>Stop windows being moved outside desktop on OSX</li>
 219      <li>Filetype associations not installed for webstart launch</li>
 220      <li>Jalview does not always retrieve progress of a JABAWS job
 221       execution in full once it is complete</li>
 222      <li>revise SHMR RSBS definition to ensure alignment is
 223       uploaded via ali_file parameter</li>
 224      <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
 225      <li>View all structures superposed fails with exception</li>
 226      <li>Jnet job queues forever if a very short sequence is
 227       submitted for prediction</li>
 228      <li>Cut and paste menu not opened when mouse clicked on
 229       desktop window</li>
 230      <li>Putting fractional value into integer text box in
 231       alignment parameter dialog causes Jalview to hang</li>
 232      <li>Structure view highlighting doesn&#39;t work on windows 7
 233      </li>
 234      <li>View all structures fails with exception shown in
 235       structure view</li>
 236      <li>Characters in filename associated with PDBEntry not
 237       escaped in a platform independent way</li>
 238      <li>Jalview desktop fails to launch with exception when using
 239       proxy</li>
 240      <li>Tree calculation reports &#39;you must have 2 or more
 241       sequences selected&#39; when selection is empty</li>
 242      <li>Jalview desktop fails to launch with jar signature failure
 243       when java web start temporary file caching is disabled</li>
 244      <li>DAS Sequence retrieval with range qualification results in
 245       sequence xref which includes range qualification</li>
 246      <li>Errors during processing of command line arguments cause
 247       progress bar (JAL-898) to be removed</li>
 248      <li>Replace comma for semi-colon option not disabled for DAS
 249       sources in sequence fetcher</li>
 250      <li>Cannot close news reader when JABAWS server warning dialog
 251       is shown</li>
 252      <li>Option widgets not updated to reflect user settings</li>
 253      <li>Edited sequence not submitted to web service</li>
 254      <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
 255      <li>InstallAnywhere installer doesn&#39;t unpack and run on
 256       OSX Mountain Lion</li>
 257      <li>Annotation panel not given a scroll bar when sequences
 258       with alignment annotation are pasted into the alignment</li>
 259      <li>Sequence associated annotation rows not associated when
 260       loaded from Jalview project</li>
 261      <li>Browser launch fails with NPE on java 1.7</li>
 262      <li>JABAWS alignment marked as finished when job was cancelled
 263       or job failed due to invalid input</li>
 264      <li>NPE with v2.7 example when clicking on Tree associated
 265       with all views</li>
 266      <li>Exceptions when copy/paste sequences with grouped
 267       annotation rows to new window</li>
 268     </ul> <em>Applet</em>
 269     <ul>
 270      <li>Sequence features are momentarily displayed before they
 271       are hidden using hidefeaturegroups applet parameter</li>
 272      <li>loading features via javascript API automatically enables
 273       feature display</li>
 274      <li>scrollToColumnIn javascript API method doesn&#39;t work</li>
 275     </ul> <em>General</em>
 276     <ul>
 277      <li>Redundancy removal fails for rna alignment</li>
 278      <li>PCA calculation fails when sequence has been selected and
 279       then deselected</li>
 280      <li>PCA window shows grey box when first opened on OSX</li>
 281      <li>Letters coloured pink in sequence logo when alignment
 282       coloured with clustalx</li>
 283      <li>Choosing fonts without letter symbols defined causes
 284       exceptions and redraw errors</li>
 285      <li>Initial PCA plot view is not same as manually reconfigured
 286       view</li>
 287      <li>Grouped annotation graph label has incorrect line colour</li>
 288      <li>Grouped annotation graph label display is corrupted for
 289       lots of labels</li>
 290     </ul>
 291   </tr>
 292   <tr>
 293    <td>
 294     <div align="center">
 295      <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
 296     </div>
 297    </td>
 298    <td><em>Application</em>
 299     <ul>
 300      <li>Jalview Desktop News Reader</li>
 301      <li>Tweaked default layout of web services menu</li>
 302      <li>View/alignment association menu to enable user to easily
 303       specify which alignment a multi-structure view takes its
 304       colours/correspondences from</li>
 305      <li>Allow properties file location to be specified as URL</li>
 306      <li>Extend Jalview project to preserve associations between
 307       many alignment views and a single Jmol display</li>
 308      <li>Store annotation row height in Jalview project file</li>
 309      <li>Annotation row column label formatting attributes stored
 310       in project file</li>
 311      <li>Annotation row order for auto-calculated annotation rows
 312       preserved in Jalview project file</li>
 313      <li>Visual progress indication when Jalview state is saved
 314       using Desktop window menu</li>
 315      <li>Visual indication that command line arguments are still
 316       being processed</li>
 317      <li>Groovy script execution from URL</li>
 318      <li>Colour by annotation default min and max colours in
 319       preferences</li>
 320      <li>Automatically associate PDB files dragged onto an
 321       alignment with sequences that have high similarity and matching
 322       IDs</li>
 323      <li>Update JGoogleAnalytics to latest release (0.3)</li>
 324      <li>&#39;view structures&#39; option to open many structures
 325       in same window</li>
 326      <li>Sort associated views menu option for tree panel</li>
 327      <li>Group all JABA and non-JABA services for a particular
 328       analysis function in its own submenu</li>
 329     </ul> <em>Applet</em>
 330     <ul>
 331      <li>Userdefined and autogenerated annotation rows for groups</li>
 332      <li>Adjustment of alignment annotation pane height</li>
 333      <li>Annotation scrollbar for annotation panel</li>
 334      <li>Drag to reorder annotation rows in annotation panel</li>
 335      <li>&#39;automaticScrolling&#39; parameter</li>
 336      <li>Allow sequences with partial ID string matches to be
 337       annotated from GFF/Jalview features files</li>
 338      <li>Sequence logo annotation row in applet</li>
 339      <li>Absolute paths relative to host server in applet
 340       parameters are treated as such</li>
 341      <li>New in the JalviewLite javascript API:
 342       <ul>
 343        <li>JalviewLite.js javascript library</li>
 344        <li>Javascript callbacks for
 345         <ul>
 346          <li>Applet initialisation</li>
 347          <li>Sequence/alignment mouse-overs and selections</li>
 348         </ul>
 349        </li>
 350        <li>scrollTo row and column alignment scrolling functions</li>
 351        <li>Select sequence/alignment regions from javascript</li>
 352        <li>javascript structure viewer harness to pass messages
 353         between Jmol and Jalview when running as distinct applets</li>
 354        <li>sortBy method</li>
 355        <li>Set of applet and application examples shipped with
 356         documentation</li>
 357        <li>New example to demonstrate JalviewLite and Jmol
 358         javascript message exchange</li>
 359       </ul>
 360     </ul> <em>General</em>
 361     <ul>
 362      <li>Enable Jmol displays to be associated with multiple
 363       multiple alignments</li>
 364      <li>Option to automatically sort alignment with new tree</li>
 365      <li>User configurable link to enable redirects to a
 366       www.Jalview.org mirror</li>
 367      <li>Jmol colours option for Jmol displays</li>
 368      <li>Configurable newline string when writing alignment and
 369       other flat files</li>
 370      <li>Allow alignment annotation description lines to contain
 371       html tags</li>
 372     </ul> <em>Documentation and Development</em>
 373     <ul>
 374      <li>Add groovy test harness for bulk load testing to examples
 375      </li>
 376      <li>Groovy script to load and align a set of sequences using a
 377       web service before displaying the result in the Jalview desktop</li>
 378      <li>Restructured javascript and applet api documentation</li>
 379      <li>Ant target to publish example html files with applet
 380       archive</li>
 381      <li>Netbeans project for building Jalview from source</li>
 382      <li>ant task to create online javadoc for Jalview source</li>
 383     </ul></td>
 384    <td><em>Application</em>
 385     <ul>
 386      <li>User defined colourscheme throws exception when current
 387       built in colourscheme is saved as new scheme</li>
 388      <li>AlignFrame-&gt;Save in application pops up save dialog for
 389       valid filename/format</li>
 390      <li>Cannot view associated structure for Uniprot sequence</li>
 391      <li>PDB file association breaks for Uniprot sequence P37173</li>
 392      <li>Associate PDB from file dialog does not tell you which
 393       sequence is to be associated with the file</li>
 394      <li>Find All raises null pointer exception when query only
 395       matches sequence IDs</li>
 396      <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
 397      <li>Jalview project with Jmol views created with Jalview 2.4
 398       cannot be loaded</li>
 399      <li>Filetype associations not installed for webstart launch</li>
 400      <li>Two or more chains in a single PDB file associated with
 401       sequences in different alignments do not get coloured by their
 402       associated sequence</li>
 403      <li>Visibility status of autocalculated annotation row not
 404       preserved when project is loaded</li>
 405      <li>Annotation row height and visibility attributes not stored
 406       in Jalview project</li>
 407      <li>Tree bootstraps are not preserved when saved as a Jalview
 408       project</li>
 409      <li>Envision2 workflow tooltips are corrupted</li>
 410      <li>Enabling show group conservation also enables colour by
 411       conservation</li>
 412      <li>Duplicate group associated conservation or consensus
 413       created on new view</li>
 414      <li>Annotation scrollbar not displayed after &#39;show all
 415       hidden annotation rows&#39; option selected</li>
 416      <li>Alignment quality not updated after alignment annotation
 417       row is hidden then shown</li>
 418      <li>Preserve colouring of structures coloured by sequences in
 419       pre Jalview 2.7 projects</li>
 420      <li>Web service job parameter dialog is not laid out properly
 421      </li>
 422      <li>Web services menu not refreshed after &#39;reset
 423       services&#39; button is pressed in preferences</li>
 424      <li>Annotation off by one in Jalview v2_3 example project</li>
 425      <li>Structures imported from file and saved in project get
 426       name like jalview_pdb1234.txt when reloaded</li>
 427      <li>Jalview does not always retrieve progress of a JABAWS job
 428       execution in full once it is complete</li>
 429     </ul> <em>Applet</em>
 430     <ul>
 431      <li>Alignment height set incorrectly when lots of annotation
 432       rows are displayed</li>
 433      <li>Relative URLs in feature HTML text not resolved to
 434       codebase</li>
 435      <li>View follows highlighting does not work for positions in
 436       sequences</li>
 437      <li>&lt;= shown as = in tooltip</li>
 438      <li>Export features raises exception when no features exist</li>
 439      <li>Separator string used for serialising lists of IDs for
 440       javascript api is modified when separator string provided as
 441       parameter</li>
 442      <li>Null pointer exception when selecting tree leaves for
 443       alignment with no existing selection</li>
 444      <li>Relative URLs for datasources assumed to be relative to
 445       applet&#39;s codebase</li>
 446      <li>Status bar not updated after finished searching and search
 447       wraps around to first result</li>
 448      <li>StructureSelectionManager instance shared between several
 449       Jalview applets causes race conditions and memory leaks</li>
 450      <li>Hover tooltip and mouseover of position on structure not
 451       sent from Jmol in applet</li>
 452      <li>Certain sequences of javascript method calls to applet API
 453       fatally hang browser</li>
 454     </ul> <em>General</em>
 455     <ul>
 456      <li>View follows structure mouseover scrolls beyond position
 457       with wrapped view and hidden regions</li>
 458      <li>Find sequence position moves to wrong residue with/without
 459       hidden columns</li>
 460      <li>Sequence length given in alignment properties window is
 461       off by 1</li>
 462      <li>InvalidNumberFormat exceptions thrown when trying to
 463       import PDB like structure files</li>
 464      <li>Positional search results are only highlighted between
 465       user-supplied sequence start/end bounds</li>
 466      <li>End attribute of sequence is not validated</li>
 467      <li>Find dialog only finds first sequence containing a given
 468       sequence position</li>
 469      <li>Sequence numbering not preserved in MSF alignment output</li>
 470      <li>Jalview PDB file reader does not extract sequence from
 471       nucleotide chains correctly</li>
 472      <li>Structure colours not updated when tree partition changed
 473       in alignment</li>
 474      <li>Sequence associated secondary structure not correctly
 475       parsed in interleaved stockholm</li>
 476      <li>Colour by annotation dialog does not restore current state
 477      </li>
 478      <li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
 479      <li>Sequences containing lowercase letters are not properly
 480       associated with their pdb files</li>
 481     </ul> <em>Documentation and Development</em>
 482     <ul>
 483      <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
 484       tool</li>
 485     </ul></td>
 486   </tr>
 487   <tr>
 488                         <td>
 489                                 <div align="center">
 490                                         <strong><a name="Jalview2.6.1">2.6.1</a>
 491                                         </strong><br> <em>15/11/2010</em>
 492                                 </div></td>
 493                         <td><em>Application</em>
 494                                 <ul>
 495                                         <li>New warning dialog when the Jalview Desktop cannot contact
 496                                                 web services</li>
 497                                         <li>JABA service parameters for a preset are shown in service
 498                                                 job window</li>
 499                                         <li>JABA Service menu entries reworded</li>
 500                                 </ul></td>
 501                         <td>
 502                                 <ul>
 503                                         <li>Modeller PIR IO broken - cannot correctly import a pir
 504                                                 file emitted by Jalview</li>
 505                                         <li>Existing feature settings transferred to new alignment
 506                                                 view created from cut'n'paste</li>
 507                                         <li>Improved test for mixed amino/nucleotide chains when
 508                                                 parsing PDB files</li>
 509                                         <li>Consensus and conservation annotation rows occasionally
 510                                                 become blank for all new windows</li>
 511                                         <li>Exception raised when right clicking above sequences in
 512                                                 wrapped view mode</li>
 513                                 </ul> <em>Application</em>
 514                                 <ul>
 515                                         <li>multiple multiply aligned structure views cause cpu usage
 516                                                 to hit 100% and computer to hang</li>
 517                                         <li>Web Service parameter layout breaks for long user
 518                                                 parameter names</li>
 519                                         <li>Jaba service discovery hangs desktop if Jaba server is
 520                                                 down</li>
 521                                 </ul></td>
 522                 </tr>
 523                 <tr>
 524                 <td>
 525                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
 526                 <em>26/9/2010</em></div>
 527                 </td>
 528                 <td><em>Application</em>
 529                 <ul>
 530                         <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
 531                         <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
 532                         <li>Web Services preference tab</li>
 533                         <li>Analysis parameters dialog box and user defined preferences</li>
 534                         <li>Improved speed and layout of Envision2 service menu</li>
 535                         <li>Superpose structures using associated sequence alignment</li>
 536                         <li>Export coordinates and projection as CSV from PCA viewer</li>
 537                 </ul>
 538                 <em>Applet</em>
 539                 <ul>
 540                         <li>enable javascript: execution by the applet via the link out
 541                         mechanism</li>
 542                 </ul>
 543                 <em>Other</em>
 544                 <ul>
 545                         <li>Updated the Jmol Jalview interface to work with Jmol series
 546                         12</li>
 547                         <li>The Jalview Desktop and JalviewLite applet now require Java
 548                         1.5</li>
 549                         <li>Allow Jalview feature colour specification for GFF sequence
 550                         annotation files</li>
 551                         <li>New 'colour by label' keword in Jalview feature file type
 552                         colour specification</li>
 553                         <li>New Jalview Desktop Groovy API method that allows a script
 554                         to check if it being run in an interactive session or in a batch
 555                         operation from the Jalview command line</li>
 556                 </ul>
 557                 </td>
 558                 <td>
 559                 <ul>
 560                         <li>clustalx colourscheme colours Ds preferentially when both
 561                         D+E are present in over 50% of the column</li>
 562                 </ul>
 563
 564                 <em>Application</em>
 565                 <ul>
 566                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 567                         selected Regions menu item</li>
 568                         <li>sequence fetcher replaces ',' for ';' when the ',' is part
 569                         of a valid accession ID</li>
 570                         <li>fatal OOM if object retrieved by sequence fetcher runs out
 571                         of memory</li>
 572                         <li>unhandled Out of Memory Error when viewing pca analysis
 573                         results</li>
 574                         <li>InstallAnywhere builds fail to launch on OS X java 10.5
 575                         update 4 (due to apple Java 1.6 update)</li>
 576                         <li>Installanywhere Jalview silently fails to launch</li>
 577                 </ul>
 578                 <em>Applet</em>
 579                 <ul>
 580                         <li>Jalview.getFeatureGroups() raises an
 581                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
 582                 </ul>
 583                 </td>
 584         </tr>
 585         <tr>
 586                 <td>
 587                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
 588                 <em>14/6/2010</em></div>
 589                 </td>
 590                 <td></td>
 591                 <td>
 592                 <ul>
 593                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
 594                         </li>
 595                         <li>clustalx colourscheme colours Ds preferentially when both
 596                         D+E are present in over 50% of the column</li>
 597                         <li>nucleic acid structures retrieved from PDB do not import
 598                         correctly</li>
 599                         <li>More columns get selected than were clicked on when a number
 600                         of columns are hidden</li>
 601                         <li>annotation label popup menu not providing correct
 602                         add/hide/show options when rows are hidden or none are present</li>
 603                         <li>Stockholm format shown in list of readable formats, and
 604                         parser copes better with alignments from RFAM.</li>
 605                         <li>CSV output of consensus only includes the percentage of all
 606                         symbols if sequence logo display is enabled</li>
 607
 608                 </ul>
 609                 <em>Applet</em>
 610                 <ul>
 611                         <li>annotation panel disappears when annotation is
 612                         hidden/removed</li>
 613                 </ul>
 614                 <em>Application</em>
 615                 <ul>
 616                         <li>Alignment view not redrawn properly when new alignment
 617                         opened where annotation panel is visible but no annotations are
 618                         present on alignment</li>
 619                         <li>pasted region containing hidden columns is incorrectly
 620                         displayed in new alignment window</li>
 621                         <li>Jalview slow to complete operations when stdout is flooded
 622                         (fix is to close the Jalview console)</li>
 623                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 624                         selected Rregions menu item.</li>
 625                         <li>inconsistent group submenu and Format submenu entry 'Un' or
 626                         'Non'conserved</li>
 627                         <li>Sequence feature settings are being shared by multiple
 628                         distinct alignments</li>
 629                         <li>group annotation not recreated when tree partition is
 630                         changed</li>
 631                         <li>double click on group annotation to select sequences does
 632                         not propagate to associated trees</li>
 633                         <li>Mac OSX specific issues:
 634                         <ul>
 635                                 <li>exception raised when mouse clicked on desktop window
 636                                 background</li>
 637                                 <li>Desktop menu placed on menu bar and application name set
 638                                 correctly</li>
 639                                 <li>sequence feature settings not wide enough for the save
 640                                 feature colourscheme button</li>
 641                         </ul>
 642                         </li>
 643                 </ul>
 644                 </td>
 645         </tr>
 646         <tr>
 647
 648                 <td>
 649                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 650                 <em>30/4/2010</em></div>
 651                 </td>
 652                 <td><em>New Capabilities</em>
 653                 <ul>
 654                         <li>URL links generated from description line for
 655                         regular-expression based URL links (applet and application)
 656                         <li>Non-positional feature URL links are shown in link menu</li>
 657                         <li>Linked viewing of nucleic acid sequences and structures</li>
 658                         <li>Automatic Scrolling option in View menu to display the
 659                         currently highlighted region of an alignment.</li>
 660                         <li>Order an alignment by sequence length, or using the average
 661                         score or total feature count for each sequence.</li>
 662                         <li>Shading features by score or associated description</li>
 663                         <li>Subdivide alignment and groups based on identity of selected
 664                         subsequence (Make Groups from Selection).</li>
 665                         <li>New hide/show options including Shift+Control+H to hide
 666                         everything but the currently selected region.</li>
 667                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 668                 </ul>
 669                 <em>Application</em>
 670                 <ul>
 671                         <li>Fetch DB References capabilities and UI expanded to support
 672                         retrieval from DAS sequence sources</li>
 673                         <li>Local DAS Sequence sources can be added via the command line
 674                         or via the Add local source dialog box.</li>
 675                         <li>DAS Dbref and DbxRef feature types are parsed as database
 676                         references and protein_name is parsed as description line (BioSapiens
 677                         terms).</li>
 678                         <li>Enable or disable non-positional feature and database
 679                         references in sequence ID tooltip from View menu in application.</li>
 680                         <!--                    <li>New hidden columns and rows and representatives capabilities
 681                         in annotations file (in progress - not yet fully implemented)</li> -->
 682                         <li>Group-associated consensus, sequence logos and conservation
 683                         plots</li>
 684                         <li>Symbol distributions for each column can be exported and
 685                         visualized as sequence logos</li>
 686                         <li>Optionally scale multi-character column labels to fit within
 687                         each column of annotation row<!-- todo for applet --></li>
 688                         <li>Optional automatic sort of associated alignment view when a
 689                         new tree is opened.</li>
 690                         <li>Jalview Java Console</li>
 691                         <li>Better placement of desktop window when moving between
 692                         different screens.</li>
 693                         <li>New preference items for sequence ID tooltip and consensus
 694                         annotation</li>
 695                         <li>Client to submit sequences and IDs to <a
 696                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 697                         <li><em>Vamsas Capabilities</em>
 698                         <ul>
 699                                 <li>Improved VAMSAS synchronization (Jalview archive used to
 700                                 preserve views, structures, and tree display settings)</li>
 701                                 <li>Import of vamsas documents from disk or URL via command
 702                                 line</li>
 703                                 <li>Sharing of selected regions between views and with other
 704                                 VAMSAS applications (Experimental feature!)</li>
 705                                 <li>Updated API to VAMSAS version 0.2</li>
 706                         </ul>
 707                         </li>
 708                 </ul>
 709                 <em>Applet</em>
 710                 <ul>
 711                         <li>Middle button resizes annotation row height</li>
 712                         <li>New Parameters
 713                         <ul>
 714                                 <li>sortByTree (true/false) - automatically sort the associated
 715                                 alignment view by the tree when a new tree is opened.</li>
 716                                 <li>showTreeBootstraps (true/false) - show or hide branch
 717                                 bootstraps (default is to show them if available)</li>
 718                                 <li>showTreeDistances (true/false) - show or hide branch
 719                                 lengths (default is to show them if available)</li>
 720                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
 721                                 unassociated nodes should be highlighted in the tree view</li>
 722                                 <li>heightScale and widthScale (1.0 or more) - increase the
 723                                 height or width of a cell in the alignment grid relative to the
 724                                 current font size.</li>
 725                         </ul>
 726                         </li>
 727                         <li>Non-positional features displayed in sequence ID tooltip</li>
 728                 </ul>
 729                 <em>Other</em>
 730                 <ul>
 731                         <li>Features format: graduated colour definitions and
 732                         specification of feature scores</li>
 733                         <li>Alignment Annotations format: new keywords for group
 734                         associated annotation (GROUP_REF) and annotation row display
 735                         properties (ROW_PROPERTIES)</li>
 736                         <li>XML formats extended to support graduated feature
 737                         colourschemes, group associated annotation, and profile visualization
 738                         settings.</li>
 739                 </td>
 740                 <td>
 741                 <ul>
 742                         <li>Source field in GFF files parsed as feature source rather
 743                         than description</li>
 744                         <li>Non-positional features are now included in sequence feature
 745                         and gff files (controlled via non-positional feature visibility in
 746                         tooltip).</li>
 747                         <li>URL links generated for all feature links (bugfix)</li>
 748                         <li>Added URL embedding instructions to features file
 749                         documentation.</li>
 750                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 751                         peptide product</li>
 752                         <li>Match case switch in find dialog box works for both sequence
 753                         ID and sequence string and query strings do not have to be in upper
 754                         case to match case-insensitively.</li>
 755                         <li>AMSA files only contain first column of multi-character
 756                         column annotation labels</li>
 757                         <li>Jalview Annotation File generation/parsing consistent with
 758                         documentation (e.g. Stockholm annotation can be exported and
 759                         re-imported)</li>
 760                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 761                         <li>Find incrementally searches ID string matches as well as
 762                         subsequence matches, and correctly reports total number of both.</li>
 763                         <li>Application:
 764                         <ul>
 765                                 <li>Better handling of exceptions during sequence retrieval</li>
 766                                 <li>Dasobert generated non-positional feature URL link text
 767                                 excludes the start_end suffix</li>
 768                                 <li>DAS feature and source retrieval buttons disabled when
 769                                 fetch or registry operations in progress.</li>
 770                                 <li>PDB files retrieved from URLs are cached properly</li>
 771                                 <li>Sequence description lines properly shared via VAMSAS</li>
 772                                 <li>Sequence fetcher fetches multiple records for all data
 773                                 sources</li>
 774                                 <li>Ensured that command line das feature retrieval completes
 775                                 before alignment figures are generated.</li>
 776                                 <li>Reduced time taken when opening file browser for first
 777                                 time.</li>
 778                                 <li>isAligned check prior to calculating tree, PCA or
 779                                 submitting an MSA to JNet now excludes hidden sequences.</li>
 780                                 <li>User defined group colours properly recovered from Jalview
 781                                 projects.</li>
 782                         </ul>
 783                         </li>
 784                 </ul>
 785                 </td>
 786
 787         </tr>
 788         <tr>
 789                 <td>
 790                 <div align="center"><strong>2.4.0.b2</strong><br>
 791                 28/10/2009</div>
 792                 </td>
 793                 <td>
 794                 <ul>
 795                         <li>Experimental support for google analytics usage tracking.</li>
 796                         <li>Jalview privacy settings (user preferences and docs).</li>
 797                 </ul>
 798                 </td>
 799                 <td>
 800                 <ul>
 801                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 802                         <li>Exception when feature created from selection beyond length
 803                         of sequence.</li>
 804                         <li>Allow synthetic PDB files to be imported gracefully</li>
 805                         <li>Sequence associated annotation rows associate with all
 806                         sequences with a given id</li>
 807                         <li>Find function matches case-insensitively for sequence ID
 808                         string searches</li>
 809                         <li>Non-standard characters do not cause pairwise alignment to
 810                         fail with exception</li>
 811                 </ul>
 812                 <em>Application Issues</em>
 813                 <ul>
 814                         <li>Sequences are now validated against EMBL database</li>
 815                         <li>Sequence fetcher fetches multiple records for all data
 816                         sources</li>
 817                 </ul>
 818                 <em>InstallAnywhere Issues</em>
 819                 <ul>
 820                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 821                         installAnywhere mechanism)</li>
 822                         <li>Command line launching of JARs from InstallAnywhere version
 823                         (java class versioning error fixed)</li>
 824                 </ul>
 825                 </td>
 826         </tr>
 827         <tr>
 828                 <td>
 829
 830                 <div align="center"><strong>2.4</strong><br>
 831                 27/8/2008</div>
 832                 </td>
 833                 <td><em>User Interface</em>
 834                 <ul>
 835                         <li>Linked highlighting of codon and amino acid from translation
 836                         and protein products</li>
 837                         <li>Linked highlighting of structure associated with residue
 838                         mapping to codon position</li>
 839                         <li>Sequence Fetcher provides example accession numbers and
 840                         'clear' button</li>
 841                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 842                         <li>Extract score function to parse whitespace separated numeric
 843                         data in description line</li>
 844                         <li>Column labels in alignment annotation can be centred.</li>
 845                         <li>Tooltip for sequence associated annotation give name of
 846                         sequence</li>
 847                 </ul>
 848                 <em>Web Services and URL fetching</em>
 849                 <ul>
 850                         <li>JPred3 web service</li>
 851                         <li>Prototype sequence search client (no public services
 852                         available yet)</li>
 853                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 854                         <li>URL Links created for matching database cross references as
 855                         well as sequence ID</li>
 856                         <li>URL Links can be created using regular-expressions</li>
 857                 </ul>
 858                 <em>Sequence Database Connectivity</em>
 859                 <ul>
 860                         <li>Retrieval of cross-referenced sequences from other databases
 861                         </li>
 862                         <li>Generalised database reference retrieval and validation to
 863                         all fetchable databases</li>
 864                         <li>Fetch sequences from DAS sources supporting the sequence
 865                         command</li>
 866                 </ul>
 867                 <em>Import and Export</em>
 868                 <li>export annotation rows as CSV for spreadsheet import</li>
 869                 <li>Jalview projects record alignment dataset associations, EMBL
 870                 products, and cDNA sequence mappings</li>
 871                 <li>Sequence Group colour can be specified in Annotation File</li>
 872                 <li>Ad-hoc colouring of group in Annotation File using RGB
 873                 triplet as name of colourscheme</li>
 874                 </ul>
 875                 <em>VAMSAS Client capabilities (Experimental)</em>
 876                 <ul>
 877                         <li>treenode binding for VAMSAS tree exchange</li>
 878                         <li>local editing and update of sequences in VAMSAS alignments
 879                         (experimental)</li>
 880                         <li>Create new or select existing session to join</li>
 881                         <li>load and save of vamsas documents</li>
 882                 </ul>
 883                 <em>Application command line</em>
 884                 <ul>
 885                         <li>-tree parameter to open trees (introduced for passing from
 886                         applet)</li>
 887                         <li>-fetchfrom command line argument to specify nicknames of DAS
 888                         servers to query for alignment features</li>
 889                         <li>-dasserver command line argument to add new servers that are
 890                         also automatically queried for features</li>
 891                         <li>-groovy command line argument executes a given groovy script
 892                         after all input data has been loaded and parsed</li>
 893                 </ul>
 894                 <em>Applet-Application data exchange</em>
 895                 <ul>
 896                         <li>Trees passed as applet parameters can be passed to
 897                         application (when using &quot;View in full application&quot;)</li>
 898                 </ul>
 899                 <em>Applet Parameters</em>
 900                 <ul>
 901                         <li>feature group display control parameter</li>
 902                         <li>debug parameter</li>
 903                         <li>showbutton parameter</li>
 904                 </ul>
 905                 <em>Applet API methods</em>
 906                 <ul>
 907                         <li>newView public method</li>
 908                         <li>Window (current view) specific get/set public methods</li>
 909                         <li>Feature display control methods</li>
 910                         <li>get list of currently selected sequences</li>
 911                 </ul>
 912                 <em>New Jalview distribution features</em>
 913                 <ul>
 914                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 915                         <li>RELEASE file gives build properties for the latest Jalview
 916                         release.</li>
 917                         <li>Java 1.1 Applet build made easier and donotobfuscate
 918                         property controls execution of obfuscator</li>
 919                         <li>Build target for generating source distribution</li>
 920                         <li>Debug flag for javacc</li>
 921                         <li>.jalview_properties file is documented (slightly) in
 922                         jalview.bin.Cache</li>
 923                         <li>Continuous Build Integration for stable and development
 924                         version of Application, Applet and source distribution</li>
 925                 </ul>
 926
 927                 </td>
 928                 <td>
 929                 <ul>
 930                         <li>selected region output includes visible annotations (for
 931                         certain formats)</li>
 932                         <li>edit label/displaychar contains existing label/char for
 933                         editing</li>
 934                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
 935                         <li>shorter peptide product names from EMBL records</li>
 936                         <li>Newick string generator makes compact representations</li>
 937                         <li>bootstrap values parsed correctly for tree files with
 938                         comments</li>
 939                         <li>pathological filechooser bug avoided by not allowing
 940                         filenames containing a ':'</li>
 941                         <li>Fixed exception when parsing GFF files containing global
 942                         sequence features</li>
 943                         <li>Alignment datasets are finalized only when number of
 944                         references from alignment sequences goes to zero</li>
 945                         <li>Close of tree branch colour box without colour selection
 946                         causes cascading exceptions</li>
 947                         <li>occasional negative imgwidth exceptions</li>
 948                         <li>better reporting of non-fatal warnings to user when file
 949                         parsing fails.</li>
 950                         <li>Save works when Jalview project is default format</li>
 951                         <li>Save as dialog opened if current alignment format is not a
 952                         valid output format</li>
 953                         <li>Uniprot canonical names introduced for both das and vamsas</li>
 954                         <li>Histidine should be midblue (not pink!) in Zappo</li>
 955                         <li>error messages passed up and output when data read fails</li>
 956                         <li>edit undo recovers previous dataset sequence when sequence
 957                         is edited</li>
 958                         <li>allow PDB files without pdb ID HEADER lines (like those
 959                         generated by MODELLER) to be read in properly</li>
 960                         <li>allow reading of JPred concise files as a normal filetype</li>
 961                         <li>Stockholm annotation parsing and alignment properties import
 962                         fixed for PFAM records</li>
 963                         <li>Structure view windows have correct name in Desktop window
 964                         list</li>
 965                         <li>annotation consisting of sequence associated scores can be
 966                         read and written correctly to annotation file</li>
 967                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
 968                         <li>Fixed display of hidden sequence markers and non-italic font
 969                         for representatives in Applet</li>
 970                         <li>Applet Menus are always embedded in applet window on Macs.</li>
 971                         <li>Newly shown features appear at top of stack (in Applet)</li>
 972                         <li>Annotations added via parameter not drawn properly due to
 973                         null pointer exceptions</li>
 974                         <li>Secondary structure lines are drawn starting from first
 975                         column of alignment</li>
 976                         <li>Uniprot XML import updated for new schema release in July
 977                         2008</li>
 978                         <li>Sequence feature to sequence ID match for Features file is
 979                         case-insensitive</li>
 980                         <li>Sequence features read from Features file appended to all
 981                         sequences with matching IDs</li>
 982                         <li>PDB structure coloured correctly for associated views
 983                         containing a sub-sequence</li>
 984                         <li>PDB files can be retrieved by applet from Jar files</li>
 985                         <li>feature and annotation file applet parameters referring to
 986                         different directories are retrieved correctly</li>
 987                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
 988                         <li>Fixed application hang whilst waiting for splash-screen
 989                         version check to complete</li>
 990                         <li>Applet properly URLencodes input parameter values when
 991                         passing them to the launchApp service</li>
 992                         <li>display name and local features preserved in results
 993                         retrieved from web service</li>
 994                         <li>Visual delay indication for sequence retrieval and sequence
 995                         fetcher initialisation</li>
 996                         <li>updated Application to use DAS 1.53e version of dasobert DAS
 997                         client</li>
 998                         <li>Re-instated Full AMSA support and .amsa file association</li>
 999                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1000                         sequences</li>
1001                 </ul>
1002                 </td>
1003         </tr>
1004         <tr>
1005                 <td>
1006                 <div align="center"><strong>2.3</strong><br>
1007                 9/5/07</div>
1008                 </td>
1009                 <td>
1010                 <ul>
1011                         <li>Jmol 11.0.2 integration</li>
1012                         <li>PDB views stored in Jalview XML files</li>
1013                         <li>Slide sequences</li>
1014                         <li>Edit sequence in place</li>
1015                         <li>EMBL CDS features</li>
1016                         <li>DAS Feature mapping</li>
1017                         <li>Feature ordering</li>
1018                         <li>Alignment Properties</li>
1019                         <li>Annotation Scores</li>
1020                         <li>Sort by scores</li>
1021                         <li>Feature/annotation editing in applet</li>
1022                 </ul>
1023                 </td>
1024                 <td>
1025                 <ul>
1026                         <li>Headless state operation in 2.2.1</li>
1027                         <li>Incorrect and unstable DNA pairwise alignment</li>
1028                         <li>Cut and paste of sequences with annotation</li>
1029                         <li>Feature group display state in XML</li>
1030                         <li>Feature ordering in XML</li>
1031                         <li>blc file iteration selection using filename # suffix</li>
1032                         <li>Stockholm alignment properties</li>
1033                         <li>Stockhom alignment secondary structure annotation</li>
1034                         <li>2.2.1 applet had no feature transparency</li>
1035                         <li>Number pad keys can be used in cursor mode</li>
1036                         <li>Structure Viewer mirror image resolved</li>
1037                 </ul>
1038                 </td>
1039
1040         </tr>
1041         <tr>
1042                 <td>
1043                 <div align="center"><strong>2.2.1</strong><br>
1044                 12/2/07</div>
1045                 </td>
1046                 <td>
1047                 <ul>
1048                         <li>Non standard characters can be read and displayed
1049                         <li>Annotations/Features can be imported/exported to the applet
1050                         via textbox
1051                         <li>Applet allows editing of sequence/annotation/group name
1052                         &amp; description
1053                         <li>Preference setting to display sequence name in italics
1054                         <li>Annotation file format extended to allow Sequence_groups to
1055                         be defined
1056                         <li>Default opening of alignment overview panel can be specified
1057                         in preferences
1058                         <li>PDB residue numbering annotation added to associated
1059                         sequences
1060                 </ul>
1061                 </td>
1062                 <td>
1063                 <ul>
1064                         <li>Applet crash under certain Linux OS with Java 1.6 installed
1065                         <li>Annotation file export / import bugs fixed
1066                         <li>PNG / EPS image output bugs fixed
1067                 </ul>
1068                 </td>
1069         </tr>
1070         <tr>
1071                 <td>
1072                 <div align="center"><strong>2.2</strong><br>
1073                 27/11/06</div>
1074                 </td>
1075                 <td>
1076                 <ul>
1077                         <li>Multiple views on alignment
1078                         <li>Sequence feature editing
1079                         <li>&quot;Reload&quot; alignment
1080                         <li>&quot;Save&quot; to current filename
1081                         <li>Background dependent text colour
1082                         <li>Right align sequence ids
1083                         <li>User-defined lower case residue colours
1084                         <li>Format Menu
1085                         <li>Select Menu
1086                         <li>Menu item accelerator keys
1087                         <li>Control-V pastes to current alignment
1088                         <li>Cancel button for DAS Feature Fetching
1089                         <li>PCA and PDB Viewers zoom via mouse roller
1090                         <li>User-defined sub-tree colours and sub-tree selection
1091                         <li>'New Window' button on the 'Output to Text box'
1092                 </ul>
1093                 </td>
1094                 <td>
1095                 <ul>
1096                         <li>New memory efficient Undo/Redo System
1097                         <li>Optimised symbol lookups and conservation/consensus
1098                         calculations
1099                         <li>Region Conservation/Consensus recalculated after edits
1100                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
1101                         alignment)
1102                         <li>Slowed DAS Feature Fetching for increased robustness.
1103                         <li>Made angle brackets in ASCII feature descriptions display
1104                         correctly
1105                         <li>Re-instated Zoom function for PCA
1106                         <li>Sequence descriptions conserved in web service analysis
1107                         results
1108                         <li>Uniprot ID discoverer uses any word separated by &#8739;
1109                         <li>WsDbFetch query/result association resolved
1110                         <li>Tree leaf to sequence mapping improved
1111                         <li>Smooth fonts switch moved to FontChooser dialog box.
1112                 </ul>
1113                 </td>
1114         </tr>
1115         <tr>
1116                 <td>
1117                 <div align="center"><strong>2.1.1</strong><br>
1118                 12/9/06</div>
1119                 </td>
1120                 <td>
1121                 <ul>
1122                         <li>Copy consensus sequence to clipboard</li>
1123                 </ul>
1124                 </td>
1125                 <td>
1126                 <ul>
1127                         <li>Image output - rightmost residues are rendered if sequence
1128                         id panel has been resized</li>
1129                         <li>Image output - all offscreen group boundaries are rendered</li>
1130                         <li>Annotation files with sequence references - all elements in
1131                         file are relative to sequence position</li>
1132                         <li>Mac Applet users can use Alt key for group editing</li>
1133                 </ul>
1134                 </td>
1135         </tr>
1136         <tr>
1137                 <td>
1138                 <div align="center"><strong>2.1</strong><br>
1139                 22/8/06</div>
1140                 </td>
1141                 <td>
1142                 <ul>
1143                         <li>MAFFT Multiple Alignment in default Web Service list</li>
1144                         <li>DAS Feature fetching</li>
1145                         <li>Hide sequences and columns</li>
1146                         <li>Export Annotations and Features</li>
1147                         <li>GFF file reading / writing</li>
1148                         <li>Associate structures with sequences from local PDB files</li>
1149                         <li>Add sequences to exisiting alignment</li>
1150                         <li>Recently opened files / URL lists</li>
1151                         <li>Applet can launch the full application</li>
1152                         <li>Applet has transparency for features (Java 1.2 required)</li>
1153                         <li>Applet has user defined colours parameter</li>
1154                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
1155                 </ul>
1156                 </td>
1157                 <td>
1158                 <ul>
1159                         <li>Redundancy Panel reinstalled in the Applet</li>
1160                         <li>Monospaced font - EPS / rescaling bug fixed</li>
1161                         <li>Annotation files with sequence references bug fixed</li>
1162                 </ul>
1163                 </td>
1164         </tr>
1165         <tr>
1166                 <td>
1167                 <div align="center"><strong>2.08.1</strong><br>
1168                 2/5/06</div>
1169                 </td>
1170                 <td>
1171                 <ul>
1172                         <li>Change case of selected region from Popup menu</li>
1173                         <li>Choose to match case when searching</li>
1174                         <li>Middle mouse button and mouse movement can compress / expand
1175                         the visible width and height of the alignment</li>
1176                 </ul>
1177                 </td>
1178                 <td>
1179                 <ul>
1180                         <li>Annotation Panel displays complete JNet results</li>
1181                 </ul>
1182                 </td>
1183         </tr>
1184         <tr>
1185                 <td>
1186                 <div align="center"><strong>2.08b</strong><br>
1187                 18/4/06</div>
1188                 </td>
1189                 <td>&nbsp;</td>
1190                 <td>
1191                 <ul>
1192                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1193                         <li>Righthand label on wrapped alignments shows correct value</li>
1194                 </ul>
1195                 </td>
1196         </tr>
1197         <tr>
1198                 <td>
1199                 <div align="center"><strong>2.08</strong><br>
1200                 10/4/06</div>
1201                 </td>
1202                 <td>
1203                 <ul>
1204                         <li>Editing can be locked to the selection area</li>
1205                         <li>Keyboard editing</li>
1206                         <li>Create sequence features from searches</li>
1207                         <li>Precalculated annotations can be loaded onto alignments</li>
1208                         <li>Features file allows grouping of features</li>
1209                         <li>Annotation Colouring scheme added</li>
1210                         <li>Smooth fonts off by default - Faster rendering</li>
1211                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
1212                 </ul>
1213                 </td>
1214                 <td>
1215                 <ul>
1216                         <li>Drag &amp; Drop fixed on Linux</li>
1217                         <li>Jalview Archive file faster to load/save, sequence
1218                         descriptions saved.</li>
1219                 </ul>
1220                 </td>
1221         </tr>
1222         <tr>
1223                 <td>
1224                 <div align="center"><strong>2.07</strong><br>
1225                 12/12/05</div>
1226                 </td>
1227                 <td>
1228                 <ul>
1229                         <li>PDB Structure Viewer enhanced</li>
1230                         <li>Sequence Feature retrieval and display enhanced</li>
1231                         <li>Choose to output sequence start-end after sequence name for
1232                         file output</li>
1233                         <li>Sequence Fetcher WSDBFetch@EBI</li>
1234                         <li>Applet can read feature files, PDB files and can be used for
1235                         HTML form input</li>
1236                 </ul>
1237                 </td>
1238                 <td>
1239                 <ul>
1240                         <li>HTML output writes groups and features</li>
1241                         <li>Group editing is Control and mouse click</li>
1242                         <li>File IO bugs</li>
1243                 </ul>
1244                 </td>
1245         </tr>
1246         <tr>
1247                 <td>
1248                 <div align="center"><strong>2.06</strong><br>
1249                 28/9/05</div>
1250                 </td>
1251                 <td>
1252                 <ul>
1253                         <li>View annotations in wrapped mode</li>
1254                         <li>More options for PCA viewer</li>
1255                 </ul>
1256                 </td>
1257                 <td>
1258                 <ul>
1259                         <li>GUI bugs resolved</li>
1260                         <li>Runs with -nodisplay from command line</li>
1261                 </ul>
1262                 </td>
1263         </tr>
1264         <tr>
1265                 <td height="63">
1266                 <div align="center"><strong>2.05b</strong><br>
1267                 15/9/05</div>
1268                 </td>
1269                 <td>
1270                 <ul>
1271                         <li>Choose EPS export as lineart or text</li>
1272                         <li>Jar files are executable</li>
1273                         <li>Can read in Uracil - maps to unknown residue</li>
1274                 </ul>
1275                 </td>
1276                 <td>
1277                 <ul>
1278                         <li>Known OutOfMemory errors give warning message</li>
1279                         <li>Overview window calculated more efficiently</li>
1280                         <li>Several GUI bugs resolved</li>
1281                 </ul>
1282                 </td>
1283         </tr>
1284         <tr>
1285                 <td>
1286                 <div align="center"><strong>2.05</strong><br>
1287                 30/8/05</div>
1288                 </td>
1289                 <td>
1290                 <ul>
1291                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
1292                 </ul>
1293                 </td>
1294                 <td>
1295                 <ul>
1296                         <li>Several GUI bugs resolved</li>
1297                 </ul>
1298                 </td>
1299         </tr>
1300         <tr>
1301                 <td>
1302                 <div align="center"><strong>2.04</strong><br>
1303                 24/8/05</div>
1304                 </td>
1305                 <td>
1306                 <ul>
1307                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
1308                 </ul>
1309                 </td>
1310                 <td>
1311                 <ul>
1312                         <li>Improved JPred client reliability</li>
1313                         <li>Improved loading of Jalview files</li>
1314                 </ul>
1315                 </td>
1316         </tr>
1317         <tr>
1318                 <td>
1319                 <div align="center"><strong>2.03</strong><br>
1320                 18/8/05</div>
1321                 </td>
1322                 <td>
1323                 <ul>
1324                         <li>Set Proxy server name and port in preferences</li>
1325                         <li>Multiple URL links from sequence ids</li>
1326                         <li>User Defined Colours can have a scheme name and added to
1327                         Colour Menu</li>
1328                         <li>Choose to ignore gaps in consensus calculation</li>
1329                         <li>Unix users can set default web browser</li>
1330                         <li>Runs without GUI for batch processing</li>
1331                         <li>Dynamically generated Web Service Menus</li>
1332                 </ul>
1333                 </td>
1334                 <td>
1335                 <ul>
1336                         <li>InstallAnywhere download for Sparc Solaris</li>
1337                 </ul>
1338                 </td>
1339         </tr>
1340         <tr>
1341                 <td>
1342                 <div align="center"><strong>2.02</strong><br>
1343                 18/7/05</div>
1344                 </td>
1345                 <td>&nbsp;</td>
1346                 <td>
1347                 <ul>
1348                         <li>Copy &amp; Paste order of sequences maintains alignment
1349                         order.</li>
1350                 </ul>
1351                 </td>
1352         </tr>
1353         <tr>
1354                 <td>
1355                 <div align="center"><strong>2.01</strong><br>
1356                 12/7/05</div>
1357                 </td>
1358                 <td>
1359                 <ul>
1360                         <li>Use delete key for deleting selection.</li>
1361                         <li>Use Mouse wheel to scroll sequences.</li>
1362                         <li>Help file updated to describe how to add alignment
1363                         annotations.</li>
1364                         <li>Version and build date written to build properties file.</li>
1365                         <li>InstallAnywhere installation will check for updates at
1366                         launch of Jalview.</li>
1367                 </ul>
1368                 </td>
1369                 <td>
1370                 <ul>
1371                         <li>Delete gaps bug fixed.</li>
1372                         <li>FileChooser sorts columns.</li>
1373                         <li>Can remove groups one by one.</li>
1374                         <li>Filechooser icons installed.</li>
1375                         <li>Finder ignores return character when searching. Return key
1376                         will initiate a search.<br>
1377                         </li>
1378                 </ul>
1379                 </td>
1380         </tr>
1381         <tr>
1382                 <td>
1383                 <div align="center"><strong>2.0</strong><br>
1384                 20/6/05</div>
1385                 </td>
1386                 <td>
1387                 <ul>
1388                         <li>New codebase</li>
1389                 </ul>
1390                 </td>
1391                 <td>&nbsp;</td>
1392         </tr>
1393 </table>
1394 <p>&nbsp;</p>
1395 </body>
1396 </html>