help/html/releases.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
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  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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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.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
  40                                 </div></td>
  41                         <td>
  42                                 <!--  New features --> <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
  43                                 <em>General</em>
  44                                 <ul>
  45                                         <li>Internationalisation of user interface (usually called
  46                                                 i18n support) and translation for Spanish locale</li>
  47                                         <li>Define/Undefine group on current selection with
  48                                                 Ctrl-G/Shift Ctrl-G</li>
  49                                         <li>Improved group creation/removal options in
  50                                                 alignment/sequence Popup menu</li>
  51                                         <li>Sensible precision for symbol distribution percentages
  52                                                 shown in logo tooltip.</li>
  53                                         <li>Annotation panel height set according to amount of
  54                                                 annotation when alignment first opened</li>
  55                                 </ul> <em>Application</em>
  56                                 <ul>
  57                                         <li>Interactive consensus RNA secondary structure prediction
  58                                                 VIENNA RNAAliFold JABA 2.1 service</li>
  59                                         <li>Select columns containing particular features from Feature
  60                                                 Settings dialog</li>
  61                                         <li>View all 'representative' PDB structures for selected
  62                                                 sequences</li>
  63                                         <li>Update Jalview project format:
  64                                                 <ul>
  65               <li>New file extension for Jalview projects '.jvp'</li>
  66                                                         <li>Preserve sequence and annotation dataset (to store
  67                                                                 secondary structure annotation,etc)</li>
  68                                                         <li>Per group and alignment annotation and RNA helix
  69                                                                 colouring</li>
  70                                                 </ul>
  71                                         </li>
  72                                         <li>New similarity measures for PCA and Tree calculation
  73                                                 (PAM250)</li>
  74                                         <li>Experimental support for retrieval and viewing of flanking
  75                                                 regions for an alignment</li>
  76                                 </ul>
  77                         </td>
  78                         <td>
  79                                 <!--  issues resolved --> <em>Application</em>
  80                                 <ul>
  81                                         <li>logo keeps spinning and status remains at queued or
  82                                                 running after job is cancelled</li>
  83                                         <li>cannot export features from alignments imported from
  84                                                 Jalview/VAMSAS projects</li>
  85                                         <li>Buggy slider for web service parameters that take float
  86                                                 values</li>
  87                                         <li>Newly created RNA secondary structure line doesn't have
  88                                                 'display all symbols' flag set</li>
  89                                         <li>T-COFFEE alignment score shading scheme and other
  90                                                 annotation shading not saved in jalview project</li>
  91                                         <li>Local file cannot be loaded in freshly downloaded Jalview</li>
  92                                         <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
  93                                         <li>Load file from desktop file browser fails</li>
  94                                         <li>Occasional NPE thrown when calculating large trees</li>
  95                                         <li>Cannot reorder or slide sequences after dragging an
  96                                                 alignment onto desktop</li>
  97                                         <li>Colour by annotation dialog throws NPE after using
  98                                                 'extract scores' function</li>
  99                                         <li>Loading/cut'n'pasting an empty file leads to a grey
 100                                                 alignment window</li>
 101                                         <li>Disorder thresholds rendered incorrectly after performing
 102                                                 IUPred disorder prediction</li>
 103                                         <li>Multiple group annotated consensus rows shown when
 104                                                 changing 'normalise logo' display setting</li>
 105                                         <li>Find shows blank dialog after 'finished searching' if
 106                                                 nothing matches query</li>
 107                                         <li>Null Pointer Exceptions raised when sorting by feature
 108                                                 with lots of groups<!--  possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
 109                                         </li>
 110                                         <li>Errors in Jmol console when structures in alignment don't
 111                                                 overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
 112                                         </li>
 113                                         <li>Not all working JABAWS services are shown in Jalview's
 114                                                 menu</li>
 115                                         <li>JAVAWS version of jalview fails to launch with 'invalid
 116                                                 literal/length code'</li>
 117                                         <li>Annotation/RNA Helix colourschemes cannot be applied to
 118                                                 alignment with groups (actually fixed in 2.8.0b1)</li>
 119             <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
 120
 121                                 </ul> <em>Applet</em>
 122                                 <ul>
 123                                         <li>Remove group option is shown even when selection is not a
 124                                                 group</li>
 125                                         <li>Apply to all groups ticked but colourscheme changes don't
 126                                                 affect groups</li>
 127                                                 <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
 128                                                 <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
 129                                                 <li>Increased font size for dropdown menus on OSX and embedded windows</li>
 130                                 </ul> <em>Other</em>
 131                                 <ul>
 132                                         <li>Consensus sequence for alignments/groups with a single
 133                                                 sequence were not calculated</li>
 134                                         <li>annotation files that contain only groups imported as
 135                                                 annotation and junk sequences</li>
 136                                         <li>Fasta files with sequences containing '*' incorrectly
 137                                                 recognised as PFAM or BLC</li>
 138                                         <li>conservation/PID slider apply all groups option doesn't
 139                                                 affect background (2.8.0b1)
 140                                         <li></li>
 141                                         <li>redundancy highlighting is erratic at 0% and 100%</li>
 142                                         <li>Remove gapped columns fails for sequences with ragged
 143                                                 trailing gaps</li>
 144                                         <li>AMSA annotation row with leading spaces is not registered
 145                                                 correctly on import</li>
 146                                         <li>Jalview crashes when selecting PCA analysis for certain
 147                                                 alignments</li>
 148                                         <li>Opening the colour by annotation dialog for an existing
 149                                                 annotation based 'use original colours' colourscheme loses
 150                                                 original colours setting</li>
 151                                 </ul>
 152                         </td>
 153                 </tr>
 154                 <tr>
 155         <td><div align="center">
 156         <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
 157         </div>
 158         </td>
 159       <td>
 160         <ul>
 161           <li>Trusted certificates for JalviewLite applet and
 162             Jalview Desktop application<br />Certificate was donated by
 163             <a href="https://www.certum.eu">Certum</a> to the Jalview
 164             open source project).
 165           </li>
 166           <li>Jalview SRS links replaced by Uniprot and EBI-search
 167           </li>
 168           <li>Output in Stockholm format</li>
 169           <li>Allow import of data from gzipped files</li>
 170           <li>Export/import group and sequence associated line
 171             graph thresholds</li>
 172           <li>Nucleotide substitution matrix that supports RNA and
 173             ambiguity codes</li>
 174           <li>Allow disorder predictions to be made on the current
 175             selection (or visible selection) in the same way that JPred
 176             works</li>
 177           <li>Groovy scripting for headless jalview operation</li>
 178         </ul> <em>Other improvements</em>
 179         <ul>
 180           <li>Upgrade desktop installer to InstallAnywhere 2013</li>
 181           <li>COMBINE statement uses current SEQUENCE_REF and
 182             GROUP_REF scope to group annotation rows</li>
 183           <li>Support &#39;&#39; style escaping of quotes in Newick
 184             files</li>
 185           <li>Group options for JABAWS service by command line name</li>
 186           <li>Empty tooltip shown for JABA service options with a
 187             link but no description</li>
 188           <li>Select primary source when selecting authority in
 189             database fetcher GUI</li>
 190           <li>Add .mfa to FASTA file extensions recognised by
 191             Jalview</li>
 192           <li>Annotation label tooltip text wrap</li>
 193         </ul>
 194       </td>
 195       <td>
 196         <ul>
 197           <li>Slow scrolling when lots of annotation rows are
 198             displayed</li>
 199           <li>Lots of NPE (and slowness) after creating RNA
 200             secondary structure annotation line</li>
 201           <li>Sequence database accessions not imported when
 202             fetching alignments from Rfam</li>
 203           <li>Incorrect SHMR submission for sequences with
 204             identical IDs</li>
 205           <li>View all structures does not always superpose
 206             structures</li>
 207           <li>Option widgets in service parameters not updated to
 208             reflect user or preset settings</li>
 209           <li>Null pointer exceptions for some services without
 210             presets or adjustable parameters</li>
 211           <li>Discover PDB IDs entry in structure menu doesn&#39;t
 212             discover PDB xRefs</li>
 213           <li>Exception encountered while trying to retrieve
 214             features with DAS</li>
 215           <li>Lowest value in annotation row isn&#39;t coloured
 216             when colour by annotation (per sequence) is coloured</li>
 217           <li>Keyboard mode P jumps to start of gapped region when
 218             residue follows a gap</li>
 219           <li>Jalview appears to hang importing an alignment with
 220             Wrap as default or after enabling Wrap</li>
 221           <li>&#39;Right click to add annotations&#39; message
 222             shown in wrap mode when no annotations present</li>
 223           <li>Disorder predictions fail with NPE if no automatic
 224             annotation already exists on alignment</li>
 225           <li>oninit javascript function should be called after
 226             initialisation completes</li>
 227           <li>Remove redundancy after disorder prediction corrupts
 228             alignment window display</li>
 229           <li>Example annotation file in documentation is invalid</li>
 230           <li>Grouped line graph annotation rows are not exported
 231             to annotation file</li>
 232           <li>Multi-harmony analysis cannot be run when only two
 233             groups created</li>
 234           <li>Cannot create multiple groups of line graphs with
 235             several &#39;combine&#39; statements in annotation file</li>
 236           <li>Pressing return several times causes Number Format
 237             exceptions in keyboard mode</li>
 238           <li>Multi-harmony (SHMMR) method doesn&#39;t submit
 239             correct partitions for input data</li>
 240           <li>Translation from DNA to Amino Acids fails</li>
 241           <li>Jalview fail to load newick tree with quoted label</li>
 242           <li>--headless flag isn&#39;t understood</li>
 243           <li>ClassCastException when generating EPS in headless
 244             mode</li>
 245           <li>Adjusting sequence-associated shading threshold only
 246             changes one row&#39;s threshold</li>
 247           <li>Preferences and Feature settings panel panel
 248             doesn&#39;t open</li>
 249                                         <li>hide consensus histogram also hides conservation and
 250                                                 quality histograms</li>
 251                                 </ul>
 252       </td>
 253     </tr>
 254   <tr>
 255    <td><div align="center">
 256      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
 257     </div></td>
 258    <td><em>Application</em>
 259     <ul><li>Support for JABAWS 2.0 Services (AACon alignment
 260      conservation, protein disorder and Clustal Omega)</li>
 261     <li>JABAWS server status indicator in Web Services preferences
 262    </li>
 263     <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
 264      Jalview alignment window</li>
 265     <li>Updated Jalview build and deploy framework for OSX mountain
 266      lion, windows 7, and 8</li>
 267     <li>Nucleotide substitution matrix for PCA that supports RNA
 268      and ambiguity codes</li>
 269
 270     <li>Improved sequence database retrieval GUI</li>
 271     <li>Support fetching and database reference look up against
 272      multiple DAS sources (Fetch all from in 'fetch db refs')</li>
 273     <li>Jalview project improvements
 274      <ul>
 275       <li>Store and retrieve the &#39;belowAlignment&#39; flag for
 276        annotation</li>
 277       <li>calcId attribute to group annotation rows on the
 278        alignment</li>
 279       <li>Store AACon calculation settings for a view in Jalview
 280        project</li>
 281
 282      </ul>
 283    </li>
 284     <li>horizontal scrolling gesture support</li>
 285     <li>Visual progress indicator when PCA calculation is running</li>
 286     <li>Simpler JABA web services menus</li>
 287     <li>visual indication that web service results are still being
 288      retrieved from server</li>
 289     <li>Serialise the dialogs that are shown when Jalview starts up
 290      for first time</li>
 291     <li>Jalview user agent string for interacting with HTTP
 292      services</li>
 293     <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
 294      library</li>
 295     <li>Examples directory and Groovy library included in
 296      InstallAnywhere distribution</li>
 297     </ul> <em>Applet</em>
 298     <ul>
 299      <li>RNA alignment and secondary structure annotation
 300       visualization applet example</li>
 301     </ul> <em>General</em>
 302     <ul>
 303      <li>Normalise option for consensus sequence logo</li>
 304      <li>Reset button in PCA window to return dimensions to
 305       defaults</li>
 306      <li>Allow seqspace or Jalview variant of alignment PCA
 307       calculation</li>
 308      <li>PCA with either nucleic acid and protein substitution
 309       matrices
 310      <li>Allow windows containing HTML reports to be exported in
 311       HTML</li>
 312      <li>Interactive display and editing of RNA secondary structure
 313       contacts</li>
 314      <li>RNA Helix Alignment Colouring</li>
 315      <li>RNA base pair logo consensus</li>
 316      <li>Parse sequence associated secondary structure information
 317       in Stockholm files</li>
 318      <li>HTML Export database accessions and annotation information
 319       presented in tooltip for sequences</li>
 320      <li>Import secondary structure from LOCARNA clustalw style RNA
 321       alignment files</li>
 322      <li>import and visualise T-COFFEE quality scores for an
 323       alignment</li>
 324      <li>&#39;colour by annotation&#39; per sequence option to
 325       shade each sequence according to its associated alignment
 326       annotation</li>
 327      <li>New Jalview Logo</li>
 328     </ul> <em>Documentation and Development</em>
 329     <ul>
 330      <li>documentation for score matrices used in Jalview</li>
 331      <li>New Website!</li>
 332     </ul></td>
 333    <td><em>Application</em>
 334     <ul>
 335      <li>PDB, Unprot and EMBL (ENA) databases retrieved via
 336       wsdbfetch REST service</li>
 337      <li>Stop windows being moved outside desktop on OSX</li>
 338      <li>Filetype associations not installed for webstart launch</li>
 339      <li>Jalview does not always retrieve progress of a JABAWS job
 340       execution in full once it is complete</li>
 341      <li>revise SHMR RSBS definition to ensure alignment is
 342       uploaded via ali_file parameter</li>
 343      <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
 344      <li>View all structures superposed fails with exception</li>
 345      <li>Jnet job queues forever if a very short sequence is
 346       submitted for prediction</li>
 347      <li>Cut and paste menu not opened when mouse clicked on
 348       desktop window</li>
 349      <li>Putting fractional value into integer text box in
 350       alignment parameter dialog causes Jalview to hang</li>
 351      <li>Structure view highlighting doesn&#39;t work on windows 7
 352      </li>
 353      <li>View all structures fails with exception shown in
 354       structure view</li>
 355      <li>Characters in filename associated with PDBEntry not
 356       escaped in a platform independent way</li>
 357      <li>Jalview desktop fails to launch with exception when using
 358       proxy</li>
 359      <li>Tree calculation reports &#39;you must have 2 or more
 360       sequences selected&#39; when selection is empty</li>
 361      <li>Jalview desktop fails to launch with jar signature failure
 362       when java web start temporary file caching is disabled</li>
 363      <li>DAS Sequence retrieval with range qualification results in
 364       sequence xref which includes range qualification</li>
 365      <li>Errors during processing of command line arguments cause
 366       progress bar (JAL-898) to be removed</li>
 367      <li>Replace comma for semi-colon option not disabled for DAS
 368       sources in sequence fetcher</li>
 369      <li>Cannot close news reader when JABAWS server warning dialog
 370       is shown</li>
 371      <li>Option widgets not updated to reflect user settings</li>
 372      <li>Edited sequence not submitted to web service</li>
 373      <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
 374      <li>InstallAnywhere installer doesn&#39;t unpack and run on
 375       OSX Mountain Lion</li>
 376      <li>Annotation panel not given a scroll bar when sequences
 377       with alignment annotation are pasted into the alignment</li>
 378      <li>Sequence associated annotation rows not associated when
 379       loaded from Jalview project</li>
 380      <li>Browser launch fails with NPE on java 1.7</li>
 381      <li>JABAWS alignment marked as finished when job was cancelled
 382       or job failed due to invalid input</li>
 383      <li>NPE with v2.7 example when clicking on Tree associated
 384       with all views</li>
 385      <li>Exceptions when copy/paste sequences with grouped
 386       annotation rows to new window</li>
 387     </ul> <em>Applet</em>
 388     <ul>
 389      <li>Sequence features are momentarily displayed before they
 390       are hidden using hidefeaturegroups applet parameter</li>
 391      <li>loading features via javascript API automatically enables
 392       feature display</li>
 393      <li>scrollToColumnIn javascript API method doesn&#39;t work</li>
 394     </ul> <em>General</em>
 395     <ul>
 396      <li>Redundancy removal fails for rna alignment</li>
 397      <li>PCA calculation fails when sequence has been selected and
 398       then deselected</li>
 399      <li>PCA window shows grey box when first opened on OSX</li>
 400      <li>Letters coloured pink in sequence logo when alignment
 401       coloured with clustalx</li>
 402      <li>Choosing fonts without letter symbols defined causes
 403       exceptions and redraw errors</li>
 404      <li>Initial PCA plot view is not same as manually reconfigured
 405       view</li>
 406      <li>Grouped annotation graph label has incorrect line colour</li>
 407      <li>Grouped annotation graph label display is corrupted for
 408       lots of labels</li>
 409     </ul>
 410   </tr>
 411   <tr>
 412    <td>
 413     <div align="center">
 414      <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
 415     </div>
 416    </td>
 417    <td><em>Application</em>
 418     <ul>
 419      <li>Jalview Desktop News Reader</li>
 420      <li>Tweaked default layout of web services menu</li>
 421      <li>View/alignment association menu to enable user to easily
 422       specify which alignment a multi-structure view takes its
 423       colours/correspondences from</li>
 424      <li>Allow properties file location to be specified as URL</li>
 425      <li>Extend Jalview project to preserve associations between
 426       many alignment views and a single Jmol display</li>
 427      <li>Store annotation row height in Jalview project file</li>
 428      <li>Annotation row column label formatting attributes stored
 429       in project file</li>
 430      <li>Annotation row order for auto-calculated annotation rows
 431       preserved in Jalview project file</li>
 432      <li>Visual progress indication when Jalview state is saved
 433       using Desktop window menu</li>
 434      <li>Visual indication that command line arguments are still
 435       being processed</li>
 436      <li>Groovy script execution from URL</li>
 437      <li>Colour by annotation default min and max colours in
 438       preferences</li>
 439      <li>Automatically associate PDB files dragged onto an
 440       alignment with sequences that have high similarity and matching
 441       IDs</li>
 442      <li>Update JGoogleAnalytics to latest release (0.3)</li>
 443      <li>&#39;view structures&#39; option to open many structures
 444       in same window</li>
 445      <li>Sort associated views menu option for tree panel</li>
 446      <li>Group all JABA and non-JABA services for a particular
 447       analysis function in its own submenu</li>
 448     </ul> <em>Applet</em>
 449     <ul>
 450      <li>Userdefined and autogenerated annotation rows for groups</li>
 451      <li>Adjustment of alignment annotation pane height</li>
 452      <li>Annotation scrollbar for annotation panel</li>
 453      <li>Drag to reorder annotation rows in annotation panel</li>
 454      <li>&#39;automaticScrolling&#39; parameter</li>
 455      <li>Allow sequences with partial ID string matches to be
 456       annotated from GFF/Jalview features files</li>
 457      <li>Sequence logo annotation row in applet</li>
 458      <li>Absolute paths relative to host server in applet
 459       parameters are treated as such</li>
 460      <li>New in the JalviewLite javascript API:
 461       <ul>
 462        <li>JalviewLite.js javascript library</li>
 463        <li>Javascript callbacks for
 464         <ul>
 465          <li>Applet initialisation</li>
 466          <li>Sequence/alignment mouse-overs and selections</li>
 467         </ul>
 468        </li>
 469        <li>scrollTo row and column alignment scrolling functions</li>
 470        <li>Select sequence/alignment regions from javascript</li>
 471        <li>javascript structure viewer harness to pass messages
 472         between Jmol and Jalview when running as distinct applets</li>
 473        <li>sortBy method</li>
 474        <li>Set of applet and application examples shipped with
 475         documentation</li>
 476        <li>New example to demonstrate JalviewLite and Jmol
 477         javascript message exchange</li>
 478       </ul>
 479     </ul> <em>General</em>
 480     <ul>
 481      <li>Enable Jmol displays to be associated with multiple
 482       multiple alignments</li>
 483      <li>Option to automatically sort alignment with new tree</li>
 484      <li>User configurable link to enable redirects to a
 485       www.Jalview.org mirror</li>
 486      <li>Jmol colours option for Jmol displays</li>
 487      <li>Configurable newline string when writing alignment and
 488       other flat files</li>
 489      <li>Allow alignment annotation description lines to contain
 490       html tags</li>
 491     </ul> <em>Documentation and Development</em>
 492     <ul>
 493      <li>Add groovy test harness for bulk load testing to examples
 494      </li>
 495      <li>Groovy script to load and align a set of sequences using a
 496       web service before displaying the result in the Jalview desktop</li>
 497      <li>Restructured javascript and applet api documentation</li>
 498      <li>Ant target to publish example html files with applet
 499       archive</li>
 500      <li>Netbeans project for building Jalview from source</li>
 501      <li>ant task to create online javadoc for Jalview source</li>
 502     </ul></td>
 503    <td><em>Application</em>
 504     <ul>
 505      <li>User defined colourscheme throws exception when current
 506       built in colourscheme is saved as new scheme</li>
 507      <li>AlignFrame-&gt;Save in application pops up save dialog for
 508       valid filename/format</li>
 509      <li>Cannot view associated structure for Uniprot sequence</li>
 510      <li>PDB file association breaks for Uniprot sequence P37173</li>
 511      <li>Associate PDB from file dialog does not tell you which
 512       sequence is to be associated with the file</li>
 513      <li>Find All raises null pointer exception when query only
 514       matches sequence IDs</li>
 515      <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
 516      <li>Jalview project with Jmol views created with Jalview 2.4
 517       cannot be loaded</li>
 518      <li>Filetype associations not installed for webstart launch</li>
 519      <li>Two or more chains in a single PDB file associated with
 520       sequences in different alignments do not get coloured by their
 521       associated sequence</li>
 522      <li>Visibility status of autocalculated annotation row not
 523       preserved when project is loaded</li>
 524      <li>Annotation row height and visibility attributes not stored
 525       in Jalview project</li>
 526      <li>Tree bootstraps are not preserved when saved as a Jalview
 527       project</li>
 528      <li>Envision2 workflow tooltips are corrupted</li>
 529      <li>Enabling show group conservation also enables colour by
 530       conservation</li>
 531      <li>Duplicate group associated conservation or consensus
 532       created on new view</li>
 533      <li>Annotation scrollbar not displayed after &#39;show all
 534       hidden annotation rows&#39; option selected</li>
 535      <li>Alignment quality not updated after alignment annotation
 536       row is hidden then shown</li>
 537      <li>Preserve colouring of structures coloured by sequences in
 538       pre Jalview 2.7 projects</li>
 539      <li>Web service job parameter dialog is not laid out properly
 540      </li>
 541      <li>Web services menu not refreshed after &#39;reset
 542       services&#39; button is pressed in preferences</li>
 543      <li>Annotation off by one in Jalview v2_3 example project</li>
 544      <li>Structures imported from file and saved in project get
 545       name like jalview_pdb1234.txt when reloaded</li>
 546      <li>Jalview does not always retrieve progress of a JABAWS job
 547       execution in full once it is complete</li>
 548     </ul> <em>Applet</em>
 549     <ul>
 550      <li>Alignment height set incorrectly when lots of annotation
 551       rows are displayed</li>
 552      <li>Relative URLs in feature HTML text not resolved to
 553       codebase</li>
 554      <li>View follows highlighting does not work for positions in
 555       sequences</li>
 556      <li>&lt;= shown as = in tooltip</li>
 557      <li>Export features raises exception when no features exist</li>
 558      <li>Separator string used for serialising lists of IDs for
 559       javascript api is modified when separator string provided as
 560       parameter</li>
 561      <li>Null pointer exception when selecting tree leaves for
 562       alignment with no existing selection</li>
 563      <li>Relative URLs for datasources assumed to be relative to
 564       applet&#39;s codebase</li>
 565      <li>Status bar not updated after finished searching and search
 566       wraps around to first result</li>
 567      <li>StructureSelectionManager instance shared between several
 568       Jalview applets causes race conditions and memory leaks</li>
 569      <li>Hover tooltip and mouseover of position on structure not
 570       sent from Jmol in applet</li>
 571      <li>Certain sequences of javascript method calls to applet API
 572       fatally hang browser</li>
 573     </ul> <em>General</em>
 574     <ul>
 575      <li>View follows structure mouseover scrolls beyond position
 576       with wrapped view and hidden regions</li>
 577      <li>Find sequence position moves to wrong residue with/without
 578       hidden columns</li>
 579      <li>Sequence length given in alignment properties window is
 580       off by 1</li>
 581      <li>InvalidNumberFormat exceptions thrown when trying to
 582       import PDB like structure files</li>
 583      <li>Positional search results are only highlighted between
 584       user-supplied sequence start/end bounds</li>
 585      <li>End attribute of sequence is not validated</li>
 586      <li>Find dialog only finds first sequence containing a given
 587       sequence position</li>
 588      <li>Sequence numbering not preserved in MSF alignment output</li>
 589      <li>Jalview PDB file reader does not extract sequence from
 590       nucleotide chains correctly</li>
 591      <li>Structure colours not updated when tree partition changed
 592       in alignment</li>
 593      <li>Sequence associated secondary structure not correctly
 594       parsed in interleaved stockholm</li>
 595      <li>Colour by annotation dialog does not restore current state
 596      </li>
 597      <li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
 598      <li>Sequences containing lowercase letters are not properly
 599       associated with their pdb files</li>
 600     </ul> <em>Documentation and Development</em>
 601     <ul>
 602      <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
 603       tool</li>
 604     </ul></td>
 605   </tr>
 606   <tr>
 607                         <td>
 608                                 <div align="center">
 609                                         <strong><a name="Jalview2.6.1">2.6.1</a>
 610                                         </strong><br> <em>15/11/2010</em>
 611                                 </div></td>
 612                         <td><em>Application</em>
 613                                 <ul>
 614                                         <li>New warning dialog when the Jalview Desktop cannot contact
 615                                                 web services</li>
 616                                         <li>JABA service parameters for a preset are shown in service
 617                                                 job window</li>
 618                                         <li>JABA Service menu entries reworded</li>
 619                                 </ul></td>
 620                         <td>
 621                                 <ul>
 622                                         <li>Modeller PIR IO broken - cannot correctly import a pir
 623                                                 file emitted by Jalview</li>
 624                                         <li>Existing feature settings transferred to new alignment
 625                                                 view created from cut'n'paste</li>
 626                                         <li>Improved test for mixed amino/nucleotide chains when
 627                                                 parsing PDB files</li>
 628                                         <li>Consensus and conservation annotation rows occasionally
 629                                                 become blank for all new windows</li>
 630                                         <li>Exception raised when right clicking above sequences in
 631                                                 wrapped view mode</li>
 632                                 </ul> <em>Application</em>
 633                                 <ul>
 634                                         <li>multiple multiply aligned structure views cause cpu usage
 635                                                 to hit 100% and computer to hang</li>
 636                                         <li>Web Service parameter layout breaks for long user
 637                                                 parameter names</li>
 638                                         <li>Jaba service discovery hangs desktop if Jaba server is
 639                                                 down</li>
 640                                 </ul></td>
 641                 </tr>
 642                 <tr>
 643                 <td>
 644                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
 645                 <em>26/9/2010</em></div>
 646                 </td>
 647                 <td><em>Application</em>
 648                 <ul>
 649                         <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
 650                         <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
 651                         <li>Web Services preference tab</li>
 652                         <li>Analysis parameters dialog box and user defined preferences</li>
 653                         <li>Improved speed and layout of Envision2 service menu</li>
 654                         <li>Superpose structures using associated sequence alignment</li>
 655                         <li>Export coordinates and projection as CSV from PCA viewer</li>
 656                 </ul>
 657                 <em>Applet</em>
 658                 <ul>
 659                         <li>enable javascript: execution by the applet via the link out
 660                         mechanism</li>
 661                 </ul>
 662                 <em>Other</em>
 663                 <ul>
 664                         <li>Updated the Jmol Jalview interface to work with Jmol series
 665                         12</li>
 666                         <li>The Jalview Desktop and JalviewLite applet now require Java
 667                         1.5</li>
 668                         <li>Allow Jalview feature colour specification for GFF sequence
 669                         annotation files</li>
 670                         <li>New 'colour by label' keword in Jalview feature file type
 671                         colour specification</li>
 672                         <li>New Jalview Desktop Groovy API method that allows a script
 673                         to check if it being run in an interactive session or in a batch
 674                         operation from the Jalview command line</li>
 675                 </ul>
 676                 </td>
 677                 <td>
 678                 <ul>
 679                         <li>clustalx colourscheme colours Ds preferentially when both
 680                         D+E are present in over 50% of the column</li>
 681                 </ul>
 682
 683                 <em>Application</em>
 684                 <ul>
 685                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 686                         selected Regions menu item</li>
 687                         <li>sequence fetcher replaces ',' for ';' when the ',' is part
 688                         of a valid accession ID</li>
 689                         <li>fatal OOM if object retrieved by sequence fetcher runs out
 690                         of memory</li>
 691                         <li>unhandled Out of Memory Error when viewing pca analysis
 692                         results</li>
 693                         <li>InstallAnywhere builds fail to launch on OS X java 10.5
 694                         update 4 (due to apple Java 1.6 update)</li>
 695                         <li>Installanywhere Jalview silently fails to launch</li>
 696                 </ul>
 697                 <em>Applet</em>
 698                 <ul>
 699                         <li>Jalview.getFeatureGroups() raises an
 700                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
 701                 </ul>
 702                 </td>
 703         </tr>
 704         <tr>
 705                 <td>
 706                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
 707                 <em>14/6/2010</em></div>
 708                 </td>
 709                 <td></td>
 710                 <td>
 711                 <ul>
 712                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
 713                         </li>
 714                         <li>clustalx colourscheme colours Ds preferentially when both
 715                         D+E are present in over 50% of the column</li>
 716                         <li>nucleic acid structures retrieved from PDB do not import
 717                         correctly</li>
 718                         <li>More columns get selected than were clicked on when a number
 719                         of columns are hidden</li>
 720                         <li>annotation label popup menu not providing correct
 721                         add/hide/show options when rows are hidden or none are present</li>
 722                         <li>Stockholm format shown in list of readable formats, and
 723                         parser copes better with alignments from RFAM.</li>
 724                         <li>CSV output of consensus only includes the percentage of all
 725                         symbols if sequence logo display is enabled</li>
 726
 727                 </ul>
 728                 <em>Applet</em>
 729                 <ul>
 730                         <li>annotation panel disappears when annotation is
 731                         hidden/removed</li>
 732                 </ul>
 733                 <em>Application</em>
 734                 <ul>
 735                         <li>Alignment view not redrawn properly when new alignment
 736                         opened where annotation panel is visible but no annotations are
 737                         present on alignment</li>
 738                         <li>pasted region containing hidden columns is incorrectly
 739                         displayed in new alignment window</li>
 740                         <li>Jalview slow to complete operations when stdout is flooded
 741                         (fix is to close the Jalview console)</li>
 742                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 743                         selected Rregions menu item.</li>
 744                         <li>inconsistent group submenu and Format submenu entry 'Un' or
 745                         'Non'conserved</li>
 746                         <li>Sequence feature settings are being shared by multiple
 747                         distinct alignments</li>
 748                         <li>group annotation not recreated when tree partition is
 749                         changed</li>
 750                         <li>double click on group annotation to select sequences does
 751                         not propagate to associated trees</li>
 752                         <li>Mac OSX specific issues:
 753                         <ul>
 754                                 <li>exception raised when mouse clicked on desktop window
 755                                 background</li>
 756                                 <li>Desktop menu placed on menu bar and application name set
 757                                 correctly</li>
 758                                 <li>sequence feature settings not wide enough for the save
 759                                 feature colourscheme button</li>
 760                         </ul>
 761                         </li>
 762                 </ul>
 763                 </td>
 764         </tr>
 765         <tr>
 766
 767                 <td>
 768                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 769                 <em>30/4/2010</em></div>
 770                 </td>
 771                 <td><em>New Capabilities</em>
 772                 <ul>
 773                         <li>URL links generated from description line for
 774                         regular-expression based URL links (applet and application)
 775                         <li>Non-positional feature URL links are shown in link menu</li>
 776                         <li>Linked viewing of nucleic acid sequences and structures</li>
 777                         <li>Automatic Scrolling option in View menu to display the
 778                         currently highlighted region of an alignment.</li>
 779                         <li>Order an alignment by sequence length, or using the average
 780                         score or total feature count for each sequence.</li>
 781                         <li>Shading features by score or associated description</li>
 782                         <li>Subdivide alignment and groups based on identity of selected
 783                         subsequence (Make Groups from Selection).</li>
 784                         <li>New hide/show options including Shift+Control+H to hide
 785                         everything but the currently selected region.</li>
 786                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 787                 </ul>
 788                 <em>Application</em>
 789                 <ul>
 790                         <li>Fetch DB References capabilities and UI expanded to support
 791                         retrieval from DAS sequence sources</li>
 792                         <li>Local DAS Sequence sources can be added via the command line
 793                         or via the Add local source dialog box.</li>
 794                         <li>DAS Dbref and DbxRef feature types are parsed as database
 795                         references and protein_name is parsed as description line (BioSapiens
 796                         terms).</li>
 797                         <li>Enable or disable non-positional feature and database
 798                         references in sequence ID tooltip from View menu in application.</li>
 799                         <!--                    <li>New hidden columns and rows and representatives capabilities
 800                         in annotations file (in progress - not yet fully implemented)</li> -->
 801                         <li>Group-associated consensus, sequence logos and conservation
 802                         plots</li>
 803                         <li>Symbol distributions for each column can be exported and
 804                         visualized as sequence logos</li>
 805                         <li>Optionally scale multi-character column labels to fit within
 806                         each column of annotation row<!-- todo for applet --></li>
 807                         <li>Optional automatic sort of associated alignment view when a
 808                         new tree is opened.</li>
 809                         <li>Jalview Java Console</li>
 810                         <li>Better placement of desktop window when moving between
 811                         different screens.</li>
 812                         <li>New preference items for sequence ID tooltip and consensus
 813                         annotation</li>
 814                         <li>Client to submit sequences and IDs to <a
 815                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 816                         <li><em>Vamsas Capabilities</em>
 817                         <ul>
 818                                 <li>Improved VAMSAS synchronization (Jalview archive used to
 819                                 preserve views, structures, and tree display settings)</li>
 820                                 <li>Import of vamsas documents from disk or URL via command
 821                                 line</li>
 822                                 <li>Sharing of selected regions between views and with other
 823                                 VAMSAS applications (Experimental feature!)</li>
 824                                 <li>Updated API to VAMSAS version 0.2</li>
 825                         </ul>
 826                         </li>
 827                 </ul>
 828                 <em>Applet</em>
 829                 <ul>
 830                         <li>Middle button resizes annotation row height</li>
 831                         <li>New Parameters
 832                         <ul>
 833                                 <li>sortByTree (true/false) - automatically sort the associated
 834                                 alignment view by the tree when a new tree is opened.</li>
 835                                 <li>showTreeBootstraps (true/false) - show or hide branch
 836                                 bootstraps (default is to show them if available)</li>
 837                                 <li>showTreeDistances (true/false) - show or hide branch
 838                                 lengths (default is to show them if available)</li>
 839                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
 840                                 unassociated nodes should be highlighted in the tree view</li>
 841                                 <li>heightScale and widthScale (1.0 or more) - increase the
 842                                 height or width of a cell in the alignment grid relative to the
 843                                 current font size.</li>
 844                         </ul>
 845                         </li>
 846                         <li>Non-positional features displayed in sequence ID tooltip</li>
 847                 </ul>
 848                 <em>Other</em>
 849                 <ul>
 850                         <li>Features format: graduated colour definitions and
 851                         specification of feature scores</li>
 852                         <li>Alignment Annotations format: new keywords for group
 853                         associated annotation (GROUP_REF) and annotation row display
 854                         properties (ROW_PROPERTIES)</li>
 855                         <li>XML formats extended to support graduated feature
 856                         colourschemes, group associated annotation, and profile visualization
 857                         settings.</li>
 858                 </td>
 859                 <td>
 860                 <ul>
 861                         <li>Source field in GFF files parsed as feature source rather
 862                         than description</li>
 863                         <li>Non-positional features are now included in sequence feature
 864                         and gff files (controlled via non-positional feature visibility in
 865                         tooltip).</li>
 866                         <li>URL links generated for all feature links (bugfix)</li>
 867                         <li>Added URL embedding instructions to features file
 868                         documentation.</li>
 869                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 870                         peptide product</li>
 871                         <li>Match case switch in find dialog box works for both sequence
 872                         ID and sequence string and query strings do not have to be in upper
 873                         case to match case-insensitively.</li>
 874                         <li>AMSA files only contain first column of multi-character
 875                         column annotation labels</li>
 876                         <li>Jalview Annotation File generation/parsing consistent with
 877                         documentation (e.g. Stockholm annotation can be exported and
 878                         re-imported)</li>
 879                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 880                         <li>Find incrementally searches ID string matches as well as
 881                         subsequence matches, and correctly reports total number of both.</li>
 882                         <li>Application:
 883                         <ul>
 884                                 <li>Better handling of exceptions during sequence retrieval</li>
 885                                 <li>Dasobert generated non-positional feature URL link text
 886                                 excludes the start_end suffix</li>
 887                                 <li>DAS feature and source retrieval buttons disabled when
 888                                 fetch or registry operations in progress.</li>
 889                                 <li>PDB files retrieved from URLs are cached properly</li>
 890                                 <li>Sequence description lines properly shared via VAMSAS</li>
 891                                 <li>Sequence fetcher fetches multiple records for all data
 892                                 sources</li>
 893                                 <li>Ensured that command line das feature retrieval completes
 894                                 before alignment figures are generated.</li>
 895                                 <li>Reduced time taken when opening file browser for first
 896                                 time.</li>
 897                                 <li>isAligned check prior to calculating tree, PCA or
 898                                 submitting an MSA to JNet now excludes hidden sequences.</li>
 899                                 <li>User defined group colours properly recovered from Jalview
 900                                 projects.</li>
 901                         </ul>
 902                         </li>
 903                 </ul>
 904                 </td>
 905
 906         </tr>
 907         <tr>
 908                 <td>
 909                 <div align="center"><strong>2.4.0.b2</strong><br>
 910                 28/10/2009</div>
 911                 </td>
 912                 <td>
 913                 <ul>
 914                         <li>Experimental support for google analytics usage tracking.</li>
 915                         <li>Jalview privacy settings (user preferences and docs).</li>
 916                 </ul>
 917                 </td>
 918                 <td>
 919                 <ul>
 920                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 921                         <li>Exception when feature created from selection beyond length
 922                         of sequence.</li>
 923                         <li>Allow synthetic PDB files to be imported gracefully</li>
 924                         <li>Sequence associated annotation rows associate with all
 925                         sequences with a given id</li>
 926                         <li>Find function matches case-insensitively for sequence ID
 927                         string searches</li>
 928                         <li>Non-standard characters do not cause pairwise alignment to
 929                         fail with exception</li>
 930                 </ul>
 931                 <em>Application Issues</em>
 932                 <ul>
 933                         <li>Sequences are now validated against EMBL database</li>
 934                         <li>Sequence fetcher fetches multiple records for all data
 935                         sources</li>
 936                 </ul>
 937                 <em>InstallAnywhere Issues</em>
 938                 <ul>
 939                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 940                         installAnywhere mechanism)</li>
 941                         <li>Command line launching of JARs from InstallAnywhere version
 942                         (java class versioning error fixed)</li>
 943                 </ul>
 944                 </td>
 945         </tr>
 946         <tr>
 947                 <td>
 948
 949                 <div align="center"><strong>2.4</strong><br>
 950                 27/8/2008</div>
 951                 </td>
 952                 <td><em>User Interface</em>
 953                 <ul>
 954                         <li>Linked highlighting of codon and amino acid from translation
 955                         and protein products</li>
 956                         <li>Linked highlighting of structure associated with residue
 957                         mapping to codon position</li>
 958                         <li>Sequence Fetcher provides example accession numbers and
 959                         'clear' button</li>
 960                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 961                         <li>Extract score function to parse whitespace separated numeric
 962                         data in description line</li>
 963                         <li>Column labels in alignment annotation can be centred.</li>
 964                         <li>Tooltip for sequence associated annotation give name of
 965                         sequence</li>
 966                 </ul>
 967                 <em>Web Services and URL fetching</em>
 968                 <ul>
 969                         <li>JPred3 web service</li>
 970                         <li>Prototype sequence search client (no public services
 971                         available yet)</li>
 972                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 973                         <li>URL Links created for matching database cross references as
 974                         well as sequence ID</li>
 975                         <li>URL Links can be created using regular-expressions</li>
 976                 </ul>
 977                 <em>Sequence Database Connectivity</em>
 978                 <ul>
 979                         <li>Retrieval of cross-referenced sequences from other databases
 980                         </li>
 981                         <li>Generalised database reference retrieval and validation to
 982                         all fetchable databases</li>
 983                         <li>Fetch sequences from DAS sources supporting the sequence
 984                         command</li>
 985                 </ul>
 986                 <em>Import and Export</em>
 987                 <li>export annotation rows as CSV for spreadsheet import</li>
 988                 <li>Jalview projects record alignment dataset associations, EMBL
 989                 products, and cDNA sequence mappings</li>
 990                 <li>Sequence Group colour can be specified in Annotation File</li>
 991                 <li>Ad-hoc colouring of group in Annotation File using RGB
 992                 triplet as name of colourscheme</li>
 993                 </ul>
 994                 <em>VAMSAS Client capabilities (Experimental)</em>
 995                 <ul>
 996                         <li>treenode binding for VAMSAS tree exchange</li>
 997                         <li>local editing and update of sequences in VAMSAS alignments
 998                         (experimental)</li>
 999                         <li>Create new or select existing session to join</li>
1000                         <li>load and save of vamsas documents</li>
1001                 </ul>
1002                 <em>Application command line</em>
1003                 <ul>
1004                         <li>-tree parameter to open trees (introduced for passing from
1005                         applet)</li>
1006                         <li>-fetchfrom command line argument to specify nicknames of DAS
1007                         servers to query for alignment features</li>
1008                         <li>-dasserver command line argument to add new servers that are
1009                         also automatically queried for features</li>
1010                         <li>-groovy command line argument executes a given groovy script
1011                         after all input data has been loaded and parsed</li>
1012                 </ul>
1013                 <em>Applet-Application data exchange</em>
1014                 <ul>
1015                         <li>Trees passed as applet parameters can be passed to
1016                         application (when using &quot;View in full application&quot;)</li>
1017                 </ul>
1018                 <em>Applet Parameters</em>
1019                 <ul>
1020                         <li>feature group display control parameter</li>
1021                         <li>debug parameter</li>
1022                         <li>showbutton parameter</li>
1023                 </ul>
1024                 <em>Applet API methods</em>
1025                 <ul>
1026                         <li>newView public method</li>
1027                         <li>Window (current view) specific get/set public methods</li>
1028                         <li>Feature display control methods</li>
1029                         <li>get list of currently selected sequences</li>
1030                 </ul>
1031                 <em>New Jalview distribution features</em>
1032                 <ul>
1033                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1034                         <li>RELEASE file gives build properties for the latest Jalview
1035                         release.</li>
1036                         <li>Java 1.1 Applet build made easier and donotobfuscate
1037                         property controls execution of obfuscator</li>
1038                         <li>Build target for generating source distribution</li>
1039                         <li>Debug flag for javacc</li>
1040                         <li>.jalview_properties file is documented (slightly) in
1041                         jalview.bin.Cache</li>
1042                         <li>Continuous Build Integration for stable and development
1043                         version of Application, Applet and source distribution</li>
1044                 </ul>
1045
1046                 </td>
1047                 <td>
1048                 <ul>
1049                         <li>selected region output includes visible annotations (for
1050                         certain formats)</li>
1051                         <li>edit label/displaychar contains existing label/char for
1052                         editing</li>
1053                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1054                         <li>shorter peptide product names from EMBL records</li>
1055                         <li>Newick string generator makes compact representations</li>
1056                         <li>bootstrap values parsed correctly for tree files with
1057                         comments</li>
1058                         <li>pathological filechooser bug avoided by not allowing
1059                         filenames containing a ':'</li>
1060                         <li>Fixed exception when parsing GFF files containing global
1061                         sequence features</li>
1062                         <li>Alignment datasets are finalized only when number of
1063                         references from alignment sequences goes to zero</li>
1064                         <li>Close of tree branch colour box without colour selection
1065                         causes cascading exceptions</li>
1066                         <li>occasional negative imgwidth exceptions</li>
1067                         <li>better reporting of non-fatal warnings to user when file
1068                         parsing fails.</li>
1069                         <li>Save works when Jalview project is default format</li>
1070                         <li>Save as dialog opened if current alignment format is not a
1071                         valid output format</li>
1072                         <li>Uniprot canonical names introduced for both das and vamsas</li>
1073                         <li>Histidine should be midblue (not pink!) in Zappo</li>
1074                         <li>error messages passed up and output when data read fails</li>
1075                         <li>edit undo recovers previous dataset sequence when sequence
1076                         is edited</li>
1077                         <li>allow PDB files without pdb ID HEADER lines (like those
1078                         generated by MODELLER) to be read in properly</li>
1079                         <li>allow reading of JPred concise files as a normal filetype</li>
1080                         <li>Stockholm annotation parsing and alignment properties import
1081                         fixed for PFAM records</li>
1082                         <li>Structure view windows have correct name in Desktop window
1083                         list</li>
1084                         <li>annotation consisting of sequence associated scores can be
1085                         read and written correctly to annotation file</li>
1086                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
1087                         <li>Fixed display of hidden sequence markers and non-italic font
1088                         for representatives in Applet</li>
1089                         <li>Applet Menus are always embedded in applet window on Macs.</li>
1090                         <li>Newly shown features appear at top of stack (in Applet)</li>
1091                         <li>Annotations added via parameter not drawn properly due to
1092                         null pointer exceptions</li>
1093                         <li>Secondary structure lines are drawn starting from first
1094                         column of alignment</li>
1095                         <li>Uniprot XML import updated for new schema release in July
1096                         2008</li>
1097                         <li>Sequence feature to sequence ID match for Features file is
1098                         case-insensitive</li>
1099                         <li>Sequence features read from Features file appended to all
1100                         sequences with matching IDs</li>
1101                         <li>PDB structure coloured correctly for associated views
1102                         containing a sub-sequence</li>
1103                         <li>PDB files can be retrieved by applet from Jar files</li>
1104                         <li>feature and annotation file applet parameters referring to
1105                         different directories are retrieved correctly</li>
1106                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1107                         <li>Fixed application hang whilst waiting for splash-screen
1108                         version check to complete</li>
1109                         <li>Applet properly URLencodes input parameter values when
1110                         passing them to the launchApp service</li>
1111                         <li>display name and local features preserved in results
1112                         retrieved from web service</li>
1113                         <li>Visual delay indication for sequence retrieval and sequence
1114                         fetcher initialisation</li>
1115                         <li>updated Application to use DAS 1.53e version of dasobert DAS
1116                         client</li>
1117                         <li>Re-instated Full AMSA support and .amsa file association</li>
1118                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1119                         sequences</li>
1120                 </ul>
1121                 </td>
1122         </tr>
1123         <tr>
1124                 <td>
1125                 <div align="center"><strong>2.3</strong><br>
1126                 9/5/07</div>
1127                 </td>
1128                 <td>
1129                 <ul>
1130                         <li>Jmol 11.0.2 integration</li>
1131                         <li>PDB views stored in Jalview XML files</li>
1132                         <li>Slide sequences</li>
1133                         <li>Edit sequence in place</li>
1134                         <li>EMBL CDS features</li>
1135                         <li>DAS Feature mapping</li>
1136                         <li>Feature ordering</li>
1137                         <li>Alignment Properties</li>
1138                         <li>Annotation Scores</li>
1139                         <li>Sort by scores</li>
1140                         <li>Feature/annotation editing in applet</li>
1141                 </ul>
1142                 </td>
1143                 <td>
1144                 <ul>
1145                         <li>Headless state operation in 2.2.1</li>
1146                         <li>Incorrect and unstable DNA pairwise alignment</li>
1147                         <li>Cut and paste of sequences with annotation</li>
1148                         <li>Feature group display state in XML</li>
1149                         <li>Feature ordering in XML</li>
1150                         <li>blc file iteration selection using filename # suffix</li>
1151                         <li>Stockholm alignment properties</li>
1152                         <li>Stockhom alignment secondary structure annotation</li>
1153                         <li>2.2.1 applet had no feature transparency</li>
1154                         <li>Number pad keys can be used in cursor mode</li>
1155                         <li>Structure Viewer mirror image resolved</li>
1156                 </ul>
1157                 </td>
1158
1159         </tr>
1160         <tr>
1161                 <td>
1162                 <div align="center"><strong>2.2.1</strong><br>
1163                 12/2/07</div>
1164                 </td>
1165                 <td>
1166                 <ul>
1167                         <li>Non standard characters can be read and displayed
1168                         <li>Annotations/Features can be imported/exported to the applet
1169                         via textbox
1170                         <li>Applet allows editing of sequence/annotation/group name
1171                         &amp; description
1172                         <li>Preference setting to display sequence name in italics
1173                         <li>Annotation file format extended to allow Sequence_groups to
1174                         be defined
1175                         <li>Default opening of alignment overview panel can be specified
1176                         in preferences
1177                         <li>PDB residue numbering annotation added to associated
1178                         sequences
1179                 </ul>
1180                 </td>
1181                 <td>
1182                 <ul>
1183                         <li>Applet crash under certain Linux OS with Java 1.6 installed
1184                         <li>Annotation file export / import bugs fixed
1185                         <li>PNG / EPS image output bugs fixed
1186                 </ul>
1187                 </td>
1188         </tr>
1189         <tr>
1190                 <td>
1191                 <div align="center"><strong>2.2</strong><br>
1192                 27/11/06</div>
1193                 </td>
1194                 <td>
1195                 <ul>
1196                         <li>Multiple views on alignment
1197                         <li>Sequence feature editing
1198                         <li>&quot;Reload&quot; alignment
1199                         <li>&quot;Save&quot; to current filename
1200                         <li>Background dependent text colour
1201                         <li>Right align sequence ids
1202                         <li>User-defined lower case residue colours
1203                         <li>Format Menu
1204                         <li>Select Menu
1205                         <li>Menu item accelerator keys
1206                         <li>Control-V pastes to current alignment
1207                         <li>Cancel button for DAS Feature Fetching
1208                         <li>PCA and PDB Viewers zoom via mouse roller
1209                         <li>User-defined sub-tree colours and sub-tree selection
1210                         <li>'New Window' button on the 'Output to Text box'
1211                 </ul>
1212                 </td>
1213                 <td>
1214                 <ul>
1215                         <li>New memory efficient Undo/Redo System
1216                         <li>Optimised symbol lookups and conservation/consensus
1217                         calculations
1218                         <li>Region Conservation/Consensus recalculated after edits
1219                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
1220                         alignment)
1221                         <li>Slowed DAS Feature Fetching for increased robustness.
1222                         <li>Made angle brackets in ASCII feature descriptions display
1223                         correctly
1224                         <li>Re-instated Zoom function for PCA
1225                         <li>Sequence descriptions conserved in web service analysis
1226                         results
1227                         <li>Uniprot ID discoverer uses any word separated by &#8739;
1228                         <li>WsDbFetch query/result association resolved
1229                         <li>Tree leaf to sequence mapping improved
1230                         <li>Smooth fonts switch moved to FontChooser dialog box.
1231                 </ul>
1232                 </td>
1233         </tr>
1234         <tr>
1235                 <td>
1236                 <div align="center"><strong>2.1.1</strong><br>
1237                 12/9/06</div>
1238                 </td>
1239                 <td>
1240                 <ul>
1241                         <li>Copy consensus sequence to clipboard</li>
1242                 </ul>
1243                 </td>
1244                 <td>
1245                 <ul>
1246                         <li>Image output - rightmost residues are rendered if sequence
1247                         id panel has been resized</li>
1248                         <li>Image output - all offscreen group boundaries are rendered</li>
1249                         <li>Annotation files with sequence references - all elements in
1250                         file are relative to sequence position</li>
1251                         <li>Mac Applet users can use Alt key for group editing</li>
1252                 </ul>
1253                 </td>
1254         </tr>
1255         <tr>
1256                 <td>
1257                 <div align="center"><strong>2.1</strong><br>
1258                 22/8/06</div>
1259                 </td>
1260                 <td>
1261                 <ul>
1262                         <li>MAFFT Multiple Alignment in default Web Service list</li>
1263                         <li>DAS Feature fetching</li>
1264                         <li>Hide sequences and columns</li>
1265                         <li>Export Annotations and Features</li>
1266                         <li>GFF file reading / writing</li>
1267                         <li>Associate structures with sequences from local PDB files</li>
1268                         <li>Add sequences to exisiting alignment</li>
1269                         <li>Recently opened files / URL lists</li>
1270                         <li>Applet can launch the full application</li>
1271                         <li>Applet has transparency for features (Java 1.2 required)</li>
1272                         <li>Applet has user defined colours parameter</li>
1273                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
1274                 </ul>
1275                 </td>
1276                 <td>
1277                 <ul>
1278                         <li>Redundancy Panel reinstalled in the Applet</li>
1279                         <li>Monospaced font - EPS / rescaling bug fixed</li>
1280                         <li>Annotation files with sequence references bug fixed</li>
1281                 </ul>
1282                 </td>
1283         </tr>
1284         <tr>
1285                 <td>
1286                 <div align="center"><strong>2.08.1</strong><br>
1287                 2/5/06</div>
1288                 </td>
1289                 <td>
1290                 <ul>
1291                         <li>Change case of selected region from Popup menu</li>
1292                         <li>Choose to match case when searching</li>
1293                         <li>Middle mouse button and mouse movement can compress / expand
1294                         the visible width and height of the alignment</li>
1295                 </ul>
1296                 </td>
1297                 <td>
1298                 <ul>
1299                         <li>Annotation Panel displays complete JNet results</li>
1300                 </ul>
1301                 </td>
1302         </tr>
1303         <tr>
1304                 <td>
1305                 <div align="center"><strong>2.08b</strong><br>
1306                 18/4/06</div>
1307                 </td>
1308                 <td>&nbsp;</td>
1309                 <td>
1310                 <ul>
1311                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1312                         <li>Righthand label on wrapped alignments shows correct value</li>
1313                 </ul>
1314                 </td>
1315         </tr>
1316         <tr>
1317                 <td>
1318                 <div align="center"><strong>2.08</strong><br>
1319                 10/4/06</div>
1320                 </td>
1321                 <td>
1322                 <ul>
1323                         <li>Editing can be locked to the selection area</li>
1324                         <li>Keyboard editing</li>
1325                         <li>Create sequence features from searches</li>
1326                         <li>Precalculated annotations can be loaded onto alignments</li>
1327                         <li>Features file allows grouping of features</li>
1328                         <li>Annotation Colouring scheme added</li>
1329                         <li>Smooth fonts off by default - Faster rendering</li>
1330                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
1331                 </ul>
1332                 </td>
1333                 <td>
1334                 <ul>
1335                         <li>Drag &amp; Drop fixed on Linux</li>
1336                         <li>Jalview Archive file faster to load/save, sequence
1337                         descriptions saved.</li>
1338                 </ul>
1339                 </td>
1340         </tr>
1341         <tr>
1342                 <td>
1343                 <div align="center"><strong>2.07</strong><br>
1344                 12/12/05</div>
1345                 </td>
1346                 <td>
1347                 <ul>
1348                         <li>PDB Structure Viewer enhanced</li>
1349                         <li>Sequence Feature retrieval and display enhanced</li>
1350                         <li>Choose to output sequence start-end after sequence name for
1351                         file output</li>
1352                         <li>Sequence Fetcher WSDBFetch@EBI</li>
1353                         <li>Applet can read feature files, PDB files and can be used for
1354                         HTML form input</li>
1355                 </ul>
1356                 </td>
1357                 <td>
1358                 <ul>
1359                         <li>HTML output writes groups and features</li>
1360                         <li>Group editing is Control and mouse click</li>
1361                         <li>File IO bugs</li>
1362                 </ul>
1363                 </td>
1364         </tr>
1365         <tr>
1366                 <td>
1367                 <div align="center"><strong>2.06</strong><br>
1368                 28/9/05</div>
1369                 </td>
1370                 <td>
1371                 <ul>
1372                         <li>View annotations in wrapped mode</li>
1373                         <li>More options for PCA viewer</li>
1374                 </ul>
1375                 </td>
1376                 <td>
1377                 <ul>
1378                         <li>GUI bugs resolved</li>
1379                         <li>Runs with -nodisplay from command line</li>
1380                 </ul>
1381                 </td>
1382         </tr>
1383         <tr>
1384                 <td height="63">
1385                 <div align="center"><strong>2.05b</strong><br>
1386                 15/9/05</div>
1387                 </td>
1388                 <td>
1389                 <ul>
1390                         <li>Choose EPS export as lineart or text</li>
1391                         <li>Jar files are executable</li>
1392                         <li>Can read in Uracil - maps to unknown residue</li>
1393                 </ul>
1394                 </td>
1395                 <td>
1396                 <ul>
1397                         <li>Known OutOfMemory errors give warning message</li>
1398                         <li>Overview window calculated more efficiently</li>
1399                         <li>Several GUI bugs resolved</li>
1400                 </ul>
1401                 </td>
1402         </tr>
1403         <tr>
1404                 <td>
1405                 <div align="center"><strong>2.05</strong><br>
1406                 30/8/05</div>
1407                 </td>
1408                 <td>
1409                 <ul>
1410                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
1411                 </ul>
1412                 </td>
1413                 <td>
1414                 <ul>
1415                         <li>Several GUI bugs resolved</li>
1416                 </ul>
1417                 </td>
1418         </tr>
1419         <tr>
1420                 <td>
1421                 <div align="center"><strong>2.04</strong><br>
1422                 24/8/05</div>
1423                 </td>
1424                 <td>
1425                 <ul>
1426                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
1427                 </ul>
1428                 </td>
1429                 <td>
1430                 <ul>
1431                         <li>Improved JPred client reliability</li>
1432                         <li>Improved loading of Jalview files</li>
1433                 </ul>
1434                 </td>
1435         </tr>
1436         <tr>
1437                 <td>
1438                 <div align="center"><strong>2.03</strong><br>
1439                 18/8/05</div>
1440                 </td>
1441                 <td>
1442                 <ul>
1443                         <li>Set Proxy server name and port in preferences</li>
1444                         <li>Multiple URL links from sequence ids</li>
1445                         <li>User Defined Colours can have a scheme name and added to
1446                         Colour Menu</li>
1447                         <li>Choose to ignore gaps in consensus calculation</li>
1448                         <li>Unix users can set default web browser</li>
1449                         <li>Runs without GUI for batch processing</li>
1450                         <li>Dynamically generated Web Service Menus</li>
1451                 </ul>
1452                 </td>
1453                 <td>
1454                 <ul>
1455                         <li>InstallAnywhere download for Sparc Solaris</li>
1456                 </ul>
1457                 </td>
1458         </tr>
1459         <tr>
1460                 <td>
1461                 <div align="center"><strong>2.02</strong><br>
1462                 18/7/05</div>
1463                 </td>
1464                 <td>&nbsp;</td>
1465                 <td>
1466                 <ul>
1467                         <li>Copy &amp; Paste order of sequences maintains alignment
1468                         order.</li>
1469                 </ul>
1470                 </td>
1471         </tr>
1472         <tr>
1473                 <td>
1474                 <div align="center"><strong>2.01</strong><br>
1475                 12/7/05</div>
1476                 </td>
1477                 <td>
1478                 <ul>
1479                         <li>Use delete key for deleting selection.</li>
1480                         <li>Use Mouse wheel to scroll sequences.</li>
1481                         <li>Help file updated to describe how to add alignment
1482                         annotations.</li>
1483                         <li>Version and build date written to build properties file.</li>
1484                         <li>InstallAnywhere installation will check for updates at
1485                         launch of Jalview.</li>
1486                 </ul>
1487                 </td>
1488                 <td>
1489                 <ul>
1490                         <li>Delete gaps bug fixed.</li>
1491                         <li>FileChooser sorts columns.</li>
1492                         <li>Can remove groups one by one.</li>
1493                         <li>Filechooser icons installed.</li>
1494                         <li>Finder ignores return character when searching. Return key
1495                         will initiate a search.<br>
1496                         </li>
1497                 </ul>
1498                 </td>
1499         </tr>
1500         <tr>
1501                 <td>
1502                 <div align="center"><strong>2.0</strong><br>
1503                 20/6/05</div>
1504                 </td>
1505                 <td>
1506                 <ul>
1507                         <li>New codebase</li>
1508                 </ul>
1509                 </td>
1510                 <td>&nbsp;</td>
1511         </tr>
1512 </table>
1513 <p>&nbsp;</p>
1514 </body>
1515 </html>