help/html/releases.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   4  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
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  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <head>
  20 <title>Release History</title>
  21 </head>
  22 <body>
  23 <p><strong>Release History</strong></p>
  24 <table border="1">
  25         <tr>
  26                 <td width="60" nowrap>
  27                 <div align="center"><em><strong>Release</strong></em></div>
  28                 </td>
  29                 <td>
  30                 <div align="center"><em><strong>New Features</strong></em></div>
  31                 </td>
  32                 <td>
  33                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
  34                 </td>
  35         </tr>
  36   <tr>
  37    <td><div align="center">
  38      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>08/11/2012</em>
  39     </div></td>
  40    <td><em>Application</em>
  41     <li>Support for JABAWS 2.0 Services (AACon alignment
  42      conservation, protein disorder and Clustal Omega) <!--[<a href='http://issues.jalview.org/browse/JAL-976'>JAL-976</a>] -         Enhance Jalview desktop to support to JABAWS v2.0 services -->
  43      <!--[<a href='http://issues.jalview.org/browse/JAL-974'>JAL-974</a>]-->
  44      <!--[<a href='http://issues.jalview.org/browse/JAL-975'>JAL-975</a>]-->
  45    </li>
  46     <li>
  47      <!--[<a href='http://issues.jalview.org/browse/JAL-1060'>JAL-1060</a>] -        -->JABAWS
  48      server status indicator in Web Services preferences
  49    </li>
  50     <li>
  51      <!--[<a href='http://issues.jalview.org/browse/JAL-842'>JAL-842</a>] -         -->VARNA
  52      (http://varna.lri.fr) viewer for RNA structures in Jalview
  53      alignment window
  54    </li>
  55     <li>
  56      <!--[<a href='http://issues.jalview.org/browse/JAL-1133'>JAL-1133</a>] -         -->Updated
  57      jalview build and deploy framework for OSX mountain lion, windows
  58      7, and 8
  59    </li>
  60     <li>Nucleotide substitution matrix for PCA that supports RNA
  61      and ambiguity codes <!--[<a href='http://issues.jalview.org/browse/JAL-1027'>JAL-1027</a>] -->
  62    </li>
  63
  64     <li>Improved sequence database retrieval GUI</li>
  65    <li>Support fetching and database reference look up against
  66      multiple DAS sources (Fetch all from in 'fetch db refs')<!--[<a href='http://issues.jalview.org/browse/JAL-1061'>JAL-1061</a>], [<a href='http://issues.jalview.org/browse/JAL-1075'>JAL-1075</a>] -         GUI elements to select one or several DAS sources to query for sequences or database references-->
  67    </li>
  68     <li>Jalview project improvements
  69      <ul>
  70       <li>
  71        <!--[<a href='http://issues.jalview.org/browse/JAL-1109'>JAL-1109</a>] -->Store
  72        and retrieve the &#39;belowAlignment&#39; flag for annotation
  73       </li>
  74       <li>
  75        <!--[<a href='http://issues.jalview.org/browse/JAL-1110'>JAL-1110</a>]-->calcId
  76        attribute to group annotation rows on the alignment
  77       </li>
  78       <li>
  79        <!--[<a href='http://issues.jalview.org/browse/JAL-1136'>JAL-1136</a>] -         -->Store
  80        AACon calculation settings for a view in Jalview project
  81       </li>
  82
  83      </ul>
  84    </li>
  85     <li>
  86      <!--[<a href='http://issues.jalview.org/browse/JAL-1160'>JAL-1160</a>] -         -->horizontal
  87      scrolling gesture support
  88    </li>
  89     <li>Visual progress indicator when PCA calculation is running<!--[<a href='http://issues.jalview.org/browse/JAL-1120'>JAL-1120</a>] -         -->
  90    </li>
  91     <li>Simpler JABA web services menus<!--[<a href='http://issues.jalview.org/browse/JAL-1137'>JAL-1137</a>] -         -->
  92    </li>
  93     <li>
  94      <!--[<a href='http://issues.jalview.org/browse/JAL-1165'>JAL-1165</a>] -         -->visual
  95      indication that web service results are still being retrieved from
  96      server
  97    </li>
  98     <li>
  99      <!--[<a href='http://issues.jalview.org/browse/JAL-1183'>JAL-1183</a>] -         -->Serialise
 100      the dialogs that are shown when jalview starts up for first time
 101    </li>
 102     <li>
 103      <!--[<a href='http://issues.jalview.org/browse/JAL-1188'>JAL-1188</a>] -         -->Jalview
 104      user agent string for interacting with HTTP services
 105    </li>
 106     <li>
 107      <!--[<a href='http://issues.jalview.org/browse/JAL-972'>JAL-972</a>] -         -->DAS
 108      1.6 and DAS 2.0 source support using new JDAS client library
 109    </li>
 110     </ul> <em>Applet</em>
 111     <ul>
 112      <li>
 113       <!--[<a href='http://issues.jalview.org/browse/JAL-963'>JAL-963</a>] -         -->RNA
 114       alignment and secondary structure annotation visualization applet
 115       example
 116      </li>
 117     </ul> <em>General</em>
 118     <ul>
 119      <li>
 120       <!--[<a href='http://issues.jalview.org/browse/JAL-958'>JAL-958</a>] -         -->Normalise
 121       option for consensus sequence logo
 122      </li>
 123      <li>
 124       <!--[<a href='http://issues.jalview.org/browse/JAL-1121'>JAL-1121</a>] -         -->Reset
 125       button in PCA window to return dimensions to defaults
 126      </li>
 127      <li>
 128       <!--[<a href='http://issues.jalview.org/browse/JAL-1125'>JAL-1125</a>] -         -->Allow
 129       seqspace or Jalview variant of alignment PCA calculation
 130      </li>
 131      <li>
 132       <!--[<a href='http://issues.jalview.org/browse/JAL-1013'>JAL-1013</a>] -->PCA
 133       with either nucleic acid and protein substitution matrices
 134      <li>
 135       <!--[<a href='http://issues.jalview.org/browse/JAL-1157'>JAL-1157</a>] -         -->Allow
 136       windows containing HTML reports to be exported in HTML
 137      </li>
 138      <li>
 139       <!--[<a href='http://issues.jalview.org/browse/JAL-970'>JAL-970</a>] -         -->Interactive
 140       display and editing of RNA secondary structure contacts
 141      </li>
 142      <li>RNA Helix Alignment Colouring</li>
 143      <li>RNA base pair logo consensus</li>
 144      <li>
 145       <!--[<a href='http://issues.jalview.org/browse/JAL-878'>JAL-878</a>] -         -->Parse
 146       sequence associated secondary structure information in Stockholm
 147       files
 148      </li>
 149      <li>
 150       <!--[<a href='http://issues.jalview.org/browse/JAL-1015'>JAL-1015</a>] -         -->HTML
 151       Export database accessions and annotation information presented in
 152       tooltip for sequences
 153      </li>
 154      <li>
 155       <!--[<a href='http://issues.jalview.org/browse/JAL-1052'>JAL-1052</a>] -        -->Import
 156       secondary structure from LOCARNA clustalw style RNA alignment
 157       files
 158      </li>
 159      <li>
 160       <!--[<a href='http://issues.jalview.org/browse/JAL-1065'>JAL-1065</a>] - [<a href='http://issues.jalview.org/browse/JAL-1078'>JAL-1078</a>]-->import
 161       and visualise T-COFFEE quality scores for an alignment
 162      </li>
 163      <li>
 164       <!--[<a href='http://issues.jalview.org/browse/JAL-1066'>JAL-1066</a>] -        -->&#39;colour
 165       by annotation&#39; per sequence option to shade each sequence
 166       according to its associated alignment annotation
 167      </li>
 168      <li>
 169       <!--[<a href='http://issues.jalview.org/browse/JAL-1130'>JAL-1130</a>] -         -->New
 170       Jalview Logo
 171      </li>
 172     </ul> <em>Documentation and Development</em>
 173     <ul>
 174      <li>
 175       <!--[<a href='http://issues.jalview.org/browse/JAL-1167'>JAL-1167</a>] -         -->documentation
 176       for score matrices used in Jalview
 177      </li>
 178      <li>New Website!</li>
 179     </ul></td>
 180    <td><em>Application</em>
 181     <ul>
 182      <li>PDB, Unprot and EMBL (ENA) databases retrieved via
 183       wsdbfetch REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
 184      </li>
 185      <li>
 186       <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] -         -->
 187       <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] -        -->Stop
 188       windows being moved outside desktop on OSX
 189      </li>
 190      <li>
 191       <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] -         -->Filetype
 192       associations not installed for webstart launch
 193      </li>
 194      <li>
 195       <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] -         -->Jalview
 196       does not always retrieve progress of a JABAWS job execution in
 197       full once it is complete
 198      </li>
 199      <li>
 200       <!--[<a href='http://issues.jalview.org/browse/JAL-979'>JAL-979</a>] -         -->revise
 201       SHMR RSBS definition to ensure alignment is uploaded via ali_file
 202       parameter
 203      </li>
 204      <li>
 205       <!--[<a href='http://issues.jalview.org/browse/JAL-980'>JAL-980</a>] -         -->Jalview
 206       2.7 is incompatible with Jmol-12.2.2
 207      </li>
 208      <li>
 209       <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] -         -->View
 210       all structures superposed fails with exception
 211      </li>
 212      <li>
 213       <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] -         -->Jnet
 214       job queues forever if a very short sequence is submitted for
 215       prediction
 216      </li>
 217      <li>
 218       <!--[<a href='http://issues.jalview.org/browse/JAL-1004'>JAL-1004</a>] -         -->Cut
 219       and paste menu not opened when mouse clicked on desktop window
 220      </li>
 221      <li>
 222       <!--[<a href='http://issues.jalview.org/browse/JAL-1010'>JAL-1010</a>] -         -->Putting
 223       fractional value into integer text box in alignment parameter
 224       dialog causes jalview to hang
 225      </li>
 226      <li>
 227       <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] -         -->Structure
 228       view highlighting doesn&#39;t work on windows 7
 229      </li>
 230      <li>
 231       <!--[<a href='http://issues.jalview.org/browse/JAL-1023'>JAL-1023</a>] -         -->View
 232       all structures fails with exception shown in structure view
 233      </li>
 234      <li>
 235       <!--[<a href='http://issues.jalview.org/browse/JAL-1025'>JAL-1025</a>] -         -->Characters
 236       in filename associated with PDBEntry not escaped in a platform
 237       independent way
 238      </li>
 239      <li>
 240       <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] -         -->Jalview
 241       desktop fails to launch with exception when using proxy
 242      </li>
 243      <li>
 244       <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] -         -->Tree
 245       calculation reports &#39;you must have 2 or more sequences
 246       selected&#39; when selection is empty
 247      </li>
 248      <li>
 249       <!--[<a href='http://issues.jalview.org/browse/JAL-1040'>JAL-1040</a>] -         -->Jalview
 250       desktop fails to launch with jar signature failure when java web
 251       start temporary file caching is disabled
 252      </li>
 253      <li>
 254       <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] -         -->DAS
 255       Sequence retrieval with range qualification results in sequence
 256       xref which includes range qualification
 257      </li>
 258      <li>
 259       <!--[<a href='http://issues.jalview.org/browse/JAL-1087'>JAL-1087</a>] -         -->Errors
 260       during processing of command line arguments cause progress bar
 261       (JAL-898) to be removed
 262      </li>
 263      <li>
 264       <!--[<a href='http://issues.jalview.org/browse/JAL-1097'>JAL-1097</a>] -         -->Replace
 265       comma for semi-colon option not disabled for DAS sources in
 266       sequence fetcher
 267      </li>
 268      <li>
 269       <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] -         -->Cannot
 270       close news reader when JABAWS server warning dialog is shown
 271      </li>
 272      <li>
 273       <!--[<a href='http://issues.jalview.org/browse/JAL-1127'>JAL-1127</a>] -         -->Option
 274       widgets not updated to reflect user settings
 275      </li>
 276      <li>
 277       <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] -         -->Edited
 278       sequence not submitted to web service
 279      </li>
 280      <li>
 281       <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] -         -->Jalview
 282       2.7 Webstart does not launch on mountain lion
 283      </li>
 284      <li>
 285       <!--[<a href='http://issues.jalview.org/browse/JAL-1135'>JAL-1135</a>] -         -->InstallAnywhere
 286       installer doesn&#39;t unpack and run on OSX Mountain Lion
 287      </li>
 288      <li>
 289       <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] -         -->Annotation
 290       panel not given a scroll bar when sequences with alignment
 291       annotation are pasted into the alignment
 292      </li>
 293      <li>
 294       <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] -         -->Sequence
 295       associated annotation rows not associated when loaded from jalview
 296       project
 297      </li>
 298      <li>
 299       <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] -         -->Browser
 300       launch fails with NPE on java 1.7
 301      </li>
 302      <li>
 303       <!--[<a href='http://issues.jalview.org/browse/JAL-1171'>JAL-1171</a>] -         -->JABAWS
 304       alignment marked as finished when job was cancelled or job failed
 305       due to invalid input
 306      </li>
 307      <li>
 308       <!--[<a href='http://issues.jalview.org/browse/JAL-1185'>JAL-1185</a>] -         -->NPE
 309       with v2.7 example when clicking on Tree associated with all views
 310      </li>
 311      <li>
 312       <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] -         -->Exceptions
 313       when copy/paste sequences with grouped annotation rows to new
 314       window
 315      </li>
 316     </ul> <em>Applet</em>
 317     <ul>
 318      <li>
 319       <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] -         -->Sequence
 320       features are momentarily displayed before they are hidden using
 321       hidefeaturegroups applet parameter
 322      </li>
 323      <li>
 324       <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] -         -->loading
 325       features via javascript API automatically enables feature display
 326      </li>
 327      <li>
 328       <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] -         -->scrollToColumnIn
 329       javascript API method doesn&#39;t work
 330      </li>
 331     </ul> <em>General</em>
 332     <ul>
 333      <li>
 334       <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] -         -->Redundancy
 335       removal fails for rna alignment
 336      </li>
 337      <li>
 338       <!--[<a href='http://issues.jalview.org/browse/JAL-1032'>JAL-1032</a>] -         -->PCA
 339       calculation fails when sequence has been selected and then
 340       deselected
 341      </li>
 342      <li>
 343       <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] -         -->PCA
 344       window shows grey box when first opened on OSX
 345      </li>
 346      <li>
 347       <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] -        -->Letters
 348       coloured pink in sequence logo when alignment coloured with
 349       clustalx
 350      </li>
 351      <li>
 352       <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] -         -->Choosing
 353       fonts without letter symbols defined causes exceptions and redraw
 354       errors
 355      </li>
 356      <li>
 357       <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] -         -->Initial
 358       PCA plot view is not same as manually reconfigured view
 359      </li>
 360      <li>
 361       <!--[<a href='http://issues.jalview.org/browse/JAL-1153'>JAL-1153</a>] -         -->Grouped
 362       annotation graph label has incorrect line colour
 363      </li>
 364      <li>
 365       <!--[<a href='http://issues.jalview.org/browse/JAL-1155'>JAL-1155</a>] -         -->Grouped
 366       annotation graph label display is corrupted for lots of labels
 367      </li>
 368     </ul>
 369   </tr>
 370   <tr>
 371    <td>
 372     <div align="center">
 373      <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
 374     </div>
 375    </td>
 376    <td><em>Application</em>
 377     <ul>
 378      <li>Jalview Desktop News Reader</li>
 379      <li>Tweaked default layout of web services menu</li>
 380      <li>View/alignment association menu to enable user to easily
 381       specify which alignment a multi-structure view takes its
 382       colours/correspondences from</li>
 383      <li>Allow properties file location to be specified as URL</li>
 384      <li>Extend jalview project to preserve associations between
 385       many alignment views and a single Jmol display</li>
 386      <li>Store annotation row height in jalview project file</li>
 387      <li>Annotation row column label formatting attributes stored
 388       in project file</li>
 389      <li>Annotation row order for auto-calculated annotation rows
 390       preserved in jalview project file</li>
 391      <li>Visual progress indication when Jalview state is saved
 392       using Desktop window menu</li>
 393      <li>Visual indication that command line arguments are still
 394       being processed</li>
 395      <li>Groovy script execution from URL</li>
 396      <li>Colour by annotation default min and max colours in
 397       preferences</li>
 398      <li>Automatically associate PDB files dragged onto an
 399       alignment with sequences that have high similarity and matching
 400       IDs</li>
 401      <li>Update JGoogleAnalytics to latest release (0.3)</li>
 402      <li>&#39;view structures&#39; option to open many structures
 403       in same window</li>
 404      <li>Sort associated views menu option for tree panel</li>
 405      <li>Group all JABA and non-JABA services for a particular
 406       analysis function in its own submenu</li>
 407     </ul> <em>Applet</em>
 408     <ul>
 409      <li>Userdefined and autogenerated annotation rows for groups</li>
 410      <li>Adjustment of alignment annotation pane height</li>
 411      <li>Annotation scrollbar for annotation panel</li>
 412      <li>Drag to reorder annotation rows in annotation panel</li>
 413      <li>&#39;automaticScrolling&#39; parameter</li>
 414      <li>Allow sequences with partial ID string matches to be
 415       annotated from GFF/jalview features files</li>
 416      <li>Sequence logo annotation row in applet</li>
 417      <li>Absolute paths relative to host server in applet
 418       parameters are treated as such</li>
 419      <li>New in the JalviewLite javascript API:
 420       <ul>
 421        <li>JalviewLite.js javascript library</li>
 422        <li>Javascript callbacks for
 423         <ul>
 424          <li>Applet initialisation</li>
 425          <li>Sequence/alignment mouse-overs and selections</li>
 426         </ul>
 427        </li>
 428        <li>scrollTo row and column alignment scrolling functions</li>
 429        <li>Select sequence/alignment regions from javascript</li>
 430        <li>javascript structure viewer harness to pass messages
 431         between Jmol and Jalview when running as distinct applets</li>
 432        <li>sortBy method</li>
 433        <li>Set of applet and application examples shipped with
 434         documentation</li>
 435        <li>New example to demonstrate jalviewLite and Jmol
 436         javascript message exchange</li>
 437       </ul>
 438     </ul> <em>General</em>
 439     <ul>
 440      <li>Enable Jmol displays to be associated with multiple
 441       multiple alignments</li>
 442      <li>Option to automatically sort alignment with new tree</li>
 443      <li>User configurable link to enable redirects to a
 444       www.jalview.org mirror</li>
 445      <li>Jmol colours option for Jmol displays</li>
 446      <li>Configurable newline string when writing alignment and
 447       other flat files</li>
 448      <li>Allow alignment annotation description lines to contain
 449       html tags</li>
 450     </ul> <em>Documentation and Development</em>
 451     <ul>
 452      <li>Add groovy test harness for bulk load testing to examples
 453      </li>
 454      <li>Groovy script to load and align a set of sequences using a
 455       web service before displaying the result in the Jalview desktop</li>
 456      <li>Restructured javascript and applet api documentation</li>
 457      <li>Ant target to publish example html files with applet
 458       archive</li>
 459      <li>Netbeans project for building jalview from source</li>
 460      <li>ant task to create online javadoc for jalview source</li>
 461     </ul></td>
 462    <td><em>Application</em>
 463     <ul>
 464      <li>User defined colourscheme throws exception when current
 465       built in colourscheme is saved as new scheme</li>
 466      <li>AlignFrame-&gt;Save in application pops up save dialog for
 467       valid filename/format</li>
 468      <li>Cannot view associated structure for Uniprot sequence</li>
 469      <li>PDB file association breaks for Uniprot sequence P37173</li>
 470      <li>Associate PDB from file dialog does not tell you which
 471       sequence is to be associated with the file</li>
 472      <li>Find All raises null pointer exception when query only
 473       matches sequence IDs</li>
 474      <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
 475      <li>Jalview project with Jmol views created with Jalview 2.4
 476       cannot be loaded</li>
 477      <li>Filetype associations not installed for webstart launch</li>
 478      <li>Two or more chains in a single PDB file associated with
 479       sequences in different alignments do not get coloured by their
 480       associated sequence</li>
 481      <li>Visibility status of autocalculated annotation row not
 482       preserved when project is loaded</li>
 483      <li>Annotation row height and visibility attributes not stored
 484       in jalview project</li>
 485      <li>Tree bootstraps are not preserved when saved as a jalview
 486       project</li>
 487      <li>Envision2 workflow tooltips are corrupted</li>
 488      <li>Enabling show group conservation also enables colour by
 489       conservation</li>
 490      <li>Duplicate group associated conservation or consensus
 491       created on new view</li>
 492      <li>Annotation scrollbar not displayed after &#39;show all
 493       hidden annotation rows&#39; option selected</li>
 494      <li>Alignment quality not updated after alignment annotation
 495       row is hidden then shown</li>
 496      <li>Preserve colouring of structures coloured by sequences in
 497       pre jalview 2.7 projects</li>
 498      <li>Web service job parameter dialog is not laid out properly
 499      </li>
 500      <li>Web services menu not refreshed after &#39;reset
 501       services&#39; button is pressed in preferences</li>
 502      <li>Annotation off by one in jalview v2_3 example project</li>
 503      <li>Structures imported from file and saved in project get
 504       name like jalview_pdb1234.txt when reloaded</li>
 505      <li>Jalview does not always retrieve progress of a JABAWS job
 506       execution in full once it is complete</li>
 507     </ul> <em>Applet</em>
 508     <ul>
 509      <li>Alignment height set incorrectly when lots of annotation
 510       rows are displayed</li>
 511      <li>Relative URLs in feature HTML text not resolved to
 512       codebase</li>
 513      <li>View follows highlighting does not work for positions in
 514       sequences</li>
 515      <li>&lt;= shown as = in tooltip</li>
 516      <li>Export features raises exception when no features exist</li>
 517      <li>Separator string used for serialising lists of IDs for
 518       javascript api is modified when separator string provided as
 519       parameter</li>
 520      <li>Null pointer exception when selecting tree leaves for
 521       alignment with no existing selection</li>
 522      <li>Relative URLs for datasources assumed to be relative to
 523       applet&#39;s codebase</li>
 524      <li>Status bar not updated after finished searching and search
 525       wraps around to first result</li>
 526      <li>StructureSelectionManager instance shared between several
 527       jalview applets causes race conditions and memory leaks</li>
 528      <li>Hover tooltip and mouseover of position on structure not
 529       sent from Jmol in applet</li>
 530      <li>Certain sequences of javascript method calls to applet API
 531       fatally hang browser</li>
 532     </ul> <em>General</em>
 533     <ul>
 534      <li>View follows structure mouseover scrolls beyond position
 535       with wrapped view and hidden regions</li>
 536      <li>Find sequence position moves to wrong residue with/without
 537       hidden columns</li>
 538      <li>Sequence length given in alignment properties window is
 539       off by 1</li>
 540      <li>InvalidNumberFormat exceptions thrown when trying to
 541       import PDB like structure files</li>
 542      <li>Positional search results are only highlighted between
 543       user-supplied sequence start/end bounds</li>
 544      <li>End attribute of sequence is not validated</li>
 545      <li>Find dialog only finds first sequence containing a given
 546       sequence position</li>
 547      <li>Sequence numbering not preserved in MSF alignment output</li>
 548      <li>Jalview PDB file reader does not extract sequence from
 549       nucleotide chains correctly</li>
 550      <li>Structure colours not updated when tree partition changed
 551       in alignment</li>
 552      <li>Sequence associated secondary structure not correctly
 553       parsed in interleaved stockholm</li>
 554      <li>Colour by annotation dialog does not restore current state
 555      </li>
 556      <li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
 557      <li>Sequences containing lowercase letters are not properly
 558       associated with their pdb files</li>
 559     </ul> <em>Documentation and Development</em>
 560     <ul>
 561      <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
 562       tool</li>
 563     </ul></td>
 564   </tr>
 565   <tr>
 566                         <td>
 567                                 <div align="center">
 568                                         <strong><a name="Jalview2.6.1">2.6.1</a>
 569                                         </strong><br> <em>15/11/2010</em>
 570                                 </div></td>
 571                         <td><em>Application</em>
 572                                 <ul>
 573                                         <li>New warning dialog when the Jalview Desktop cannot contact
 574                                                 web services</li>
 575                                         <li>JABA service parameters for a preset are shown in service
 576                                                 job window</li>
 577                                         <li>JABA Service menu entries reworded</li>
 578                                 </ul></td>
 579                         <td>
 580                                 <ul>
 581                                         <li>Modeller PIR IO broken - cannot correctly import a pir
 582                                                 file emitted by jalview</li>
 583                                         <li>Existing feature settings transferred to new alignment
 584                                                 view created from cut'n'paste</li>
 585                                         <li>Improved test for mixed amino/nucleotide chains when
 586                                                 parsing PDB files</li>
 587                                         <li>Consensus and conservation annotation rows occasionally
 588                                                 become blank for all new windows</li>
 589                                         <li>Exception raised when right clicking above sequences in
 590                                                 wrapped view mode</li>
 591                                 </ul> <em>Application</em>
 592                                 <ul>
 593                                         <li>multiple multiply aligned structure views cause cpu usage
 594                                                 to hit 100% and computer to hang</li>
 595                                         <li>Web Service parameter layout breaks for long user
 596                                                 parameter names</li>
 597                                         <li>Jaba service discovery hangs desktop if Jaba server is
 598                                                 down</li>
 599                                 </ul></td>
 600                 </tr>
 601                 <tr>
 602                 <td>
 603                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
 604                 <em>26/9/2010</em></div>
 605                 </td>
 606                 <td><em>Application</em>
 607                 <ul>
 608                         <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
 609                         <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
 610                         <li>Web Services preference tab</li>
 611                         <li>Analysis parameters dialog box and user defined preferences</li>
 612                         <li>Improved speed and layout of Envision2 service menu</li>
 613                         <li>Superpose structures using associated sequence alignment</li>
 614                         <li>Export coordinates and projection as CSV from PCA viewer</li>
 615                 </ul>
 616                 <em>Applet</em>
 617                 <ul>
 618                         <li>enable javascript: execution by the applet via the link out
 619                         mechanism</li>
 620                 </ul>
 621                 <em>Other</em>
 622                 <ul>
 623                         <li>Updated the Jmol Jalview interface to work with Jmol series
 624                         12</li>
 625                         <li>The Jalview Desktop and JalviewLite applet now require Java
 626                         1.5</li>
 627                         <li>Allow Jalview feature colour specification for GFF sequence
 628                         annotation files</li>
 629                         <li>New 'colour by label' keword in jalview feature file type
 630                         colour specification</li>
 631                         <li>New Jalview Desktop Groovy API method that allows a script
 632                         to check if it being run in an interactive session or in a batch
 633                         operation from the jalview command line</li>
 634                 </ul>
 635                 </td>
 636                 <td>
 637                 <ul>
 638                         <li>clustalx colourscheme colours Ds preferentially when both
 639                         D+E are present in over 50% of the column</li>
 640                 </ul>
 641
 642                 <em>Application</em>
 643                 <ul>
 644                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 645                         selected Regions menu item</li>
 646                         <li>sequence fetcher replaces ',' for ';' when the ',' is part
 647                         of a valid accession ID</li>
 648                         <li>fatal OOM if object retrieved by sequence fetcher runs out
 649                         of memory</li>
 650                         <li>unhandled Out of Memory Error when viewing pca analysis
 651                         results</li>
 652                         <li>InstallAnywhere builds fail to launch on OS X java 10.5
 653                         update 4 (due to apple Java 1.6 update)</li>
 654                         <li>Installanywhere Jalview silently fails to launch</li>
 655                 </ul>
 656                 <em>Applet</em>
 657                 <ul>
 658                         <li>Jalview.getFeatureGroups() raises an
 659                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
 660                 </ul>
 661                 </td>
 662         </tr>
 663         <tr>
 664                 <td>
 665                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
 666                 <em>14/6/2010</em></div>
 667                 </td>
 668                 <td></td>
 669                 <td>
 670                 <ul>
 671                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
 672                         </li>
 673                         <li>clustalx colourscheme colours Ds preferentially when both
 674                         D+E are present in over 50% of the column</li>
 675                         <li>nucleic acid structures retrieved from PDB do not import
 676                         correctly</li>
 677                         <li>More columns get selected than were clicked on when a number
 678                         of columns are hidden</li>
 679                         <li>annotation label popup menu not providing correct
 680                         add/hide/show options when rows are hidden or none are present</li>
 681                         <li>Stockholm format shown in list of readable formats, and
 682                         parser copes better with alignments from RFAM.</li>
 683                         <li>CSV output of consensus only includes the percentage of all
 684                         symbols if sequence logo display is enabled</li>
 685
 686                 </ul>
 687                 <em>Applet</em>
 688                 <ul>
 689                         <li>annotation panel disappears when annotation is
 690                         hidden/removed</li>
 691                 </ul>
 692                 <em>Application</em>
 693                 <ul>
 694                         <li>Alignment view not redrawn properly when new alignment
 695                         opened where annotation panel is visible but no annotations are
 696                         present on alignment</li>
 697                         <li>pasted region containing hidden columns is incorrectly
 698                         displayed in new alignment window</li>
 699                         <li>Jalview slow to complete operations when stdout is flooded
 700                         (fix is to close the Jalview console)</li>
 701                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
 702                         selected Rregions menu item.</li>
 703                         <li>inconsistent group submenu and Format submenu entry 'Un' or
 704                         'Non'conserved</li>
 705                         <li>Sequence feature settings are being shared by multiple
 706                         distinct alignments</li>
 707                         <li>group annotation not recreated when tree partition is
 708                         changed</li>
 709                         <li>double click on group annotation to select sequences does
 710                         not propagate to associated trees</li>
 711                         <li>Mac OSX specific issues:
 712                         <ul>
 713                                 <li>exception raised when mouse clicked on desktop window
 714                                 background</li>
 715                                 <li>Desktop menu placed on menu bar and application name set
 716                                 correctly</li>
 717                                 <li>sequence feature settings not wide enough for the save
 718                                 feature colourscheme button</li>
 719                         </ul>
 720                         </li>
 721                 </ul>
 722                 </td>
 723         </tr>
 724         <tr>
 725
 726                 <td>
 727                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
 728                 <em>30/4/2010</em></div>
 729                 </td>
 730                 <td><em>New Capabilities</em>
 731                 <ul>
 732                         <li>URL links generated from description line for
 733                         regular-expression based URL links (applet and application)
 734                         <li>Non-positional feature URL links are shown in link menu</li>
 735                         <li>Linked viewing of nucleic acid sequences and structures</li>
 736                         <li>Automatic Scrolling option in View menu to display the
 737                         currently highlighted region of an alignment.</li>
 738                         <li>Order an alignment by sequence length, or using the average
 739                         score or total feature count for each sequence.</li>
 740                         <li>Shading features by score or associated description</li>
 741                         <li>Subdivide alignment and groups based on identity of selected
 742                         subsequence (Make Groups from Selection).</li>
 743                         <li>New hide/show options including Shift+Control+H to hide
 744                         everything but the currently selected region.</li>
 745                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
 746                 </ul>
 747                 <em>Application</em>
 748                 <ul>
 749                         <li>Fetch DB References capabilities and UI expanded to support
 750                         retrieval from DAS sequence sources</li>
 751                         <li>Local DAS Sequence sources can be added via the command line
 752                         or via the Add local source dialog box.</li>
 753                         <li>DAS Dbref and DbxRef feature types are parsed as database
 754                         references and protein_name is parsed as description line (BioSapiens
 755                         terms).</li>
 756                         <li>Enable or disable non-positional feature and database
 757                         references in sequence ID tooltip from View menu in application.</li>
 758                         <!--                    <li>New hidden columns and rows and representatives capabilities
 759                         in annotations file (in progress - not yet fully implemented)</li> -->
 760                         <li>Group-associated consensus, sequence logos and conservation
 761                         plots</li>
 762                         <li>Symbol distributions for each column can be exported and
 763                         visualized as sequence logos</li>
 764                         <li>Optionally scale multi-character column labels to fit within
 765                         each column of annotation row<!-- todo for applet --></li>
 766                         <li>Optional automatic sort of associated alignment view when a
 767                         new tree is opened.</li>
 768                         <li>Jalview Java Console</li>
 769                         <li>Better placement of desktop window when moving between
 770                         different screens.</li>
 771                         <li>New preference items for sequence ID tooltip and consensus
 772                         annotation</li>
 773                         <li>Client to submit sequences and IDs to <a
 774                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
 775                         <li><em>Vamsas Capabilities</em>
 776                         <ul>
 777                                 <li>Improved VAMSAS synchronization (jalview archive used to
 778                                 preserve views, structures, and tree display settings)</li>
 779                                 <li>Import of vamsas documents from disk or URL via command
 780                                 line</li>
 781                                 <li>Sharing of selected regions between views and with other
 782                                 VAMSAS applications (Experimental feature!)</li>
 783                                 <li>Updated API to VAMSAS version 0.2</li>
 784                         </ul>
 785                         </li>
 786                 </ul>
 787                 <em>Applet</em>
 788                 <ul>
 789                         <li>Middle button resizes annotation row height</li>
 790                         <li>New Parameters
 791                         <ul>
 792                                 <li>sortByTree (true/false) - automatically sort the associated
 793                                 alignment view by the tree when a new tree is opened.</li>
 794                                 <li>showTreeBootstraps (true/false) - show or hide branch
 795                                 bootstraps (default is to show them if available)</li>
 796                                 <li>showTreeDistances (true/false) - show or hide branch
 797                                 lengths (default is to show them if available)</li>
 798                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
 799                                 unassociated nodes should be highlighted in the tree view</li>
 800                                 <li>heightScale and widthScale (1.0 or more) - increase the
 801                                 height or width of a cell in the alignment grid relative to the
 802                                 current font size.</li>
 803                         </ul>
 804                         </li>
 805                         <li>Non-positional features displayed in sequence ID tooltip</li>
 806                 </ul>
 807                 <em>Other</em>
 808                 <ul>
 809                         <li>Features format: graduated colour definitions and
 810                         specification of feature scores</li>
 811                         <li>Alignment Annotations format: new keywords for group
 812                         associated annotation (GROUP_REF) and annotation row display
 813                         properties (ROW_PROPERTIES)</li>
 814                         <li>XML formats extended to support graduated feature
 815                         colourschemes, group associated annotation, and profile visualization
 816                         settings.</li>
 817                 </td>
 818                 <td>
 819                 <ul>
 820                         <li>Source field in GFF files parsed as feature source rather
 821                         than description</li>
 822                         <li>Non-positional features are now included in sequence feature
 823                         and gff files (controlled via non-positional feature visibility in
 824                         tooltip).</li>
 825                         <li>URL links generated for all feature links (bugfix)</li>
 826                         <li>Added URL embedding instructions to features file
 827                         documentation.</li>
 828                         <li>Codons containing ambiguous nucleotides translated as 'X' in
 829                         peptide product</li>
 830                         <li>Match case switch in find dialog box works for both sequence
 831                         ID and sequence string and query strings do not have to be in upper
 832                         case to match case-insensitively.</li>
 833                         <li>AMSA files only contain first column of multi-character
 834                         column annotation labels</li>
 835                         <li>Jalview Annotation File generation/parsing consistent with
 836                         documentation (e.g. Stockholm annotation can be exported and
 837                         re-imported)</li>
 838                         <li>PDB files without embedded PDB IDs given a friendly name</li>
 839                         <li>Find incrementally searches ID string matches as well as
 840                         subsequence matches, and correctly reports total number of both.</li>
 841                         <li>Application:
 842                         <ul>
 843                                 <li>Better handling of exceptions during sequence retrieval</li>
 844                                 <li>Dasobert generated non-positional feature URL link text
 845                                 excludes the start_end suffix</li>
 846                                 <li>DAS feature and source retrieval buttons disabled when
 847                                 fetch or registry operations in progress.</li>
 848                                 <li>PDB files retrieved from URLs are cached properly</li>
 849                                 <li>Sequence description lines properly shared via VAMSAS</li>
 850                                 <li>Sequence fetcher fetches multiple records for all data
 851                                 sources</li>
 852                                 <li>Ensured that command line das feature retrieval completes
 853                                 before alignment figures are generated.</li>
 854                                 <li>Reduced time taken when opening file browser for first
 855                                 time.</li>
 856                                 <li>isAligned check prior to calculating tree, PCA or
 857                                 submitting an MSA to JNet now excludes hidden sequences.</li>
 858                                 <li>User defined group colours properly recovered from Jalview
 859                                 projects.</li>
 860                         </ul>
 861                         </li>
 862                 </ul>
 863                 </td>
 864
 865         </tr>
 866         <tr>
 867                 <td>
 868                 <div align="center"><strong>2.4.0.b2</strong><br>
 869                 28/10/2009</div>
 870                 </td>
 871                 <td>
 872                 <ul>
 873                         <li>Experimental support for google analytics usage tracking.</li>
 874                         <li>Jalview privacy settings (user preferences and docs).</li>
 875                 </ul>
 876                 </td>
 877                 <td>
 878                 <ul>
 879                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
 880                         <li>Exception when feature created from selection beyond length
 881                         of sequence.</li>
 882                         <li>Allow synthetic PDB files to be imported gracefully</li>
 883                         <li>Sequence associated annotation rows associate with all
 884                         sequences with a given id</li>
 885                         <li>Find function matches case-insensitively for sequence ID
 886                         string searches</li>
 887                         <li>Non-standard characters do not cause pairwise alignment to
 888                         fail with exception</li>
 889                 </ul>
 890                 <em>Application Issues</em>
 891                 <ul>
 892                         <li>Sequences are now validated against EMBL database</li>
 893                         <li>Sequence fetcher fetches multiple records for all data
 894                         sources</li>
 895                 </ul>
 896                 <em>InstallAnywhere Issues</em>
 897                 <ul>
 898                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
 899                         installAnywhere mechanism)</li>
 900                         <li>Command line launching of JARs from InstallAnywhere version
 901                         (java class versioning error fixed)</li>
 902                 </ul>
 903                 </td>
 904         </tr>
 905         <tr>
 906                 <td>
 907
 908                 <div align="center"><strong>2.4</strong><br>
 909                 27/8/2008</div>
 910                 </td>
 911                 <td><em>User Interface</em>
 912                 <ul>
 913                         <li>Linked highlighting of codon and amino acid from translation
 914                         and protein products</li>
 915                         <li>Linked highlighting of structure associated with residue
 916                         mapping to codon position</li>
 917                         <li>Sequence Fetcher provides example accession numbers and
 918                         'clear' button</li>
 919                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
 920                         <li>Extract score function to parse whitespace separated numeric
 921                         data in description line</li>
 922                         <li>Column labels in alignment annotation can be centred.</li>
 923                         <li>Tooltip for sequence associated annotation give name of
 924                         sequence</li>
 925                 </ul>
 926                 <em>Web Services and URL fetching</em>
 927                 <ul>
 928                         <li>JPred3 web service</li>
 929                         <li>Prototype sequence search client (no public services
 930                         available yet)</li>
 931                         <li>Fetch either seed alignment or full alignment from PFAM</li>
 932                         <li>URL Links created for matching database cross references as
 933                         well as sequence ID</li>
 934                         <li>URL Links can be created using regular-expressions</li>
 935                 </ul>
 936                 <em>Sequence Database Connectivity</em>
 937                 <ul>
 938                         <li>Retrieval of cross-referenced sequences from other databases
 939                         </li>
 940                         <li>Generalised database reference retrieval and validation to
 941                         all fetchable databases</li>
 942                         <li>Fetch sequences from DAS sources supporting the sequence
 943                         command</li>
 944                 </ul>
 945                 <em>Import and Export</em>
 946                 <li>export annotation rows as CSV for spreadsheet import</li>
 947                 <li>Jalview projects record alignment dataset associations, EMBL
 948                 products, and cDNA sequence mappings</li>
 949                 <li>Sequence Group colour can be specified in Annotation File</li>
 950                 <li>Ad-hoc colouring of group in Annotation File using RGB
 951                 triplet as name of colourscheme</li>
 952                 </ul>
 953                 <em>VAMSAS Client capabilities (Experimental)</em>
 954                 <ul>
 955                         <li>treenode binding for VAMSAS tree exchange</li>
 956                         <li>local editing and update of sequences in VAMSAS alignments
 957                         (experimental)</li>
 958                         <li>Create new or select existing session to join</li>
 959                         <li>load and save of vamsas documents</li>
 960                 </ul>
 961                 <em>Application command line</em>
 962                 <ul>
 963                         <li>-tree parameter to open trees (introduced for passing from
 964                         applet)</li>
 965                         <li>-fetchfrom command line argument to specify nicknames of DAS
 966                         servers to query for alignment features</li>
 967                         <li>-dasserver command line argument to add new servers that are
 968                         also automatically queried for features</li>
 969                         <li>-groovy command line argument executes a given groovy script
 970                         after all input data has been loaded and parsed</li>
 971                 </ul>
 972                 <em>Applet-Application data exchange</em>
 973                 <ul>
 974                         <li>Trees passed as applet parameters can be passed to
 975                         application (when using &quot;View in full application&quot;)</li>
 976                 </ul>
 977                 <em>Applet Parameters</em>
 978                 <ul>
 979                         <li>feature group display control parameter</li>
 980                         <li>debug parameter</li>
 981                         <li>showbutton parameter</li>
 982                 </ul>
 983                 <em>Applet API methods</em>
 984                 <ul>
 985                         <li>newView public method</li>
 986                         <li>Window (current view) specific get/set public methods</li>
 987                         <li>Feature display control methods</li>
 988                         <li>get list of currently selected sequences</li>
 989                 </ul>
 990                 <em>New Jalview distribution features</em>
 991                 <ul>
 992                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
 993                         <li>RELEASE file gives build properties for the latest Jalview
 994                         release.</li>
 995                         <li>Java 1.1 Applet build made easier and donotobfuscate
 996                         property controls execution of obfuscator</li>
 997                         <li>Build target for generating source distribution</li>
 998                         <li>Debug flag for javacc</li>
 999                         <li>.jalview_properties file is documented (slightly) in
1000                         jalview.bin.Cache</li>
1001                         <li>Continuous Build Integration for stable and development
1002                         version of Application, Applet and source distribution</li>
1003                 </ul>
1004
1005                 </td>
1006                 <td>
1007                 <ul>
1008                         <li>selected region output includes visible annotations (for
1009                         certain formats)</li>
1010                         <li>edit label/displaychar contains existing label/char for
1011                         editing</li>
1012                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1013                         <li>shorter peptide product names from EMBL records</li>
1014                         <li>Newick string generator makes compact representations</li>
1015                         <li>bootstrap values parsed correctly for tree files with
1016                         comments</li>
1017                         <li>pathological filechooser bug avoided by not allowing
1018                         filenames containing a ':'</li>
1019                         <li>Fixed exception when parsing GFF files containing global
1020                         sequence features</li>
1021                         <li>Alignment datasets are finalized only when number of
1022                         references from alignment sequences goes to zero</li>
1023                         <li>Close of tree branch colour box without colour selection
1024                         causes cascading exceptions</li>
1025                         <li>occasional negative imgwidth exceptions</li>
1026                         <li>better reporting of non-fatal warnings to user when file
1027                         parsing fails.</li>
1028                         <li>Save works when Jalview project is default format</li>
1029                         <li>Save as dialog opened if current alignment format is not a
1030                         valid output format</li>
1031                         <li>Uniprot canonical names introduced for both das and vamsas</li>
1032                         <li>Histidine should be midblue (not pink!) in Zappo</li>
1033                         <li>error messages passed up and output when data read fails</li>
1034                         <li>edit undo recovers previous dataset sequence when sequence
1035                         is edited</li>
1036                         <li>allow PDB files without pdb ID HEADER lines (like those
1037                         generated by MODELLER) to be read in properly</li>
1038                         <li>allow reading of JPred concise files as a normal filetype</li>
1039                         <li>Stockholm annotation parsing and alignment properties import
1040                         fixed for PFAM records</li>
1041                         <li>Structure view windows have correct name in Desktop window
1042                         list</li>
1043                         <li>annotation consisting of sequence associated scores can be
1044                         read and written correctly to annotation file</li>
1045                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
1046                         <li>Fixed display of hidden sequence markers and non-italic font
1047                         for representatives in Applet</li>
1048                         <li>Applet Menus are always embedded in applet window on Macs.</li>
1049                         <li>Newly shown features appear at top of stack (in Applet)</li>
1050                         <li>Annotations added via parameter not drawn properly due to
1051                         null pointer exceptions</li>
1052                         <li>Secondary structure lines are drawn starting from first
1053                         column of alignment</li>
1054                         <li>Uniprot XML import updated for new schema release in July
1055                         2008</li>
1056                         <li>Sequence feature to sequence ID match for Features file is
1057                         case-insensitive</li>
1058                         <li>Sequence features read from Features file appended to all
1059                         sequences with matching IDs</li>
1060                         <li>PDB structure coloured correctly for associated views
1061                         containing a sub-sequence</li>
1062                         <li>PDB files can be retrieved by applet from Jar files</li>
1063                         <li>feature and annotation file applet parameters referring to
1064                         different directories are retrieved correctly</li>
1065                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1066                         <li>Fixed application hang whilst waiting for splash-screen
1067                         version check to complete</li>
1068                         <li>Applet properly URLencodes input parameter values when
1069                         passing them to the launchApp service</li>
1070                         <li>display name and local features preserved in results
1071                         retrieved from web service</li>
1072                         <li>Visual delay indication for sequence retrieval and sequence
1073                         fetcher initialisation</li>
1074                         <li>updated Application to use DAS 1.53e version of dasobert DAS
1075                         client</li>
1076                         <li>Re-instated Full AMSA support and .amsa file association</li>
1077                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1078                         sequences</li>
1079                 </ul>
1080                 </td>
1081         </tr>
1082         <tr>
1083                 <td>
1084                 <div align="center"><strong>2.3</strong><br>
1085                 9/5/07</div>
1086                 </td>
1087                 <td>
1088                 <ul>
1089                         <li>Jmol 11.0.2 integration</li>
1090                         <li>PDB views stored in Jalview XML files</li>
1091                         <li>Slide sequences</li>
1092                         <li>Edit sequence in place</li>
1093                         <li>EMBL CDS features</li>
1094                         <li>DAS Feature mapping</li>
1095                         <li>Feature ordering</li>
1096                         <li>Alignment Properties</li>
1097                         <li>Annotation Scores</li>
1098                         <li>Sort by scores</li>
1099                         <li>Feature/annotation editing in applet</li>
1100                 </ul>
1101                 </td>
1102                 <td>
1103                 <ul>
1104                         <li>Headless state operation in 2.2.1</li>
1105                         <li>Incorrect and unstable DNA pairwise alignment</li>
1106                         <li>Cut and paste of sequences with annotation</li>
1107                         <li>Feature group display state in XML</li>
1108                         <li>Feature ordering in XML</li>
1109                         <li>blc file iteration selection using filename # suffix</li>
1110                         <li>Stockholm alignment properties</li>
1111                         <li>Stockhom alignment secondary structure annotation</li>
1112                         <li>2.2.1 applet had no feature transparency</li>
1113                         <li>Number pad keys can be used in cursor mode</li>
1114                         <li>Structure Viewer mirror image resolved</li>
1115                 </ul>
1116                 </td>
1117
1118         </tr>
1119         <tr>
1120                 <td>
1121                 <div align="center"><strong>2.2.1</strong><br>
1122                 12/2/07</div>
1123                 </td>
1124                 <td>
1125                 <ul>
1126                         <li>Non standard characters can be read and displayed
1127                         <li>Annotations/Features can be imported/exported to the applet
1128                         via textbox
1129                         <li>Applet allows editing of sequence/annotation/group name
1130                         &amp; description
1131                         <li>Preference setting to display sequence name in italics
1132                         <li>Annotation file format extended to allow Sequence_groups to
1133                         be defined
1134                         <li>Default opening of alignment overview panel can be specified
1135                         in preferences
1136                         <li>PDB residue numbering annotation added to associated
1137                         sequences
1138                 </ul>
1139                 </td>
1140                 <td>
1141                 <ul>
1142                         <li>Applet crash under certain Linux OS with Java 1.6 installed
1143                         <li>Annotation file export / import bugs fixed
1144                         <li>PNG / EPS image output bugs fixed
1145                 </ul>
1146                 </td>
1147         </tr>
1148         <tr>
1149                 <td>
1150                 <div align="center"><strong>2.2</strong><br>
1151                 27/11/06</div>
1152                 </td>
1153                 <td>
1154                 <ul>
1155                         <li>Multiple views on alignment
1156                         <li>Sequence feature editing
1157                         <li>&quot;Reload&quot; alignment
1158                         <li>&quot;Save&quot; to current filename
1159                         <li>Background dependent text colour
1160                         <li>Right align sequence ids
1161                         <li>User-defined lower case residue colours
1162                         <li>Format Menu
1163                         <li>Select Menu
1164                         <li>Menu item accelerator keys
1165                         <li>Control-V pastes to current alignment
1166                         <li>Cancel button for DAS Feature Fetching
1167                         <li>PCA and PDB Viewers zoom via mouse roller
1168                         <li>User-defined sub-tree colours and sub-tree selection
1169                         <li>'New Window' button on the 'Output to Text box'
1170                 </ul>
1171                 </td>
1172                 <td>
1173                 <ul>
1174                         <li>New memory efficient Undo/Redo System
1175                         <li>Optimised symbol lookups and conservation/consensus
1176                         calculations
1177                         <li>Region Conservation/Consensus recalculated after edits
1178                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
1179                         alignment)
1180                         <li>Slowed DAS Feature Fetching for increased robustness.
1181                         <li>Made angle brackets in ASCII feature descriptions display
1182                         correctly
1183                         <li>Re-instated Zoom function for PCA
1184                         <li>Sequence descriptions conserved in web service analysis
1185                         results
1186                         <li>Uniprot ID discoverer uses any word separated by &#8739;
1187                         <li>WsDbFetch query/result association resolved
1188                         <li>Tree leaf to sequence mapping improved
1189                         <li>Smooth fonts switch moved to FontChooser dialog box.
1190                 </ul>
1191                 </td>
1192         </tr>
1193         <tr>
1194                 <td>
1195                 <div align="center"><strong>2.1.1</strong><br>
1196                 12/9/06</div>
1197                 </td>
1198                 <td>
1199                 <ul>
1200                         <li>Copy consensus sequence to clipboard</li>
1201                 </ul>
1202                 </td>
1203                 <td>
1204                 <ul>
1205                         <li>Image output - rightmost residues are rendered if sequence
1206                         id panel has been resized</li>
1207                         <li>Image output - all offscreen group boundaries are rendered</li>
1208                         <li>Annotation files with sequence references - all elements in
1209                         file are relative to sequence position</li>
1210                         <li>Mac Applet users can use Alt key for group editing</li>
1211                 </ul>
1212                 </td>
1213         </tr>
1214         <tr>
1215                 <td>
1216                 <div align="center"><strong>2.1</strong><br>
1217                 22/8/06</div>
1218                 </td>
1219                 <td>
1220                 <ul>
1221                         <li>MAFFT Multiple Alignment in default Web Service list</li>
1222                         <li>DAS Feature fetching</li>
1223                         <li>Hide sequences and columns</li>
1224                         <li>Export Annotations and Features</li>
1225                         <li>GFF file reading / writing</li>
1226                         <li>Associate structures with sequences from local PDB files</li>
1227                         <li>Add sequences to exisiting alignment</li>
1228                         <li>Recently opened files / URL lists</li>
1229                         <li>Applet can launch the full application</li>
1230                         <li>Applet has transparency for features (Java 1.2 required)</li>
1231                         <li>Applet has user defined colours parameter</li>
1232                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
1233                 </ul>
1234                 </td>
1235                 <td>
1236                 <ul>
1237                         <li>Redundancy Panel reinstalled in the Applet</li>
1238                         <li>Monospaced font - EPS / rescaling bug fixed</li>
1239                         <li>Annotation files with sequence references bug fixed</li>
1240                 </ul>
1241                 </td>
1242         </tr>
1243         <tr>
1244                 <td>
1245                 <div align="center"><strong>2.08.1</strong><br>
1246                 2/5/06</div>
1247                 </td>
1248                 <td>
1249                 <ul>
1250                         <li>Change case of selected region from Popup menu</li>
1251                         <li>Choose to match case when searching</li>
1252                         <li>Middle mouse button and mouse movement can compress / expand
1253                         the visible width and height of the alignment</li>
1254                 </ul>
1255                 </td>
1256                 <td>
1257                 <ul>
1258                         <li>Annotation Panel displays complete JNet results</li>
1259                 </ul>
1260                 </td>
1261         </tr>
1262         <tr>
1263                 <td>
1264                 <div align="center"><strong>2.08b</strong><br>
1265                 18/4/06</div>
1266                 </td>
1267                 <td>&nbsp;</td>
1268                 <td>
1269                 <ul>
1270                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1271                         <li>Righthand label on wrapped alignments shows correct value</li>
1272                 </ul>
1273                 </td>
1274         </tr>
1275         <tr>
1276                 <td>
1277                 <div align="center"><strong>2.08</strong><br>
1278                 10/4/06</div>
1279                 </td>
1280                 <td>
1281                 <ul>
1282                         <li>Editing can be locked to the selection area</li>
1283                         <li>Keyboard editing</li>
1284                         <li>Create sequence features from searches</li>
1285                         <li>Precalculated annotations can be loaded onto alignments</li>
1286                         <li>Features file allows grouping of features</li>
1287                         <li>Annotation Colouring scheme added</li>
1288                         <li>Smooth fonts off by default - Faster rendering</li>
1289                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
1290                 </ul>
1291                 </td>
1292                 <td>
1293                 <ul>
1294                         <li>Drag &amp; Drop fixed on Linux</li>
1295                         <li>Jalview Archive file faster to load/save, sequence
1296                         descriptions saved.</li>
1297                 </ul>
1298                 </td>
1299         </tr>
1300         <tr>
1301                 <td>
1302                 <div align="center"><strong>2.07</strong><br>
1303                 12/12/05</div>
1304                 </td>
1305                 <td>
1306                 <ul>
1307                         <li>PDB Structure Viewer enhanced</li>
1308                         <li>Sequence Feature retrieval and display enhanced</li>
1309                         <li>Choose to output sequence start-end after sequence name for
1310                         file output</li>
1311                         <li>Sequence Fetcher WSDBFetch@EBI</li>
1312                         <li>Applet can read feature files, PDB files and can be used for
1313                         HTML form input</li>
1314                 </ul>
1315                 </td>
1316                 <td>
1317                 <ul>
1318                         <li>HTML output writes groups and features</li>
1319                         <li>Group editing is Control and mouse click</li>
1320                         <li>File IO bugs</li>
1321                 </ul>
1322                 </td>
1323         </tr>
1324         <tr>
1325                 <td>
1326                 <div align="center"><strong>2.06</strong><br>
1327                 28/9/05</div>
1328                 </td>
1329                 <td>
1330                 <ul>
1331                         <li>View annotations in wrapped mode</li>
1332                         <li>More options for PCA viewer</li>
1333                 </ul>
1334                 </td>
1335                 <td>
1336                 <ul>
1337                         <li>GUI bugs resolved</li>
1338                         <li>Runs with -nodisplay from command line</li>
1339                 </ul>
1340                 </td>
1341         </tr>
1342         <tr>
1343                 <td height="63">
1344                 <div align="center"><strong>2.05b</strong><br>
1345                 15/9/05</div>
1346                 </td>
1347                 <td>
1348                 <ul>
1349                         <li>Choose EPS export as lineart or text</li>
1350                         <li>Jar files are executable</li>
1351                         <li>Can read in Uracil - maps to unknown residue</li>
1352                 </ul>
1353                 </td>
1354                 <td>
1355                 <ul>
1356                         <li>Known OutOfMemory errors give warning message</li>
1357                         <li>Overview window calculated more efficiently</li>
1358                         <li>Several GUI bugs resolved</li>
1359                 </ul>
1360                 </td>
1361         </tr>
1362         <tr>
1363                 <td>
1364                 <div align="center"><strong>2.05</strong><br>
1365                 30/8/05</div>
1366                 </td>
1367                 <td>
1368                 <ul>
1369                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
1370                 </ul>
1371                 </td>
1372                 <td>
1373                 <ul>
1374                         <li>Several GUI bugs resolved</li>
1375                 </ul>
1376                 </td>
1377         </tr>
1378         <tr>
1379                 <td>
1380                 <div align="center"><strong>2.04</strong><br>
1381                 24/8/05</div>
1382                 </td>
1383                 <td>
1384                 <ul>
1385                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
1386                 </ul>
1387                 </td>
1388                 <td>
1389                 <ul>
1390                         <li>Improved JPred client reliability</li>
1391                         <li>Improved loading of Jalview files</li>
1392                 </ul>
1393                 </td>
1394         </tr>
1395         <tr>
1396                 <td>
1397                 <div align="center"><strong>2.03</strong><br>
1398                 18/8/05</div>
1399                 </td>
1400                 <td>
1401                 <ul>
1402                         <li>Set Proxy server name and port in preferences</li>
1403                         <li>Multiple URL links from sequence ids</li>
1404                         <li>User Defined Colours can have a scheme name and added to
1405                         Colour Menu</li>
1406                         <li>Choose to ignore gaps in consensus calculation</li>
1407                         <li>Unix users can set default web browser</li>
1408                         <li>Runs without GUI for batch processing</li>
1409                         <li>Dynamically generated Web Service Menus</li>
1410                 </ul>
1411                 </td>
1412                 <td>
1413                 <ul>
1414                         <li>InstallAnywhere download for Sparc Solaris</li>
1415                 </ul>
1416                 </td>
1417         </tr>
1418         <tr>
1419                 <td>
1420                 <div align="center"><strong>2.02</strong><br>
1421                 18/7/05</div>
1422                 </td>
1423                 <td>&nbsp;</td>
1424                 <td>
1425                 <ul>
1426                         <li>Copy &amp; Paste order of sequences maintains alignment
1427                         order.</li>
1428                 </ul>
1429                 </td>
1430         </tr>
1431         <tr>
1432                 <td>
1433                 <div align="center"><strong>2.01</strong><br>
1434                 12/7/05</div>
1435                 </td>
1436                 <td>
1437                 <ul>
1438                         <li>Use delete key for deleting selection.</li>
1439                         <li>Use Mouse wheel to scroll sequences.</li>
1440                         <li>Help file updated to describe how to add alignment
1441                         annotations.</li>
1442                         <li>Version and build date written to build properties file.</li>
1443                         <li>InstallAnywhere installation will check for updates at
1444                         launch of Jalview.</li>
1445                 </ul>
1446                 </td>
1447                 <td>
1448                 <ul>
1449                         <li>Delete gaps bug fixed.</li>
1450                         <li>FileChooser sorts columns.</li>
1451                         <li>Can remove groups one by one.</li>
1452                         <li>Filechooser icons installed.</li>
1453                         <li>Finder ignores return character when searching. Return key
1454                         will initiate a search.<br>
1455                         </li>
1456                 </ul>
1457                 </td>
1458         </tr>
1459         <tr>
1460                 <td>
1461                 <div align="center"><strong>2.0</strong><br>
1462                 20/6/05</div>
1463                 </td>
1464                 <td>
1465                 <ul>
1466                         <li>New codebase</li>
1467                 </ul>
1468                 </td>
1469                 <td>&nbsp;</td>
1470         </tr>
1471 </table>
1472 <p>&nbsp;</p>
1473 </body>
1474 </html>