help/html/releases.html

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