help/html/releases.html

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   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
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   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3
  11  * of the License, or (at your option) any later version.
  12  *
  13  * Jalview is distributed in the hope that it will be useful, but
  14  * WITHOUT ANY WARRANTY; without even the implied warranty
  15  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  16  * PURPOSE.  See the GNU General Public License for more details.
  17  *
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  19  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  20  * The Jalview Authors are detailed in the 'AUTHORS' file.
  21  -->
  22 <head>
  23 <title>Release History</title>
  24 </head>
  25 <body>
  26 <p><strong>Release History</strong></p>
  27 <table border="1">
  28                 <tr>
  29                         <td width="60" nowrap>
  30                                 <div align="center">
  31                                         <em><strong>Release</strong></em>
  32                                 </div>
  33                         </td>
  34                         <td>
  35                                 <div align="center">
  36                                         <em><strong>New Features</strong></em>
  37                                 </div>
  38                         </td>
  39                         <td>
  40                                 <div align="center">
  41                                         <em><strong>Issues Resolved</strong></em>
  42                                 </div>
  43                         </td>
  44                 </tr>
  45     <tr>
  46       <td><div align="center">
  47           <strong><a name="Jalview.2.9">2.9</a><br /> <em>9/9/2015</em></strong>
  48         </div></td>
  49       <td><em>General</em>
  50         <ul>
  51           <li>Linked visualisation and analysis of DNA and Protein
  52             alignments:
  53             <ul>
  54               <li>Translated cDNA alignments shown as split protein
  55                 and DNA alignment views</li>
  56               <li>Codon consensus annotation for linked protein and
  57                 cDNA alignment views</li>
  58               <li>Link cDNA or Protein product sequences by loading
  59                 them onto Protein or cDNA alignments</li>
  60               <li>Reconstruct linked cDNA alignment from aligned
  61                 protein sequences</li>
  62             </ul>
  63           </li>
  64           <li>Jmol integration updated to Jmol v14.2.14</li>
  65           <li>Import and export of Jalview alignment views as <a href="">BioJSON</a></li>
  66           <li>New alignment annotation file statements for
  67             reference sequences and marking hidden columns</li>
  68           <li>Assign an alignment reference sequence to highlight
  69             variation</li>
  70           <li>Select or hide columns according to alignment
  71             annotation</li>
  72           <li>Find option for locating sequences by
  73             description</li>
  74           <li>Conserved physicochemical properties shown in amino
  75             acid conservation row</li>
  76           <li>Alignments can be sorted by number of RNA helices</li>
  77         </ul>
  78         <em>Application</em>
  79         <ul>
  80           <li>Optional embedding of BioJSON data when exporting
  81             alignment figures to HTML</li>
  82           <li>New Export Settings dialog to control hidden region
  83             export in flat file generation</li>
  84           <li>New cDNA/Protein analysis capabilities
  85             <ul>
  86               <li>Get Cross-References should open a Split Frame
  87                 view with cDNA/Protein</li>
  88               <li>Detect when nucleotide sequences and protein
  89                 sequences are placed in the same alignment</li>
  90               <li>Split cDNA/Protein views are saved in Jalview
  91                 projects</li>
  92             </ul>
  93           </li>
  94
  95           <li>Use REST API to talk to Chimera</li>
  96           <li>Selected regions in Chimera are highlighted in linked Jalview windows</li>
  97
  98           <li>Calculate UPGMA and NJ trees using sequence feature
  99             similarity</li>
 100
 101           <li>VARNA RNA viewer updated to v3.93</li>
 102           <li>VARNA views are saved in Jalview
 103             Projects</li>
 104           <li>Pseudoknots displayed as Jalview RNA annotation can be shown in VARNA</li>
 105
 106           <li>changed 'View nucleotide structure' submenu to 'View VARNA 2D Structure'</li>
 107           <li>change "View protein structure" menu option to "3D Structure ..."</li>
 108
 109           <li>Make groups for selection uses marked columns as well
 110             as the active selected region</li>
 111
 112           <li>allow different similarity matrix calculations for
 113             tree building and PCA</li>
 114
 115           <li>Export alignment views for display with the <a
 116             href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
 117
 118           <li>Export scrollable SVG in HTML page</li>
 119
 120           <li>Interactive free text and structured queries with the
 121             PDBe Search API for PDB data retrieval</li>
 122           <li>PDBe Search API based discovery and selection of PDB structures to
 123             view for a sequence set</li>
 124
 125           <li>JPred4 employed for protein secondary structure
 126             predictions</li>
 127           <li>Hide Insertions menu option to hide unaligned columns
 128             for one or a group of sequences</li>
 129           <li>Automatically hide insertions in alignments imported from the JPred4 web server</li>
 130           <li>(Nearly) Native 'Quaqua' dialogs for browsing file
 131             system on OSX<br />LGPL libraries courtesy of <a
 132             href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
 133           </li>
 134         </ul> <em>Applet</em>
 135         <ul>
 136           <li>New parameters to enable SplitFrame view (file2, scaleProteinAsCdna)</li>
 137           <li>New example demonstrating linked viewing of cDNA and
 138             Protein alignments</li>
 139           <li>New layout for applet example pages</li>
 140         </ul>
 141         <em>Development and deployment</em>
 142         <li>Java 1.7 minimum requirement for Jalview 2.9</li>
 143         <li>Include installation type and git revision in build
 144           properties and console log output</li>
 145         <li>Github project and web URL for storing BioJsMSA
 146           Templates</li>
 147         <li>Jalview's unit tests now managed with TestNG</li></td>
 148       <td>
 149         <!-- <em>General</em>
 150         <ul>
 151         </ul>  -->
 152         <!--  issues resolved --> <em>Application</em>
 153         <ul>
 154           <li>Escape should close any open find dialogs</li>
 155           <li>Typo in select-by-features status report</li>
 156           <li>Consensus RNA secondary secondary structure
 157             predictions are not highlighted in amber</li>
 158           <li>Missing gap character in v2.7 example file means
 159             alignment appears unaligned when pad-gaps is not enabled</li>
 160           <li>First switch to RNA Helices colouring doesn't colour
 161             associated structure views</li>
 162           <li>ID width preference option is greyed out when auto
 163             width checkbox not enabled</li>
 164           <li>Stopped a warning dialog from being shown when
 165             creating user defined colours</li>
 166           <li>'View Mapping' in structure viewer shows sequence
 167             mappings for just that viewer's sequences</li>
 168           <li>Workaround for superposing PDB files containing
 169             multiple models in Chimera</li>
 170           <li>Report sequence position in status bar when hovering
 171             over Jmol structure</li>
 172           <li>Cannot output gaps as '.' symbols with Selection ->
 173             output to text box</li>
 174           <li>Flat file exports of alignments with hidden columns
 175             have incorrect sequence start/end</li>
 176           <li>'Aligning' a second chain to a Chimera structure from
 177             Jalview fails</li>
 178           <li>Colour schemes applied to structure viewers don't
 179             work for nucleotide</li>
 180           <li>Loading/cut'n'pasting an empty or invalid file leads
 181             to a grey/invisible alignment window</li>
 182           <li>Exported Jpred annotation from a sequence region
 183             imports to different position</li>
 184           <li>Space at beginning of sequence feature tooltips shown
 185             on some platforms</li>
 186           <li>Chimera viewer 'View | Show Chain' menu is not
 187             populated</li>
 188           <li>'New View' fails with a Null Pointer Exception in
 189             console if Chimera has been opened</li>
 190           <li>Mouseover to Chimera not working</li>
 191           <li>Miscellaneous ENA XML feature qualifiers not
 192             retrieved</li>
 193           <li>NPE in annotation renderer after 'Extract Scores'</li>
 194           <li>If two structures in one Chimera window, mouseover of
 195             either sequence shows on first structure</li>
 196           <li>'Show annotations' options should not make
 197             non-positional annotations visible</li>
 198           <li>Subsequence secondary structure annotation not shown
 199             in right place after 'view flanking regions'</li>
 200           <li>File Save As type unset when current file format is
 201             unknown</li>
 202           <li>Save as '.jar' option removed for saving Jalview
 203             projects</li>
 204           <li>Colour by Sequence colouring in Chimera more
 205             responsive</li>
 206           <li>Cannot 'add reference annotation' for a sequence in
 207             several views on same alignment</li>
 208           <li>Cannot show linked products for EMBL / ENA records</li>
 209           <li>Jalview's tooltip wraps long texts containing no
 210             spaces</li>
 211         </ul> <em>Applet</em>
 212         <li>Jmol to JalviewLite mouseover/link not working</li>
 213         <li>JalviewLite can't import sequences with ID descriptions
 214           containing angle brackets</li>
 215         <ul>
 216         </ul> <em>General</em>
 217         <ul>
 218           <li>Cannot export and reimport RNA secondary structure
 219             via jalview annotation file</li>
 220           <li>Random helix colour palette for colour by annotation
 221             with RNA secondary structure</li>
 222           <li>Mouseover to cDNA from STOP residue in protein
 223             translation doesn't work.</li>
 224           <li>hints when using the select by annotation dialog box</li>
 225           <li>Jmol alignment incorrect if PDB file has alternate CA
 226             positions</li>
 227           <li>FontChooser message dialog appears to hang after
 228             choosing 1pt font</li>
 229           <li>Peptide secondary structure incorrectly imported from
 230             annotation file when annotation display text includes 'e' or
 231             'h'</li>
 232           <li>Cannot set colour of new feature type whilst creating
 233             new feature</li>
 234           <li>cDNA translation alignment should not be sequence
 235             order dependent</li>
 236           <li>'Show unconserved' doesn't work for lower case
 237             sequences</li>
 238           <li>Nucleotide ambiguity codes involving R not recognised</li>
 239         </ul> <em>Deployment and Documentation</em>
 240         <ul>
 241           <li>Applet example pages appear different to the rest of
 242             www.jalview.org</li>
 243         </ul> <em>Application Known issues</em>
 244         <ul>
 245           <li>Incomplete sequence extracted from PDB entry 3a6s</li>
 246           <li>Misleading message appears after trying to delete
 247             solid column.</li>
 248           <li>Jalview icon not shown in dock after InstallAnywhere
 249             version launches</li>
 250           <li>Fetching EMBL reference for an RNA sequence results
 251             fails with a sequence mismatch</li>
 252           <li>Corrupted or unreadable alignment display when
 253             scrolling alignment to right</li>
 254           <li>ArrayIndexOutOfBoundsException thrown when remove
 255             empty columns called on alignment with ragged gapped ends</li>
 256           <li>auto calculated alignment annotation rows do not get
 257             placed above or below non-autocalculated rows</li>
 258           <li>Jalview dekstop becomes sluggish at full screen in
 259             ultra-high resolution</li>
 260           <li>Cannot disable consensus calculation independently of
 261             quality and conservation</li>
 262           <li>Mouseover highlighting between cDNA and protein can
 263             become sluggish with more than one splitframe shown</li>
 264         </ul> <em>Applet Known Issues</em>
 265         <ul>
 266           <li>Core PDB parsing code requires Jmol</li>
 267           <li>Sequence canvas panel goes white when alignment
 268             window is being resized
 269           <li>
 270         </ul>
 271       </td>
 272     </tr>
 273     <tr>
 274                         <td width="60" nowrap>
 275                                 <div align="center">
 276                                         <strong><a name="Jalview.2.8.2b1">2.8.2b1</a><br /> <em>15/12/2014</em></strong>
 277                                 </div>
 278                         </td>
 279                         <td>
 280                                 <div align="center">
 281                                 </div>
 282                         </td>
 283                         <td>
 284                                 <div align="center">
 285                                         <ul><li>Reinstated the display of default example file on startup</li>
 286                                         <li>All pairs shown in Jalview window when viewing result of pairwise alignment</li>
 287                                         </ul>
 288                                 </div>
 289                         </td>
 290                 </tr>
 291                 <tr>
 292                         <td><div align="center">
 293                                         <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
 294                                 </div></td>
 295                         <td><em>General</em>
 296                                 <ul>
 297                                 <li>Updated Java code signing certificate donated by Certum.PL.</li>
 298                                         <li>Features and annotation preserved when performing pairwise
 299                                                 alignment</li>
 300                                         <li>RNA pseudoknot annotation can be
 301                                                 imported/exported/displayed</li>
 302                                         <li>&#39;colour by annotation&#39; can colour by RNA and
 303                                           protein secondary structure</li>
 304                                 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned post-hoc with 2.9 release</em>)</li>
 305
 306                                 </ul> <em>Application</em>
 307                                 <ul>
 308                                         <li>Extract and display secondary structure for sequences with
 309                                                 3D structures</li>
 310                                         <li>Support for parsing RNAML</li>
 311                                         <li>Annotations menu for layout
 312                                                 <ul>
 313                                                         <li>sort sequence annotation rows by alignment</li>
 314                                                         <li>place sequence annotation above/below alignment
 315                                                                 annotation</li>
 316                                                 </ul>
 317                                         <li>Output in Stockholm format</li>
 318                                         <li>Internationalisation: improved Spanish (es) translation</li>
 319                                         <li>Structure viewer preferences tab</li>
 320                                         <li>Disorder and Secondary Structure annotation tracks shared
 321                                                 between alignments</li>
 322                                         <li>UCSF Chimera launch and linked highlighting from Jalview</li>
 323                                         <li>Show/hide all sequence associated annotation rows for all
 324                                                 or current selection</li>
 325                                         <li>disorder and secondary structure predictions available as
 326                                                 dataset annotation</li>
 327                                         <li>Per-sequence rna helices colouring</li>
 328
 329
 330                                         <li>Sequence database accessions imported when fetching
 331                                                 alignments from Rfam</li>
 332                                         <li>update VARNA version to 3.91</li>
 333
 334                                         <li>New groovy scripts for exporting aligned positions,
 335                                                 conservation values, and calculating sum of pairs scores.</li>
 336                                         <li>Command line argument to set default JABAWS server</li>
 337                                         <li>include installation type in build properties and console
 338                                                 log output</li>
 339                                         <li>Updated Jalview project format to preserve dataset annotation</li>
 340                                 </ul></td>
 341                         <td>
 342                                 <!--  issues resolved --> <em>Application</em>
 343                                 <ul>
 344                                         <li>Distinguish alignment and sequence associated RNA
 345                                                 structure in structure-&gt;view-&gt;VARNA</li>
 346                                         <li>Raise dialog box if user deletes all sequences in an
 347                                                 alignment</li>
 348                                         <li>Pressing F1 results in documentation opening twice</li>
 349                                         <li>Sequence feature tooltip is wrapped</li>
 350                                         <li>Double click on sequence associated annotation selects
 351                                                 only first column</li>
 352                                         <li>Redundancy removal doesn&#39;t result in unlinked leaves
 353                                                 shown in tree</li>
 354                                         <li>Undos after several redundancy removals don't undo
 355                                                 properly</li>
 356                                         <li>Hide sequence doesn&#39;t hide associated annotation</li>
 357                                         <li>User defined colours dialog box too big to fit on screen
 358                                                 and buttons not visible</li>
 359                                         <li>author list isn't updated if already written to Jalview
 360                                                 properties</li>
 361                                         <li>Popup menu won&#39;t open after retrieving sequence from
 362                                                 database</li>
 363                                         <li>File open window for associate PDB doesn&#39;t open</li>
 364                                         <li>Left-then-right click on a sequence id opens a browser
 365                                                 search window</li>
 366                                         <li>Cannot open sequence feature shading/sort popup menu in
 367                                                 feature settings dialog</li>
 368                                         <li>better tooltip placement for some areas of Jalview desktop</li>
 369                                         <li>Allow addition of JABAWS Server which doesn&#39;t pass
 370                                                 validation</li>
 371                                         <li>Web services parameters dialog box is too large to fit on
 372                                                 screen</li>
 373                                         <li>Muscle nucleotide alignment preset obscured by tooltip</li>
 374                                         <li>JABAWS preset submenus don&#39;t contain newly defined
 375                                                 user preset</li>
 376                                         <li>MSA web services warns user if they were launched with
 377                                                 invalid input</li>
 378                                         <li>Jalview cannot contact DAS Registy when running on Java 8</li>
 379                                         <li>
 380                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
 381                                                 &#39;Superpose with&#39; submenu not shown when new view created
 382                                         </li>
 383
 384                                 </ul> <!--  <em>Applet</em>
 385                                 <ul>
 386                                 </ul> <em>General</em>
 387                                 <ul>
 388                                 </ul>--> <em>Deployment and Documentation</em>
 389                                 <ul>
 390                                         <li>2G and 1G options in launchApp have no effect on memory
 391                                                 allocation</li>
 392                                         <li>launchApp service doesn't automatically open
 393                                                 www.jalview.org/examples/exampleFile.jar if no file is given</li>
 394                                         <li>
 395                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
 396                                                 InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is
 397                                                 available
 398                                         </li>
 399                                 </ul> <em>Application Known issues</em>
 400                                 <ul>
 401                                         <li>
 402                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
 403                                                 corrupted or unreadable alignment display when scrolling alignment
 404                                                 to right
 405                                         </li>
 406                                         <li>
 407                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
 408                                                 retrieval fails but progress bar continues for DAS retrieval with
 409                                                 large number of ID
 410                                         </li>
 411                                         <li>
 412                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
 413                                                 flatfile output of visible region has incorrect sequence start/end
 414                                         </li>
 415                                         <li>
 416                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
 417                                                 rna structure consensus doesn&#39;t update when secondary
 418                                                 structure tracks are rearranged
 419                                         </li>
 420                                         <li>
 421                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
 422                                                 invalid rna structure positional highlighting does not highlight
 423                                                 position of invalid base pairs
 424                                         </li>
 425                                         <li>
 426                                                 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
 427                                                 out of memory errors are not raised when saving Jalview project
 428                                                 from alignment window file menu
 429                                         </li>
 430                                         <li>
 431                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
 432                                                 Switching to RNA Helices colouring doesn&#39;t propagate to
 433                                                 structures
 434                                         </li>
 435                                         <li>
 436                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
 437                                                 colour by RNA Helices not enabled when user created annotation
 438                                                 added to alignment
 439                                         </li>
 440                                         <li>
 441                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
 442                                                 Jalview icon not shown on dock in Mountain Lion/Webstart
 443                                         </li>
 444                                 </ul> <em>Applet Known Issues</em>
 445                                 <ul>
 446                                         <li>
 447                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
 448                                                 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
 449                                         </li>
 450                                         <li>
 451                                                 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
 452                                                 Jalview and Jmol example not compatible with IE9
 453                                         </li>
 454
 455                                         <li>Sort by annotation score doesn&#39;t reverse order when
 456                                                 selected</li>
 457                                 </ul>
 458                         </td>
 459                 </tr>
 460                 <tr>
 461                         <td><div align="center">
 462                                         <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
 463                                 </div></td>
 464                         <td>
 465                                 <!--  New features --> <!--  For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
 466                                 <em>General</em>
 467                                 <ul>
 468                                         <li>Internationalisation of user interface (usually called
 469                                                 i18n support) and translation for Spanish locale</li>
 470                                         <li>Define/Undefine group on current selection with
 471                                                 Ctrl-G/Shift Ctrl-G</li>
 472                                         <li>Improved group creation/removal options in
 473                                                 alignment/sequence Popup menu</li>
 474                                         <li>Sensible precision for symbol distribution percentages
 475                                                 shown in logo tooltip.</li>
 476                                         <li>Annotation panel height set according to amount of
 477                                                 annotation when alignment first opened</li>
 478                                 </ul> <em>Application</em>
 479                                 <ul>
 480                                         <li>Interactive consensus RNA secondary structure prediction
 481                                                 VIENNA RNAAliFold JABA 2.1 service</li>
 482                                         <li>Select columns containing particular features from Feature
 483                                                 Settings dialog</li>
 484                                         <li>View all 'representative' PDB structures for selected
 485                                                 sequences</li>
 486                                         <li>Update Jalview project format:
 487                                                 <ul>
 488               <li>New file extension for Jalview projects '.jvp'</li>
 489                                                         <li>Preserve sequence and annotation dataset (to store
 490                                                                 secondary structure annotation,etc)</li>
 491                                                         <li>Per group and alignment annotation and RNA helix
 492                                                                 colouring</li>
 493                                                 </ul>
 494                                         </li>
 495                                         <li>New similarity measures for PCA and Tree calculation
 496                                                 (PAM250)</li>
 497                                         <li>Experimental support for retrieval and viewing of flanking
 498                                                 regions for an alignment</li>
 499                                 </ul>
 500                         </td>
 501                         <td>
 502                                 <!--  issues resolved --> <em>Application</em>
 503                                 <ul>
 504                                         <li>logo keeps spinning and status remains at queued or
 505                                                 running after job is cancelled</li>
 506                                         <li>cannot export features from alignments imported from
 507                                                 Jalview/VAMSAS projects</li>
 508                                         <li>Buggy slider for web service parameters that take float
 509                                                 values</li>
 510                                         <li>Newly created RNA secondary structure line doesn't have
 511                                                 'display all symbols' flag set</li>
 512                                         <li>T-COFFEE alignment score shading scheme and other
 513                                                 annotation shading not saved in Jalview project</li>
 514                                         <li>Local file cannot be loaded in freshly downloaded Jalview</li>
 515                                         <li>Jalview icon not shown on dock in Mountain Lion/Webstart</li>
 516                                         <li>Load file from desktop file browser fails</li>
 517                                         <li>Occasional NPE thrown when calculating large trees</li>
 518                                         <li>Cannot reorder or slide sequences after dragging an
 519                                                 alignment onto desktop</li>
 520                                         <li>Colour by annotation dialog throws NPE after using
 521                                                 'extract scores' function</li>
 522                                         <li>Loading/cut'n'pasting an empty file leads to a grey
 523                                                 alignment window</li>
 524                                         <li>Disorder thresholds rendered incorrectly after performing
 525                                                 IUPred disorder prediction</li>
 526                                         <li>Multiple group annotated consensus rows shown when
 527                                                 changing 'normalise logo' display setting</li>
 528                                         <li>Find shows blank dialog after 'finished searching' if
 529                                                 nothing matches query</li>
 530                                         <li>Null Pointer Exceptions raised when sorting by feature
 531                                                 with lots of groups<!--  possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
 532                                         </li>
 533                                         <li>Errors in Jmol console when structures in alignment don't
 534                                                 overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
 535                                         </li>
 536                                         <li>Not all working JABAWS services are shown in Jalview's
 537                                                 menu</li>
 538                                         <li>JAVAWS version of Jalview fails to launch with 'invalid
 539                                                 literal/length code'</li>
 540                                         <li>Annotation/RNA Helix colourschemes cannot be applied to
 541                                                 alignment with groups (actually fixed in 2.8.0b1)</li>
 542             <li>RNA Helices and T-Coffee Scores available as default colourscheme</li>
 543
 544                                 </ul> <em>Applet</em>
 545                                 <ul>
 546                                         <li>Remove group option is shown even when selection is not a
 547                                                 group</li>
 548                                         <li>Apply to all groups ticked but colourscheme changes don't
 549                                                 affect groups</li>
 550                                                 <li>Documented RNA Helices and T-Coffee Scores as valid colourscheme name</li>
 551                                                 <li>Annotation labels drawn on sequence IDs when Annotation panel is not displayed</li>
 552                                                 <li>Increased font size for dropdown menus on OSX and embedded windows</li>
 553                                 </ul> <em>Other</em>
 554                                 <ul>
 555                                         <li>Consensus sequence for alignments/groups with a single
 556                                                 sequence were not calculated</li>
 557                                         <li>annotation files that contain only groups imported as
 558                                                 annotation and junk sequences</li>
 559                                         <li>Fasta files with sequences containing '*' incorrectly
 560                                                 recognised as PFAM or BLC</li>
 561                                         <li>conservation/PID slider apply all groups option doesn't
 562                                                 affect background (2.8.0b1)
 563                                         <li></li>
 564                                         <li>redundancy highlighting is erratic at 0% and 100%</li>
 565                                         <li>Remove gapped columns fails for sequences with ragged
 566                                                 trailing gaps</li>
 567                                         <li>AMSA annotation row with leading spaces is not registered
 568                                                 correctly on import</li>
 569                                         <li>Jalview crashes when selecting PCA analysis for certain
 570                                                 alignments</li>
 571                                         <li>Opening the colour by annotation dialog for an existing
 572                                                 annotation based 'use original colours' colourscheme loses
 573                                                 original colours setting</li>
 574                                 </ul>
 575                         </td>
 576                 </tr>
 577                 <tr>
 578         <td><div align="center">
 579         <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br/><em>30/1/2014</em></strong>
 580         </div>
 581         </td>
 582       <td>
 583         <ul>
 584           <li>Trusted certificates for JalviewLite applet and
 585             Jalview Desktop application<br />Certificate was donated by
 586             <a href="https://www.certum.eu">Certum</a> to the Jalview
 587             open source project).
 588           </li>
 589           <li>Jalview SRS links replaced by Uniprot and EBI-search
 590           </li>
 591           <li>Output in Stockholm format</li>
 592           <li>Allow import of data from gzipped files</li>
 593           <li>Export/import group and sequence associated line
 594             graph thresholds</li>
 595           <li>Nucleotide substitution matrix that supports RNA and
 596             ambiguity codes</li>
 597           <li>Allow disorder predictions to be made on the current
 598             selection (or visible selection) in the same way that JPred
 599             works</li>
 600           <li>Groovy scripting for headless Jalview operation</li>
 601         </ul> <em>Other improvements</em>
 602         <ul>
 603           <li>Upgrade desktop installer to InstallAnywhere 2013</li>
 604           <li>COMBINE statement uses current SEQUENCE_REF and
 605             GROUP_REF scope to group annotation rows</li>
 606           <li>Support &#39;&#39; style escaping of quotes in Newick
 607             files</li>
 608           <li>Group options for JABAWS service by command line name</li>
 609           <li>Empty tooltip shown for JABA service options with a
 610             link but no description</li>
 611           <li>Select primary source when selecting authority in
 612             database fetcher GUI</li>
 613           <li>Add .mfa to FASTA file extensions recognised by
 614             Jalview</li>
 615           <li>Annotation label tooltip text wrap</li>
 616         </ul>
 617       </td>
 618       <td>
 619         <ul>
 620           <li>Slow scrolling when lots of annotation rows are
 621             displayed</li>
 622           <li>Lots of NPE (and slowness) after creating RNA
 623             secondary structure annotation line</li>
 624           <li>Sequence database accessions not imported when
 625             fetching alignments from Rfam</li>
 626           <li>Incorrect SHMR submission for sequences with
 627             identical IDs</li>
 628           <li>View all structures does not always superpose
 629             structures</li>
 630           <li>Option widgets in service parameters not updated to
 631             reflect user or preset settings</li>
 632           <li>Null pointer exceptions for some services without
 633             presets or adjustable parameters</li>
 634           <li>Discover PDB IDs entry in structure menu doesn&#39;t
 635             discover PDB xRefs</li>
 636           <li>Exception encountered while trying to retrieve
 637             features with DAS</li>
 638           <li>Lowest value in annotation row isn&#39;t coloured
 639             when colour by annotation (per sequence) is coloured</li>
 640           <li>Keyboard mode P jumps to start of gapped region when
 641             residue follows a gap</li>
 642           <li>Jalview appears to hang importing an alignment with
 643             Wrap as default or after enabling Wrap</li>
 644           <li>&#39;Right click to add annotations&#39; message
 645             shown in wrap mode when no annotations present</li>
 646           <li>Disorder predictions fail with NPE if no automatic
 647             annotation already exists on alignment</li>
 648           <li>oninit javascript function should be called after
 649             initialisation completes</li>
 650           <li>Remove redundancy after disorder prediction corrupts
 651             alignment window display</li>
 652           <li>Example annotation file in documentation is invalid</li>
 653           <li>Grouped line graph annotation rows are not exported
 654             to annotation file</li>
 655           <li>Multi-harmony analysis cannot be run when only two
 656             groups created</li>
 657           <li>Cannot create multiple groups of line graphs with
 658             several &#39;combine&#39; statements in annotation file</li>
 659           <li>Pressing return several times causes Number Format
 660             exceptions in keyboard mode</li>
 661           <li>Multi-harmony (SHMMR) method doesn&#39;t submit
 662             correct partitions for input data</li>
 663           <li>Translation from DNA to Amino Acids fails</li>
 664           <li>Jalview fail to load newick tree with quoted label</li>
 665           <li>--headless flag isn&#39;t understood</li>
 666           <li>ClassCastException when generating EPS in headless
 667             mode</li>
 668           <li>Adjusting sequence-associated shading threshold only
 669             changes one row&#39;s threshold</li>
 670           <li>Preferences and Feature settings panel panel
 671             doesn&#39;t open</li>
 672                                         <li>hide consensus histogram also hides conservation and
 673                                                 quality histograms</li>
 674                                 </ul>
 675       </td>
 676     </tr>
 677   <tr>
 678    <td><div align="center">
 679      <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
 680     </div></td>
 681    <td><em>Application</em>
 682     <ul><li>Support for JABAWS 2.0 Services (AACon alignment
 683      conservation, protein disorder and Clustal Omega)</li>
 684     <li>JABAWS server status indicator in Web Services preferences
 685    </li>
 686     <li>VARNA (http://varna.lri.fr) viewer for RNA structures in
 687      Jalview alignment window</li>
 688     <li>Updated Jalview build and deploy framework for OSX mountain
 689      lion, windows 7, and 8</li>
 690     <li>Nucleotide substitution matrix for PCA that supports RNA
 691      and ambiguity codes</li>
 692
 693     <li>Improved sequence database retrieval GUI</li>
 694     <li>Support fetching and database reference look up against
 695      multiple DAS sources (Fetch all from in 'fetch db refs')</li>
 696     <li>Jalview project improvements
 697      <ul>
 698       <li>Store and retrieve the &#39;belowAlignment&#39; flag for
 699        annotation</li>
 700       <li>calcId attribute to group annotation rows on the
 701        alignment</li>
 702       <li>Store AACon calculation settings for a view in Jalview
 703        project</li>
 704
 705      </ul>
 706    </li>
 707     <li>horizontal scrolling gesture support</li>
 708     <li>Visual progress indicator when PCA calculation is running</li>
 709     <li>Simpler JABA web services menus</li>
 710     <li>visual indication that web service results are still being
 711      retrieved from server</li>
 712     <li>Serialise the dialogs that are shown when Jalview starts up
 713      for first time</li>
 714     <li>Jalview user agent string for interacting with HTTP
 715      services</li>
 716     <li>DAS 1.6 and DAS 2.0 source support using new JDAS client
 717      library</li>
 718     <li>Examples directory and Groovy library included in
 719      InstallAnywhere distribution</li>
 720     </ul> <em>Applet</em>
 721     <ul>
 722      <li>RNA alignment and secondary structure annotation
 723       visualization applet example</li>
 724     </ul> <em>General</em>
 725     <ul>
 726      <li>Normalise option for consensus sequence logo</li>
 727      <li>Reset button in PCA window to return dimensions to
 728       defaults</li>
 729      <li>Allow seqspace or Jalview variant of alignment PCA
 730       calculation</li>
 731      <li>PCA with either nucleic acid and protein substitution
 732       matrices
 733      <li>Allow windows containing HTML reports to be exported in
 734       HTML</li>
 735      <li>Interactive display and editing of RNA secondary structure
 736       contacts</li>
 737      <li>RNA Helix Alignment Colouring</li>
 738      <li>RNA base pair logo consensus</li>
 739      <li>Parse sequence associated secondary structure information
 740       in Stockholm files</li>
 741      <li>HTML Export database accessions and annotation information
 742       presented in tooltip for sequences</li>
 743      <li>Import secondary structure from LOCARNA clustalw style RNA
 744       alignment files</li>
 745      <li>import and visualise T-COFFEE quality scores for an
 746       alignment</li>
 747      <li>&#39;colour by annotation&#39; per sequence option to
 748       shade each sequence according to its associated alignment
 749       annotation</li>
 750      <li>New Jalview Logo</li>
 751     </ul> <em>Documentation and Development</em>
 752     <ul>
 753      <li>documentation for score matrices used in Jalview</li>
 754      <li>New Website!</li>
 755     </ul></td>
 756    <td><em>Application</em>
 757     <ul>
 758      <li>PDB, Unprot and EMBL (ENA) databases retrieved via
 759       wsdbfetch REST service</li>
 760      <li>Stop windows being moved outside desktop on OSX</li>
 761      <li>Filetype associations not installed for webstart launch</li>
 762      <li>Jalview does not always retrieve progress of a JABAWS job
 763       execution in full once it is complete</li>
 764      <li>revise SHMR RSBS definition to ensure alignment is
 765       uploaded via ali_file parameter</li>
 766      <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
 767      <li>View all structures superposed fails with exception</li>
 768      <li>Jnet job queues forever if a very short sequence is
 769       submitted for prediction</li>
 770      <li>Cut and paste menu not opened when mouse clicked on
 771       desktop window</li>
 772      <li>Putting fractional value into integer text box in
 773       alignment parameter dialog causes Jalview to hang</li>
 774      <li>Structure view highlighting doesn&#39;t work on windows 7
 775      </li>
 776      <li>View all structures fails with exception shown in
 777       structure view</li>
 778      <li>Characters in filename associated with PDBEntry not
 779       escaped in a platform independent way</li>
 780      <li>Jalview desktop fails to launch with exception when using
 781       proxy</li>
 782      <li>Tree calculation reports &#39;you must have 2 or more
 783       sequences selected&#39; when selection is empty</li>
 784      <li>Jalview desktop fails to launch with jar signature failure
 785       when java web start temporary file caching is disabled</li>
 786      <li>DAS Sequence retrieval with range qualification results in
 787       sequence xref which includes range qualification</li>
 788      <li>Errors during processing of command line arguments cause
 789       progress bar (JAL-898) to be removed</li>
 790      <li>Replace comma for semi-colon option not disabled for DAS
 791       sources in sequence fetcher</li>
 792      <li>Cannot close news reader when JABAWS server warning dialog
 793       is shown</li>
 794      <li>Option widgets not updated to reflect user settings</li>
 795      <li>Edited sequence not submitted to web service</li>
 796      <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
 797      <li>InstallAnywhere installer doesn&#39;t unpack and run on
 798       OSX Mountain Lion</li>
 799      <li>Annotation panel not given a scroll bar when sequences
 800       with alignment annotation are pasted into the alignment</li>
 801      <li>Sequence associated annotation rows not associated when
 802       loaded from Jalview project</li>
 803      <li>Browser launch fails with NPE on java 1.7</li>
 804      <li>JABAWS alignment marked as finished when job was cancelled
 805       or job failed due to invalid input</li>
 806      <li>NPE with v2.7 example when clicking on Tree associated
 807       with all views</li>
 808      <li>Exceptions when copy/paste sequences with grouped
 809       annotation rows to new window</li>
 810     </ul> <em>Applet</em>
 811     <ul>
 812      <li>Sequence features are momentarily displayed before they
 813       are hidden using hidefeaturegroups applet parameter</li>
 814      <li>loading features via javascript API automatically enables
 815       feature display</li>
 816      <li>scrollToColumnIn javascript API method doesn&#39;t work</li>
 817     </ul> <em>General</em>
 818     <ul>
 819      <li>Redundancy removal fails for rna alignment</li>
 820      <li>PCA calculation fails when sequence has been selected and
 821       then deselected</li>
 822      <li>PCA window shows grey box when first opened on OSX</li>
 823      <li>Letters coloured pink in sequence logo when alignment
 824       coloured with clustalx</li>
 825      <li>Choosing fonts without letter symbols defined causes
 826       exceptions and redraw errors</li>
 827      <li>Initial PCA plot view is not same as manually reconfigured
 828       view</li>
 829      <li>Grouped annotation graph label has incorrect line colour</li>
 830      <li>Grouped annotation graph label display is corrupted for
 831       lots of labels</li>
 832     </ul>
 833   </tr>
 834   <tr>
 835    <td>
 836     <div align="center">
 837      <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
 838     </div>
 839    </td>
 840    <td><em>Application</em>
 841     <ul>
 842      <li>Jalview Desktop News Reader</li>
 843      <li>Tweaked default layout of web services menu</li>
 844      <li>View/alignment association menu to enable user to easily
 845       specify which alignment a multi-structure view takes its
 846       colours/correspondences from</li>
 847      <li>Allow properties file location to be specified as URL</li>
 848      <li>Extend Jalview project to preserve associations between
 849       many alignment views and a single Jmol display</li>
 850      <li>Store annotation row height in Jalview project file</li>
 851      <li>Annotation row column label formatting attributes stored
 852       in project file</li>
 853      <li>Annotation row order for auto-calculated annotation rows
 854       preserved in Jalview project file</li>
 855      <li>Visual progress indication when Jalview state is saved
 856       using Desktop window menu</li>
 857      <li>Visual indication that command line arguments are still
 858       being processed</li>
 859      <li>Groovy script execution from URL</li>
 860      <li>Colour by annotation default min and max colours in
 861       preferences</li>
 862      <li>Automatically associate PDB files dragged onto an
 863       alignment with sequences that have high similarity and matching
 864       IDs</li>
 865      <li>Update JGoogleAnalytics to latest release (0.3)</li>
 866      <li>&#39;view structures&#39; option to open many structures
 867       in same window</li>
 868      <li>Sort associated views menu option for tree panel</li>
 869      <li>Group all JABA and non-JABA services for a particular
 870       analysis function in its own submenu</li>
 871     </ul> <em>Applet</em>
 872     <ul>
 873      <li>Userdefined and autogenerated annotation rows for groups</li>
 874      <li>Adjustment of alignment annotation pane height</li>
 875      <li>Annotation scrollbar for annotation panel</li>
 876      <li>Drag to reorder annotation rows in annotation panel</li>
 877      <li>&#39;automaticScrolling&#39; parameter</li>
 878      <li>Allow sequences with partial ID string matches to be
 879       annotated from GFF/Jalview features files</li>
 880      <li>Sequence logo annotation row in applet</li>
 881      <li>Absolute paths relative to host server in applet
 882       parameters are treated as such</li>
 883      <li>New in the JalviewLite javascript API:
 884       <ul>
 885        <li>JalviewLite.js javascript library</li>
 886        <li>Javascript callbacks for
 887         <ul>
 888          <li>Applet initialisation</li>
 889          <li>Sequence/alignment mouse-overs and selections</li>
 890         </ul>
 891        </li>
 892        <li>scrollTo row and column alignment scrolling functions</li>
 893        <li>Select sequence/alignment regions from javascript</li>
 894        <li>javascript structure viewer harness to pass messages
 895         between Jmol and Jalview when running as distinct applets</li>
 896        <li>sortBy method</li>
 897        <li>Set of applet and application examples shipped with
 898         documentation</li>
 899        <li>New example to demonstrate JalviewLite and Jmol
 900         javascript message exchange</li>
 901       </ul>
 902     </ul> <em>General</em>
 903     <ul>
 904      <li>Enable Jmol displays to be associated with multiple
 905       multiple alignments</li>
 906      <li>Option to automatically sort alignment with new tree</li>
 907      <li>User configurable link to enable redirects to a
 908       www.Jalview.org mirror</li>
 909      <li>Jmol colours option for Jmol displays</li>
 910      <li>Configurable newline string when writing alignment and
 911       other flat files</li>
 912      <li>Allow alignment annotation description lines to contain
 913       html tags</li>
 914     </ul> <em>Documentation and Development</em>
 915     <ul>
 916      <li>Add groovy test harness for bulk load testing to examples
 917      </li>
 918      <li>Groovy script to load and align a set of sequences using a
 919       web service before displaying the result in the Jalview desktop</li>
 920      <li>Restructured javascript and applet api documentation</li>
 921      <li>Ant target to publish example html files with applet
 922       archive</li>
 923      <li>Netbeans project for building Jalview from source</li>
 924      <li>ant task to create online javadoc for Jalview source</li>
 925     </ul></td>
 926    <td><em>Application</em>
 927     <ul>
 928      <li>User defined colourscheme throws exception when current
 929       built in colourscheme is saved as new scheme</li>
 930      <li>AlignFrame-&gt;Save in application pops up save dialog for
 931       valid filename/format</li>
 932      <li>Cannot view associated structure for Uniprot sequence</li>
 933      <li>PDB file association breaks for Uniprot sequence P37173</li>
 934      <li>Associate PDB from file dialog does not tell you which
 935       sequence is to be associated with the file</li>
 936      <li>Find All raises null pointer exception when query only
 937       matches sequence IDs</li>
 938      <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
 939      <li>Jalview project with Jmol views created with Jalview 2.4
 940       cannot be loaded</li>
 941      <li>Filetype associations not installed for webstart launch</li>
 942      <li>Two or more chains in a single PDB file associated with
 943       sequences in different alignments do not get coloured by their
 944       associated sequence</li>
 945      <li>Visibility status of autocalculated annotation row not
 946       preserved when project is loaded</li>
 947      <li>Annotation row height and visibility attributes not stored
 948       in Jalview project</li>
 949      <li>Tree bootstraps are not preserved when saved as a Jalview
 950       project</li>
 951      <li>Envision2 workflow tooltips are corrupted</li>
 952      <li>Enabling show group conservation also enables colour by
 953       conservation</li>
 954      <li>Duplicate group associated conservation or consensus
 955       created on new view</li>
 956      <li>Annotation scrollbar not displayed after &#39;show all
 957       hidden annotation rows&#39; option selected</li>
 958      <li>Alignment quality not updated after alignment annotation
 959       row is hidden then shown</li>
 960      <li>Preserve colouring of structures coloured by sequences in
 961       pre Jalview 2.7 projects</li>
 962      <li>Web service job parameter dialog is not laid out properly
 963      </li>
 964      <li>Web services menu not refreshed after &#39;reset
 965       services&#39; button is pressed in preferences</li>
 966      <li>Annotation off by one in Jalview v2_3 example project</li>
 967      <li>Structures imported from file and saved in project get
 968       name like jalview_pdb1234.txt when reloaded</li>
 969      <li>Jalview does not always retrieve progress of a JABAWS job
 970       execution in full once it is complete</li>
 971     </ul> <em>Applet</em>
 972     <ul>
 973      <li>Alignment height set incorrectly when lots of annotation
 974       rows are displayed</li>
 975      <li>Relative URLs in feature HTML text not resolved to
 976       codebase</li>
 977      <li>View follows highlighting does not work for positions in
 978       sequences</li>
 979      <li>&lt;= shown as = in tooltip</li>
 980      <li>Export features raises exception when no features exist</li>
 981      <li>Separator string used for serialising lists of IDs for
 982       javascript api is modified when separator string provided as
 983       parameter</li>
 984      <li>Null pointer exception when selecting tree leaves for
 985       alignment with no existing selection</li>
 986      <li>Relative URLs for datasources assumed to be relative to
 987       applet&#39;s codebase</li>
 988      <li>Status bar not updated after finished searching and search
 989       wraps around to first result</li>
 990      <li>StructureSelectionManager instance shared between several
 991       Jalview applets causes race conditions and memory leaks</li>
 992      <li>Hover tooltip and mouseover of position on structure not
 993       sent from Jmol in applet</li>
 994      <li>Certain sequences of javascript method calls to applet API
 995       fatally hang browser</li>
 996     </ul> <em>General</em>
 997     <ul>
 998      <li>View follows structure mouseover scrolls beyond position
 999       with wrapped view and hidden regions</li>
1000      <li>Find sequence position moves to wrong residue with/without
1001       hidden columns</li>
1002      <li>Sequence length given in alignment properties window is
1003       off by 1</li>
1004      <li>InvalidNumberFormat exceptions thrown when trying to
1005       import PDB like structure files</li>
1006      <li>Positional search results are only highlighted between
1007       user-supplied sequence start/end bounds</li>
1008      <li>End attribute of sequence is not validated</li>
1009      <li>Find dialog only finds first sequence containing a given
1010       sequence position</li>
1011      <li>Sequence numbering not preserved in MSF alignment output</li>
1012      <li>Jalview PDB file reader does not extract sequence from
1013       nucleotide chains correctly</li>
1014      <li>Structure colours not updated when tree partition changed
1015       in alignment</li>
1016      <li>Sequence associated secondary structure not correctly
1017       parsed in interleaved stockholm</li>
1018      <li>Colour by annotation dialog does not restore current state
1019      </li>
1020      <li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
1021      <li>Sequences containing lowercase letters are not properly
1022       associated with their pdb files</li>
1023     </ul> <em>Documentation and Development</em>
1024     <ul>
1025      <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
1026       tool</li>
1027     </ul></td>
1028   </tr>
1029   <tr>
1030                         <td>
1031                                 <div align="center">
1032                                         <strong><a name="Jalview2.6.1">2.6.1</a>
1033                                         </strong><br> <em>15/11/2010</em>
1034                                 </div></td>
1035                         <td><em>Application</em>
1036                                 <ul>
1037                                         <li>New warning dialog when the Jalview Desktop cannot contact
1038                                                 web services</li>
1039                                         <li>JABA service parameters for a preset are shown in service
1040                                                 job window</li>
1041                                         <li>JABA Service menu entries reworded</li>
1042                                 </ul></td>
1043                         <td>
1044                                 <ul>
1045                                         <li>Modeller PIR IO broken - cannot correctly import a pir
1046                                                 file emitted by Jalview</li>
1047                                         <li>Existing feature settings transferred to new alignment
1048                                                 view created from cut'n'paste</li>
1049                                         <li>Improved test for mixed amino/nucleotide chains when
1050                                                 parsing PDB files</li>
1051                                         <li>Consensus and conservation annotation rows occasionally
1052                                                 become blank for all new windows</li>
1053                                         <li>Exception raised when right clicking above sequences in
1054                                                 wrapped view mode</li>
1055                                 </ul> <em>Application</em>
1056                                 <ul>
1057                                         <li>multiple multiply aligned structure views cause cpu usage
1058                                                 to hit 100% and computer to hang</li>
1059                                         <li>Web Service parameter layout breaks for long user
1060                                                 parameter names</li>
1061                                         <li>Jaba service discovery hangs desktop if Jaba server is
1062                                                 down</li>
1063                                 </ul></td>
1064                 </tr>
1065                 <tr>
1066                 <td>
1067                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
1068                 <em>26/9/2010</em></div>
1069                 </td>
1070                 <td><em>Application</em>
1071                 <ul>
1072                         <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1073                         <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
1074                         <li>Web Services preference tab</li>
1075                         <li>Analysis parameters dialog box and user defined preferences</li>
1076                         <li>Improved speed and layout of Envision2 service menu</li>
1077                         <li>Superpose structures using associated sequence alignment</li>
1078                         <li>Export coordinates and projection as CSV from PCA viewer</li>
1079                 </ul>
1080                 <em>Applet</em>
1081                 <ul>
1082                         <li>enable javascript: execution by the applet via the link out
1083                         mechanism</li>
1084                 </ul>
1085                 <em>Other</em>
1086                 <ul>
1087                         <li>Updated the Jmol Jalview interface to work with Jmol series
1088                         12</li>
1089                         <li>The Jalview Desktop and JalviewLite applet now require Java
1090                         1.5</li>
1091                         <li>Allow Jalview feature colour specification for GFF sequence
1092                         annotation files</li>
1093                         <li>New 'colour by label' keword in Jalview feature file type
1094                         colour specification</li>
1095                         <li>New Jalview Desktop Groovy API method that allows a script
1096                         to check if it being run in an interactive session or in a batch
1097                         operation from the Jalview command line</li>
1098                 </ul>
1099                 </td>
1100                 <td>
1101                 <ul>
1102                         <li>clustalx colourscheme colours Ds preferentially when both
1103                         D+E are present in over 50% of the column</li>
1104                 </ul>
1105
1106                 <em>Application</em>
1107                 <ul>
1108                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
1109                         selected Regions menu item</li>
1110                         <li>sequence fetcher replaces ',' for ';' when the ',' is part
1111                         of a valid accession ID</li>
1112                         <li>fatal OOM if object retrieved by sequence fetcher runs out
1113                         of memory</li>
1114                         <li>unhandled Out of Memory Error when viewing pca analysis
1115                         results</li>
1116                         <li>InstallAnywhere builds fail to launch on OS X java 10.5
1117                         update 4 (due to apple Java 1.6 update)</li>
1118                         <li>Installanywhere Jalview silently fails to launch</li>
1119                 </ul>
1120                 <em>Applet</em>
1121                 <ul>
1122                         <li>Jalview.getFeatureGroups() raises an
1123                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
1124                 </ul>
1125                 </td>
1126         </tr>
1127         <tr>
1128                 <td>
1129                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
1130                 <em>14/6/2010</em></div>
1131                 </td>
1132                 <td></td>
1133                 <td>
1134                 <ul>
1135                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
1136                         </li>
1137                         <li>clustalx colourscheme colours Ds preferentially when both
1138                         D+E are present in over 50% of the column</li>
1139                         <li>nucleic acid structures retrieved from PDB do not import
1140                         correctly</li>
1141                         <li>More columns get selected than were clicked on when a number
1142                         of columns are hidden</li>
1143                         <li>annotation label popup menu not providing correct
1144                         add/hide/show options when rows are hidden or none are present</li>
1145                         <li>Stockholm format shown in list of readable formats, and
1146                         parser copes better with alignments from RFAM.</li>
1147                         <li>CSV output of consensus only includes the percentage of all
1148                         symbols if sequence logo display is enabled</li>
1149
1150                 </ul>
1151                 <em>Applet</em>
1152                 <ul>
1153                         <li>annotation panel disappears when annotation is
1154                         hidden/removed</li>
1155                 </ul>
1156                 <em>Application</em>
1157                 <ul>
1158                         <li>Alignment view not redrawn properly when new alignment
1159                         opened where annotation panel is visible but no annotations are
1160                         present on alignment</li>
1161                         <li>pasted region containing hidden columns is incorrectly
1162                         displayed in new alignment window</li>
1163                         <li>Jalview slow to complete operations when stdout is flooded
1164                         (fix is to close the Jalview console)</li>
1165                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
1166                         selected Rregions menu item.</li>
1167                         <li>inconsistent group submenu and Format submenu entry 'Un' or
1168                         'Non'conserved</li>
1169                         <li>Sequence feature settings are being shared by multiple
1170                         distinct alignments</li>
1171                         <li>group annotation not recreated when tree partition is
1172                         changed</li>
1173                         <li>double click on group annotation to select sequences does
1174                         not propagate to associated trees</li>
1175                         <li>Mac OSX specific issues:
1176                         <ul>
1177                                 <li>exception raised when mouse clicked on desktop window
1178                                 background</li>
1179                                 <li>Desktop menu placed on menu bar and application name set
1180                                 correctly</li>
1181                                 <li>sequence feature settings not wide enough for the save
1182                                 feature colourscheme button</li>
1183                         </ul>
1184                         </li>
1185                 </ul>
1186                 </td>
1187         </tr>
1188         <tr>
1189
1190                 <td>
1191                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
1192                 <em>30/4/2010</em></div>
1193                 </td>
1194                 <td><em>New Capabilities</em>
1195                 <ul>
1196                         <li>URL links generated from description line for
1197                         regular-expression based URL links (applet and application)
1198                         <li>Non-positional feature URL links are shown in link menu</li>
1199                         <li>Linked viewing of nucleic acid sequences and structures</li>
1200                         <li>Automatic Scrolling option in View menu to display the
1201                         currently highlighted region of an alignment.</li>
1202                         <li>Order an alignment by sequence length, or using the average
1203                         score or total feature count for each sequence.</li>
1204                         <li>Shading features by score or associated description</li>
1205                         <li>Subdivide alignment and groups based on identity of selected
1206                         subsequence (Make Groups from Selection).</li>
1207                         <li>New hide/show options including Shift+Control+H to hide
1208                         everything but the currently selected region.</li>
1209                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1210                 </ul>
1211                 <em>Application</em>
1212                 <ul>
1213                         <li>Fetch DB References capabilities and UI expanded to support
1214                         retrieval from DAS sequence sources</li>
1215                         <li>Local DAS Sequence sources can be added via the command line
1216                         or via the Add local source dialog box.</li>
1217                         <li>DAS Dbref and DbxRef feature types are parsed as database
1218                         references and protein_name is parsed as description line (BioSapiens
1219                         terms).</li>
1220                         <li>Enable or disable non-positional feature and database
1221                         references in sequence ID tooltip from View menu in application.</li>
1222                         <!--                    <li>New hidden columns and rows and representatives capabilities
1223                         in annotations file (in progress - not yet fully implemented)</li> -->
1224                         <li>Group-associated consensus, sequence logos and conservation
1225                         plots</li>
1226                         <li>Symbol distributions for each column can be exported and
1227                         visualized as sequence logos</li>
1228                         <li>Optionally scale multi-character column labels to fit within
1229                         each column of annotation row<!-- todo for applet --></li>
1230                         <li>Optional automatic sort of associated alignment view when a
1231                         new tree is opened.</li>
1232                         <li>Jalview Java Console</li>
1233                         <li>Better placement of desktop window when moving between
1234                         different screens.</li>
1235                         <li>New preference items for sequence ID tooltip and consensus
1236                         annotation</li>
1237                         <li>Client to submit sequences and IDs to <a
1238                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
1239                         <li><em>Vamsas Capabilities</em>
1240                         <ul>
1241                                 <li>Improved VAMSAS synchronization (Jalview archive used to
1242                                 preserve views, structures, and tree display settings)</li>
1243                                 <li>Import of vamsas documents from disk or URL via command
1244                                 line</li>
1245                                 <li>Sharing of selected regions between views and with other
1246                                 VAMSAS applications (Experimental feature!)</li>
1247                                 <li>Updated API to VAMSAS version 0.2</li>
1248                         </ul>
1249                         </li>
1250                 </ul>
1251                 <em>Applet</em>
1252                 <ul>
1253                         <li>Middle button resizes annotation row height</li>
1254                         <li>New Parameters
1255                         <ul>
1256                                 <li>sortByTree (true/false) - automatically sort the associated
1257                                 alignment view by the tree when a new tree is opened.</li>
1258                                 <li>showTreeBootstraps (true/false) - show or hide branch
1259                                 bootstraps (default is to show them if available)</li>
1260                                 <li>showTreeDistances (true/false) - show or hide branch
1261                                 lengths (default is to show them if available)</li>
1262                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
1263                                 unassociated nodes should be highlighted in the tree view</li>
1264                                 <li>heightScale and widthScale (1.0 or more) - increase the
1265                                 height or width of a cell in the alignment grid relative to the
1266                                 current font size.</li>
1267                         </ul>
1268                         </li>
1269                         <li>Non-positional features displayed in sequence ID tooltip</li>
1270                 </ul>
1271                 <em>Other</em>
1272                 <ul>
1273                         <li>Features format: graduated colour definitions and
1274                         specification of feature scores</li>
1275                         <li>Alignment Annotations format: new keywords for group
1276                         associated annotation (GROUP_REF) and annotation row display
1277                         properties (ROW_PROPERTIES)</li>
1278                         <li>XML formats extended to support graduated feature
1279                         colourschemes, group associated annotation, and profile visualization
1280                         settings.</li>
1281                 </td>
1282                 <td>
1283                 <ul>
1284                         <li>Source field in GFF files parsed as feature source rather
1285                         than description</li>
1286                         <li>Non-positional features are now included in sequence feature
1287                         and gff files (controlled via non-positional feature visibility in
1288                         tooltip).</li>
1289                         <li>URL links generated for all feature links (bugfix)</li>
1290                         <li>Added URL embedding instructions to features file
1291                         documentation.</li>
1292                         <li>Codons containing ambiguous nucleotides translated as 'X' in
1293                         peptide product</li>
1294                         <li>Match case switch in find dialog box works for both sequence
1295                         ID and sequence string and query strings do not have to be in upper
1296                         case to match case-insensitively.</li>
1297                         <li>AMSA files only contain first column of multi-character
1298                         column annotation labels</li>
1299                         <li>Jalview Annotation File generation/parsing consistent with
1300                         documentation (e.g. Stockholm annotation can be exported and
1301                         re-imported)</li>
1302                         <li>PDB files without embedded PDB IDs given a friendly name</li>
1303                         <li>Find incrementally searches ID string matches as well as
1304                         subsequence matches, and correctly reports total number of both.</li>
1305                         <li>Application:
1306                         <ul>
1307                                 <li>Better handling of exceptions during sequence retrieval</li>
1308                                 <li>Dasobert generated non-positional feature URL link text
1309                                 excludes the start_end suffix</li>
1310                                 <li>DAS feature and source retrieval buttons disabled when
1311                                 fetch or registry operations in progress.</li>
1312                                 <li>PDB files retrieved from URLs are cached properly</li>
1313                                 <li>Sequence description lines properly shared via VAMSAS</li>
1314                                 <li>Sequence fetcher fetches multiple records for all data
1315                                 sources</li>
1316                                 <li>Ensured that command line das feature retrieval completes
1317                                 before alignment figures are generated.</li>
1318                                 <li>Reduced time taken when opening file browser for first
1319                                 time.</li>
1320                                 <li>isAligned check prior to calculating tree, PCA or
1321                                 submitting an MSA to JNet now excludes hidden sequences.</li>
1322                                 <li>User defined group colours properly recovered from Jalview
1323                                 projects.</li>
1324                         </ul>
1325                         </li>
1326                 </ul>
1327                 </td>
1328
1329         </tr>
1330         <tr>
1331                 <td>
1332                 <div align="center"><strong>2.4.0.b2</strong><br>
1333                 28/10/2009</div>
1334                 </td>
1335                 <td>
1336                 <ul>
1337                         <li>Experimental support for google analytics usage tracking.</li>
1338                         <li>Jalview privacy settings (user preferences and docs).</li>
1339                 </ul>
1340                 </td>
1341                 <td>
1342                 <ul>
1343                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
1344                         <li>Exception when feature created from selection beyond length
1345                         of sequence.</li>
1346                         <li>Allow synthetic PDB files to be imported gracefully</li>
1347                         <li>Sequence associated annotation rows associate with all
1348                         sequences with a given id</li>
1349                         <li>Find function matches case-insensitively for sequence ID
1350                         string searches</li>
1351                         <li>Non-standard characters do not cause pairwise alignment to
1352                         fail with exception</li>
1353                 </ul>
1354                 <em>Application Issues</em>
1355                 <ul>
1356                         <li>Sequences are now validated against EMBL database</li>
1357                         <li>Sequence fetcher fetches multiple records for all data
1358                         sources</li>
1359                 </ul>
1360                 <em>InstallAnywhere Issues</em>
1361                 <ul>
1362                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
1363                         installAnywhere mechanism)</li>
1364                         <li>Command line launching of JARs from InstallAnywhere version
1365                         (java class versioning error fixed)</li>
1366                 </ul>
1367                 </td>
1368         </tr>
1369         <tr>
1370                 <td>
1371
1372                 <div align="center"><strong>2.4</strong><br>
1373                 27/8/2008</div>
1374                 </td>
1375                 <td><em>User Interface</em>
1376                 <ul>
1377                         <li>Linked highlighting of codon and amino acid from translation
1378                         and protein products</li>
1379                         <li>Linked highlighting of structure associated with residue
1380                         mapping to codon position</li>
1381                         <li>Sequence Fetcher provides example accession numbers and
1382                         'clear' button</li>
1383                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
1384                         <li>Extract score function to parse whitespace separated numeric
1385                         data in description line</li>
1386                         <li>Column labels in alignment annotation can be centred.</li>
1387                         <li>Tooltip for sequence associated annotation give name of
1388                         sequence</li>
1389                 </ul>
1390                 <em>Web Services and URL fetching</em>
1391                 <ul>
1392                         <li>JPred3 web service</li>
1393                         <li>Prototype sequence search client (no public services
1394                         available yet)</li>
1395                         <li>Fetch either seed alignment or full alignment from PFAM</li>
1396                         <li>URL Links created for matching database cross references as
1397                         well as sequence ID</li>
1398                         <li>URL Links can be created using regular-expressions</li>
1399                 </ul>
1400                 <em>Sequence Database Connectivity</em>
1401                 <ul>
1402                         <li>Retrieval of cross-referenced sequences from other databases
1403                         </li>
1404                         <li>Generalised database reference retrieval and validation to
1405                         all fetchable databases</li>
1406                         <li>Fetch sequences from DAS sources supporting the sequence
1407                         command</li>
1408                 </ul>
1409                 <em>Import and Export</em>
1410                 <li>export annotation rows as CSV for spreadsheet import</li>
1411                 <li>Jalview projects record alignment dataset associations, EMBL
1412                 products, and cDNA sequence mappings</li>
1413                 <li>Sequence Group colour can be specified in Annotation File</li>
1414                 <li>Ad-hoc colouring of group in Annotation File using RGB
1415                 triplet as name of colourscheme</li>
1416                 </ul>
1417                 <em>VAMSAS Client capabilities (Experimental)</em>
1418                 <ul>
1419                         <li>treenode binding for VAMSAS tree exchange</li>
1420                         <li>local editing and update of sequences in VAMSAS alignments
1421                         (experimental)</li>
1422                         <li>Create new or select existing session to join</li>
1423                         <li>load and save of vamsas documents</li>
1424                 </ul>
1425                 <em>Application command line</em>
1426                 <ul>
1427                         <li>-tree parameter to open trees (introduced for passing from
1428                         applet)</li>
1429                         <li>-fetchfrom command line argument to specify nicknames of DAS
1430                         servers to query for alignment features</li>
1431                         <li>-dasserver command line argument to add new servers that are
1432                         also automatically queried for features</li>
1433                         <li>-groovy command line argument executes a given groovy script
1434                         after all input data has been loaded and parsed</li>
1435                 </ul>
1436                 <em>Applet-Application data exchange</em>
1437                 <ul>
1438                         <li>Trees passed as applet parameters can be passed to
1439                         application (when using &quot;View in full application&quot;)</li>
1440                 </ul>
1441                 <em>Applet Parameters</em>
1442                 <ul>
1443                         <li>feature group display control parameter</li>
1444                         <li>debug parameter</li>
1445                         <li>showbutton parameter</li>
1446                 </ul>
1447                 <em>Applet API methods</em>
1448                 <ul>
1449                         <li>newView public method</li>
1450                         <li>Window (current view) specific get/set public methods</li>
1451                         <li>Feature display control methods</li>
1452                         <li>get list of currently selected sequences</li>
1453                 </ul>
1454                 <em>New Jalview distribution features</em>
1455                 <ul>
1456                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1457                         <li>RELEASE file gives build properties for the latest Jalview
1458                         release.</li>
1459                         <li>Java 1.1 Applet build made easier and donotobfuscate
1460                         property controls execution of obfuscator</li>
1461                         <li>Build target for generating source distribution</li>
1462                         <li>Debug flag for javacc</li>
1463                         <li>.jalview_properties file is documented (slightly) in
1464                         jalview.bin.Cache</li>
1465                         <li>Continuous Build Integration for stable and development
1466                         version of Application, Applet and source distribution</li>
1467                 </ul>
1468
1469                 </td>
1470                 <td>
1471                 <ul>
1472                         <li>selected region output includes visible annotations (for
1473                         certain formats)</li>
1474                         <li>edit label/displaychar contains existing label/char for
1475                         editing</li>
1476                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1477                         <li>shorter peptide product names from EMBL records</li>
1478                         <li>Newick string generator makes compact representations</li>
1479                         <li>bootstrap values parsed correctly for tree files with
1480                         comments</li>
1481                         <li>pathological filechooser bug avoided by not allowing
1482                         filenames containing a ':'</li>
1483                         <li>Fixed exception when parsing GFF files containing global
1484                         sequence features</li>
1485                         <li>Alignment datasets are finalized only when number of
1486                         references from alignment sequences goes to zero</li>
1487                         <li>Close of tree branch colour box without colour selection
1488                         causes cascading exceptions</li>
1489                         <li>occasional negative imgwidth exceptions</li>
1490                         <li>better reporting of non-fatal warnings to user when file
1491                         parsing fails.</li>
1492                         <li>Save works when Jalview project is default format</li>
1493                         <li>Save as dialog opened if current alignment format is not a
1494                         valid output format</li>
1495                         <li>Uniprot canonical names introduced for both das and vamsas</li>
1496                         <li>Histidine should be midblue (not pink!) in Zappo</li>
1497                         <li>error messages passed up and output when data read fails</li>
1498                         <li>edit undo recovers previous dataset sequence when sequence
1499                         is edited</li>
1500                         <li>allow PDB files without pdb ID HEADER lines (like those
1501                         generated by MODELLER) to be read in properly</li>
1502                         <li>allow reading of JPred concise files as a normal filetype</li>
1503                         <li>Stockholm annotation parsing and alignment properties import
1504                         fixed for PFAM records</li>
1505                         <li>Structure view windows have correct name in Desktop window
1506                         list</li>
1507                         <li>annotation consisting of sequence associated scores can be
1508                         read and written correctly to annotation file</li>
1509                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
1510                         <li>Fixed display of hidden sequence markers and non-italic font
1511                         for representatives in Applet</li>
1512                         <li>Applet Menus are always embedded in applet window on Macs.</li>
1513                         <li>Newly shown features appear at top of stack (in Applet)</li>
1514                         <li>Annotations added via parameter not drawn properly due to
1515                         null pointer exceptions</li>
1516                         <li>Secondary structure lines are drawn starting from first
1517                         column of alignment</li>
1518                         <li>Uniprot XML import updated for new schema release in July
1519                         2008</li>
1520                         <li>Sequence feature to sequence ID match for Features file is
1521                         case-insensitive</li>
1522                         <li>Sequence features read from Features file appended to all
1523                         sequences with matching IDs</li>
1524                         <li>PDB structure coloured correctly for associated views
1525                         containing a sub-sequence</li>
1526                         <li>PDB files can be retrieved by applet from Jar files</li>
1527                         <li>feature and annotation file applet parameters referring to
1528                         different directories are retrieved correctly</li>
1529                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1530                         <li>Fixed application hang whilst waiting for splash-screen
1531                         version check to complete</li>
1532                         <li>Applet properly URLencodes input parameter values when
1533                         passing them to the launchApp service</li>
1534                         <li>display name and local features preserved in results
1535                         retrieved from web service</li>
1536                         <li>Visual delay indication for sequence retrieval and sequence
1537                         fetcher initialisation</li>
1538                         <li>updated Application to use DAS 1.53e version of dasobert DAS
1539                         client</li>
1540                         <li>Re-instated Full AMSA support and .amsa file association</li>
1541                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1542                         sequences</li>
1543                 </ul>
1544                 </td>
1545         </tr>
1546         <tr>
1547                 <td>
1548                 <div align="center"><strong>2.3</strong><br>
1549                 9/5/07</div>
1550                 </td>
1551                 <td>
1552                 <ul>
1553                         <li>Jmol 11.0.2 integration</li>
1554                         <li>PDB views stored in Jalview XML files</li>
1555                         <li>Slide sequences</li>
1556                         <li>Edit sequence in place</li>
1557                         <li>EMBL CDS features</li>
1558                         <li>DAS Feature mapping</li>
1559                         <li>Feature ordering</li>
1560                         <li>Alignment Properties</li>
1561                         <li>Annotation Scores</li>
1562                         <li>Sort by scores</li>
1563                         <li>Feature/annotation editing in applet</li>
1564                 </ul>
1565                 </td>
1566                 <td>
1567                 <ul>
1568                         <li>Headless state operation in 2.2.1</li>
1569                         <li>Incorrect and unstable DNA pairwise alignment</li>
1570                         <li>Cut and paste of sequences with annotation</li>
1571                         <li>Feature group display state in XML</li>
1572                         <li>Feature ordering in XML</li>
1573                         <li>blc file iteration selection using filename # suffix</li>
1574                         <li>Stockholm alignment properties</li>
1575                         <li>Stockhom alignment secondary structure annotation</li>
1576                         <li>2.2.1 applet had no feature transparency</li>
1577                         <li>Number pad keys can be used in cursor mode</li>
1578                         <li>Structure Viewer mirror image resolved</li>
1579                 </ul>
1580                 </td>
1581
1582         </tr>
1583         <tr>
1584                 <td>
1585                 <div align="center"><strong>2.2.1</strong><br>
1586                 12/2/07</div>
1587                 </td>
1588                 <td>
1589                 <ul>
1590                         <li>Non standard characters can be read and displayed
1591                         <li>Annotations/Features can be imported/exported to the applet
1592                         via textbox
1593                         <li>Applet allows editing of sequence/annotation/group name
1594                         &amp; description
1595                         <li>Preference setting to display sequence name in italics
1596                         <li>Annotation file format extended to allow Sequence_groups to
1597                         be defined
1598                         <li>Default opening of alignment overview panel can be specified
1599                         in preferences
1600                         <li>PDB residue numbering annotation added to associated
1601                         sequences
1602                 </ul>
1603                 </td>
1604                 <td>
1605                 <ul>
1606                         <li>Applet crash under certain Linux OS with Java 1.6 installed
1607                         <li>Annotation file export / import bugs fixed
1608                         <li>PNG / EPS image output bugs fixed
1609                 </ul>
1610                 </td>
1611         </tr>
1612         <tr>
1613                 <td>
1614                 <div align="center"><strong>2.2</strong><br>
1615                 27/11/06</div>
1616                 </td>
1617                 <td>
1618                 <ul>
1619                         <li>Multiple views on alignment
1620                         <li>Sequence feature editing
1621                         <li>&quot;Reload&quot; alignment
1622                         <li>&quot;Save&quot; to current filename
1623                         <li>Background dependent text colour
1624                         <li>Right align sequence ids
1625                         <li>User-defined lower case residue colours
1626                         <li>Format Menu
1627                         <li>Select Menu
1628                         <li>Menu item accelerator keys
1629                         <li>Control-V pastes to current alignment
1630                         <li>Cancel button for DAS Feature Fetching
1631                         <li>PCA and PDB Viewers zoom via mouse roller
1632                         <li>User-defined sub-tree colours and sub-tree selection
1633                         <li>'New Window' button on the 'Output to Text box'
1634                 </ul>
1635                 </td>
1636                 <td>
1637                 <ul>
1638                         <li>New memory efficient Undo/Redo System
1639                         <li>Optimised symbol lookups and conservation/consensus
1640                         calculations
1641                         <li>Region Conservation/Consensus recalculated after edits
1642                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
1643                         alignment)
1644                         <li>Slowed DAS Feature Fetching for increased robustness.
1645                         <li>Made angle brackets in ASCII feature descriptions display
1646                         correctly
1647                         <li>Re-instated Zoom function for PCA
1648                         <li>Sequence descriptions conserved in web service analysis
1649                         results
1650                         <li>Uniprot ID discoverer uses any word separated by &#8739;
1651                         <li>WsDbFetch query/result association resolved
1652                         <li>Tree leaf to sequence mapping improved
1653                         <li>Smooth fonts switch moved to FontChooser dialog box.
1654                 </ul>
1655                 </td>
1656         </tr>
1657         <tr>
1658                 <td>
1659                 <div align="center"><strong>2.1.1</strong><br>
1660                 12/9/06</div>
1661                 </td>
1662                 <td>
1663                 <ul>
1664                         <li>Copy consensus sequence to clipboard</li>
1665                 </ul>
1666                 </td>
1667                 <td>
1668                 <ul>
1669                         <li>Image output - rightmost residues are rendered if sequence
1670                         id panel has been resized</li>
1671                         <li>Image output - all offscreen group boundaries are rendered</li>
1672                         <li>Annotation files with sequence references - all elements in
1673                         file are relative to sequence position</li>
1674                         <li>Mac Applet users can use Alt key for group editing</li>
1675                 </ul>
1676                 </td>
1677         </tr>
1678         <tr>
1679                 <td>
1680                 <div align="center"><strong>2.1</strong><br>
1681                 22/8/06</div>
1682                 </td>
1683                 <td>
1684                 <ul>
1685                         <li>MAFFT Multiple Alignment in default Web Service list</li>
1686                         <li>DAS Feature fetching</li>
1687                         <li>Hide sequences and columns</li>
1688                         <li>Export Annotations and Features</li>
1689                         <li>GFF file reading / writing</li>
1690                         <li>Associate structures with sequences from local PDB files</li>
1691                         <li>Add sequences to exisiting alignment</li>
1692                         <li>Recently opened files / URL lists</li>
1693                         <li>Applet can launch the full application</li>
1694                         <li>Applet has transparency for features (Java 1.2 required)</li>
1695                         <li>Applet has user defined colours parameter</li>
1696                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
1697                 </ul>
1698                 </td>
1699                 <td>
1700                 <ul>
1701                         <li>Redundancy Panel reinstalled in the Applet</li>
1702                         <li>Monospaced font - EPS / rescaling bug fixed</li>
1703                         <li>Annotation files with sequence references bug fixed</li>
1704                 </ul>
1705                 </td>
1706         </tr>
1707         <tr>
1708                 <td>
1709                 <div align="center"><strong>2.08.1</strong><br>
1710                 2/5/06</div>
1711                 </td>
1712                 <td>
1713                 <ul>
1714                         <li>Change case of selected region from Popup menu</li>
1715                         <li>Choose to match case when searching</li>
1716                         <li>Middle mouse button and mouse movement can compress / expand
1717                         the visible width and height of the alignment</li>
1718                 </ul>
1719                 </td>
1720                 <td>
1721                 <ul>
1722                         <li>Annotation Panel displays complete JNet results</li>
1723                 </ul>
1724                 </td>
1725         </tr>
1726         <tr>
1727                 <td>
1728                 <div align="center"><strong>2.08b</strong><br>
1729                 18/4/06</div>
1730                 </td>
1731                 <td>&nbsp;</td>
1732                 <td>
1733                 <ul>
1734                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1735                         <li>Righthand label on wrapped alignments shows correct value</li>
1736                 </ul>
1737                 </td>
1738         </tr>
1739         <tr>
1740                 <td>
1741                 <div align="center"><strong>2.08</strong><br>
1742                 10/4/06</div>
1743                 </td>
1744                 <td>
1745                 <ul>
1746                         <li>Editing can be locked to the selection area</li>
1747                         <li>Keyboard editing</li>
1748                         <li>Create sequence features from searches</li>
1749                         <li>Precalculated annotations can be loaded onto alignments</li>
1750                         <li>Features file allows grouping of features</li>
1751                         <li>Annotation Colouring scheme added</li>
1752                         <li>Smooth fonts off by default - Faster rendering</li>
1753                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
1754                 </ul>
1755                 </td>
1756                 <td>
1757                 <ul>
1758                         <li>Drag &amp; Drop fixed on Linux</li>
1759                         <li>Jalview Archive file faster to load/save, sequence
1760                         descriptions saved.</li>
1761                 </ul>
1762                 </td>
1763         </tr>
1764         <tr>
1765                 <td>
1766                 <div align="center"><strong>2.07</strong><br>
1767                 12/12/05</div>
1768                 </td>
1769                 <td>
1770                 <ul>
1771                         <li>PDB Structure Viewer enhanced</li>
1772                         <li>Sequence Feature retrieval and display enhanced</li>
1773                         <li>Choose to output sequence start-end after sequence name for
1774                         file output</li>
1775                         <li>Sequence Fetcher WSDBFetch@EBI</li>
1776                         <li>Applet can read feature files, PDB files and can be used for
1777                         HTML form input</li>
1778                 </ul>
1779                 </td>
1780                 <td>
1781                 <ul>
1782                         <li>HTML output writes groups and features</li>
1783                         <li>Group editing is Control and mouse click</li>
1784                         <li>File IO bugs</li>
1785                 </ul>
1786                 </td>
1787         </tr>
1788         <tr>
1789                 <td>
1790                 <div align="center"><strong>2.06</strong><br>
1791                 28/9/05</div>
1792                 </td>
1793                 <td>
1794                 <ul>
1795                         <li>View annotations in wrapped mode</li>
1796                         <li>More options for PCA viewer</li>
1797                 </ul>
1798                 </td>
1799                 <td>
1800                 <ul>
1801                         <li>GUI bugs resolved</li>
1802                         <li>Runs with -nodisplay from command line</li>
1803                 </ul>
1804                 </td>
1805         </tr>
1806         <tr>
1807                 <td height="63">
1808                 <div align="center"><strong>2.05b</strong><br>
1809                 15/9/05</div>
1810                 </td>
1811                 <td>
1812                 <ul>
1813                         <li>Choose EPS export as lineart or text</li>
1814                         <li>Jar files are executable</li>
1815                         <li>Can read in Uracil - maps to unknown residue</li>
1816                 </ul>
1817                 </td>
1818                 <td>
1819                 <ul>
1820                         <li>Known OutOfMemory errors give warning message</li>
1821                         <li>Overview window calculated more efficiently</li>
1822                         <li>Several GUI bugs resolved</li>
1823                 </ul>
1824                 </td>
1825         </tr>
1826         <tr>
1827                 <td>
1828                 <div align="center"><strong>2.05</strong><br>
1829                 30/8/05</div>
1830                 </td>
1831                 <td>
1832                 <ul>
1833                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
1834                 </ul>
1835                 </td>
1836                 <td>
1837                 <ul>
1838                         <li>Several GUI bugs resolved</li>
1839                 </ul>
1840                 </td>
1841         </tr>
1842         <tr>
1843                 <td>
1844                 <div align="center"><strong>2.04</strong><br>
1845                 24/8/05</div>
1846                 </td>
1847                 <td>
1848                 <ul>
1849                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
1850                 </ul>
1851                 </td>
1852                 <td>
1853                 <ul>
1854                         <li>Improved JPred client reliability</li>
1855                         <li>Improved loading of Jalview files</li>
1856                 </ul>
1857                 </td>
1858         </tr>
1859         <tr>
1860                 <td>
1861                 <div align="center"><strong>2.03</strong><br>
1862                 18/8/05</div>
1863                 </td>
1864                 <td>
1865                 <ul>
1866                         <li>Set Proxy server name and port in preferences</li>
1867                         <li>Multiple URL links from sequence ids</li>
1868                         <li>User Defined Colours can have a scheme name and added to
1869                         Colour Menu</li>
1870                         <li>Choose to ignore gaps in consensus calculation</li>
1871                         <li>Unix users can set default web browser</li>
1872                         <li>Runs without GUI for batch processing</li>
1873                         <li>Dynamically generated Web Service Menus</li>
1874                 </ul>
1875                 </td>
1876                 <td>
1877                 <ul>
1878                         <li>InstallAnywhere download for Sparc Solaris</li>
1879                 </ul>
1880                 </td>
1881         </tr>
1882         <tr>
1883                 <td>
1884                 <div align="center"><strong>2.02</strong><br>
1885                 18/7/05</div>
1886                 </td>
1887                 <td>&nbsp;</td>
1888                 <td>
1889                 <ul>
1890                         <li>Copy &amp; Paste order of sequences maintains alignment
1891                         order.</li>
1892                 </ul>
1893                 </td>
1894         </tr>
1895         <tr>
1896                 <td>
1897                 <div align="center"><strong>2.01</strong><br>
1898                 12/7/05</div>
1899                 </td>
1900                 <td>
1901                 <ul>
1902                         <li>Use delete key for deleting selection.</li>
1903                         <li>Use Mouse wheel to scroll sequences.</li>
1904                         <li>Help file updated to describe how to add alignment
1905                         annotations.</li>
1906                         <li>Version and build date written to build properties file.</li>
1907                         <li>InstallAnywhere installation will check for updates at
1908                         launch of Jalview.</li>
1909                 </ul>
1910                 </td>
1911                 <td>
1912                 <ul>
1913                         <li>Delete gaps bug fixed.</li>
1914                         <li>FileChooser sorts columns.</li>
1915                         <li>Can remove groups one by one.</li>
1916                         <li>Filechooser icons installed.</li>
1917                         <li>Finder ignores return character when searching. Return key
1918                         will initiate a search.<br>
1919                         </li>
1920                 </ul>
1921                 </td>
1922         </tr>
1923         <tr>
1924                 <td>
1925                 <div align="center"><strong>2.0</strong><br>
1926                 20/6/05</div>
1927                 </td>
1928                 <td>
1929                 <ul>
1930                         <li>New codebase</li>
1931                 </ul>
1932                 </td>
1933                 <td>&nbsp;</td>
1934         </tr>
1935 </table>
1936 <p>&nbsp;</p>
1937 </body>
1938 </html>