3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Release History</title>
23 <p><strong>Release History</strong></p>
26 <td width="60" nowrap>
27 <div align="center"><em><strong>Release</strong></em></div>
30 <div align="center"><em><strong>New Features</strong></em></div>
33 <div align="center"><em><strong>Issues Resolved</strong></em></div>
37 <td><div align="center">
38 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>08/11/2012</em>
40 <td><em>Application</em>
41 <li>Support for JABAWS 2.0 Services (AACon alignment
42 conservation, protein disorder and Clustal Omega) <!--[<a href='http://issues.jalview.org/browse/JAL-976'>JAL-976</a>] - Enhance Jalview desktop to support to JABAWS v2.0 services -->
43 <!--[<a href='http://issues.jalview.org/browse/JAL-974'>JAL-974</a>]-->
44 <!--[<a href='http://issues.jalview.org/browse/JAL-975'>JAL-975</a>]-->
47 <!--[<a href='http://issues.jalview.org/browse/JAL-1060'>JAL-1060</a>] - -->JABAWS
48 server status indicator in Web Services preferences
51 <!--[<a href='http://issues.jalview.org/browse/JAL-842'>JAL-842</a>] - -->VARNA
52 (http://varna.lri.fr) viewer for RNA structures in Jalview
56 <!--[<a href='http://issues.jalview.org/browse/JAL-1133'>JAL-1133</a>] - -->Updated
57 jalview build and deploy framework for OSX mountain lion, windows
60 <li>Nucleotide substitution matrix for PCA that supports RNA
61 and ambiguity codes <!--[<a href='http://issues.jalview.org/browse/JAL-1027'>JAL-1027</a>] -->
64 <li>Improved sequence database retrieval GUI</li>
65 <li>Support fetching and database reference look up against
66 multiple DAS sources (Fetch all from in 'fetch db refs')<!--[<a href='http://issues.jalview.org/browse/JAL-1061'>JAL-1061</a>], [<a href='http://issues.jalview.org/browse/JAL-1075'>JAL-1075</a>] - GUI elements to select one or several DAS sources to query for sequences or database references-->
68 <li>Jalview project improvements
71 <!--[<a href='http://issues.jalview.org/browse/JAL-1109'>JAL-1109</a>] -->Store
72 and retrieve the 'belowAlignment' flag for annotation
75 <!--[<a href='http://issues.jalview.org/browse/JAL-1110'>JAL-1110</a>]-->calcId
76 attribute to group annotation rows on the alignment
79 <!--[<a href='http://issues.jalview.org/browse/JAL-1136'>JAL-1136</a>] - -->Store
80 AACon calculation settings for a view in Jalview project
86 <!--[<a href='http://issues.jalview.org/browse/JAL-1160'>JAL-1160</a>] - -->horizontal
87 scrolling gesture support
89 <li>Visual progress indicator when PCA calculation is running<!--[<a href='http://issues.jalview.org/browse/JAL-1120'>JAL-1120</a>] - -->
91 <li>Simpler JABA web services menus<!--[<a href='http://issues.jalview.org/browse/JAL-1137'>JAL-1137</a>] - -->
94 <!--[<a href='http://issues.jalview.org/browse/JAL-1165'>JAL-1165</a>] - -->visual
95 indication that web service results are still being retrieved from
99 <!--[<a href='http://issues.jalview.org/browse/JAL-1183'>JAL-1183</a>] - -->Serialise
100 the dialogs that are shown when jalview starts up for first time
103 <!--[<a href='http://issues.jalview.org/browse/JAL-1188'>JAL-1188</a>] - -->Jalview
104 user agent string for interacting with HTTP services
107 <!--[<a href='http://issues.jalview.org/browse/JAL-972'>JAL-972</a>] - -->DAS
108 1.6 and DAS 2.0 source support using new JDAS client library
111 <!--[<a href='http://issues.jalview.org/browse/JAL-1202'>JAL-1202</a>] - -->Examples
112 directory and Groovy library included in InstallAnywhere
115 </ul> <em>Applet</em>
118 <!--[<a href='http://issues.jalview.org/browse/JAL-963'>JAL-963</a>] - -->RNA
119 alignment and secondary structure annotation visualization applet
122 </ul> <em>General</em>
125 <!--[<a href='http://issues.jalview.org/browse/JAL-958'>JAL-958</a>] - -->Normalise
126 option for consensus sequence logo
129 <!--[<a href='http://issues.jalview.org/browse/JAL-1121'>JAL-1121</a>] - -->Reset
130 button in PCA window to return dimensions to defaults
133 <!--[<a href='http://issues.jalview.org/browse/JAL-1125'>JAL-1125</a>] - -->Allow
134 seqspace or Jalview variant of alignment PCA calculation
137 <!--[<a href='http://issues.jalview.org/browse/JAL-1013'>JAL-1013</a>] -->PCA
138 with either nucleic acid and protein substitution matrices
140 <!--[<a href='http://issues.jalview.org/browse/JAL-1157'>JAL-1157</a>] - -->Allow
141 windows containing HTML reports to be exported in HTML
144 <!--[<a href='http://issues.jalview.org/browse/JAL-970'>JAL-970</a>] - -->Interactive
145 display and editing of RNA secondary structure contacts
147 <li>RNA Helix Alignment Colouring</li>
148 <li>RNA base pair logo consensus</li>
150 <!--[<a href='http://issues.jalview.org/browse/JAL-878'>JAL-878</a>] - -->Parse
151 sequence associated secondary structure information in Stockholm
155 <!--[<a href='http://issues.jalview.org/browse/JAL-1015'>JAL-1015</a>] - -->HTML
156 Export database accessions and annotation information presented in
157 tooltip for sequences
160 <!--[<a href='http://issues.jalview.org/browse/JAL-1052'>JAL-1052</a>] - -->Import
161 secondary structure from LOCARNA clustalw style RNA alignment
165 <!--[<a href='http://issues.jalview.org/browse/JAL-1065'>JAL-1065</a>] - [<a href='http://issues.jalview.org/browse/JAL-1078'>JAL-1078</a>]-->import
166 and visualise T-COFFEE quality scores for an alignment
169 <!--[<a href='http://issues.jalview.org/browse/JAL-1066'>JAL-1066</a>] - -->'colour
170 by annotation' per sequence option to shade each sequence
171 according to its associated alignment annotation
174 <!--[<a href='http://issues.jalview.org/browse/JAL-1130'>JAL-1130</a>] - -->New
177 </ul> <em>Documentation and Development</em>
180 <!--[<a href='http://issues.jalview.org/browse/JAL-1167'>JAL-1167</a>] - -->documentation
181 for score matrices used in Jalview
183 <li>New Website!</li>
185 <td><em>Application</em>
187 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
188 wsdbfetch REST service<!--<a href='http://issues.jalview.org/browse/JAL-636'>JAL-636</a>-->
191 <!--[<a href='http://issues.jalview.org/browse/JAL-368'>JAL-368</a>] - -->
192 <!--[<a href='http://issues.jalview.org/browse/JAL-153'>JAL-153</a>] - -->Stop
193 windows being moved outside desktop on OSX
196 <!--[<a href='http://issues.jalview.org/browse/JAL-758'>JAL-758</a>] - -->Filetype
197 associations not installed for webstart launch
200 <!--[<a href='http://issues.jalview.org/browse/JAL-849'>JAL-849</a>] - -->Jalview
201 does not always retrieve progress of a JABAWS job execution in
202 full once it is complete
205 <!--[<a href='http://issues.jalview.org/browse/JAL-979'>JAL-979</a>] - -->revise
206 SHMR RSBS definition to ensure alignment is uploaded via ali_file
210 <!--[<a href='http://issues.jalview.org/browse/JAL-980'>JAL-980</a>] - -->Jalview
211 2.7 is incompatible with Jmol-12.2.2
214 <!--[<a href='http://issues.jalview.org/browse/JAL-983'>JAL-983</a>] - -->View
215 all structures superposed fails with exception
218 <!--[<a href='http://issues.jalview.org/browse/JAL-994'>JAL-994</a>] - -->Jnet
219 job queues forever if a very short sequence is submitted for
223 <!--[<a href='http://issues.jalview.org/browse/JAL-1004'>JAL-1004</a>] - -->Cut
224 and paste menu not opened when mouse clicked on desktop window
227 <!--[<a href='http://issues.jalview.org/browse/JAL-1010'>JAL-1010</a>] - -->Putting
228 fractional value into integer text box in alignment parameter
229 dialog causes jalview to hang
232 <!--[<a href='http://issues.jalview.org/browse/JAL-1022'>JAL-1022</a>] - -->Structure
233 view highlighting doesn't work on windows 7
236 <!--[<a href='http://issues.jalview.org/browse/JAL-1023'>JAL-1023</a>] - -->View
237 all structures fails with exception shown in structure view
240 <!--[<a href='http://issues.jalview.org/browse/JAL-1025'>JAL-1025</a>] - -->Characters
241 in filename associated with PDBEntry not escaped in a platform
245 <!--[<a href='http://issues.jalview.org/browse/JAL-1026'>JAL-1026</a>] - -->Jalview
246 desktop fails to launch with exception when using proxy
249 <!--[<a href='http://issues.jalview.org/browse/JAL-1031'>JAL-1031</a>] - -->Tree
250 calculation reports 'you must have 2 or more sequences
251 selected' when selection is empty
254 <!--[<a href='http://issues.jalview.org/browse/JAL-1040'>JAL-1040</a>] - -->Jalview
255 desktop fails to launch with jar signature failure when java web
256 start temporary file caching is disabled
259 <!--[<a href='http://issues.jalview.org/browse/JAL-1062'>JAL-1062</a>] - -->DAS
260 Sequence retrieval with range qualification results in sequence
261 xref which includes range qualification
264 <!--[<a href='http://issues.jalview.org/browse/JAL-1087'>JAL-1087</a>] - -->Errors
265 during processing of command line arguments cause progress bar
266 (JAL-898) to be removed
269 <!--[<a href='http://issues.jalview.org/browse/JAL-1097'>JAL-1097</a>] - -->Replace
270 comma for semi-colon option not disabled for DAS sources in
274 <!--[<a href='http://issues.jalview.org/browse/JAL-1111'>JAL-1111</a>] - -->Cannot
275 close news reader when JABAWS server warning dialog is shown
278 <!--[<a href='http://issues.jalview.org/browse/JAL-1127'>JAL-1127</a>] - -->Option
279 widgets not updated to reflect user settings
282 <!--[<a href='http://issues.jalview.org/browse/JAL-1131'>JAL-1131</a>] - -->Edited
283 sequence not submitted to web service
286 <!--[<a href='http://issues.jalview.org/browse/JAL-1134'>JAL-1134</a>] - -->Jalview
287 2.7 Webstart does not launch on mountain lion
290 <!--[<a href='http://issues.jalview.org/browse/JAL-1135'>JAL-1135</a>] - -->InstallAnywhere
291 installer doesn't unpack and run on OSX Mountain Lion
294 <!--[<a href='http://issues.jalview.org/browse/JAL-1144'>JAL-1144</a>] - -->Annotation
295 panel not given a scroll bar when sequences with alignment
296 annotation are pasted into the alignment
299 <!--[<a href='http://issues.jalview.org/browse/JAL-1148'>JAL-1148</a>] - -->Sequence
300 associated annotation rows not associated when loaded from jalview
304 <!--[<a href='http://issues.jalview.org/browse/JAL-1149'>JAL-1149</a>] - -->Browser
305 launch fails with NPE on java 1.7
308 <!--[<a href='http://issues.jalview.org/browse/JAL-1171'>JAL-1171</a>] - -->JABAWS
309 alignment marked as finished when job was cancelled or job failed
313 <!--[<a href='http://issues.jalview.org/browse/JAL-1185'>JAL-1185</a>] - -->NPE
314 with v2.7 example when clicking on Tree associated with all views
317 <!--[<a href='http://issues.jalview.org/browse/JAL-1145'>JAL-1145</a>] - -->Exceptions
318 when copy/paste sequences with grouped annotation rows to new
321 </ul> <em>Applet</em>
324 <!--[<a href='http://issues.jalview.org/browse/JAL-962'>JAL-962</a>] - -->Sequence
325 features are momentarily displayed before they are hidden using
326 hidefeaturegroups applet parameter
329 <!--[<a href='http://issues.jalview.org/browse/JAL-965'>JAL-965</a>] - -->loading
330 features via javascript API automatically enables feature display
333 <!--[<a href='http://issues.jalview.org/browse/JAL-1170'>JAL-1170</a>] - -->scrollToColumnIn
334 javascript API method doesn't work
336 </ul> <em>General</em>
339 <!--[<a href='http://issues.jalview.org/browse/JAL-1007'>JAL-1007</a>] - -->Redundancy
340 removal fails for rna alignment
343 <!--[<a href='http://issues.jalview.org/browse/JAL-1032'>JAL-1032</a>] - -->PCA
344 calculation fails when sequence has been selected and then
348 <!--[<a href='http://issues.jalview.org/browse/JAL-1033'>JAL-1033</a>] - -->PCA
349 window shows grey box when first opened on OSX
352 <!--[<a href='http://issues.jalview.org/browse/JAL-1086'>JAL-1086</a>] - -->Letters
353 coloured pink in sequence logo when alignment coloured with
357 <!--[<a href='http://issues.jalview.org/browse/JAL-1099'>JAL-1099</a>] - -->Choosing
358 fonts without letter symbols defined causes exceptions and redraw
362 <!--[<a href='http://issues.jalview.org/browse/JAL-1123'>JAL-1123</a>] - -->Initial
363 PCA plot view is not same as manually reconfigured view
366 <!--[<a href='http://issues.jalview.org/browse/JAL-1153'>JAL-1153</a>] - -->Grouped
367 annotation graph label has incorrect line colour
370 <!--[<a href='http://issues.jalview.org/browse/JAL-1155'>JAL-1155</a>] - -->Grouped
371 annotation graph label display is corrupted for lots of labels
378 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
381 <td><em>Application</em>
383 <li>Jalview Desktop News Reader</li>
384 <li>Tweaked default layout of web services menu</li>
385 <li>View/alignment association menu to enable user to easily
386 specify which alignment a multi-structure view takes its
387 colours/correspondences from</li>
388 <li>Allow properties file location to be specified as URL</li>
389 <li>Extend jalview project to preserve associations between
390 many alignment views and a single Jmol display</li>
391 <li>Store annotation row height in jalview project file</li>
392 <li>Annotation row column label formatting attributes stored
394 <li>Annotation row order for auto-calculated annotation rows
395 preserved in jalview project file</li>
396 <li>Visual progress indication when Jalview state is saved
397 using Desktop window menu</li>
398 <li>Visual indication that command line arguments are still
400 <li>Groovy script execution from URL</li>
401 <li>Colour by annotation default min and max colours in
403 <li>Automatically associate PDB files dragged onto an
404 alignment with sequences that have high similarity and matching
406 <li>Update JGoogleAnalytics to latest release (0.3)</li>
407 <li>'view structures' option to open many structures
409 <li>Sort associated views menu option for tree panel</li>
410 <li>Group all JABA and non-JABA services for a particular
411 analysis function in its own submenu</li>
412 </ul> <em>Applet</em>
414 <li>Userdefined and autogenerated annotation rows for groups</li>
415 <li>Adjustment of alignment annotation pane height</li>
416 <li>Annotation scrollbar for annotation panel</li>
417 <li>Drag to reorder annotation rows in annotation panel</li>
418 <li>'automaticScrolling' parameter</li>
419 <li>Allow sequences with partial ID string matches to be
420 annotated from GFF/jalview features files</li>
421 <li>Sequence logo annotation row in applet</li>
422 <li>Absolute paths relative to host server in applet
423 parameters are treated as such</li>
424 <li>New in the JalviewLite javascript API:
426 <li>JalviewLite.js javascript library</li>
427 <li>Javascript callbacks for
429 <li>Applet initialisation</li>
430 <li>Sequence/alignment mouse-overs and selections</li>
433 <li>scrollTo row and column alignment scrolling functions</li>
434 <li>Select sequence/alignment regions from javascript</li>
435 <li>javascript structure viewer harness to pass messages
436 between Jmol and Jalview when running as distinct applets</li>
437 <li>sortBy method</li>
438 <li>Set of applet and application examples shipped with
440 <li>New example to demonstrate jalviewLite and Jmol
441 javascript message exchange</li>
443 </ul> <em>General</em>
445 <li>Enable Jmol displays to be associated with multiple
446 multiple alignments</li>
447 <li>Option to automatically sort alignment with new tree</li>
448 <li>User configurable link to enable redirects to a
449 www.jalview.org mirror</li>
450 <li>Jmol colours option for Jmol displays</li>
451 <li>Configurable newline string when writing alignment and
452 other flat files</li>
453 <li>Allow alignment annotation description lines to contain
455 </ul> <em>Documentation and Development</em>
457 <li>Add groovy test harness for bulk load testing to examples
459 <li>Groovy script to load and align a set of sequences using a
460 web service before displaying the result in the Jalview desktop</li>
461 <li>Restructured javascript and applet api documentation</li>
462 <li>Ant target to publish example html files with applet
464 <li>Netbeans project for building jalview from source</li>
465 <li>ant task to create online javadoc for jalview source</li>
467 <td><em>Application</em>
469 <li>User defined colourscheme throws exception when current
470 built in colourscheme is saved as new scheme</li>
471 <li>AlignFrame->Save in application pops up save dialog for
472 valid filename/format</li>
473 <li>Cannot view associated structure for Uniprot sequence</li>
474 <li>PDB file association breaks for Uniprot sequence P37173</li>
475 <li>Associate PDB from file dialog does not tell you which
476 sequence is to be associated with the file</li>
477 <li>Find All raises null pointer exception when query only
478 matches sequence IDs</li>
479 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
480 <li>Jalview project with Jmol views created with Jalview 2.4
481 cannot be loaded</li>
482 <li>Filetype associations not installed for webstart launch</li>
483 <li>Two or more chains in a single PDB file associated with
484 sequences in different alignments do not get coloured by their
485 associated sequence</li>
486 <li>Visibility status of autocalculated annotation row not
487 preserved when project is loaded</li>
488 <li>Annotation row height and visibility attributes not stored
489 in jalview project</li>
490 <li>Tree bootstraps are not preserved when saved as a jalview
492 <li>Envision2 workflow tooltips are corrupted</li>
493 <li>Enabling show group conservation also enables colour by
495 <li>Duplicate group associated conservation or consensus
496 created on new view</li>
497 <li>Annotation scrollbar not displayed after 'show all
498 hidden annotation rows' option selected</li>
499 <li>Alignment quality not updated after alignment annotation
500 row is hidden then shown</li>
501 <li>Preserve colouring of structures coloured by sequences in
502 pre jalview 2.7 projects</li>
503 <li>Web service job parameter dialog is not laid out properly
505 <li>Web services menu not refreshed after 'reset
506 services' button is pressed in preferences</li>
507 <li>Annotation off by one in jalview v2_3 example project</li>
508 <li>Structures imported from file and saved in project get
509 name like jalview_pdb1234.txt when reloaded</li>
510 <li>Jalview does not always retrieve progress of a JABAWS job
511 execution in full once it is complete</li>
512 </ul> <em>Applet</em>
514 <li>Alignment height set incorrectly when lots of annotation
515 rows are displayed</li>
516 <li>Relative URLs in feature HTML text not resolved to
518 <li>View follows highlighting does not work for positions in
520 <li><= shown as = in tooltip</li>
521 <li>Export features raises exception when no features exist</li>
522 <li>Separator string used for serialising lists of IDs for
523 javascript api is modified when separator string provided as
525 <li>Null pointer exception when selecting tree leaves for
526 alignment with no existing selection</li>
527 <li>Relative URLs for datasources assumed to be relative to
528 applet's codebase</li>
529 <li>Status bar not updated after finished searching and search
530 wraps around to first result</li>
531 <li>StructureSelectionManager instance shared between several
532 jalview applets causes race conditions and memory leaks</li>
533 <li>Hover tooltip and mouseover of position on structure not
534 sent from Jmol in applet</li>
535 <li>Certain sequences of javascript method calls to applet API
536 fatally hang browser</li>
537 </ul> <em>General</em>
539 <li>View follows structure mouseover scrolls beyond position
540 with wrapped view and hidden regions</li>
541 <li>Find sequence position moves to wrong residue with/without
543 <li>Sequence length given in alignment properties window is
545 <li>InvalidNumberFormat exceptions thrown when trying to
546 import PDB like structure files</li>
547 <li>Positional search results are only highlighted between
548 user-supplied sequence start/end bounds</li>
549 <li>End attribute of sequence is not validated</li>
550 <li>Find dialog only finds first sequence containing a given
551 sequence position</li>
552 <li>Sequence numbering not preserved in MSF alignment output</li>
553 <li>Jalview PDB file reader does not extract sequence from
554 nucleotide chains correctly</li>
555 <li>Structure colours not updated when tree partition changed
557 <li>Sequence associated secondary structure not correctly
558 parsed in interleaved stockholm</li>
559 <li>Colour by annotation dialog does not restore current state
561 <li>Hiding (nearly) all sequences doesn't work properly</li>
562 <li>Sequences containing lowercase letters are not properly
563 associated with their pdb files</li>
564 </ul> <em>Documentation and Development</em>
566 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
573 <strong><a name="Jalview2.6.1">2.6.1</a>
574 </strong><br> <em>15/11/2010</em>
576 <td><em>Application</em>
578 <li>New warning dialog when the Jalview Desktop cannot contact
580 <li>JABA service parameters for a preset are shown in service
582 <li>JABA Service menu entries reworded</li>
586 <li>Modeller PIR IO broken - cannot correctly import a pir
587 file emitted by jalview</li>
588 <li>Existing feature settings transferred to new alignment
589 view created from cut'n'paste</li>
590 <li>Improved test for mixed amino/nucleotide chains when
591 parsing PDB files</li>
592 <li>Consensus and conservation annotation rows occasionally
593 become blank for all new windows</li>
594 <li>Exception raised when right clicking above sequences in
595 wrapped view mode</li>
596 </ul> <em>Application</em>
598 <li>multiple multiply aligned structure views cause cpu usage
599 to hit 100% and computer to hang</li>
600 <li>Web Service parameter layout breaks for long user
602 <li>Jaba service discovery hangs desktop if Jaba server is
608 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
609 <em>26/9/2010</em></div>
611 <td><em>Application</em>
613 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
614 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
615 <li>Web Services preference tab</li>
616 <li>Analysis parameters dialog box and user defined preferences</li>
617 <li>Improved speed and layout of Envision2 service menu</li>
618 <li>Superpose structures using associated sequence alignment</li>
619 <li>Export coordinates and projection as CSV from PCA viewer</li>
623 <li>enable javascript: execution by the applet via the link out
628 <li>Updated the Jmol Jalview interface to work with Jmol series
630 <li>The Jalview Desktop and JalviewLite applet now require Java
632 <li>Allow Jalview feature colour specification for GFF sequence
633 annotation files</li>
634 <li>New 'colour by label' keword in jalview feature file type
635 colour specification</li>
636 <li>New Jalview Desktop Groovy API method that allows a script
637 to check if it being run in an interactive session or in a batch
638 operation from the jalview command line</li>
643 <li>clustalx colourscheme colours Ds preferentially when both
644 D+E are present in over 50% of the column</li>
649 <li>typo in AlignmentFrame->View->Hide->all but
650 selected Regions menu item</li>
651 <li>sequence fetcher replaces ',' for ';' when the ',' is part
652 of a valid accession ID</li>
653 <li>fatal OOM if object retrieved by sequence fetcher runs out
655 <li>unhandled Out of Memory Error when viewing pca analysis
657 <li>InstallAnywhere builds fail to launch on OS X java 10.5
658 update 4 (due to apple Java 1.6 update)</li>
659 <li>Installanywhere Jalview silently fails to launch</li>
663 <li>Jalview.getFeatureGroups() raises an
664 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
670 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
671 <em>14/6/2010</em></div>
676 <li>Alignment prettyprinter doesn't cope with long sequence IDs
678 <li>clustalx colourscheme colours Ds preferentially when both
679 D+E are present in over 50% of the column</li>
680 <li>nucleic acid structures retrieved from PDB do not import
682 <li>More columns get selected than were clicked on when a number
683 of columns are hidden</li>
684 <li>annotation label popup menu not providing correct
685 add/hide/show options when rows are hidden or none are present</li>
686 <li>Stockholm format shown in list of readable formats, and
687 parser copes better with alignments from RFAM.</li>
688 <li>CSV output of consensus only includes the percentage of all
689 symbols if sequence logo display is enabled</li>
694 <li>annotation panel disappears when annotation is
699 <li>Alignment view not redrawn properly when new alignment
700 opened where annotation panel is visible but no annotations are
701 present on alignment</li>
702 <li>pasted region containing hidden columns is incorrectly
703 displayed in new alignment window</li>
704 <li>Jalview slow to complete operations when stdout is flooded
705 (fix is to close the Jalview console)</li>
706 <li>typo in AlignmentFrame->View->Hide->all but
707 selected Rregions menu item.</li>
708 <li>inconsistent group submenu and Format submenu entry 'Un' or
710 <li>Sequence feature settings are being shared by multiple
711 distinct alignments</li>
712 <li>group annotation not recreated when tree partition is
714 <li>double click on group annotation to select sequences does
715 not propagate to associated trees</li>
716 <li>Mac OSX specific issues:
718 <li>exception raised when mouse clicked on desktop window
720 <li>Desktop menu placed on menu bar and application name set
722 <li>sequence feature settings not wide enough for the save
723 feature colourscheme button</li>
732 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
733 <em>30/4/2010</em></div>
735 <td><em>New Capabilities</em>
737 <li>URL links generated from description line for
738 regular-expression based URL links (applet and application)
739 <li>Non-positional feature URL links are shown in link menu</li>
740 <li>Linked viewing of nucleic acid sequences and structures</li>
741 <li>Automatic Scrolling option in View menu to display the
742 currently highlighted region of an alignment.</li>
743 <li>Order an alignment by sequence length, or using the average
744 score or total feature count for each sequence.</li>
745 <li>Shading features by score or associated description</li>
746 <li>Subdivide alignment and groups based on identity of selected
747 subsequence (Make Groups from Selection).</li>
748 <li>New hide/show options including Shift+Control+H to hide
749 everything but the currently selected region.</li>
750 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
754 <li>Fetch DB References capabilities and UI expanded to support
755 retrieval from DAS sequence sources</li>
756 <li>Local DAS Sequence sources can be added via the command line
757 or via the Add local source dialog box.</li>
758 <li>DAS Dbref and DbxRef feature types are parsed as database
759 references and protein_name is parsed as description line (BioSapiens
761 <li>Enable or disable non-positional feature and database
762 references in sequence ID tooltip from View menu in application.</li>
763 <!-- <li>New hidden columns and rows and representatives capabilities
764 in annotations file (in progress - not yet fully implemented)</li> -->
765 <li>Group-associated consensus, sequence logos and conservation
767 <li>Symbol distributions for each column can be exported and
768 visualized as sequence logos</li>
769 <li>Optionally scale multi-character column labels to fit within
770 each column of annotation row<!-- todo for applet --></li>
771 <li>Optional automatic sort of associated alignment view when a
772 new tree is opened.</li>
773 <li>Jalview Java Console</li>
774 <li>Better placement of desktop window when moving between
775 different screens.</li>
776 <li>New preference items for sequence ID tooltip and consensus
778 <li>Client to submit sequences and IDs to <a
779 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
780 <li><em>Vamsas Capabilities</em>
782 <li>Improved VAMSAS synchronization (jalview archive used to
783 preserve views, structures, and tree display settings)</li>
784 <li>Import of vamsas documents from disk or URL via command
786 <li>Sharing of selected regions between views and with other
787 VAMSAS applications (Experimental feature!)</li>
788 <li>Updated API to VAMSAS version 0.2</li>
794 <li>Middle button resizes annotation row height</li>
797 <li>sortByTree (true/false) - automatically sort the associated
798 alignment view by the tree when a new tree is opened.</li>
799 <li>showTreeBootstraps (true/false) - show or hide branch
800 bootstraps (default is to show them if available)</li>
801 <li>showTreeDistances (true/false) - show or hide branch
802 lengths (default is to show them if available)</li>
803 <li>showUnlinkedTreeNodes (true/false) - indicate if
804 unassociated nodes should be highlighted in the tree view</li>
805 <li>heightScale and widthScale (1.0 or more) - increase the
806 height or width of a cell in the alignment grid relative to the
807 current font size.</li>
810 <li>Non-positional features displayed in sequence ID tooltip</li>
814 <li>Features format: graduated colour definitions and
815 specification of feature scores</li>
816 <li>Alignment Annotations format: new keywords for group
817 associated annotation (GROUP_REF) and annotation row display
818 properties (ROW_PROPERTIES)</li>
819 <li>XML formats extended to support graduated feature
820 colourschemes, group associated annotation, and profile visualization
825 <li>Source field in GFF files parsed as feature source rather
826 than description</li>
827 <li>Non-positional features are now included in sequence feature
828 and gff files (controlled via non-positional feature visibility in
830 <li>URL links generated for all feature links (bugfix)</li>
831 <li>Added URL embedding instructions to features file
833 <li>Codons containing ambiguous nucleotides translated as 'X' in
835 <li>Match case switch in find dialog box works for both sequence
836 ID and sequence string and query strings do not have to be in upper
837 case to match case-insensitively.</li>
838 <li>AMSA files only contain first column of multi-character
839 column annotation labels</li>
840 <li>Jalview Annotation File generation/parsing consistent with
841 documentation (e.g. Stockholm annotation can be exported and
843 <li>PDB files without embedded PDB IDs given a friendly name</li>
844 <li>Find incrementally searches ID string matches as well as
845 subsequence matches, and correctly reports total number of both.</li>
848 <li>Better handling of exceptions during sequence retrieval</li>
849 <li>Dasobert generated non-positional feature URL link text
850 excludes the start_end suffix</li>
851 <li>DAS feature and source retrieval buttons disabled when
852 fetch or registry operations in progress.</li>
853 <li>PDB files retrieved from URLs are cached properly</li>
854 <li>Sequence description lines properly shared via VAMSAS</li>
855 <li>Sequence fetcher fetches multiple records for all data
857 <li>Ensured that command line das feature retrieval completes
858 before alignment figures are generated.</li>
859 <li>Reduced time taken when opening file browser for first
861 <li>isAligned check prior to calculating tree, PCA or
862 submitting an MSA to JNet now excludes hidden sequences.</li>
863 <li>User defined group colours properly recovered from Jalview
873 <div align="center"><strong>2.4.0.b2</strong><br>
878 <li>Experimental support for google analytics usage tracking.</li>
879 <li>Jalview privacy settings (user preferences and docs).</li>
884 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
885 <li>Exception when feature created from selection beyond length
887 <li>Allow synthetic PDB files to be imported gracefully</li>
888 <li>Sequence associated annotation rows associate with all
889 sequences with a given id</li>
890 <li>Find function matches case-insensitively for sequence ID
892 <li>Non-standard characters do not cause pairwise alignment to
893 fail with exception</li>
895 <em>Application Issues</em>
897 <li>Sequences are now validated against EMBL database</li>
898 <li>Sequence fetcher fetches multiple records for all data
901 <em>InstallAnywhere Issues</em>
903 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
904 installAnywhere mechanism)</li>
905 <li>Command line launching of JARs from InstallAnywhere version
906 (java class versioning error fixed)</li>
913 <div align="center"><strong>2.4</strong><br>
916 <td><em>User Interface</em>
918 <li>Linked highlighting of codon and amino acid from translation
919 and protein products</li>
920 <li>Linked highlighting of structure associated with residue
921 mapping to codon position</li>
922 <li>Sequence Fetcher provides example accession numbers and
924 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
925 <li>Extract score function to parse whitespace separated numeric
926 data in description line</li>
927 <li>Column labels in alignment annotation can be centred.</li>
928 <li>Tooltip for sequence associated annotation give name of
931 <em>Web Services and URL fetching</em>
933 <li>JPred3 web service</li>
934 <li>Prototype sequence search client (no public services
936 <li>Fetch either seed alignment or full alignment from PFAM</li>
937 <li>URL Links created for matching database cross references as
938 well as sequence ID</li>
939 <li>URL Links can be created using regular-expressions</li>
941 <em>Sequence Database Connectivity</em>
943 <li>Retrieval of cross-referenced sequences from other databases
945 <li>Generalised database reference retrieval and validation to
946 all fetchable databases</li>
947 <li>Fetch sequences from DAS sources supporting the sequence
950 <em>Import and Export</em>
951 <li>export annotation rows as CSV for spreadsheet import</li>
952 <li>Jalview projects record alignment dataset associations, EMBL
953 products, and cDNA sequence mappings</li>
954 <li>Sequence Group colour can be specified in Annotation File</li>
955 <li>Ad-hoc colouring of group in Annotation File using RGB
956 triplet as name of colourscheme</li>
958 <em>VAMSAS Client capabilities (Experimental)</em>
960 <li>treenode binding for VAMSAS tree exchange</li>
961 <li>local editing and update of sequences in VAMSAS alignments
963 <li>Create new or select existing session to join</li>
964 <li>load and save of vamsas documents</li>
966 <em>Application command line</em>
968 <li>-tree parameter to open trees (introduced for passing from
970 <li>-fetchfrom command line argument to specify nicknames of DAS
971 servers to query for alignment features</li>
972 <li>-dasserver command line argument to add new servers that are
973 also automatically queried for features</li>
974 <li>-groovy command line argument executes a given groovy script
975 after all input data has been loaded and parsed</li>
977 <em>Applet-Application data exchange</em>
979 <li>Trees passed as applet parameters can be passed to
980 application (when using "View in full application")</li>
982 <em>Applet Parameters</em>
984 <li>feature group display control parameter</li>
985 <li>debug parameter</li>
986 <li>showbutton parameter</li>
988 <em>Applet API methods</em>
990 <li>newView public method</li>
991 <li>Window (current view) specific get/set public methods</li>
992 <li>Feature display control methods</li>
993 <li>get list of currently selected sequences</li>
995 <em>New Jalview distribution features</em>
997 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
998 <li>RELEASE file gives build properties for the latest Jalview
1000 <li>Java 1.1 Applet build made easier and donotobfuscate
1001 property controls execution of obfuscator</li>
1002 <li>Build target for generating source distribution</li>
1003 <li>Debug flag for javacc</li>
1004 <li>.jalview_properties file is documented (slightly) in
1005 jalview.bin.Cache</li>
1006 <li>Continuous Build Integration for stable and development
1007 version of Application, Applet and source distribution</li>
1013 <li>selected region output includes visible annotations (for
1014 certain formats)</li>
1015 <li>edit label/displaychar contains existing label/char for
1017 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1018 <li>shorter peptide product names from EMBL records</li>
1019 <li>Newick string generator makes compact representations</li>
1020 <li>bootstrap values parsed correctly for tree files with
1022 <li>pathological filechooser bug avoided by not allowing
1023 filenames containing a ':'</li>
1024 <li>Fixed exception when parsing GFF files containing global
1025 sequence features</li>
1026 <li>Alignment datasets are finalized only when number of
1027 references from alignment sequences goes to zero</li>
1028 <li>Close of tree branch colour box without colour selection
1029 causes cascading exceptions</li>
1030 <li>occasional negative imgwidth exceptions</li>
1031 <li>better reporting of non-fatal warnings to user when file
1033 <li>Save works when Jalview project is default format</li>
1034 <li>Save as dialog opened if current alignment format is not a
1035 valid output format</li>
1036 <li>Uniprot canonical names introduced for both das and vamsas</li>
1037 <li>Histidine should be midblue (not pink!) in Zappo</li>
1038 <li>error messages passed up and output when data read fails</li>
1039 <li>edit undo recovers previous dataset sequence when sequence
1041 <li>allow PDB files without pdb ID HEADER lines (like those
1042 generated by MODELLER) to be read in properly</li>
1043 <li>allow reading of JPred concise files as a normal filetype</li>
1044 <li>Stockholm annotation parsing and alignment properties import
1045 fixed for PFAM records</li>
1046 <li>Structure view windows have correct name in Desktop window
1048 <li>annotation consisting of sequence associated scores can be
1049 read and written correctly to annotation file</li>
1050 <li>Aligned cDNA translation to aligned peptide works correctly</li>
1051 <li>Fixed display of hidden sequence markers and non-italic font
1052 for representatives in Applet</li>
1053 <li>Applet Menus are always embedded in applet window on Macs.</li>
1054 <li>Newly shown features appear at top of stack (in Applet)</li>
1055 <li>Annotations added via parameter not drawn properly due to
1056 null pointer exceptions</li>
1057 <li>Secondary structure lines are drawn starting from first
1058 column of alignment</li>
1059 <li>Uniprot XML import updated for new schema release in July
1061 <li>Sequence feature to sequence ID match for Features file is
1062 case-insensitive</li>
1063 <li>Sequence features read from Features file appended to all
1064 sequences with matching IDs</li>
1065 <li>PDB structure coloured correctly for associated views
1066 containing a sub-sequence</li>
1067 <li>PDB files can be retrieved by applet from Jar files</li>
1068 <li>feature and annotation file applet parameters referring to
1069 different directories are retrieved correctly</li>
1070 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1071 <li>Fixed application hang whilst waiting for splash-screen
1072 version check to complete</li>
1073 <li>Applet properly URLencodes input parameter values when
1074 passing them to the launchApp service</li>
1075 <li>display name and local features preserved in results
1076 retrieved from web service</li>
1077 <li>Visual delay indication for sequence retrieval and sequence
1078 fetcher initialisation</li>
1079 <li>updated Application to use DAS 1.53e version of dasobert DAS
1081 <li>Re-instated Full AMSA support and .amsa file association</li>
1082 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1089 <div align="center"><strong>2.3</strong><br>
1094 <li>Jmol 11.0.2 integration</li>
1095 <li>PDB views stored in Jalview XML files</li>
1096 <li>Slide sequences</li>
1097 <li>Edit sequence in place</li>
1098 <li>EMBL CDS features</li>
1099 <li>DAS Feature mapping</li>
1100 <li>Feature ordering</li>
1101 <li>Alignment Properties</li>
1102 <li>Annotation Scores</li>
1103 <li>Sort by scores</li>
1104 <li>Feature/annotation editing in applet</li>
1109 <li>Headless state operation in 2.2.1</li>
1110 <li>Incorrect and unstable DNA pairwise alignment</li>
1111 <li>Cut and paste of sequences with annotation</li>
1112 <li>Feature group display state in XML</li>
1113 <li>Feature ordering in XML</li>
1114 <li>blc file iteration selection using filename # suffix</li>
1115 <li>Stockholm alignment properties</li>
1116 <li>Stockhom alignment secondary structure annotation</li>
1117 <li>2.2.1 applet had no feature transparency</li>
1118 <li>Number pad keys can be used in cursor mode</li>
1119 <li>Structure Viewer mirror image resolved</li>
1126 <div align="center"><strong>2.2.1</strong><br>
1131 <li>Non standard characters can be read and displayed
1132 <li>Annotations/Features can be imported/exported to the applet
1134 <li>Applet allows editing of sequence/annotation/group name
1136 <li>Preference setting to display sequence name in italics
1137 <li>Annotation file format extended to allow Sequence_groups to
1139 <li>Default opening of alignment overview panel can be specified
1141 <li>PDB residue numbering annotation added to associated
1147 <li>Applet crash under certain Linux OS with Java 1.6 installed
1148 <li>Annotation file export / import bugs fixed
1149 <li>PNG / EPS image output bugs fixed
1155 <div align="center"><strong>2.2</strong><br>
1160 <li>Multiple views on alignment
1161 <li>Sequence feature editing
1162 <li>"Reload" alignment
1163 <li>"Save" to current filename
1164 <li>Background dependent text colour
1165 <li>Right align sequence ids
1166 <li>User-defined lower case residue colours
1169 <li>Menu item accelerator keys
1170 <li>Control-V pastes to current alignment
1171 <li>Cancel button for DAS Feature Fetching
1172 <li>PCA and PDB Viewers zoom via mouse roller
1173 <li>User-defined sub-tree colours and sub-tree selection
1174 <li>'New Window' button on the 'Output to Text box'
1179 <li>New memory efficient Undo/Redo System
1180 <li>Optimised symbol lookups and conservation/consensus
1182 <li>Region Conservation/Consensus recalculated after edits
1183 <li>Fixed Remove Empty Columns Bug (empty columns at end of
1185 <li>Slowed DAS Feature Fetching for increased robustness.
1186 <li>Made angle brackets in ASCII feature descriptions display
1188 <li>Re-instated Zoom function for PCA
1189 <li>Sequence descriptions conserved in web service analysis
1191 <li>Uniprot ID discoverer uses any word separated by ∣
1192 <li>WsDbFetch query/result association resolved
1193 <li>Tree leaf to sequence mapping improved
1194 <li>Smooth fonts switch moved to FontChooser dialog box.
1200 <div align="center"><strong>2.1.1</strong><br>
1205 <li>Copy consensus sequence to clipboard</li>
1210 <li>Image output - rightmost residues are rendered if sequence
1211 id panel has been resized</li>
1212 <li>Image output - all offscreen group boundaries are rendered</li>
1213 <li>Annotation files with sequence references - all elements in
1214 file are relative to sequence position</li>
1215 <li>Mac Applet users can use Alt key for group editing</li>
1221 <div align="center"><strong>2.1</strong><br>
1226 <li>MAFFT Multiple Alignment in default Web Service list</li>
1227 <li>DAS Feature fetching</li>
1228 <li>Hide sequences and columns</li>
1229 <li>Export Annotations and Features</li>
1230 <li>GFF file reading / writing</li>
1231 <li>Associate structures with sequences from local PDB files</li>
1232 <li>Add sequences to exisiting alignment</li>
1233 <li>Recently opened files / URL lists</li>
1234 <li>Applet can launch the full application</li>
1235 <li>Applet has transparency for features (Java 1.2 required)</li>
1236 <li>Applet has user defined colours parameter</li>
1237 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
1242 <li>Redundancy Panel reinstalled in the Applet</li>
1243 <li>Monospaced font - EPS / rescaling bug fixed</li>
1244 <li>Annotation files with sequence references bug fixed</li>
1250 <div align="center"><strong>2.08.1</strong><br>
1255 <li>Change case of selected region from Popup menu</li>
1256 <li>Choose to match case when searching</li>
1257 <li>Middle mouse button and mouse movement can compress / expand
1258 the visible width and height of the alignment</li>
1263 <li>Annotation Panel displays complete JNet results</li>
1269 <div align="center"><strong>2.08b</strong><br>
1275 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1276 <li>Righthand label on wrapped alignments shows correct value</li>
1282 <div align="center"><strong>2.08</strong><br>
1287 <li>Editing can be locked to the selection area</li>
1288 <li>Keyboard editing</li>
1289 <li>Create sequence features from searches</li>
1290 <li>Precalculated annotations can be loaded onto alignments</li>
1291 <li>Features file allows grouping of features</li>
1292 <li>Annotation Colouring scheme added</li>
1293 <li>Smooth fonts off by default - Faster rendering</li>
1294 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1299 <li>Drag & Drop fixed on Linux</li>
1300 <li>Jalview Archive file faster to load/save, sequence
1301 descriptions saved.</li>
1307 <div align="center"><strong>2.07</strong><br>
1312 <li>PDB Structure Viewer enhanced</li>
1313 <li>Sequence Feature retrieval and display enhanced</li>
1314 <li>Choose to output sequence start-end after sequence name for
1316 <li>Sequence Fetcher WSDBFetch@EBI</li>
1317 <li>Applet can read feature files, PDB files and can be used for
1318 HTML form input</li>
1323 <li>HTML output writes groups and features</li>
1324 <li>Group editing is Control and mouse click</li>
1325 <li>File IO bugs</li>
1331 <div align="center"><strong>2.06</strong><br>
1336 <li>View annotations in wrapped mode</li>
1337 <li>More options for PCA viewer</li>
1342 <li>GUI bugs resolved</li>
1343 <li>Runs with -nodisplay from command line</li>
1349 <div align="center"><strong>2.05b</strong><br>
1354 <li>Choose EPS export as lineart or text</li>
1355 <li>Jar files are executable</li>
1356 <li>Can read in Uracil - maps to unknown residue</li>
1361 <li>Known OutOfMemory errors give warning message</li>
1362 <li>Overview window calculated more efficiently</li>
1363 <li>Several GUI bugs resolved</li>
1369 <div align="center"><strong>2.05</strong><br>
1374 <li>Edit and annotate in "Wrapped" view</li>
1379 <li>Several GUI bugs resolved</li>
1385 <div align="center"><strong>2.04</strong><br>
1390 <li>Hold down mouse wheel & scroll to change font size</li>
1395 <li>Improved JPred client reliability</li>
1396 <li>Improved loading of Jalview files</li>
1402 <div align="center"><strong>2.03</strong><br>
1407 <li>Set Proxy server name and port in preferences</li>
1408 <li>Multiple URL links from sequence ids</li>
1409 <li>User Defined Colours can have a scheme name and added to
1411 <li>Choose to ignore gaps in consensus calculation</li>
1412 <li>Unix users can set default web browser</li>
1413 <li>Runs without GUI for batch processing</li>
1414 <li>Dynamically generated Web Service Menus</li>
1419 <li>InstallAnywhere download for Sparc Solaris</li>
1425 <div align="center"><strong>2.02</strong><br>
1431 <li>Copy & Paste order of sequences maintains alignment
1438 <div align="center"><strong>2.01</strong><br>
1443 <li>Use delete key for deleting selection.</li>
1444 <li>Use Mouse wheel to scroll sequences.</li>
1445 <li>Help file updated to describe how to add alignment
1447 <li>Version and build date written to build properties file.</li>
1448 <li>InstallAnywhere installation will check for updates at
1449 launch of Jalview.</li>
1454 <li>Delete gaps bug fixed.</li>
1455 <li>FileChooser sorts columns.</li>
1456 <li>Can remove groups one by one.</li>
1457 <li>Filechooser icons installed.</li>
1458 <li>Finder ignores return character when searching. Return key
1459 will initiate a search.<br>
1466 <div align="center"><strong>2.0</strong><br>
1471 <li>New codebase</li>