3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
11 * of the License, or (at your option) any later version.
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.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
27 <strong>Release History</strong>
31 <td width="60" nowrap>
33 <em><strong>Release</strong></em>
38 <em><strong>New Features</strong></em>
43 <em><strong>Issues Resolved</strong></em>
48 <td width="60" nowrap>
50 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>20/9/2016</em></strong>
55 <li><!-- JAL-2164,JAL-1919,-->Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.</li>
56 <li><!-- JAL-192 --->Alignment ruler shows positions relative to reference sequence</li>
57 <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
58 </ul> <em>Application</em>
66 <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
67 <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
68 <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
69 <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
70 <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
71 <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
72 <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
73 <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
74 <li><!-- JAL-2183-->Free-text search client for UniProt using the UniProt web API</li>
85 <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
86 <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
87 <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
88 <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
89 <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
90 <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
91 <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
92 <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
93 <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
94 <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
99 <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
100 <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
101 <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
102 <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
103 <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
104 <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
105 <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
106 <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
107 <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
109 <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
119 <td width="60" nowrap>
121 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
122 <em>16/10/2015</em></strong>
127 <li>Time stamps for signed Jalview application and applet
134 <li>Duplicate group consensus and conservation rows
135 shown when tree is partitioned</li>
136 <li>Erratic behaviour when tree partitions made with
137 multiple cDNA/Protein split views</li>
143 <td width="60" nowrap>
145 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
146 <em>8/10/2015</em></strong>
151 <li>Updated Spanish translations of localized text for
153 </ul> <em>Application</em>
155 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
156 <li>Signed OSX InstallAnywhere installer<br></li>
157 <li>Support for per-sequence based annotations in BioJSON</li>
158 </ul> <em>Applet</em>
160 <li>Split frame example added to applet examples page</li>
166 <li>Mapping of cDNA to protein in split frames
167 incorrect when sequence start > 1</li>
168 <li>Broken images in filter column by annotation dialog
170 <li>Feature colours not parsed from features file</li>
171 <li>Exceptions and incomplete link URLs recovered when
172 loading a features file containing HTML tags in feature
178 <li>Annotations corrupted after BioJS export and
180 <li>Incorrect sequence limits after Fetch DB References
181 with 'trim retrieved sequences'</li>
182 <li>Incorrect warning about deleting all data when
183 deleting selected columns</li>
184 <li>Patch to build system for shipping properly signed
185 JNLP templates for webstart launch</li>
186 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
187 unreleased structures for download or viewing</li>
188 <li>Tab/space/return keystroke operation of EMBL-PDBe
189 fetcher/viewer dialogs works correctly</li>
190 <li>Disabled 'minimise' button on Jalview windows
191 running on OSX to workaround redraw hang bug</li>
192 <li>Split cDNA/Protein view position and geometry not
193 recovered from jalview project</li>
194 <li>Initial enabled/disabled state of annotation menu
195 sorter 'show autocalculated first/last' corresponds to
197 <li>Restoring of Clustal, RNA Helices and T-Coffee
198 color schemes from BioJSON</li>
202 <li>Reorder sequences mirrored in cDNA/Protein split
204 <li>Applet with Jmol examples not loading correctly</li>
210 <td><div align="center">
211 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
215 <li>Linked visualisation and analysis of DNA and Protein
218 <li>Translated cDNA alignments shown as split protein
219 and DNA alignment views</li>
220 <li>Codon consensus annotation for linked protein and
221 cDNA alignment views</li>
222 <li>Link cDNA or Protein product sequences by loading
223 them onto Protein or cDNA alignments</li>
224 <li>Reconstruct linked cDNA alignment from aligned
225 protein sequences</li>
228 <li>Jmol integration updated to Jmol v14.2.14</li>
229 <li>Import and export of Jalview alignment views as <a
230 href="features/bioJsonFormat.html">BioJSON</a></li>
231 <li>New alignment annotation file statements for
232 reference sequences and marking hidden columns</li>
233 <li>Reference sequence based alignment shading to
234 highlight variation</li>
235 <li>Select or hide columns according to alignment
237 <li>Find option for locating sequences by description</li>
238 <li>Conserved physicochemical properties shown in amino
239 acid conservation row</li>
240 <li>Alignments can be sorted by number of RNA helices</li>
241 </ul> <em>Application</em>
243 <li>New cDNA/Protein analysis capabilities
245 <li>Get Cross-References should open a Split Frame
246 view with cDNA/Protein</li>
247 <li>Detect when nucleotide sequences and protein
248 sequences are placed in the same alignment</li>
249 <li>Split cDNA/Protein views are saved in Jalview
254 <li>Use REST API to talk to Chimera</li>
255 <li>Selected regions in Chimera are highlighted in linked
258 <li>VARNA RNA viewer updated to v3.93</li>
259 <li>VARNA views are saved in Jalview Projects</li>
260 <li>Pseudoknots displayed as Jalview RNA annotation can
261 be shown in VARNA</li>
263 <li>Make groups for selection uses marked columns as well
264 as the active selected region</li>
266 <li>Calculate UPGMA and NJ trees using sequence feature
268 <li>New Export options
270 <li>New Export Settings dialog to control hidden
271 region export in flat file generation</li>
273 <li>Export alignment views for display with the <a
274 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
276 <li>Export scrollable SVG in HTML page</li>
277 <li>Optional embedding of BioJSON data when exporting
278 alignment figures to HTML</li>
280 <li>3D structure retrieval and display
282 <li>Free text and structured queries with the PDBe
284 <li>PDBe Search API based discovery and selection of
285 PDB structures for a sequence set</li>
289 <li>JPred4 employed for protein secondary structure
291 <li>Hide Insertions menu option to hide unaligned columns
292 for one or a group of sequences</li>
293 <li>Automatically hide insertions in alignments imported
294 from the JPred4 web server</li>
295 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
296 system on OSX<br />LGPL libraries courtesy of <a
297 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
299 <li>changed 'View nucleotide structure' submenu to 'View
300 VARNA 2D Structure'</li>
301 <li>change "View protein structure" menu option to "3D
304 </ul> <em>Applet</em>
306 <li>New layout for applet example pages</li>
307 <li>New parameters to enable SplitFrame view
308 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
309 <li>New example demonstrating linked viewing of cDNA and
310 Protein alignments</li>
311 </ul> <em>Development and deployment</em>
313 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
314 <li>Include installation type and git revision in build
315 properties and console log output</li>
316 <li>Jalview Github organisation, and new github site for
317 storing BioJsMSA Templates</li>
318 <li>Jalview's unit tests now managed with TestNG</li>
321 <!-- <em>General</em>
323 </ul> --> <!-- issues resolved --> <em>Application</em>
325 <li>Escape should close any open find dialogs</li>
326 <li>Typo in select-by-features status report</li>
327 <li>Consensus RNA secondary secondary structure
328 predictions are not highlighted in amber</li>
329 <li>Missing gap character in v2.7 example file means
330 alignment appears unaligned when pad-gaps is not enabled</li>
331 <li>First switch to RNA Helices colouring doesn't colour
332 associated structure views</li>
333 <li>ID width preference option is greyed out when auto
334 width checkbox not enabled</li>
335 <li>Stopped a warning dialog from being shown when
336 creating user defined colours</li>
337 <li>'View Mapping' in structure viewer shows sequence
338 mappings for just that viewer's sequences</li>
339 <li>Workaround for superposing PDB files containing
340 multiple models in Chimera</li>
341 <li>Report sequence position in status bar when hovering
342 over Jmol structure</li>
343 <li>Cannot output gaps as '.' symbols with Selection ->
344 output to text box</li>
345 <li>Flat file exports of alignments with hidden columns
346 have incorrect sequence start/end</li>
347 <li>'Aligning' a second chain to a Chimera structure from
349 <li>Colour schemes applied to structure viewers don't
350 work for nucleotide</li>
351 <li>Loading/cut'n'pasting an empty or invalid file leads
352 to a grey/invisible alignment window</li>
353 <li>Exported Jpred annotation from a sequence region
354 imports to different position</li>
355 <li>Space at beginning of sequence feature tooltips shown
356 on some platforms</li>
357 <li>Chimera viewer 'View | Show Chain' menu is not
359 <li>'New View' fails with a Null Pointer Exception in
360 console if Chimera has been opened</li>
361 <li>Mouseover to Chimera not working</li>
362 <li>Miscellaneous ENA XML feature qualifiers not
364 <li>NPE in annotation renderer after 'Extract Scores'</li>
365 <li>If two structures in one Chimera window, mouseover of
366 either sequence shows on first structure</li>
367 <li>'Show annotations' options should not make
368 non-positional annotations visible</li>
369 <li>Subsequence secondary structure annotation not shown
370 in right place after 'view flanking regions'</li>
371 <li>File Save As type unset when current file format is
373 <li>Save as '.jar' option removed for saving Jalview
375 <li>Colour by Sequence colouring in Chimera more
377 <li>Cannot 'add reference annotation' for a sequence in
378 several views on same alignment</li>
379 <li>Cannot show linked products for EMBL / ENA records</li>
380 <li>Jalview's tooltip wraps long texts containing no
382 </ul> <em>Applet</em>
384 <li>Jmol to JalviewLite mouseover/link not working</li>
385 <li>JalviewLite can't import sequences with ID
386 descriptions containing angle brackets</li>
387 </ul> <em>General</em>
389 <li>Cannot export and reimport RNA secondary structure
390 via jalview annotation file</li>
391 <li>Random helix colour palette for colour by annotation
392 with RNA secondary structure</li>
393 <li>Mouseover to cDNA from STOP residue in protein
394 translation doesn't work.</li>
395 <li>hints when using the select by annotation dialog box</li>
396 <li>Jmol alignment incorrect if PDB file has alternate CA
398 <li>FontChooser message dialog appears to hang after
399 choosing 1pt font</li>
400 <li>Peptide secondary structure incorrectly imported from
401 annotation file when annotation display text includes 'e' or
403 <li>Cannot set colour of new feature type whilst creating
405 <li>cDNA translation alignment should not be sequence
407 <li>'Show unconserved' doesn't work for lower case
409 <li>Nucleotide ambiguity codes involving R not recognised</li>
410 </ul> <em>Deployment and Documentation</em>
412 <li>Applet example pages appear different to the rest of
414 </ul> <em>Application Known issues</em>
416 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
417 <li>Misleading message appears after trying to delete
419 <li>Jalview icon not shown in dock after InstallAnywhere
420 version launches</li>
421 <li>Fetching EMBL reference for an RNA sequence results
422 fails with a sequence mismatch</li>
423 <li>Corrupted or unreadable alignment display when
424 scrolling alignment to right</li>
425 <li>ArrayIndexOutOfBoundsException thrown when remove
426 empty columns called on alignment with ragged gapped ends</li>
427 <li>auto calculated alignment annotation rows do not get
428 placed above or below non-autocalculated rows</li>
429 <li>Jalview dekstop becomes sluggish at full screen in
430 ultra-high resolution</li>
431 <li>Cannot disable consensus calculation independently of
432 quality and conservation</li>
433 <li>Mouseover highlighting between cDNA and protein can
434 become sluggish with more than one splitframe shown</li>
435 </ul> <em>Applet Known Issues</em>
437 <li>Core PDB parsing code requires Jmol</li>
438 <li>Sequence canvas panel goes white when alignment
439 window is being resized</li>
445 <td><div align="center">
446 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
450 <li>Updated Java code signing certificate donated by
452 <li>Features and annotation preserved when performing
453 pairwise alignment</li>
454 <li>RNA pseudoknot annotation can be
455 imported/exported/displayed</li>
456 <li>'colour by annotation' can colour by RNA and
457 protein secondary structure</li>
458 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
459 post-hoc with 2.9 release</em>)
462 </ul> <em>Application</em>
464 <li>Extract and display secondary structure for sequences
465 with 3D structures</li>
466 <li>Support for parsing RNAML</li>
467 <li>Annotations menu for layout
469 <li>sort sequence annotation rows by alignment</li>
470 <li>place sequence annotation above/below alignment
473 <li>Output in Stockholm format</li>
474 <li>Internationalisation: improved Spanish (es)
476 <li>Structure viewer preferences tab</li>
477 <li>Disorder and Secondary Structure annotation tracks
478 shared between alignments</li>
479 <li>UCSF Chimera launch and linked highlighting from
481 <li>Show/hide all sequence associated annotation rows for
482 all or current selection</li>
483 <li>disorder and secondary structure predictions
484 available as dataset annotation</li>
485 <li>Per-sequence rna helices colouring</li>
488 <li>Sequence database accessions imported when fetching
489 alignments from Rfam</li>
490 <li>update VARNA version to 3.91</li>
492 <li>New groovy scripts for exporting aligned positions,
493 conservation values, and calculating sum of pairs scores.</li>
494 <li>Command line argument to set default JABAWS server</li>
495 <li>include installation type in build properties and
496 console log output</li>
497 <li>Updated Jalview project format to preserve dataset
501 <!-- issues resolved --> <em>Application</em>
503 <li>Distinguish alignment and sequence associated RNA
504 structure in structure->view->VARNA</li>
505 <li>Raise dialog box if user deletes all sequences in an
507 <li>Pressing F1 results in documentation opening twice</li>
508 <li>Sequence feature tooltip is wrapped</li>
509 <li>Double click on sequence associated annotation
510 selects only first column</li>
511 <li>Redundancy removal doesn't result in unlinked
512 leaves shown in tree</li>
513 <li>Undos after several redundancy removals don't undo
515 <li>Hide sequence doesn't hide associated annotation</li>
516 <li>User defined colours dialog box too big to fit on
517 screen and buttons not visible</li>
518 <li>author list isn't updated if already written to
519 Jalview properties</li>
520 <li>Popup menu won't open after retrieving sequence
522 <li>File open window for associate PDB doesn't open</li>
523 <li>Left-then-right click on a sequence id opens a
524 browser search window</li>
525 <li>Cannot open sequence feature shading/sort popup menu
526 in feature settings dialog</li>
527 <li>better tooltip placement for some areas of Jalview
529 <li>Allow addition of JABAWS Server which doesn't
531 <li>Web services parameters dialog box is too large to
533 <li>Muscle nucleotide alignment preset obscured by
535 <li>JABAWS preset submenus don't contain newly
536 defined user preset</li>
537 <li>MSA web services warns user if they were launched
538 with invalid input</li>
539 <li>Jalview cannot contact DAS Registy when running on
542 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
543 'Superpose with' submenu not shown when new view
547 </ul> <!-- <em>Applet</em>
549 </ul> <em>General</em>
551 </ul>--> <em>Deployment and Documentation</em>
553 <li>2G and 1G options in launchApp have no effect on
554 memory allocation</li>
555 <li>launchApp service doesn't automatically open
556 www.jalview.org/examples/exampleFile.jar if no file is given</li>
558 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
559 InstallAnywhere reports cannot find valid JVM when Java
562 </ul> <em>Application Known issues</em>
565 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
566 corrupted or unreadable alignment display when scrolling
570 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
571 retrieval fails but progress bar continues for DAS retrieval
572 with large number of ID
575 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
576 flatfile output of visible region has incorrect sequence
580 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
581 rna structure consensus doesn't update when secondary
582 structure tracks are rearranged
585 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
586 invalid rna structure positional highlighting does not
587 highlight position of invalid base pairs
590 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
591 out of memory errors are not raised when saving Jalview
592 project from alignment window file menu
595 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
596 Switching to RNA Helices colouring doesn't propagate to
600 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
601 colour by RNA Helices not enabled when user created
602 annotation added to alignment
605 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
606 Jalview icon not shown on dock in Mountain Lion/Webstart
608 </ul> <em>Applet Known Issues</em>
611 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
612 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
615 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
616 Jalview and Jmol example not compatible with IE9
619 <li>Sort by annotation score doesn't reverse order
625 <td><div align="center">
626 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
629 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
632 <li>Internationalisation of user interface (usually
633 called i18n support) and translation for Spanish locale</li>
634 <li>Define/Undefine group on current selection with
635 Ctrl-G/Shift Ctrl-G</li>
636 <li>Improved group creation/removal options in
637 alignment/sequence Popup menu</li>
638 <li>Sensible precision for symbol distribution
639 percentages shown in logo tooltip.</li>
640 <li>Annotation panel height set according to amount of
641 annotation when alignment first opened</li>
642 </ul> <em>Application</em>
644 <li>Interactive consensus RNA secondary structure
645 prediction VIENNA RNAAliFold JABA 2.1 service</li>
646 <li>Select columns containing particular features from
647 Feature Settings dialog</li>
648 <li>View all 'representative' PDB structures for selected
650 <li>Update Jalview project format:
652 <li>New file extension for Jalview projects '.jvp'</li>
653 <li>Preserve sequence and annotation dataset (to
654 store secondary structure annotation,etc)</li>
655 <li>Per group and alignment annotation and RNA helix
659 <li>New similarity measures for PCA and Tree calculation
661 <li>Experimental support for retrieval and viewing of
662 flanking regions for an alignment</li>
666 <!-- issues resolved --> <em>Application</em>
668 <li>logo keeps spinning and status remains at queued or
669 running after job is cancelled</li>
670 <li>cannot export features from alignments imported from
671 Jalview/VAMSAS projects</li>
672 <li>Buggy slider for web service parameters that take
674 <li>Newly created RNA secondary structure line doesn't
675 have 'display all symbols' flag set</li>
676 <li>T-COFFEE alignment score shading scheme and other
677 annotation shading not saved in Jalview project</li>
678 <li>Local file cannot be loaded in freshly downloaded
680 <li>Jalview icon not shown on dock in Mountain
682 <li>Load file from desktop file browser fails</li>
683 <li>Occasional NPE thrown when calculating large trees</li>
684 <li>Cannot reorder or slide sequences after dragging an
685 alignment onto desktop</li>
686 <li>Colour by annotation dialog throws NPE after using
687 'extract scores' function</li>
688 <li>Loading/cut'n'pasting an empty file leads to a grey
689 alignment window</li>
690 <li>Disorder thresholds rendered incorrectly after
691 performing IUPred disorder prediction</li>
692 <li>Multiple group annotated consensus rows shown when
693 changing 'normalise logo' display setting</li>
694 <li>Find shows blank dialog after 'finished searching' if
695 nothing matches query</li>
696 <li>Null Pointer Exceptions raised when sorting by
697 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
699 <li>Errors in Jmol console when structures in alignment
700 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
702 <li>Not all working JABAWS services are shown in
704 <li>JAVAWS version of Jalview fails to launch with
705 'invalid literal/length code'</li>
706 <li>Annotation/RNA Helix colourschemes cannot be applied
707 to alignment with groups (actually fixed in 2.8.0b1)</li>
708 <li>RNA Helices and T-Coffee Scores available as default
711 </ul> <em>Applet</em>
713 <li>Remove group option is shown even when selection is
715 <li>Apply to all groups ticked but colourscheme changes
716 don't affect groups</li>
717 <li>Documented RNA Helices and T-Coffee Scores as valid
718 colourscheme name</li>
719 <li>Annotation labels drawn on sequence IDs when
720 Annotation panel is not displayed</li>
721 <li>Increased font size for dropdown menus on OSX and
722 embedded windows</li>
725 <li>Consensus sequence for alignments/groups with a
726 single sequence were not calculated</li>
727 <li>annotation files that contain only groups imported as
728 annotation and junk sequences</li>
729 <li>Fasta files with sequences containing '*' incorrectly
730 recognised as PFAM or BLC</li>
731 <li>conservation/PID slider apply all groups option
732 doesn't affect background (2.8.0b1)
734 <li>redundancy highlighting is erratic at 0% and 100%</li>
735 <li>Remove gapped columns fails for sequences with ragged
737 <li>AMSA annotation row with leading spaces is not
738 registered correctly on import</li>
739 <li>Jalview crashes when selecting PCA analysis for
740 certain alignments</li>
741 <li>Opening the colour by annotation dialog for an
742 existing annotation based 'use original colours'
743 colourscheme loses original colours setting</li>
748 <td><div align="center">
749 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
750 <em>30/1/2014</em></strong>
754 <li>Trusted certificates for JalviewLite applet and
755 Jalview Desktop application<br />Certificate was donated by
756 <a href="https://www.certum.eu">Certum</a> to the Jalview
757 open source project).
759 <li>Jalview SRS links replaced by UniProt and EBI-search
761 <li>Output in Stockholm format</li>
762 <li>Allow import of data from gzipped files</li>
763 <li>Export/import group and sequence associated line
764 graph thresholds</li>
765 <li>Nucleotide substitution matrix that supports RNA and
767 <li>Allow disorder predictions to be made on the current
768 selection (or visible selection) in the same way that JPred
770 <li>Groovy scripting for headless Jalview operation</li>
771 </ul> <em>Other improvements</em>
773 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
774 <li>COMBINE statement uses current SEQUENCE_REF and
775 GROUP_REF scope to group annotation rows</li>
776 <li>Support '' style escaping of quotes in Newick
778 <li>Group options for JABAWS service by command line name</li>
779 <li>Empty tooltip shown for JABA service options with a
780 link but no description</li>
781 <li>Select primary source when selecting authority in
782 database fetcher GUI</li>
783 <li>Add .mfa to FASTA file extensions recognised by
785 <li>Annotation label tooltip text wrap</li>
790 <li>Slow scrolling when lots of annotation rows are
792 <li>Lots of NPE (and slowness) after creating RNA
793 secondary structure annotation line</li>
794 <li>Sequence database accessions not imported when
795 fetching alignments from Rfam</li>
796 <li>Incorrect SHMR submission for sequences with
798 <li>View all structures does not always superpose
800 <li>Option widgets in service parameters not updated to
801 reflect user or preset settings</li>
802 <li>Null pointer exceptions for some services without
803 presets or adjustable parameters</li>
804 <li>Discover PDB IDs entry in structure menu doesn't
805 discover PDB xRefs</li>
806 <li>Exception encountered while trying to retrieve
807 features with DAS</li>
808 <li>Lowest value in annotation row isn't coloured
809 when colour by annotation (per sequence) is coloured</li>
810 <li>Keyboard mode P jumps to start of gapped region when
811 residue follows a gap</li>
812 <li>Jalview appears to hang importing an alignment with
813 Wrap as default or after enabling Wrap</li>
814 <li>'Right click to add annotations' message
815 shown in wrap mode when no annotations present</li>
816 <li>Disorder predictions fail with NPE if no automatic
817 annotation already exists on alignment</li>
818 <li>oninit javascript function should be called after
819 initialisation completes</li>
820 <li>Remove redundancy after disorder prediction corrupts
821 alignment window display</li>
822 <li>Example annotation file in documentation is invalid</li>
823 <li>Grouped line graph annotation rows are not exported
824 to annotation file</li>
825 <li>Multi-harmony analysis cannot be run when only two
827 <li>Cannot create multiple groups of line graphs with
828 several 'combine' statements in annotation file</li>
829 <li>Pressing return several times causes Number Format
830 exceptions in keyboard mode</li>
831 <li>Multi-harmony (SHMMR) method doesn't submit
832 correct partitions for input data</li>
833 <li>Translation from DNA to Amino Acids fails</li>
834 <li>Jalview fail to load newick tree with quoted label</li>
835 <li>--headless flag isn't understood</li>
836 <li>ClassCastException when generating EPS in headless
838 <li>Adjusting sequence-associated shading threshold only
839 changes one row's threshold</li>
840 <li>Preferences and Feature settings panel panel
841 doesn't open</li>
842 <li>hide consensus histogram also hides conservation and
843 quality histograms</li>
848 <td><div align="center">
849 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
851 <td><em>Application</em>
853 <li>Support for JABAWS 2.0 Services (AACon alignment
854 conservation, protein disorder and Clustal Omega)</li>
855 <li>JABAWS server status indicator in Web Services
857 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
858 in Jalview alignment window</li>
859 <li>Updated Jalview build and deploy framework for OSX
860 mountain lion, windows 7, and 8</li>
861 <li>Nucleotide substitution matrix for PCA that supports
862 RNA and ambiguity codes</li>
864 <li>Improved sequence database retrieval GUI</li>
865 <li>Support fetching and database reference look up
866 against multiple DAS sources (Fetch all from in 'fetch db
868 <li>Jalview project improvements
870 <li>Store and retrieve the 'belowAlignment'
871 flag for annotation</li>
872 <li>calcId attribute to group annotation rows on the
874 <li>Store AACon calculation settings for a view in
879 <li>horizontal scrolling gesture support</li>
880 <li>Visual progress indicator when PCA calculation is
882 <li>Simpler JABA web services menus</li>
883 <li>visual indication that web service results are still
884 being retrieved from server</li>
885 <li>Serialise the dialogs that are shown when Jalview
886 starts up for first time</li>
887 <li>Jalview user agent string for interacting with HTTP
889 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
891 <li>Examples directory and Groovy library included in
892 InstallAnywhere distribution</li>
893 </ul> <em>Applet</em>
895 <li>RNA alignment and secondary structure annotation
896 visualization applet example</li>
897 </ul> <em>General</em>
899 <li>Normalise option for consensus sequence logo</li>
900 <li>Reset button in PCA window to return dimensions to
902 <li>Allow seqspace or Jalview variant of alignment PCA
904 <li>PCA with either nucleic acid and protein substitution
906 <li>Allow windows containing HTML reports to be exported
908 <li>Interactive display and editing of RNA secondary
909 structure contacts</li>
910 <li>RNA Helix Alignment Colouring</li>
911 <li>RNA base pair logo consensus</li>
912 <li>Parse sequence associated secondary structure
913 information in Stockholm files</li>
914 <li>HTML Export database accessions and annotation
915 information presented in tooltip for sequences</li>
916 <li>Import secondary structure from LOCARNA clustalw
917 style RNA alignment files</li>
918 <li>import and visualise T-COFFEE quality scores for an
920 <li>'colour by annotation' per sequence option to
921 shade each sequence according to its associated alignment
923 <li>New Jalview Logo</li>
924 </ul> <em>Documentation and Development</em>
926 <li>documentation for score matrices used in Jalview</li>
927 <li>New Website!</li>
929 <td><em>Application</em>
931 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
932 wsdbfetch REST service</li>
933 <li>Stop windows being moved outside desktop on OSX</li>
934 <li>Filetype associations not installed for webstart
936 <li>Jalview does not always retrieve progress of a JABAWS
937 job execution in full once it is complete</li>
938 <li>revise SHMR RSBS definition to ensure alignment is
939 uploaded via ali_file parameter</li>
940 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
941 <li>View all structures superposed fails with exception</li>
942 <li>Jnet job queues forever if a very short sequence is
943 submitted for prediction</li>
944 <li>Cut and paste menu not opened when mouse clicked on
946 <li>Putting fractional value into integer text box in
947 alignment parameter dialog causes Jalview to hang</li>
948 <li>Structure view highlighting doesn't work on
950 <li>View all structures fails with exception shown in
952 <li>Characters in filename associated with PDBEntry not
953 escaped in a platform independent way</li>
954 <li>Jalview desktop fails to launch with exception when
956 <li>Tree calculation reports 'you must have 2 or more
957 sequences selected' when selection is empty</li>
958 <li>Jalview desktop fails to launch with jar signature
959 failure when java web start temporary file caching is
961 <li>DAS Sequence retrieval with range qualification
962 results in sequence xref which includes range qualification</li>
963 <li>Errors during processing of command line arguments
964 cause progress bar (JAL-898) to be removed</li>
965 <li>Replace comma for semi-colon option not disabled for
966 DAS sources in sequence fetcher</li>
967 <li>Cannot close news reader when JABAWS server warning
969 <li>Option widgets not updated to reflect user settings</li>
970 <li>Edited sequence not submitted to web service</li>
971 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
972 <li>InstallAnywhere installer doesn't unpack and run
973 on OSX Mountain Lion</li>
974 <li>Annotation panel not given a scroll bar when
975 sequences with alignment annotation are pasted into the
977 <li>Sequence associated annotation rows not associated
978 when loaded from Jalview project</li>
979 <li>Browser launch fails with NPE on java 1.7</li>
980 <li>JABAWS alignment marked as finished when job was
981 cancelled or job failed due to invalid input</li>
982 <li>NPE with v2.7 example when clicking on Tree
983 associated with all views</li>
984 <li>Exceptions when copy/paste sequences with grouped
985 annotation rows to new window</li>
986 </ul> <em>Applet</em>
988 <li>Sequence features are momentarily displayed before
989 they are hidden using hidefeaturegroups applet parameter</li>
990 <li>loading features via javascript API automatically
991 enables feature display</li>
992 <li>scrollToColumnIn javascript API method doesn't
994 </ul> <em>General</em>
996 <li>Redundancy removal fails for rna alignment</li>
997 <li>PCA calculation fails when sequence has been selected
998 and then deselected</li>
999 <li>PCA window shows grey box when first opened on OSX</li>
1000 <li>Letters coloured pink in sequence logo when alignment
1001 coloured with clustalx</li>
1002 <li>Choosing fonts without letter symbols defined causes
1003 exceptions and redraw errors</li>
1004 <li>Initial PCA plot view is not same as manually
1005 reconfigured view</li>
1006 <li>Grouped annotation graph label has incorrect line
1008 <li>Grouped annotation graph label display is corrupted
1009 for lots of labels</li>
1014 <div align="center">
1015 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1018 <td><em>Application</em>
1020 <li>Jalview Desktop News Reader</li>
1021 <li>Tweaked default layout of web services menu</li>
1022 <li>View/alignment association menu to enable user to
1023 easily specify which alignment a multi-structure view takes
1024 its colours/correspondences from</li>
1025 <li>Allow properties file location to be specified as URL</li>
1026 <li>Extend Jalview project to preserve associations
1027 between many alignment views and a single Jmol display</li>
1028 <li>Store annotation row height in Jalview project file</li>
1029 <li>Annotation row column label formatting attributes
1030 stored in project file</li>
1031 <li>Annotation row order for auto-calculated annotation
1032 rows preserved in Jalview project file</li>
1033 <li>Visual progress indication when Jalview state is
1034 saved using Desktop window menu</li>
1035 <li>Visual indication that command line arguments are
1036 still being processed</li>
1037 <li>Groovy script execution from URL</li>
1038 <li>Colour by annotation default min and max colours in
1040 <li>Automatically associate PDB files dragged onto an
1041 alignment with sequences that have high similarity and
1043 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1044 <li>'view structures' option to open many
1045 structures in same window</li>
1046 <li>Sort associated views menu option for tree panel</li>
1047 <li>Group all JABA and non-JABA services for a particular
1048 analysis function in its own submenu</li>
1049 </ul> <em>Applet</em>
1051 <li>Userdefined and autogenerated annotation rows for
1053 <li>Adjustment of alignment annotation pane height</li>
1054 <li>Annotation scrollbar for annotation panel</li>
1055 <li>Drag to reorder annotation rows in annotation panel</li>
1056 <li>'automaticScrolling' parameter</li>
1057 <li>Allow sequences with partial ID string matches to be
1058 annotated from GFF/Jalview features files</li>
1059 <li>Sequence logo annotation row in applet</li>
1060 <li>Absolute paths relative to host server in applet
1061 parameters are treated as such</li>
1062 <li>New in the JalviewLite javascript API:
1064 <li>JalviewLite.js javascript library</li>
1065 <li>Javascript callbacks for
1067 <li>Applet initialisation</li>
1068 <li>Sequence/alignment mouse-overs and selections</li>
1071 <li>scrollTo row and column alignment scrolling
1073 <li>Select sequence/alignment regions from javascript</li>
1074 <li>javascript structure viewer harness to pass
1075 messages between Jmol and Jalview when running as
1076 distinct applets</li>
1077 <li>sortBy method</li>
1078 <li>Set of applet and application examples shipped
1079 with documentation</li>
1080 <li>New example to demonstrate JalviewLite and Jmol
1081 javascript message exchange</li>
1083 </ul> <em>General</em>
1085 <li>Enable Jmol displays to be associated with multiple
1086 multiple alignments</li>
1087 <li>Option to automatically sort alignment with new tree</li>
1088 <li>User configurable link to enable redirects to a
1089 www.Jalview.org mirror</li>
1090 <li>Jmol colours option for Jmol displays</li>
1091 <li>Configurable newline string when writing alignment
1092 and other flat files</li>
1093 <li>Allow alignment annotation description lines to
1094 contain html tags</li>
1095 </ul> <em>Documentation and Development</em>
1097 <li>Add groovy test harness for bulk load testing to
1099 <li>Groovy script to load and align a set of sequences
1100 using a web service before displaying the result in the
1101 Jalview desktop</li>
1102 <li>Restructured javascript and applet api documentation</li>
1103 <li>Ant target to publish example html files with applet
1105 <li>Netbeans project for building Jalview from source</li>
1106 <li>ant task to create online javadoc for Jalview source</li>
1108 <td><em>Application</em>
1110 <li>User defined colourscheme throws exception when
1111 current built in colourscheme is saved as new scheme</li>
1112 <li>AlignFrame->Save in application pops up save
1113 dialog for valid filename/format</li>
1114 <li>Cannot view associated structure for UniProt sequence</li>
1115 <li>PDB file association breaks for UniProt sequence
1117 <li>Associate PDB from file dialog does not tell you
1118 which sequence is to be associated with the file</li>
1119 <li>Find All raises null pointer exception when query
1120 only matches sequence IDs</li>
1121 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1122 <li>Jalview project with Jmol views created with Jalview
1123 2.4 cannot be loaded</li>
1124 <li>Filetype associations not installed for webstart
1126 <li>Two or more chains in a single PDB file associated
1127 with sequences in different alignments do not get coloured
1128 by their associated sequence</li>
1129 <li>Visibility status of autocalculated annotation row
1130 not preserved when project is loaded</li>
1131 <li>Annotation row height and visibility attributes not
1132 stored in Jalview project</li>
1133 <li>Tree bootstraps are not preserved when saved as a
1134 Jalview project</li>
1135 <li>Envision2 workflow tooltips are corrupted</li>
1136 <li>Enabling show group conservation also enables colour
1137 by conservation</li>
1138 <li>Duplicate group associated conservation or consensus
1139 created on new view</li>
1140 <li>Annotation scrollbar not displayed after 'show
1141 all hidden annotation rows' option selected</li>
1142 <li>Alignment quality not updated after alignment
1143 annotation row is hidden then shown</li>
1144 <li>Preserve colouring of structures coloured by
1145 sequences in pre Jalview 2.7 projects</li>
1146 <li>Web service job parameter dialog is not laid out
1148 <li>Web services menu not refreshed after 'reset
1149 services' button is pressed in preferences</li>
1150 <li>Annotation off by one in Jalview v2_3 example project</li>
1151 <li>Structures imported from file and saved in project
1152 get name like jalview_pdb1234.txt when reloaded</li>
1153 <li>Jalview does not always retrieve progress of a JABAWS
1154 job execution in full once it is complete</li>
1155 </ul> <em>Applet</em>
1157 <li>Alignment height set incorrectly when lots of
1158 annotation rows are displayed</li>
1159 <li>Relative URLs in feature HTML text not resolved to
1161 <li>View follows highlighting does not work for positions
1163 <li><= shown as = in tooltip</li>
1164 <li>Export features raises exception when no features
1166 <li>Separator string used for serialising lists of IDs
1167 for javascript api is modified when separator string
1168 provided as parameter</li>
1169 <li>Null pointer exception when selecting tree leaves for
1170 alignment with no existing selection</li>
1171 <li>Relative URLs for datasources assumed to be relative
1172 to applet's codebase</li>
1173 <li>Status bar not updated after finished searching and
1174 search wraps around to first result</li>
1175 <li>StructureSelectionManager instance shared between
1176 several Jalview applets causes race conditions and memory
1178 <li>Hover tooltip and mouseover of position on structure
1179 not sent from Jmol in applet</li>
1180 <li>Certain sequences of javascript method calls to
1181 applet API fatally hang browser</li>
1182 </ul> <em>General</em>
1184 <li>View follows structure mouseover scrolls beyond
1185 position with wrapped view and hidden regions</li>
1186 <li>Find sequence position moves to wrong residue
1187 with/without hidden columns</li>
1188 <li>Sequence length given in alignment properties window
1190 <li>InvalidNumberFormat exceptions thrown when trying to
1191 import PDB like structure files</li>
1192 <li>Positional search results are only highlighted
1193 between user-supplied sequence start/end bounds</li>
1194 <li>End attribute of sequence is not validated</li>
1195 <li>Find dialog only finds first sequence containing a
1196 given sequence position</li>
1197 <li>Sequence numbering not preserved in MSF alignment
1199 <li>Jalview PDB file reader does not extract sequence
1200 from nucleotide chains correctly</li>
1201 <li>Structure colours not updated when tree partition
1202 changed in alignment</li>
1203 <li>Sequence associated secondary structure not correctly
1204 parsed in interleaved stockholm</li>
1205 <li>Colour by annotation dialog does not restore current
1207 <li>Hiding (nearly) all sequences doesn't work
1209 <li>Sequences containing lowercase letters are not
1210 properly associated with their pdb files</li>
1211 </ul> <em>Documentation and Development</em>
1213 <li>schemas/JalviewWsParamSet.xsd corrupted by
1214 ApplyCopyright tool</li>
1219 <div align="center">
1220 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1223 <td><em>Application</em>
1225 <li>New warning dialog when the Jalview Desktop cannot
1226 contact web services</li>
1227 <li>JABA service parameters for a preset are shown in
1228 service job window</li>
1229 <li>JABA Service menu entries reworded</li>
1233 <li>Modeller PIR IO broken - cannot correctly import a
1234 pir file emitted by Jalview</li>
1235 <li>Existing feature settings transferred to new
1236 alignment view created from cut'n'paste</li>
1237 <li>Improved test for mixed amino/nucleotide chains when
1238 parsing PDB files</li>
1239 <li>Consensus and conservation annotation rows
1240 occasionally become blank for all new windows</li>
1241 <li>Exception raised when right clicking above sequences
1242 in wrapped view mode</li>
1243 </ul> <em>Application</em>
1245 <li>multiple multiply aligned structure views cause cpu
1246 usage to hit 100% and computer to hang</li>
1247 <li>Web Service parameter layout breaks for long user
1248 parameter names</li>
1249 <li>Jaba service discovery hangs desktop if Jaba server
1256 <div align="center">
1257 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1260 <td><em>Application</em>
1262 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1263 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1266 <li>Web Services preference tab</li>
1267 <li>Analysis parameters dialog box and user defined
1269 <li>Improved speed and layout of Envision2 service menu</li>
1270 <li>Superpose structures using associated sequence
1272 <li>Export coordinates and projection as CSV from PCA
1274 </ul> <em>Applet</em>
1276 <li>enable javascript: execution by the applet via the
1277 link out mechanism</li>
1278 </ul> <em>Other</em>
1280 <li>Updated the Jmol Jalview interface to work with Jmol
1282 <li>The Jalview Desktop and JalviewLite applet now
1283 require Java 1.5</li>
1284 <li>Allow Jalview feature colour specification for GFF
1285 sequence annotation files</li>
1286 <li>New 'colour by label' keword in Jalview feature file
1287 type colour specification</li>
1288 <li>New Jalview Desktop Groovy API method that allows a
1289 script to check if it being run in an interactive session or
1290 in a batch operation from the Jalview command line</li>
1294 <li>clustalx colourscheme colours Ds preferentially when
1295 both D+E are present in over 50% of the column</li>
1296 </ul> <em>Application</em>
1298 <li>typo in AlignmentFrame->View->Hide->all but
1299 selected Regions menu item</li>
1300 <li>sequence fetcher replaces ',' for ';' when the ',' is
1301 part of a valid accession ID</li>
1302 <li>fatal OOM if object retrieved by sequence fetcher
1303 runs out of memory</li>
1304 <li>unhandled Out of Memory Error when viewing pca
1305 analysis results</li>
1306 <li>InstallAnywhere builds fail to launch on OS X java
1307 10.5 update 4 (due to apple Java 1.6 update)</li>
1308 <li>Installanywhere Jalview silently fails to launch</li>
1309 </ul> <em>Applet</em>
1311 <li>Jalview.getFeatureGroups() raises an
1312 ArrayIndexOutOfBoundsException if no feature groups are
1319 <div align="center">
1320 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1326 <li>Alignment prettyprinter doesn't cope with long
1328 <li>clustalx colourscheme colours Ds preferentially when
1329 both D+E are present in over 50% of the column</li>
1330 <li>nucleic acid structures retrieved from PDB do not
1331 import correctly</li>
1332 <li>More columns get selected than were clicked on when a
1333 number of columns are hidden</li>
1334 <li>annotation label popup menu not providing correct
1335 add/hide/show options when rows are hidden or none are
1337 <li>Stockholm format shown in list of readable formats,
1338 and parser copes better with alignments from RFAM.</li>
1339 <li>CSV output of consensus only includes the percentage
1340 of all symbols if sequence logo display is enabled</li>
1342 </ul> <em>Applet</em>
1344 <li>annotation panel disappears when annotation is
1346 </ul> <em>Application</em>
1348 <li>Alignment view not redrawn properly when new
1349 alignment opened where annotation panel is visible but no
1350 annotations are present on alignment</li>
1351 <li>pasted region containing hidden columns is
1352 incorrectly displayed in new alignment window</li>
1353 <li>Jalview slow to complete operations when stdout is
1354 flooded (fix is to close the Jalview console)</li>
1355 <li>typo in AlignmentFrame->View->Hide->all but
1356 selected Rregions menu item.</li>
1357 <li>inconsistent group submenu and Format submenu entry
1358 'Un' or 'Non'conserved</li>
1359 <li>Sequence feature settings are being shared by
1360 multiple distinct alignments</li>
1361 <li>group annotation not recreated when tree partition is
1363 <li>double click on group annotation to select sequences
1364 does not propagate to associated trees</li>
1365 <li>Mac OSX specific issues:
1367 <li>exception raised when mouse clicked on desktop
1368 window background</li>
1369 <li>Desktop menu placed on menu bar and application
1370 name set correctly</li>
1371 <li>sequence feature settings not wide enough for the
1372 save feature colourscheme button</li>
1381 <div align="center">
1382 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1385 <td><em>New Capabilities</em>
1387 <li>URL links generated from description line for
1388 regular-expression based URL links (applet and application)
1391 <li>Non-positional feature URL links are shown in link
1393 <li>Linked viewing of nucleic acid sequences and
1395 <li>Automatic Scrolling option in View menu to display
1396 the currently highlighted region of an alignment.</li>
1397 <li>Order an alignment by sequence length, or using the
1398 average score or total feature count for each sequence.</li>
1399 <li>Shading features by score or associated description</li>
1400 <li>Subdivide alignment and groups based on identity of
1401 selected subsequence (Make Groups from Selection).</li>
1402 <li>New hide/show options including Shift+Control+H to
1403 hide everything but the currently selected region.</li>
1404 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1405 </ul> <em>Application</em>
1407 <li>Fetch DB References capabilities and UI expanded to
1408 support retrieval from DAS sequence sources</li>
1409 <li>Local DAS Sequence sources can be added via the
1410 command line or via the Add local source dialog box.</li>
1411 <li>DAS Dbref and DbxRef feature types are parsed as
1412 database references and protein_name is parsed as
1413 description line (BioSapiens terms).</li>
1414 <li>Enable or disable non-positional feature and database
1415 references in sequence ID tooltip from View menu in
1417 <!-- <li>New hidden columns and rows and representatives capabilities
1418 in annotations file (in progress - not yet fully implemented)</li> -->
1419 <li>Group-associated consensus, sequence logos and
1420 conservation plots</li>
1421 <li>Symbol distributions for each column can be exported
1422 and visualized as sequence logos</li>
1423 <li>Optionally scale multi-character column labels to fit
1424 within each column of annotation row<!-- todo for applet -->
1426 <li>Optional automatic sort of associated alignment view
1427 when a new tree is opened.</li>
1428 <li>Jalview Java Console</li>
1429 <li>Better placement of desktop window when moving
1430 between different screens.</li>
1431 <li>New preference items for sequence ID tooltip and
1432 consensus annotation</li>
1433 <li>Client to submit sequences and IDs to Envision2 Workflows</li>
1434 <li><em>Vamsas Capabilities</em>
1436 <li>Improved VAMSAS synchronization (Jalview archive
1437 used to preserve views, structures, and tree display
1439 <li>Import of vamsas documents from disk or URL via
1441 <li>Sharing of selected regions between views and
1442 with other VAMSAS applications (Experimental feature!)</li>
1443 <li>Updated API to VAMSAS version 0.2</li>
1445 </ul> <em>Applet</em>
1447 <li>Middle button resizes annotation row height</li>
1450 <li>sortByTree (true/false) - automatically sort the
1451 associated alignment view by the tree when a new tree is
1453 <li>showTreeBootstraps (true/false) - show or hide
1454 branch bootstraps (default is to show them if available)</li>
1455 <li>showTreeDistances (true/false) - show or hide
1456 branch lengths (default is to show them if available)</li>
1457 <li>showUnlinkedTreeNodes (true/false) - indicate if
1458 unassociated nodes should be highlighted in the tree
1460 <li>heightScale and widthScale (1.0 or more) -
1461 increase the height or width of a cell in the alignment
1462 grid relative to the current font size.</li>
1465 <li>Non-positional features displayed in sequence ID
1467 </ul> <em>Other</em>
1469 <li>Features format: graduated colour definitions and
1470 specification of feature scores</li>
1471 <li>Alignment Annotations format: new keywords for group
1472 associated annotation (GROUP_REF) and annotation row display
1473 properties (ROW_PROPERTIES)</li>
1474 <li>XML formats extended to support graduated feature
1475 colourschemes, group associated annotation, and profile
1476 visualization settings.</li></td>
1479 <li>Source field in GFF files parsed as feature source
1480 rather than description</li>
1481 <li>Non-positional features are now included in sequence
1482 feature and gff files (controlled via non-positional feature
1483 visibility in tooltip).</li>
1484 <li>URL links generated for all feature links (bugfix)</li>
1485 <li>Added URL embedding instructions to features file
1487 <li>Codons containing ambiguous nucleotides translated as
1488 'X' in peptide product</li>
1489 <li>Match case switch in find dialog box works for both
1490 sequence ID and sequence string and query strings do not
1491 have to be in upper case to match case-insensitively.</li>
1492 <li>AMSA files only contain first column of
1493 multi-character column annotation labels</li>
1494 <li>Jalview Annotation File generation/parsing consistent
1495 with documentation (e.g. Stockholm annotation can be
1496 exported and re-imported)</li>
1497 <li>PDB files without embedded PDB IDs given a friendly
1499 <li>Find incrementally searches ID string matches as well
1500 as subsequence matches, and correctly reports total number
1504 <li>Better handling of exceptions during sequence
1506 <li>Dasobert generated non-positional feature URL
1507 link text excludes the start_end suffix</li>
1508 <li>DAS feature and source retrieval buttons disabled
1509 when fetch or registry operations in progress.</li>
1510 <li>PDB files retrieved from URLs are cached properly</li>
1511 <li>Sequence description lines properly shared via
1513 <li>Sequence fetcher fetches multiple records for all
1515 <li>Ensured that command line das feature retrieval
1516 completes before alignment figures are generated.</li>
1517 <li>Reduced time taken when opening file browser for
1519 <li>isAligned check prior to calculating tree, PCA or
1520 submitting an MSA to JNet now excludes hidden sequences.</li>
1521 <li>User defined group colours properly recovered
1522 from Jalview projects.</li>
1531 <div align="center">
1532 <strong>2.4.0.b2</strong><br> 28/10/2009
1537 <li>Experimental support for google analytics usage
1539 <li>Jalview privacy settings (user preferences and docs).</li>
1544 <li>Race condition in applet preventing startup in
1546 <li>Exception when feature created from selection beyond
1547 length of sequence.</li>
1548 <li>Allow synthetic PDB files to be imported gracefully</li>
1549 <li>Sequence associated annotation rows associate with
1550 all sequences with a given id</li>
1551 <li>Find function matches case-insensitively for sequence
1552 ID string searches</li>
1553 <li>Non-standard characters do not cause pairwise
1554 alignment to fail with exception</li>
1555 </ul> <em>Application Issues</em>
1557 <li>Sequences are now validated against EMBL database</li>
1558 <li>Sequence fetcher fetches multiple records for all
1560 </ul> <em>InstallAnywhere Issues</em>
1562 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1563 issue with installAnywhere mechanism)</li>
1564 <li>Command line launching of JARs from InstallAnywhere
1565 version (java class versioning error fixed)</li>
1572 <div align="center">
1573 <strong>2.4</strong><br> 27/8/2008
1576 <td><em>User Interface</em>
1578 <li>Linked highlighting of codon and amino acid from
1579 translation and protein products</li>
1580 <li>Linked highlighting of structure associated with
1581 residue mapping to codon position</li>
1582 <li>Sequence Fetcher provides example accession numbers
1583 and 'clear' button</li>
1584 <li>MemoryMonitor added as an option under Desktop's
1586 <li>Extract score function to parse whitespace separated
1587 numeric data in description line</li>
1588 <li>Column labels in alignment annotation can be centred.</li>
1589 <li>Tooltip for sequence associated annotation give name
1591 </ul> <em>Web Services and URL fetching</em>
1593 <li>JPred3 web service</li>
1594 <li>Prototype sequence search client (no public services
1596 <li>Fetch either seed alignment or full alignment from
1598 <li>URL Links created for matching database cross
1599 references as well as sequence ID</li>
1600 <li>URL Links can be created using regular-expressions</li>
1601 </ul> <em>Sequence Database Connectivity</em>
1603 <li>Retrieval of cross-referenced sequences from other
1605 <li>Generalised database reference retrieval and
1606 validation to all fetchable databases</li>
1607 <li>Fetch sequences from DAS sources supporting the
1608 sequence command</li>
1609 </ul> <em>Import and Export</em>
1610 <li>export annotation rows as CSV for spreadsheet import</li>
1611 <li>Jalview projects record alignment dataset associations,
1612 EMBL products, and cDNA sequence mappings</li>
1613 <li>Sequence Group colour can be specified in Annotation
1615 <li>Ad-hoc colouring of group in Annotation File using RGB
1616 triplet as name of colourscheme</li>
1617 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1619 <li>treenode binding for VAMSAS tree exchange</li>
1620 <li>local editing and update of sequences in VAMSAS
1621 alignments (experimental)</li>
1622 <li>Create new or select existing session to join</li>
1623 <li>load and save of vamsas documents</li>
1624 </ul> <em>Application command line</em>
1626 <li>-tree parameter to open trees (introduced for passing
1628 <li>-fetchfrom command line argument to specify nicknames
1629 of DAS servers to query for alignment features</li>
1630 <li>-dasserver command line argument to add new servers
1631 that are also automatically queried for features</li>
1632 <li>-groovy command line argument executes a given groovy
1633 script after all input data has been loaded and parsed</li>
1634 </ul> <em>Applet-Application data exchange</em>
1636 <li>Trees passed as applet parameters can be passed to
1637 application (when using "View in full
1638 application")</li>
1639 </ul> <em>Applet Parameters</em>
1641 <li>feature group display control parameter</li>
1642 <li>debug parameter</li>
1643 <li>showbutton parameter</li>
1644 </ul> <em>Applet API methods</em>
1646 <li>newView public method</li>
1647 <li>Window (current view) specific get/set public methods</li>
1648 <li>Feature display control methods</li>
1649 <li>get list of currently selected sequences</li>
1650 </ul> <em>New Jalview distribution features</em>
1652 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1653 <li>RELEASE file gives build properties for the latest
1654 Jalview release.</li>
1655 <li>Java 1.1 Applet build made easier and donotobfuscate
1656 property controls execution of obfuscator</li>
1657 <li>Build target for generating source distribution</li>
1658 <li>Debug flag for javacc</li>
1659 <li>.jalview_properties file is documented (slightly) in
1660 jalview.bin.Cache</li>
1661 <li>Continuous Build Integration for stable and
1662 development version of Application, Applet and source
1667 <li>selected region output includes visible annotations
1668 (for certain formats)</li>
1669 <li>edit label/displaychar contains existing label/char
1671 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1672 <li>shorter peptide product names from EMBL records</li>
1673 <li>Newick string generator makes compact representations</li>
1674 <li>bootstrap values parsed correctly for tree files with
1676 <li>pathological filechooser bug avoided by not allowing
1677 filenames containing a ':'</li>
1678 <li>Fixed exception when parsing GFF files containing
1679 global sequence features</li>
1680 <li>Alignment datasets are finalized only when number of
1681 references from alignment sequences goes to zero</li>
1682 <li>Close of tree branch colour box without colour
1683 selection causes cascading exceptions</li>
1684 <li>occasional negative imgwidth exceptions</li>
1685 <li>better reporting of non-fatal warnings to user when
1686 file parsing fails.</li>
1687 <li>Save works when Jalview project is default format</li>
1688 <li>Save as dialog opened if current alignment format is
1689 not a valid output format</li>
1690 <li>UniProt canonical names introduced for both das and
1692 <li>Histidine should be midblue (not pink!) in Zappo</li>
1693 <li>error messages passed up and output when data read
1695 <li>edit undo recovers previous dataset sequence when
1696 sequence is edited</li>
1697 <li>allow PDB files without pdb ID HEADER lines (like
1698 those generated by MODELLER) to be read in properly</li>
1699 <li>allow reading of JPred concise files as a normal
1701 <li>Stockholm annotation parsing and alignment properties
1702 import fixed for PFAM records</li>
1703 <li>Structure view windows have correct name in Desktop
1705 <li>annotation consisting of sequence associated scores
1706 can be read and written correctly to annotation file</li>
1707 <li>Aligned cDNA translation to aligned peptide works
1709 <li>Fixed display of hidden sequence markers and
1710 non-italic font for representatives in Applet</li>
1711 <li>Applet Menus are always embedded in applet window on
1713 <li>Newly shown features appear at top of stack (in
1715 <li>Annotations added via parameter not drawn properly
1716 due to null pointer exceptions</li>
1717 <li>Secondary structure lines are drawn starting from
1718 first column of alignment</li>
1719 <li>UniProt XML import updated for new schema release in
1721 <li>Sequence feature to sequence ID match for Features
1722 file is case-insensitive</li>
1723 <li>Sequence features read from Features file appended to
1724 all sequences with matching IDs</li>
1725 <li>PDB structure coloured correctly for associated views
1726 containing a sub-sequence</li>
1727 <li>PDB files can be retrieved by applet from Jar files</li>
1728 <li>feature and annotation file applet parameters
1729 referring to different directories are retrieved correctly</li>
1730 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1731 <li>Fixed application hang whilst waiting for
1732 splash-screen version check to complete</li>
1733 <li>Applet properly URLencodes input parameter values
1734 when passing them to the launchApp service</li>
1735 <li>display name and local features preserved in results
1736 retrieved from web service</li>
1737 <li>Visual delay indication for sequence retrieval and
1738 sequence fetcher initialisation</li>
1739 <li>updated Application to use DAS 1.53e version of
1740 dasobert DAS client</li>
1741 <li>Re-instated Full AMSA support and .amsa file
1743 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1751 <div align="center">
1752 <strong>2.3</strong><br> 9/5/07
1757 <li>Jmol 11.0.2 integration</li>
1758 <li>PDB views stored in Jalview XML files</li>
1759 <li>Slide sequences</li>
1760 <li>Edit sequence in place</li>
1761 <li>EMBL CDS features</li>
1762 <li>DAS Feature mapping</li>
1763 <li>Feature ordering</li>
1764 <li>Alignment Properties</li>
1765 <li>Annotation Scores</li>
1766 <li>Sort by scores</li>
1767 <li>Feature/annotation editing in applet</li>
1772 <li>Headless state operation in 2.2.1</li>
1773 <li>Incorrect and unstable DNA pairwise alignment</li>
1774 <li>Cut and paste of sequences with annotation</li>
1775 <li>Feature group display state in XML</li>
1776 <li>Feature ordering in XML</li>
1777 <li>blc file iteration selection using filename # suffix</li>
1778 <li>Stockholm alignment properties</li>
1779 <li>Stockhom alignment secondary structure annotation</li>
1780 <li>2.2.1 applet had no feature transparency</li>
1781 <li>Number pad keys can be used in cursor mode</li>
1782 <li>Structure Viewer mirror image resolved</li>
1789 <div align="center">
1790 <strong>2.2.1</strong><br> 12/2/07
1795 <li>Non standard characters can be read and displayed
1796 <li>Annotations/Features can be imported/exported to the
1798 <li>Applet allows editing of sequence/annotation/group
1799 name & description
1800 <li>Preference setting to display sequence name in
1802 <li>Annotation file format extended to allow
1803 Sequence_groups to be defined
1804 <li>Default opening of alignment overview panel can be
1805 specified in preferences
1806 <li>PDB residue numbering annotation added to associated
1812 <li>Applet crash under certain Linux OS with Java 1.6
1814 <li>Annotation file export / import bugs fixed
1815 <li>PNG / EPS image output bugs fixed
1821 <div align="center">
1822 <strong>2.2</strong><br> 27/11/06
1827 <li>Multiple views on alignment
1828 <li>Sequence feature editing
1829 <li>"Reload" alignment
1830 <li>"Save" to current filename
1831 <li>Background dependent text colour
1832 <li>Right align sequence ids
1833 <li>User-defined lower case residue colours
1836 <li>Menu item accelerator keys
1837 <li>Control-V pastes to current alignment
1838 <li>Cancel button for DAS Feature Fetching
1839 <li>PCA and PDB Viewers zoom via mouse roller
1840 <li>User-defined sub-tree colours and sub-tree selection
1843 <li>'New Window' button on the 'Output to Text box'
1848 <li>New memory efficient Undo/Redo System
1849 <li>Optimised symbol lookups and conservation/consensus
1851 <li>Region Conservation/Consensus recalculated after
1853 <li>Fixed Remove Empty Columns Bug (empty columns at end
1855 <li>Slowed DAS Feature Fetching for increased robustness.
1858 <li>Made angle brackets in ASCII feature descriptions
1860 <li>Re-instated Zoom function for PCA
1861 <li>Sequence descriptions conserved in web service
1863 <li>UniProt ID discoverer uses any word separated by
1865 <li>WsDbFetch query/result association resolved
1866 <li>Tree leaf to sequence mapping improved
1867 <li>Smooth fonts switch moved to FontChooser dialog box.
1875 <div align="center">
1876 <strong>2.1.1</strong><br> 12/9/06
1881 <li>Copy consensus sequence to clipboard</li>
1886 <li>Image output - rightmost residues are rendered if
1887 sequence id panel has been resized</li>
1888 <li>Image output - all offscreen group boundaries are
1890 <li>Annotation files with sequence references - all
1891 elements in file are relative to sequence position</li>
1892 <li>Mac Applet users can use Alt key for group editing</li>
1898 <div align="center">
1899 <strong>2.1</strong><br> 22/8/06
1904 <li>MAFFT Multiple Alignment in default Web Service list</li>
1905 <li>DAS Feature fetching</li>
1906 <li>Hide sequences and columns</li>
1907 <li>Export Annotations and Features</li>
1908 <li>GFF file reading / writing</li>
1909 <li>Associate structures with sequences from local PDB
1911 <li>Add sequences to exisiting alignment</li>
1912 <li>Recently opened files / URL lists</li>
1913 <li>Applet can launch the full application</li>
1914 <li>Applet has transparency for features (Java 1.2
1916 <li>Applet has user defined colours parameter</li>
1917 <li>Applet can load sequences from parameter
1918 "sequence<em>x</em>"
1924 <li>Redundancy Panel reinstalled in the Applet</li>
1925 <li>Monospaced font - EPS / rescaling bug fixed</li>
1926 <li>Annotation files with sequence references bug fixed</li>
1932 <div align="center">
1933 <strong>2.08.1</strong><br> 2/5/06
1938 <li>Change case of selected region from Popup menu</li>
1939 <li>Choose to match case when searching</li>
1940 <li>Middle mouse button and mouse movement can compress /
1941 expand the visible width and height of the alignment</li>
1946 <li>Annotation Panel displays complete JNet results</li>
1952 <div align="center">
1953 <strong>2.08b</strong><br> 18/4/06
1959 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1960 <li>Righthand label on wrapped alignments shows correct
1967 <div align="center">
1968 <strong>2.08</strong><br> 10/4/06
1973 <li>Editing can be locked to the selection area</li>
1974 <li>Keyboard editing</li>
1975 <li>Create sequence features from searches</li>
1976 <li>Precalculated annotations can be loaded onto
1978 <li>Features file allows grouping of features</li>
1979 <li>Annotation Colouring scheme added</li>
1980 <li>Smooth fonts off by default - Faster rendering</li>
1981 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1986 <li>Drag & Drop fixed on Linux</li>
1987 <li>Jalview Archive file faster to load/save, sequence
1988 descriptions saved.</li>
1994 <div align="center">
1995 <strong>2.07</strong><br> 12/12/05
2000 <li>PDB Structure Viewer enhanced</li>
2001 <li>Sequence Feature retrieval and display enhanced</li>
2002 <li>Choose to output sequence start-end after sequence
2003 name for file output</li>
2004 <li>Sequence Fetcher WSDBFetch@EBI</li>
2005 <li>Applet can read feature files, PDB files and can be
2006 used for HTML form input</li>
2011 <li>HTML output writes groups and features</li>
2012 <li>Group editing is Control and mouse click</li>
2013 <li>File IO bugs</li>
2019 <div align="center">
2020 <strong>2.06</strong><br> 28/9/05
2025 <li>View annotations in wrapped mode</li>
2026 <li>More options for PCA viewer</li>
2031 <li>GUI bugs resolved</li>
2032 <li>Runs with -nodisplay from command line</li>
2038 <div align="center">
2039 <strong>2.05b</strong><br> 15/9/05
2044 <li>Choose EPS export as lineart or text</li>
2045 <li>Jar files are executable</li>
2046 <li>Can read in Uracil - maps to unknown residue</li>
2051 <li>Known OutOfMemory errors give warning message</li>
2052 <li>Overview window calculated more efficiently</li>
2053 <li>Several GUI bugs resolved</li>
2059 <div align="center">
2060 <strong>2.05</strong><br> 30/8/05
2065 <li>Edit and annotate in "Wrapped" view</li>
2070 <li>Several GUI bugs resolved</li>
2076 <div align="center">
2077 <strong>2.04</strong><br> 24/8/05
2082 <li>Hold down mouse wheel & scroll to change font
2088 <li>Improved JPred client reliability</li>
2089 <li>Improved loading of Jalview files</li>
2095 <div align="center">
2096 <strong>2.03</strong><br> 18/8/05
2101 <li>Set Proxy server name and port in preferences</li>
2102 <li>Multiple URL links from sequence ids</li>
2103 <li>User Defined Colours can have a scheme name and added
2105 <li>Choose to ignore gaps in consensus calculation</li>
2106 <li>Unix users can set default web browser</li>
2107 <li>Runs without GUI for batch processing</li>
2108 <li>Dynamically generated Web Service Menus</li>
2113 <li>InstallAnywhere download for Sparc Solaris</li>
2119 <div align="center">
2120 <strong>2.02</strong><br> 18/7/05
2126 <li>Copy & Paste order of sequences maintains
2127 alignment order.</li>
2133 <div align="center">
2134 <strong>2.01</strong><br> 12/7/05
2139 <li>Use delete key for deleting selection.</li>
2140 <li>Use Mouse wheel to scroll sequences.</li>
2141 <li>Help file updated to describe how to add alignment
2143 <li>Version and build date written to build properties
2145 <li>InstallAnywhere installation will check for updates
2146 at launch of Jalview.</li>
2151 <li>Delete gaps bug fixed.</li>
2152 <li>FileChooser sorts columns.</li>
2153 <li>Can remove groups one by one.</li>
2154 <li>Filechooser icons installed.</li>
2155 <li>Finder ignores return character when searching.
2156 Return key will initiate a search.<br>
2163 <div align="center">
2164 <strong>2.0</strong><br> 20/6/05
2169 <li>New codebase</li>