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>
65 <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
66 <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
67 <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
68 <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
69 <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
70 <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
71 <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
72 <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
73 <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
74 <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
75 <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
76 <li><!-- JAL-1563-->Free-text search client for UniProt using the UniProt REST API</li>
87 <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
88 <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
89 <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
90 <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
91 <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
92 <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
93 <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
94 <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
95 <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
96 <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
97 <li><!-- JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
102 <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
103 <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
104 <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
105 <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
106 <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
107 <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
108 <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
109 <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
110 <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
111 <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
113 <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
123 <td width="60" nowrap>
125 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
126 <em>16/10/2015</em></strong>
131 <li>Time stamps for signed Jalview application and applet
138 <li>Duplicate group consensus and conservation rows
139 shown when tree is partitioned</li>
140 <li>Erratic behaviour when tree partitions made with
141 multiple cDNA/Protein split views</li>
147 <td width="60" nowrap>
149 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
150 <em>8/10/2015</em></strong>
155 <li>Updated Spanish translations of localized text for
157 </ul> <em>Application</em>
159 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
160 <li>Signed OSX InstallAnywhere installer<br></li>
161 <li>Support for per-sequence based annotations in BioJSON</li>
162 </ul> <em>Applet</em>
164 <li>Split frame example added to applet examples page</li>
170 <li>Mapping of cDNA to protein in split frames
171 incorrect when sequence start > 1</li>
172 <li>Broken images in filter column by annotation dialog
174 <li>Feature colours not parsed from features file</li>
175 <li>Exceptions and incomplete link URLs recovered when
176 loading a features file containing HTML tags in feature
182 <li>Annotations corrupted after BioJS export and
184 <li>Incorrect sequence limits after Fetch DB References
185 with 'trim retrieved sequences'</li>
186 <li>Incorrect warning about deleting all data when
187 deleting selected columns</li>
188 <li>Patch to build system for shipping properly signed
189 JNLP templates for webstart launch</li>
190 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
191 unreleased structures for download or viewing</li>
192 <li>Tab/space/return keystroke operation of EMBL-PDBe
193 fetcher/viewer dialogs works correctly</li>
194 <li>Disabled 'minimise' button on Jalview windows
195 running on OSX to workaround redraw hang bug</li>
196 <li>Split cDNA/Protein view position and geometry not
197 recovered from jalview project</li>
198 <li>Initial enabled/disabled state of annotation menu
199 sorter 'show autocalculated first/last' corresponds to
201 <li>Restoring of Clustal, RNA Helices and T-Coffee
202 color schemes from BioJSON</li>
206 <li>Reorder sequences mirrored in cDNA/Protein split
208 <li>Applet with Jmol examples not loading correctly</li>
214 <td><div align="center">
215 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
219 <li>Linked visualisation and analysis of DNA and Protein
222 <li>Translated cDNA alignments shown as split protein
223 and DNA alignment views</li>
224 <li>Codon consensus annotation for linked protein and
225 cDNA alignment views</li>
226 <li>Link cDNA or Protein product sequences by loading
227 them onto Protein or cDNA alignments</li>
228 <li>Reconstruct linked cDNA alignment from aligned
229 protein sequences</li>
232 <li>Jmol integration updated to Jmol v14.2.14</li>
233 <li>Import and export of Jalview alignment views as <a
234 href="features/bioJsonFormat.html">BioJSON</a></li>
235 <li>New alignment annotation file statements for
236 reference sequences and marking hidden columns</li>
237 <li>Reference sequence based alignment shading to
238 highlight variation</li>
239 <li>Select or hide columns according to alignment
241 <li>Find option for locating sequences by description</li>
242 <li>Conserved physicochemical properties shown in amino
243 acid conservation row</li>
244 <li>Alignments can be sorted by number of RNA helices</li>
245 </ul> <em>Application</em>
247 <li>New cDNA/Protein analysis capabilities
249 <li>Get Cross-References should open a Split Frame
250 view with cDNA/Protein</li>
251 <li>Detect when nucleotide sequences and protein
252 sequences are placed in the same alignment</li>
253 <li>Split cDNA/Protein views are saved in Jalview
258 <li>Use REST API to talk to Chimera</li>
259 <li>Selected regions in Chimera are highlighted in linked
262 <li>VARNA RNA viewer updated to v3.93</li>
263 <li>VARNA views are saved in Jalview Projects</li>
264 <li>Pseudoknots displayed as Jalview RNA annotation can
265 be shown in VARNA</li>
267 <li>Make groups for selection uses marked columns as well
268 as the active selected region</li>
270 <li>Calculate UPGMA and NJ trees using sequence feature
272 <li>New Export options
274 <li>New Export Settings dialog to control hidden
275 region export in flat file generation</li>
277 <li>Export alignment views for display with the <a
278 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
280 <li>Export scrollable SVG in HTML page</li>
281 <li>Optional embedding of BioJSON data when exporting
282 alignment figures to HTML</li>
284 <li>3D structure retrieval and display
286 <li>Free text and structured queries with the PDBe
288 <li>PDBe Search API based discovery and selection of
289 PDB structures for a sequence set</li>
293 <li>JPred4 employed for protein secondary structure
295 <li>Hide Insertions menu option to hide unaligned columns
296 for one or a group of sequences</li>
297 <li>Automatically hide insertions in alignments imported
298 from the JPred4 web server</li>
299 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
300 system on OSX<br />LGPL libraries courtesy of <a
301 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
303 <li>changed 'View nucleotide structure' submenu to 'View
304 VARNA 2D Structure'</li>
305 <li>change "View protein structure" menu option to "3D
308 </ul> <em>Applet</em>
310 <li>New layout for applet example pages</li>
311 <li>New parameters to enable SplitFrame view
312 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
313 <li>New example demonstrating linked viewing of cDNA and
314 Protein alignments</li>
315 </ul> <em>Development and deployment</em>
317 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
318 <li>Include installation type and git revision in build
319 properties and console log output</li>
320 <li>Jalview Github organisation, and new github site for
321 storing BioJsMSA Templates</li>
322 <li>Jalview's unit tests now managed with TestNG</li>
325 <!-- <em>General</em>
327 </ul> --> <!-- issues resolved --> <em>Application</em>
329 <li>Escape should close any open find dialogs</li>
330 <li>Typo in select-by-features status report</li>
331 <li>Consensus RNA secondary secondary structure
332 predictions are not highlighted in amber</li>
333 <li>Missing gap character in v2.7 example file means
334 alignment appears unaligned when pad-gaps is not enabled</li>
335 <li>First switch to RNA Helices colouring doesn't colour
336 associated structure views</li>
337 <li>ID width preference option is greyed out when auto
338 width checkbox not enabled</li>
339 <li>Stopped a warning dialog from being shown when
340 creating user defined colours</li>
341 <li>'View Mapping' in structure viewer shows sequence
342 mappings for just that viewer's sequences</li>
343 <li>Workaround for superposing PDB files containing
344 multiple models in Chimera</li>
345 <li>Report sequence position in status bar when hovering
346 over Jmol structure</li>
347 <li>Cannot output gaps as '.' symbols with Selection ->
348 output to text box</li>
349 <li>Flat file exports of alignments with hidden columns
350 have incorrect sequence start/end</li>
351 <li>'Aligning' a second chain to a Chimera structure from
353 <li>Colour schemes applied to structure viewers don't
354 work for nucleotide</li>
355 <li>Loading/cut'n'pasting an empty or invalid file leads
356 to a grey/invisible alignment window</li>
357 <li>Exported Jpred annotation from a sequence region
358 imports to different position</li>
359 <li>Space at beginning of sequence feature tooltips shown
360 on some platforms</li>
361 <li>Chimera viewer 'View | Show Chain' menu is not
363 <li>'New View' fails with a Null Pointer Exception in
364 console if Chimera has been opened</li>
365 <li>Mouseover to Chimera not working</li>
366 <li>Miscellaneous ENA XML feature qualifiers not
368 <li>NPE in annotation renderer after 'Extract Scores'</li>
369 <li>If two structures in one Chimera window, mouseover of
370 either sequence shows on first structure</li>
371 <li>'Show annotations' options should not make
372 non-positional annotations visible</li>
373 <li>Subsequence secondary structure annotation not shown
374 in right place after 'view flanking regions'</li>
375 <li>File Save As type unset when current file format is
377 <li>Save as '.jar' option removed for saving Jalview
379 <li>Colour by Sequence colouring in Chimera more
381 <li>Cannot 'add reference annotation' for a sequence in
382 several views on same alignment</li>
383 <li>Cannot show linked products for EMBL / ENA records</li>
384 <li>Jalview's tooltip wraps long texts containing no
386 </ul> <em>Applet</em>
388 <li>Jmol to JalviewLite mouseover/link not working</li>
389 <li>JalviewLite can't import sequences with ID
390 descriptions containing angle brackets</li>
391 </ul> <em>General</em>
393 <li>Cannot export and reimport RNA secondary structure
394 via jalview annotation file</li>
395 <li>Random helix colour palette for colour by annotation
396 with RNA secondary structure</li>
397 <li>Mouseover to cDNA from STOP residue in protein
398 translation doesn't work.</li>
399 <li>hints when using the select by annotation dialog box</li>
400 <li>Jmol alignment incorrect if PDB file has alternate CA
402 <li>FontChooser message dialog appears to hang after
403 choosing 1pt font</li>
404 <li>Peptide secondary structure incorrectly imported from
405 annotation file when annotation display text includes 'e' or
407 <li>Cannot set colour of new feature type whilst creating
409 <li>cDNA translation alignment should not be sequence
411 <li>'Show unconserved' doesn't work for lower case
413 <li>Nucleotide ambiguity codes involving R not recognised</li>
414 </ul> <em>Deployment and Documentation</em>
416 <li>Applet example pages appear different to the rest of
418 </ul> <em>Application Known issues</em>
420 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
421 <li>Misleading message appears after trying to delete
423 <li>Jalview icon not shown in dock after InstallAnywhere
424 version launches</li>
425 <li>Fetching EMBL reference for an RNA sequence results
426 fails with a sequence mismatch</li>
427 <li>Corrupted or unreadable alignment display when
428 scrolling alignment to right</li>
429 <li>ArrayIndexOutOfBoundsException thrown when remove
430 empty columns called on alignment with ragged gapped ends</li>
431 <li>auto calculated alignment annotation rows do not get
432 placed above or below non-autocalculated rows</li>
433 <li>Jalview dekstop becomes sluggish at full screen in
434 ultra-high resolution</li>
435 <li>Cannot disable consensus calculation independently of
436 quality and conservation</li>
437 <li>Mouseover highlighting between cDNA and protein can
438 become sluggish with more than one splitframe shown</li>
439 </ul> <em>Applet Known Issues</em>
441 <li>Core PDB parsing code requires Jmol</li>
442 <li>Sequence canvas panel goes white when alignment
443 window is being resized</li>
449 <td><div align="center">
450 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
454 <li>Updated Java code signing certificate donated by
456 <li>Features and annotation preserved when performing
457 pairwise alignment</li>
458 <li>RNA pseudoknot annotation can be
459 imported/exported/displayed</li>
460 <li>'colour by annotation' can colour by RNA and
461 protein secondary structure</li>
462 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
463 post-hoc with 2.9 release</em>)
466 </ul> <em>Application</em>
468 <li>Extract and display secondary structure for sequences
469 with 3D structures</li>
470 <li>Support for parsing RNAML</li>
471 <li>Annotations menu for layout
473 <li>sort sequence annotation rows by alignment</li>
474 <li>place sequence annotation above/below alignment
477 <li>Output in Stockholm format</li>
478 <li>Internationalisation: improved Spanish (es)
480 <li>Structure viewer preferences tab</li>
481 <li>Disorder and Secondary Structure annotation tracks
482 shared between alignments</li>
483 <li>UCSF Chimera launch and linked highlighting from
485 <li>Show/hide all sequence associated annotation rows for
486 all or current selection</li>
487 <li>disorder and secondary structure predictions
488 available as dataset annotation</li>
489 <li>Per-sequence rna helices colouring</li>
492 <li>Sequence database accessions imported when fetching
493 alignments from Rfam</li>
494 <li>update VARNA version to 3.91</li>
496 <li>New groovy scripts for exporting aligned positions,
497 conservation values, and calculating sum of pairs scores.</li>
498 <li>Command line argument to set default JABAWS server</li>
499 <li>include installation type in build properties and
500 console log output</li>
501 <li>Updated Jalview project format to preserve dataset
505 <!-- issues resolved --> <em>Application</em>
507 <li>Distinguish alignment and sequence associated RNA
508 structure in structure->view->VARNA</li>
509 <li>Raise dialog box if user deletes all sequences in an
511 <li>Pressing F1 results in documentation opening twice</li>
512 <li>Sequence feature tooltip is wrapped</li>
513 <li>Double click on sequence associated annotation
514 selects only first column</li>
515 <li>Redundancy removal doesn't result in unlinked
516 leaves shown in tree</li>
517 <li>Undos after several redundancy removals don't undo
519 <li>Hide sequence doesn't hide associated annotation</li>
520 <li>User defined colours dialog box too big to fit on
521 screen and buttons not visible</li>
522 <li>author list isn't updated if already written to
523 Jalview properties</li>
524 <li>Popup menu won't open after retrieving sequence
526 <li>File open window for associate PDB doesn't open</li>
527 <li>Left-then-right click on a sequence id opens a
528 browser search window</li>
529 <li>Cannot open sequence feature shading/sort popup menu
530 in feature settings dialog</li>
531 <li>better tooltip placement for some areas of Jalview
533 <li>Allow addition of JABAWS Server which doesn't
535 <li>Web services parameters dialog box is too large to
537 <li>Muscle nucleotide alignment preset obscured by
539 <li>JABAWS preset submenus don't contain newly
540 defined user preset</li>
541 <li>MSA web services warns user if they were launched
542 with invalid input</li>
543 <li>Jalview cannot contact DAS Registy when running on
546 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
547 'Superpose with' submenu not shown when new view
551 </ul> <!-- <em>Applet</em>
553 </ul> <em>General</em>
555 </ul>--> <em>Deployment and Documentation</em>
557 <li>2G and 1G options in launchApp have no effect on
558 memory allocation</li>
559 <li>launchApp service doesn't automatically open
560 www.jalview.org/examples/exampleFile.jar if no file is given</li>
562 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
563 InstallAnywhere reports cannot find valid JVM when Java
566 </ul> <em>Application Known issues</em>
569 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
570 corrupted or unreadable alignment display when scrolling
574 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
575 retrieval fails but progress bar continues for DAS retrieval
576 with large number of ID
579 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
580 flatfile output of visible region has incorrect sequence
584 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
585 rna structure consensus doesn't update when secondary
586 structure tracks are rearranged
589 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
590 invalid rna structure positional highlighting does not
591 highlight position of invalid base pairs
594 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
595 out of memory errors are not raised when saving Jalview
596 project from alignment window file menu
599 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
600 Switching to RNA Helices colouring doesn't propagate to
604 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
605 colour by RNA Helices not enabled when user created
606 annotation added to alignment
609 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
610 Jalview icon not shown on dock in Mountain Lion/Webstart
612 </ul> <em>Applet Known Issues</em>
615 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
616 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
619 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
620 Jalview and Jmol example not compatible with IE9
623 <li>Sort by annotation score doesn't reverse order
629 <td><div align="center">
630 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
633 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
636 <li>Internationalisation of user interface (usually
637 called i18n support) and translation for Spanish locale</li>
638 <li>Define/Undefine group on current selection with
639 Ctrl-G/Shift Ctrl-G</li>
640 <li>Improved group creation/removal options in
641 alignment/sequence Popup menu</li>
642 <li>Sensible precision for symbol distribution
643 percentages shown in logo tooltip.</li>
644 <li>Annotation panel height set according to amount of
645 annotation when alignment first opened</li>
646 </ul> <em>Application</em>
648 <li>Interactive consensus RNA secondary structure
649 prediction VIENNA RNAAliFold JABA 2.1 service</li>
650 <li>Select columns containing particular features from
651 Feature Settings dialog</li>
652 <li>View all 'representative' PDB structures for selected
654 <li>Update Jalview project format:
656 <li>New file extension for Jalview projects '.jvp'</li>
657 <li>Preserve sequence and annotation dataset (to
658 store secondary structure annotation,etc)</li>
659 <li>Per group and alignment annotation and RNA helix
663 <li>New similarity measures for PCA and Tree calculation
665 <li>Experimental support for retrieval and viewing of
666 flanking regions for an alignment</li>
670 <!-- issues resolved --> <em>Application</em>
672 <li>logo keeps spinning and status remains at queued or
673 running after job is cancelled</li>
674 <li>cannot export features from alignments imported from
675 Jalview/VAMSAS projects</li>
676 <li>Buggy slider for web service parameters that take
678 <li>Newly created RNA secondary structure line doesn't
679 have 'display all symbols' flag set</li>
680 <li>T-COFFEE alignment score shading scheme and other
681 annotation shading not saved in Jalview project</li>
682 <li>Local file cannot be loaded in freshly downloaded
684 <li>Jalview icon not shown on dock in Mountain
686 <li>Load file from desktop file browser fails</li>
687 <li>Occasional NPE thrown when calculating large trees</li>
688 <li>Cannot reorder or slide sequences after dragging an
689 alignment onto desktop</li>
690 <li>Colour by annotation dialog throws NPE after using
691 'extract scores' function</li>
692 <li>Loading/cut'n'pasting an empty file leads to a grey
693 alignment window</li>
694 <li>Disorder thresholds rendered incorrectly after
695 performing IUPred disorder prediction</li>
696 <li>Multiple group annotated consensus rows shown when
697 changing 'normalise logo' display setting</li>
698 <li>Find shows blank dialog after 'finished searching' if
699 nothing matches query</li>
700 <li>Null Pointer Exceptions raised when sorting by
701 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
703 <li>Errors in Jmol console when structures in alignment
704 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
706 <li>Not all working JABAWS services are shown in
708 <li>JAVAWS version of Jalview fails to launch with
709 'invalid literal/length code'</li>
710 <li>Annotation/RNA Helix colourschemes cannot be applied
711 to alignment with groups (actually fixed in 2.8.0b1)</li>
712 <li>RNA Helices and T-Coffee Scores available as default
715 </ul> <em>Applet</em>
717 <li>Remove group option is shown even when selection is
719 <li>Apply to all groups ticked but colourscheme changes
720 don't affect groups</li>
721 <li>Documented RNA Helices and T-Coffee Scores as valid
722 colourscheme name</li>
723 <li>Annotation labels drawn on sequence IDs when
724 Annotation panel is not displayed</li>
725 <li>Increased font size for dropdown menus on OSX and
726 embedded windows</li>
729 <li>Consensus sequence for alignments/groups with a
730 single sequence were not calculated</li>
731 <li>annotation files that contain only groups imported as
732 annotation and junk sequences</li>
733 <li>Fasta files with sequences containing '*' incorrectly
734 recognised as PFAM or BLC</li>
735 <li>conservation/PID slider apply all groups option
736 doesn't affect background (2.8.0b1)
738 <li>redundancy highlighting is erratic at 0% and 100%</li>
739 <li>Remove gapped columns fails for sequences with ragged
741 <li>AMSA annotation row with leading spaces is not
742 registered correctly on import</li>
743 <li>Jalview crashes when selecting PCA analysis for
744 certain alignments</li>
745 <li>Opening the colour by annotation dialog for an
746 existing annotation based 'use original colours'
747 colourscheme loses original colours setting</li>
752 <td><div align="center">
753 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
754 <em>30/1/2014</em></strong>
758 <li>Trusted certificates for JalviewLite applet and
759 Jalview Desktop application<br />Certificate was donated by
760 <a href="https://www.certum.eu">Certum</a> to the Jalview
761 open source project).
763 <li>Jalview SRS links replaced by UniProt and EBI-search
765 <li>Output in Stockholm format</li>
766 <li>Allow import of data from gzipped files</li>
767 <li>Export/import group and sequence associated line
768 graph thresholds</li>
769 <li>Nucleotide substitution matrix that supports RNA and
771 <li>Allow disorder predictions to be made on the current
772 selection (or visible selection) in the same way that JPred
774 <li>Groovy scripting for headless Jalview operation</li>
775 </ul> <em>Other improvements</em>
777 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
778 <li>COMBINE statement uses current SEQUENCE_REF and
779 GROUP_REF scope to group annotation rows</li>
780 <li>Support '' style escaping of quotes in Newick
782 <li>Group options for JABAWS service by command line name</li>
783 <li>Empty tooltip shown for JABA service options with a
784 link but no description</li>
785 <li>Select primary source when selecting authority in
786 database fetcher GUI</li>
787 <li>Add .mfa to FASTA file extensions recognised by
789 <li>Annotation label tooltip text wrap</li>
794 <li>Slow scrolling when lots of annotation rows are
796 <li>Lots of NPE (and slowness) after creating RNA
797 secondary structure annotation line</li>
798 <li>Sequence database accessions not imported when
799 fetching alignments from Rfam</li>
800 <li>Incorrect SHMR submission for sequences with
802 <li>View all structures does not always superpose
804 <li>Option widgets in service parameters not updated to
805 reflect user or preset settings</li>
806 <li>Null pointer exceptions for some services without
807 presets or adjustable parameters</li>
808 <li>Discover PDB IDs entry in structure menu doesn't
809 discover PDB xRefs</li>
810 <li>Exception encountered while trying to retrieve
811 features with DAS</li>
812 <li>Lowest value in annotation row isn't coloured
813 when colour by annotation (per sequence) is coloured</li>
814 <li>Keyboard mode P jumps to start of gapped region when
815 residue follows a gap</li>
816 <li>Jalview appears to hang importing an alignment with
817 Wrap as default or after enabling Wrap</li>
818 <li>'Right click to add annotations' message
819 shown in wrap mode when no annotations present</li>
820 <li>Disorder predictions fail with NPE if no automatic
821 annotation already exists on alignment</li>
822 <li>oninit javascript function should be called after
823 initialisation completes</li>
824 <li>Remove redundancy after disorder prediction corrupts
825 alignment window display</li>
826 <li>Example annotation file in documentation is invalid</li>
827 <li>Grouped line graph annotation rows are not exported
828 to annotation file</li>
829 <li>Multi-harmony analysis cannot be run when only two
831 <li>Cannot create multiple groups of line graphs with
832 several 'combine' statements in annotation file</li>
833 <li>Pressing return several times causes Number Format
834 exceptions in keyboard mode</li>
835 <li>Multi-harmony (SHMMR) method doesn't submit
836 correct partitions for input data</li>
837 <li>Translation from DNA to Amino Acids fails</li>
838 <li>Jalview fail to load newick tree with quoted label</li>
839 <li>--headless flag isn't understood</li>
840 <li>ClassCastException when generating EPS in headless
842 <li>Adjusting sequence-associated shading threshold only
843 changes one row's threshold</li>
844 <li>Preferences and Feature settings panel panel
845 doesn't open</li>
846 <li>hide consensus histogram also hides conservation and
847 quality histograms</li>
852 <td><div align="center">
853 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
855 <td><em>Application</em>
857 <li>Support for JABAWS 2.0 Services (AACon alignment
858 conservation, protein disorder and Clustal Omega)</li>
859 <li>JABAWS server status indicator in Web Services
861 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
862 in Jalview alignment window</li>
863 <li>Updated Jalview build and deploy framework for OSX
864 mountain lion, windows 7, and 8</li>
865 <li>Nucleotide substitution matrix for PCA that supports
866 RNA and ambiguity codes</li>
868 <li>Improved sequence database retrieval GUI</li>
869 <li>Support fetching and database reference look up
870 against multiple DAS sources (Fetch all from in 'fetch db
872 <li>Jalview project improvements
874 <li>Store and retrieve the 'belowAlignment'
875 flag for annotation</li>
876 <li>calcId attribute to group annotation rows on the
878 <li>Store AACon calculation settings for a view in
883 <li>horizontal scrolling gesture support</li>
884 <li>Visual progress indicator when PCA calculation is
886 <li>Simpler JABA web services menus</li>
887 <li>visual indication that web service results are still
888 being retrieved from server</li>
889 <li>Serialise the dialogs that are shown when Jalview
890 starts up for first time</li>
891 <li>Jalview user agent string for interacting with HTTP
893 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
895 <li>Examples directory and Groovy library included in
896 InstallAnywhere distribution</li>
897 </ul> <em>Applet</em>
899 <li>RNA alignment and secondary structure annotation
900 visualization applet example</li>
901 </ul> <em>General</em>
903 <li>Normalise option for consensus sequence logo</li>
904 <li>Reset button in PCA window to return dimensions to
906 <li>Allow seqspace or Jalview variant of alignment PCA
908 <li>PCA with either nucleic acid and protein substitution
910 <li>Allow windows containing HTML reports to be exported
912 <li>Interactive display and editing of RNA secondary
913 structure contacts</li>
914 <li>RNA Helix Alignment Colouring</li>
915 <li>RNA base pair logo consensus</li>
916 <li>Parse sequence associated secondary structure
917 information in Stockholm files</li>
918 <li>HTML Export database accessions and annotation
919 information presented in tooltip for sequences</li>
920 <li>Import secondary structure from LOCARNA clustalw
921 style RNA alignment files</li>
922 <li>import and visualise T-COFFEE quality scores for an
924 <li>'colour by annotation' per sequence option to
925 shade each sequence according to its associated alignment
927 <li>New Jalview Logo</li>
928 </ul> <em>Documentation and Development</em>
930 <li>documentation for score matrices used in Jalview</li>
931 <li>New Website!</li>
933 <td><em>Application</em>
935 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
936 wsdbfetch REST service</li>
937 <li>Stop windows being moved outside desktop on OSX</li>
938 <li>Filetype associations not installed for webstart
940 <li>Jalview does not always retrieve progress of a JABAWS
941 job execution in full once it is complete</li>
942 <li>revise SHMR RSBS definition to ensure alignment is
943 uploaded via ali_file parameter</li>
944 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
945 <li>View all structures superposed fails with exception</li>
946 <li>Jnet job queues forever if a very short sequence is
947 submitted for prediction</li>
948 <li>Cut and paste menu not opened when mouse clicked on
950 <li>Putting fractional value into integer text box in
951 alignment parameter dialog causes Jalview to hang</li>
952 <li>Structure view highlighting doesn't work on
954 <li>View all structures fails with exception shown in
956 <li>Characters in filename associated with PDBEntry not
957 escaped in a platform independent way</li>
958 <li>Jalview desktop fails to launch with exception when
960 <li>Tree calculation reports 'you must have 2 or more
961 sequences selected' when selection is empty</li>
962 <li>Jalview desktop fails to launch with jar signature
963 failure when java web start temporary file caching is
965 <li>DAS Sequence retrieval with range qualification
966 results in sequence xref which includes range qualification</li>
967 <li>Errors during processing of command line arguments
968 cause progress bar (JAL-898) to be removed</li>
969 <li>Replace comma for semi-colon option not disabled for
970 DAS sources in sequence fetcher</li>
971 <li>Cannot close news reader when JABAWS server warning
973 <li>Option widgets not updated to reflect user settings</li>
974 <li>Edited sequence not submitted to web service</li>
975 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
976 <li>InstallAnywhere installer doesn't unpack and run
977 on OSX Mountain Lion</li>
978 <li>Annotation panel not given a scroll bar when
979 sequences with alignment annotation are pasted into the
981 <li>Sequence associated annotation rows not associated
982 when loaded from Jalview project</li>
983 <li>Browser launch fails with NPE on java 1.7</li>
984 <li>JABAWS alignment marked as finished when job was
985 cancelled or job failed due to invalid input</li>
986 <li>NPE with v2.7 example when clicking on Tree
987 associated with all views</li>
988 <li>Exceptions when copy/paste sequences with grouped
989 annotation rows to new window</li>
990 </ul> <em>Applet</em>
992 <li>Sequence features are momentarily displayed before
993 they are hidden using hidefeaturegroups applet parameter</li>
994 <li>loading features via javascript API automatically
995 enables feature display</li>
996 <li>scrollToColumnIn javascript API method doesn't
998 </ul> <em>General</em>
1000 <li>Redundancy removal fails for rna alignment</li>
1001 <li>PCA calculation fails when sequence has been selected
1002 and then deselected</li>
1003 <li>PCA window shows grey box when first opened on OSX</li>
1004 <li>Letters coloured pink in sequence logo when alignment
1005 coloured with clustalx</li>
1006 <li>Choosing fonts without letter symbols defined causes
1007 exceptions and redraw errors</li>
1008 <li>Initial PCA plot view is not same as manually
1009 reconfigured view</li>
1010 <li>Grouped annotation graph label has incorrect line
1012 <li>Grouped annotation graph label display is corrupted
1013 for lots of labels</li>
1018 <div align="center">
1019 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1022 <td><em>Application</em>
1024 <li>Jalview Desktop News Reader</li>
1025 <li>Tweaked default layout of web services menu</li>
1026 <li>View/alignment association menu to enable user to
1027 easily specify which alignment a multi-structure view takes
1028 its colours/correspondences from</li>
1029 <li>Allow properties file location to be specified as URL</li>
1030 <li>Extend Jalview project to preserve associations
1031 between many alignment views and a single Jmol display</li>
1032 <li>Store annotation row height in Jalview project file</li>
1033 <li>Annotation row column label formatting attributes
1034 stored in project file</li>
1035 <li>Annotation row order for auto-calculated annotation
1036 rows preserved in Jalview project file</li>
1037 <li>Visual progress indication when Jalview state is
1038 saved using Desktop window menu</li>
1039 <li>Visual indication that command line arguments are
1040 still being processed</li>
1041 <li>Groovy script execution from URL</li>
1042 <li>Colour by annotation default min and max colours in
1044 <li>Automatically associate PDB files dragged onto an
1045 alignment with sequences that have high similarity and
1047 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1048 <li>'view structures' option to open many
1049 structures in same window</li>
1050 <li>Sort associated views menu option for tree panel</li>
1051 <li>Group all JABA and non-JABA services for a particular
1052 analysis function in its own submenu</li>
1053 </ul> <em>Applet</em>
1055 <li>Userdefined and autogenerated annotation rows for
1057 <li>Adjustment of alignment annotation pane height</li>
1058 <li>Annotation scrollbar for annotation panel</li>
1059 <li>Drag to reorder annotation rows in annotation panel</li>
1060 <li>'automaticScrolling' parameter</li>
1061 <li>Allow sequences with partial ID string matches to be
1062 annotated from GFF/Jalview features files</li>
1063 <li>Sequence logo annotation row in applet</li>
1064 <li>Absolute paths relative to host server in applet
1065 parameters are treated as such</li>
1066 <li>New in the JalviewLite javascript API:
1068 <li>JalviewLite.js javascript library</li>
1069 <li>Javascript callbacks for
1071 <li>Applet initialisation</li>
1072 <li>Sequence/alignment mouse-overs and selections</li>
1075 <li>scrollTo row and column alignment scrolling
1077 <li>Select sequence/alignment regions from javascript</li>
1078 <li>javascript structure viewer harness to pass
1079 messages between Jmol and Jalview when running as
1080 distinct applets</li>
1081 <li>sortBy method</li>
1082 <li>Set of applet and application examples shipped
1083 with documentation</li>
1084 <li>New example to demonstrate JalviewLite and Jmol
1085 javascript message exchange</li>
1087 </ul> <em>General</em>
1089 <li>Enable Jmol displays to be associated with multiple
1090 multiple alignments</li>
1091 <li>Option to automatically sort alignment with new tree</li>
1092 <li>User configurable link to enable redirects to a
1093 www.Jalview.org mirror</li>
1094 <li>Jmol colours option for Jmol displays</li>
1095 <li>Configurable newline string when writing alignment
1096 and other flat files</li>
1097 <li>Allow alignment annotation description lines to
1098 contain html tags</li>
1099 </ul> <em>Documentation and Development</em>
1101 <li>Add groovy test harness for bulk load testing to
1103 <li>Groovy script to load and align a set of sequences
1104 using a web service before displaying the result in the
1105 Jalview desktop</li>
1106 <li>Restructured javascript and applet api documentation</li>
1107 <li>Ant target to publish example html files with applet
1109 <li>Netbeans project for building Jalview from source</li>
1110 <li>ant task to create online javadoc for Jalview source</li>
1112 <td><em>Application</em>
1114 <li>User defined colourscheme throws exception when
1115 current built in colourscheme is saved as new scheme</li>
1116 <li>AlignFrame->Save in application pops up save
1117 dialog for valid filename/format</li>
1118 <li>Cannot view associated structure for UniProt sequence</li>
1119 <li>PDB file association breaks for UniProt sequence
1121 <li>Associate PDB from file dialog does not tell you
1122 which sequence is to be associated with the file</li>
1123 <li>Find All raises null pointer exception when query
1124 only matches sequence IDs</li>
1125 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1126 <li>Jalview project with Jmol views created with Jalview
1127 2.4 cannot be loaded</li>
1128 <li>Filetype associations not installed for webstart
1130 <li>Two or more chains in a single PDB file associated
1131 with sequences in different alignments do not get coloured
1132 by their associated sequence</li>
1133 <li>Visibility status of autocalculated annotation row
1134 not preserved when project is loaded</li>
1135 <li>Annotation row height and visibility attributes not
1136 stored in Jalview project</li>
1137 <li>Tree bootstraps are not preserved when saved as a
1138 Jalview project</li>
1139 <li>Envision2 workflow tooltips are corrupted</li>
1140 <li>Enabling show group conservation also enables colour
1141 by conservation</li>
1142 <li>Duplicate group associated conservation or consensus
1143 created on new view</li>
1144 <li>Annotation scrollbar not displayed after 'show
1145 all hidden annotation rows' option selected</li>
1146 <li>Alignment quality not updated after alignment
1147 annotation row is hidden then shown</li>
1148 <li>Preserve colouring of structures coloured by
1149 sequences in pre Jalview 2.7 projects</li>
1150 <li>Web service job parameter dialog is not laid out
1152 <li>Web services menu not refreshed after 'reset
1153 services' button is pressed in preferences</li>
1154 <li>Annotation off by one in Jalview v2_3 example project</li>
1155 <li>Structures imported from file and saved in project
1156 get name like jalview_pdb1234.txt when reloaded</li>
1157 <li>Jalview does not always retrieve progress of a JABAWS
1158 job execution in full once it is complete</li>
1159 </ul> <em>Applet</em>
1161 <li>Alignment height set incorrectly when lots of
1162 annotation rows are displayed</li>
1163 <li>Relative URLs in feature HTML text not resolved to
1165 <li>View follows highlighting does not work for positions
1167 <li><= shown as = in tooltip</li>
1168 <li>Export features raises exception when no features
1170 <li>Separator string used for serialising lists of IDs
1171 for javascript api is modified when separator string
1172 provided as parameter</li>
1173 <li>Null pointer exception when selecting tree leaves for
1174 alignment with no existing selection</li>
1175 <li>Relative URLs for datasources assumed to be relative
1176 to applet's codebase</li>
1177 <li>Status bar not updated after finished searching and
1178 search wraps around to first result</li>
1179 <li>StructureSelectionManager instance shared between
1180 several Jalview applets causes race conditions and memory
1182 <li>Hover tooltip and mouseover of position on structure
1183 not sent from Jmol in applet</li>
1184 <li>Certain sequences of javascript method calls to
1185 applet API fatally hang browser</li>
1186 </ul> <em>General</em>
1188 <li>View follows structure mouseover scrolls beyond
1189 position with wrapped view and hidden regions</li>
1190 <li>Find sequence position moves to wrong residue
1191 with/without hidden columns</li>
1192 <li>Sequence length given in alignment properties window
1194 <li>InvalidNumberFormat exceptions thrown when trying to
1195 import PDB like structure files</li>
1196 <li>Positional search results are only highlighted
1197 between user-supplied sequence start/end bounds</li>
1198 <li>End attribute of sequence is not validated</li>
1199 <li>Find dialog only finds first sequence containing a
1200 given sequence position</li>
1201 <li>Sequence numbering not preserved in MSF alignment
1203 <li>Jalview PDB file reader does not extract sequence
1204 from nucleotide chains correctly</li>
1205 <li>Structure colours not updated when tree partition
1206 changed in alignment</li>
1207 <li>Sequence associated secondary structure not correctly
1208 parsed in interleaved stockholm</li>
1209 <li>Colour by annotation dialog does not restore current
1211 <li>Hiding (nearly) all sequences doesn't work
1213 <li>Sequences containing lowercase letters are not
1214 properly associated with their pdb files</li>
1215 </ul> <em>Documentation and Development</em>
1217 <li>schemas/JalviewWsParamSet.xsd corrupted by
1218 ApplyCopyright tool</li>
1223 <div align="center">
1224 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1227 <td><em>Application</em>
1229 <li>New warning dialog when the Jalview Desktop cannot
1230 contact web services</li>
1231 <li>JABA service parameters for a preset are shown in
1232 service job window</li>
1233 <li>JABA Service menu entries reworded</li>
1237 <li>Modeller PIR IO broken - cannot correctly import a
1238 pir file emitted by Jalview</li>
1239 <li>Existing feature settings transferred to new
1240 alignment view created from cut'n'paste</li>
1241 <li>Improved test for mixed amino/nucleotide chains when
1242 parsing PDB files</li>
1243 <li>Consensus and conservation annotation rows
1244 occasionally become blank for all new windows</li>
1245 <li>Exception raised when right clicking above sequences
1246 in wrapped view mode</li>
1247 </ul> <em>Application</em>
1249 <li>multiple multiply aligned structure views cause cpu
1250 usage to hit 100% and computer to hang</li>
1251 <li>Web Service parameter layout breaks for long user
1252 parameter names</li>
1253 <li>Jaba service discovery hangs desktop if Jaba server
1260 <div align="center">
1261 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1264 <td><em>Application</em>
1266 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1267 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1270 <li>Web Services preference tab</li>
1271 <li>Analysis parameters dialog box and user defined
1273 <li>Improved speed and layout of Envision2 service menu</li>
1274 <li>Superpose structures using associated sequence
1276 <li>Export coordinates and projection as CSV from PCA
1278 </ul> <em>Applet</em>
1280 <li>enable javascript: execution by the applet via the
1281 link out mechanism</li>
1282 </ul> <em>Other</em>
1284 <li>Updated the Jmol Jalview interface to work with Jmol
1286 <li>The Jalview Desktop and JalviewLite applet now
1287 require Java 1.5</li>
1288 <li>Allow Jalview feature colour specification for GFF
1289 sequence annotation files</li>
1290 <li>New 'colour by label' keword in Jalview feature file
1291 type colour specification</li>
1292 <li>New Jalview Desktop Groovy API method that allows a
1293 script to check if it being run in an interactive session or
1294 in a batch operation from the Jalview command line</li>
1298 <li>clustalx colourscheme colours Ds preferentially when
1299 both D+E are present in over 50% of the column</li>
1300 </ul> <em>Application</em>
1302 <li>typo in AlignmentFrame->View->Hide->all but
1303 selected Regions menu item</li>
1304 <li>sequence fetcher replaces ',' for ';' when the ',' is
1305 part of a valid accession ID</li>
1306 <li>fatal OOM if object retrieved by sequence fetcher
1307 runs out of memory</li>
1308 <li>unhandled Out of Memory Error when viewing pca
1309 analysis results</li>
1310 <li>InstallAnywhere builds fail to launch on OS X java
1311 10.5 update 4 (due to apple Java 1.6 update)</li>
1312 <li>Installanywhere Jalview silently fails to launch</li>
1313 </ul> <em>Applet</em>
1315 <li>Jalview.getFeatureGroups() raises an
1316 ArrayIndexOutOfBoundsException if no feature groups are
1323 <div align="center">
1324 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1330 <li>Alignment prettyprinter doesn't cope with long
1332 <li>clustalx colourscheme colours Ds preferentially when
1333 both D+E are present in over 50% of the column</li>
1334 <li>nucleic acid structures retrieved from PDB do not
1335 import correctly</li>
1336 <li>More columns get selected than were clicked on when a
1337 number of columns are hidden</li>
1338 <li>annotation label popup menu not providing correct
1339 add/hide/show options when rows are hidden or none are
1341 <li>Stockholm format shown in list of readable formats,
1342 and parser copes better with alignments from RFAM.</li>
1343 <li>CSV output of consensus only includes the percentage
1344 of all symbols if sequence logo display is enabled</li>
1346 </ul> <em>Applet</em>
1348 <li>annotation panel disappears when annotation is
1350 </ul> <em>Application</em>
1352 <li>Alignment view not redrawn properly when new
1353 alignment opened where annotation panel is visible but no
1354 annotations are present on alignment</li>
1355 <li>pasted region containing hidden columns is
1356 incorrectly displayed in new alignment window</li>
1357 <li>Jalview slow to complete operations when stdout is
1358 flooded (fix is to close the Jalview console)</li>
1359 <li>typo in AlignmentFrame->View->Hide->all but
1360 selected Rregions menu item.</li>
1361 <li>inconsistent group submenu and Format submenu entry
1362 'Un' or 'Non'conserved</li>
1363 <li>Sequence feature settings are being shared by
1364 multiple distinct alignments</li>
1365 <li>group annotation not recreated when tree partition is
1367 <li>double click on group annotation to select sequences
1368 does not propagate to associated trees</li>
1369 <li>Mac OSX specific issues:
1371 <li>exception raised when mouse clicked on desktop
1372 window background</li>
1373 <li>Desktop menu placed on menu bar and application
1374 name set correctly</li>
1375 <li>sequence feature settings not wide enough for the
1376 save feature colourscheme button</li>
1385 <div align="center">
1386 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1389 <td><em>New Capabilities</em>
1391 <li>URL links generated from description line for
1392 regular-expression based URL links (applet and application)
1395 <li>Non-positional feature URL links are shown in link
1397 <li>Linked viewing of nucleic acid sequences and
1399 <li>Automatic Scrolling option in View menu to display
1400 the currently highlighted region of an alignment.</li>
1401 <li>Order an alignment by sequence length, or using the
1402 average score or total feature count for each sequence.</li>
1403 <li>Shading features by score or associated description</li>
1404 <li>Subdivide alignment and groups based on identity of
1405 selected subsequence (Make Groups from Selection).</li>
1406 <li>New hide/show options including Shift+Control+H to
1407 hide everything but the currently selected region.</li>
1408 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1409 </ul> <em>Application</em>
1411 <li>Fetch DB References capabilities and UI expanded to
1412 support retrieval from DAS sequence sources</li>
1413 <li>Local DAS Sequence sources can be added via the
1414 command line or via the Add local source dialog box.</li>
1415 <li>DAS Dbref and DbxRef feature types are parsed as
1416 database references and protein_name is parsed as
1417 description line (BioSapiens terms).</li>
1418 <li>Enable or disable non-positional feature and database
1419 references in sequence ID tooltip from View menu in
1421 <!-- <li>New hidden columns and rows and representatives capabilities
1422 in annotations file (in progress - not yet fully implemented)</li> -->
1423 <li>Group-associated consensus, sequence logos and
1424 conservation plots</li>
1425 <li>Symbol distributions for each column can be exported
1426 and visualized as sequence logos</li>
1427 <li>Optionally scale multi-character column labels to fit
1428 within each column of annotation row<!-- todo for applet -->
1430 <li>Optional automatic sort of associated alignment view
1431 when a new tree is opened.</li>
1432 <li>Jalview Java Console</li>
1433 <li>Better placement of desktop window when moving
1434 between different screens.</li>
1435 <li>New preference items for sequence ID tooltip and
1436 consensus annotation</li>
1437 <li>Client to submit sequences and IDs to Envision2 Workflows</li>
1438 <li><em>Vamsas Capabilities</em>
1440 <li>Improved VAMSAS synchronization (Jalview archive
1441 used to preserve views, structures, and tree display
1443 <li>Import of vamsas documents from disk or URL via
1445 <li>Sharing of selected regions between views and
1446 with other VAMSAS applications (Experimental feature!)</li>
1447 <li>Updated API to VAMSAS version 0.2</li>
1449 </ul> <em>Applet</em>
1451 <li>Middle button resizes annotation row height</li>
1454 <li>sortByTree (true/false) - automatically sort the
1455 associated alignment view by the tree when a new tree is
1457 <li>showTreeBootstraps (true/false) - show or hide
1458 branch bootstraps (default is to show them if available)</li>
1459 <li>showTreeDistances (true/false) - show or hide
1460 branch lengths (default is to show them if available)</li>
1461 <li>showUnlinkedTreeNodes (true/false) - indicate if
1462 unassociated nodes should be highlighted in the tree
1464 <li>heightScale and widthScale (1.0 or more) -
1465 increase the height or width of a cell in the alignment
1466 grid relative to the current font size.</li>
1469 <li>Non-positional features displayed in sequence ID
1471 </ul> <em>Other</em>
1473 <li>Features format: graduated colour definitions and
1474 specification of feature scores</li>
1475 <li>Alignment Annotations format: new keywords for group
1476 associated annotation (GROUP_REF) and annotation row display
1477 properties (ROW_PROPERTIES)</li>
1478 <li>XML formats extended to support graduated feature
1479 colourschemes, group associated annotation, and profile
1480 visualization settings.</li></td>
1483 <li>Source field in GFF files parsed as feature source
1484 rather than description</li>
1485 <li>Non-positional features are now included in sequence
1486 feature and gff files (controlled via non-positional feature
1487 visibility in tooltip).</li>
1488 <li>URL links generated for all feature links (bugfix)</li>
1489 <li>Added URL embedding instructions to features file
1491 <li>Codons containing ambiguous nucleotides translated as
1492 'X' in peptide product</li>
1493 <li>Match case switch in find dialog box works for both
1494 sequence ID and sequence string and query strings do not
1495 have to be in upper case to match case-insensitively.</li>
1496 <li>AMSA files only contain first column of
1497 multi-character column annotation labels</li>
1498 <li>Jalview Annotation File generation/parsing consistent
1499 with documentation (e.g. Stockholm annotation can be
1500 exported and re-imported)</li>
1501 <li>PDB files without embedded PDB IDs given a friendly
1503 <li>Find incrementally searches ID string matches as well
1504 as subsequence matches, and correctly reports total number
1508 <li>Better handling of exceptions during sequence
1510 <li>Dasobert generated non-positional feature URL
1511 link text excludes the start_end suffix</li>
1512 <li>DAS feature and source retrieval buttons disabled
1513 when fetch or registry operations in progress.</li>
1514 <li>PDB files retrieved from URLs are cached properly</li>
1515 <li>Sequence description lines properly shared via
1517 <li>Sequence fetcher fetches multiple records for all
1519 <li>Ensured that command line das feature retrieval
1520 completes before alignment figures are generated.</li>
1521 <li>Reduced time taken when opening file browser for
1523 <li>isAligned check prior to calculating tree, PCA or
1524 submitting an MSA to JNet now excludes hidden sequences.</li>
1525 <li>User defined group colours properly recovered
1526 from Jalview projects.</li>
1535 <div align="center">
1536 <strong>2.4.0.b2</strong><br> 28/10/2009
1541 <li>Experimental support for google analytics usage
1543 <li>Jalview privacy settings (user preferences and docs).</li>
1548 <li>Race condition in applet preventing startup in
1550 <li>Exception when feature created from selection beyond
1551 length of sequence.</li>
1552 <li>Allow synthetic PDB files to be imported gracefully</li>
1553 <li>Sequence associated annotation rows associate with
1554 all sequences with a given id</li>
1555 <li>Find function matches case-insensitively for sequence
1556 ID string searches</li>
1557 <li>Non-standard characters do not cause pairwise
1558 alignment to fail with exception</li>
1559 </ul> <em>Application Issues</em>
1561 <li>Sequences are now validated against EMBL database</li>
1562 <li>Sequence fetcher fetches multiple records for all
1564 </ul> <em>InstallAnywhere Issues</em>
1566 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1567 issue with installAnywhere mechanism)</li>
1568 <li>Command line launching of JARs from InstallAnywhere
1569 version (java class versioning error fixed)</li>
1576 <div align="center">
1577 <strong>2.4</strong><br> 27/8/2008
1580 <td><em>User Interface</em>
1582 <li>Linked highlighting of codon and amino acid from
1583 translation and protein products</li>
1584 <li>Linked highlighting of structure associated with
1585 residue mapping to codon position</li>
1586 <li>Sequence Fetcher provides example accession numbers
1587 and 'clear' button</li>
1588 <li>MemoryMonitor added as an option under Desktop's
1590 <li>Extract score function to parse whitespace separated
1591 numeric data in description line</li>
1592 <li>Column labels in alignment annotation can be centred.</li>
1593 <li>Tooltip for sequence associated annotation give name
1595 </ul> <em>Web Services and URL fetching</em>
1597 <li>JPred3 web service</li>
1598 <li>Prototype sequence search client (no public services
1600 <li>Fetch either seed alignment or full alignment from
1602 <li>URL Links created for matching database cross
1603 references as well as sequence ID</li>
1604 <li>URL Links can be created using regular-expressions</li>
1605 </ul> <em>Sequence Database Connectivity</em>
1607 <li>Retrieval of cross-referenced sequences from other
1609 <li>Generalised database reference retrieval and
1610 validation to all fetchable databases</li>
1611 <li>Fetch sequences from DAS sources supporting the
1612 sequence command</li>
1613 </ul> <em>Import and Export</em>
1614 <li>export annotation rows as CSV for spreadsheet import</li>
1615 <li>Jalview projects record alignment dataset associations,
1616 EMBL products, and cDNA sequence mappings</li>
1617 <li>Sequence Group colour can be specified in Annotation
1619 <li>Ad-hoc colouring of group in Annotation File using RGB
1620 triplet as name of colourscheme</li>
1621 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1623 <li>treenode binding for VAMSAS tree exchange</li>
1624 <li>local editing and update of sequences in VAMSAS
1625 alignments (experimental)</li>
1626 <li>Create new or select existing session to join</li>
1627 <li>load and save of vamsas documents</li>
1628 </ul> <em>Application command line</em>
1630 <li>-tree parameter to open trees (introduced for passing
1632 <li>-fetchfrom command line argument to specify nicknames
1633 of DAS servers to query for alignment features</li>
1634 <li>-dasserver command line argument to add new servers
1635 that are also automatically queried for features</li>
1636 <li>-groovy command line argument executes a given groovy
1637 script after all input data has been loaded and parsed</li>
1638 </ul> <em>Applet-Application data exchange</em>
1640 <li>Trees passed as applet parameters can be passed to
1641 application (when using "View in full
1642 application")</li>
1643 </ul> <em>Applet Parameters</em>
1645 <li>feature group display control parameter</li>
1646 <li>debug parameter</li>
1647 <li>showbutton parameter</li>
1648 </ul> <em>Applet API methods</em>
1650 <li>newView public method</li>
1651 <li>Window (current view) specific get/set public methods</li>
1652 <li>Feature display control methods</li>
1653 <li>get list of currently selected sequences</li>
1654 </ul> <em>New Jalview distribution features</em>
1656 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1657 <li>RELEASE file gives build properties for the latest
1658 Jalview release.</li>
1659 <li>Java 1.1 Applet build made easier and donotobfuscate
1660 property controls execution of obfuscator</li>
1661 <li>Build target for generating source distribution</li>
1662 <li>Debug flag for javacc</li>
1663 <li>.jalview_properties file is documented (slightly) in
1664 jalview.bin.Cache</li>
1665 <li>Continuous Build Integration for stable and
1666 development version of Application, Applet and source
1671 <li>selected region output includes visible annotations
1672 (for certain formats)</li>
1673 <li>edit label/displaychar contains existing label/char
1675 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1676 <li>shorter peptide product names from EMBL records</li>
1677 <li>Newick string generator makes compact representations</li>
1678 <li>bootstrap values parsed correctly for tree files with
1680 <li>pathological filechooser bug avoided by not allowing
1681 filenames containing a ':'</li>
1682 <li>Fixed exception when parsing GFF files containing
1683 global sequence features</li>
1684 <li>Alignment datasets are finalized only when number of
1685 references from alignment sequences goes to zero</li>
1686 <li>Close of tree branch colour box without colour
1687 selection causes cascading exceptions</li>
1688 <li>occasional negative imgwidth exceptions</li>
1689 <li>better reporting of non-fatal warnings to user when
1690 file parsing fails.</li>
1691 <li>Save works when Jalview project is default format</li>
1692 <li>Save as dialog opened if current alignment format is
1693 not a valid output format</li>
1694 <li>UniProt canonical names introduced for both das and
1696 <li>Histidine should be midblue (not pink!) in Zappo</li>
1697 <li>error messages passed up and output when data read
1699 <li>edit undo recovers previous dataset sequence when
1700 sequence is edited</li>
1701 <li>allow PDB files without pdb ID HEADER lines (like
1702 those generated by MODELLER) to be read in properly</li>
1703 <li>allow reading of JPred concise files as a normal
1705 <li>Stockholm annotation parsing and alignment properties
1706 import fixed for PFAM records</li>
1707 <li>Structure view windows have correct name in Desktop
1709 <li>annotation consisting of sequence associated scores
1710 can be read and written correctly to annotation file</li>
1711 <li>Aligned cDNA translation to aligned peptide works
1713 <li>Fixed display of hidden sequence markers and
1714 non-italic font for representatives in Applet</li>
1715 <li>Applet Menus are always embedded in applet window on
1717 <li>Newly shown features appear at top of stack (in
1719 <li>Annotations added via parameter not drawn properly
1720 due to null pointer exceptions</li>
1721 <li>Secondary structure lines are drawn starting from
1722 first column of alignment</li>
1723 <li>UniProt XML import updated for new schema release in
1725 <li>Sequence feature to sequence ID match for Features
1726 file is case-insensitive</li>
1727 <li>Sequence features read from Features file appended to
1728 all sequences with matching IDs</li>
1729 <li>PDB structure coloured correctly for associated views
1730 containing a sub-sequence</li>
1731 <li>PDB files can be retrieved by applet from Jar files</li>
1732 <li>feature and annotation file applet parameters
1733 referring to different directories are retrieved correctly</li>
1734 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1735 <li>Fixed application hang whilst waiting for
1736 splash-screen version check to complete</li>
1737 <li>Applet properly URLencodes input parameter values
1738 when passing them to the launchApp service</li>
1739 <li>display name and local features preserved in results
1740 retrieved from web service</li>
1741 <li>Visual delay indication for sequence retrieval and
1742 sequence fetcher initialisation</li>
1743 <li>updated Application to use DAS 1.53e version of
1744 dasobert DAS client</li>
1745 <li>Re-instated Full AMSA support and .amsa file
1747 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1755 <div align="center">
1756 <strong>2.3</strong><br> 9/5/07
1761 <li>Jmol 11.0.2 integration</li>
1762 <li>PDB views stored in Jalview XML files</li>
1763 <li>Slide sequences</li>
1764 <li>Edit sequence in place</li>
1765 <li>EMBL CDS features</li>
1766 <li>DAS Feature mapping</li>
1767 <li>Feature ordering</li>
1768 <li>Alignment Properties</li>
1769 <li>Annotation Scores</li>
1770 <li>Sort by scores</li>
1771 <li>Feature/annotation editing in applet</li>
1776 <li>Headless state operation in 2.2.1</li>
1777 <li>Incorrect and unstable DNA pairwise alignment</li>
1778 <li>Cut and paste of sequences with annotation</li>
1779 <li>Feature group display state in XML</li>
1780 <li>Feature ordering in XML</li>
1781 <li>blc file iteration selection using filename # suffix</li>
1782 <li>Stockholm alignment properties</li>
1783 <li>Stockhom alignment secondary structure annotation</li>
1784 <li>2.2.1 applet had no feature transparency</li>
1785 <li>Number pad keys can be used in cursor mode</li>
1786 <li>Structure Viewer mirror image resolved</li>
1793 <div align="center">
1794 <strong>2.2.1</strong><br> 12/2/07
1799 <li>Non standard characters can be read and displayed
1800 <li>Annotations/Features can be imported/exported to the
1802 <li>Applet allows editing of sequence/annotation/group
1803 name & description
1804 <li>Preference setting to display sequence name in
1806 <li>Annotation file format extended to allow
1807 Sequence_groups to be defined
1808 <li>Default opening of alignment overview panel can be
1809 specified in preferences
1810 <li>PDB residue numbering annotation added to associated
1816 <li>Applet crash under certain Linux OS with Java 1.6
1818 <li>Annotation file export / import bugs fixed
1819 <li>PNG / EPS image output bugs fixed
1825 <div align="center">
1826 <strong>2.2</strong><br> 27/11/06
1831 <li>Multiple views on alignment
1832 <li>Sequence feature editing
1833 <li>"Reload" alignment
1834 <li>"Save" to current filename
1835 <li>Background dependent text colour
1836 <li>Right align sequence ids
1837 <li>User-defined lower case residue colours
1840 <li>Menu item accelerator keys
1841 <li>Control-V pastes to current alignment
1842 <li>Cancel button for DAS Feature Fetching
1843 <li>PCA and PDB Viewers zoom via mouse roller
1844 <li>User-defined sub-tree colours and sub-tree selection
1847 <li>'New Window' button on the 'Output to Text box'
1852 <li>New memory efficient Undo/Redo System
1853 <li>Optimised symbol lookups and conservation/consensus
1855 <li>Region Conservation/Consensus recalculated after
1857 <li>Fixed Remove Empty Columns Bug (empty columns at end
1859 <li>Slowed DAS Feature Fetching for increased robustness.
1862 <li>Made angle brackets in ASCII feature descriptions
1864 <li>Re-instated Zoom function for PCA
1865 <li>Sequence descriptions conserved in web service
1867 <li>UniProt ID discoverer uses any word separated by
1869 <li>WsDbFetch query/result association resolved
1870 <li>Tree leaf to sequence mapping improved
1871 <li>Smooth fonts switch moved to FontChooser dialog box.
1879 <div align="center">
1880 <strong>2.1.1</strong><br> 12/9/06
1885 <li>Copy consensus sequence to clipboard</li>
1890 <li>Image output - rightmost residues are rendered if
1891 sequence id panel has been resized</li>
1892 <li>Image output - all offscreen group boundaries are
1894 <li>Annotation files with sequence references - all
1895 elements in file are relative to sequence position</li>
1896 <li>Mac Applet users can use Alt key for group editing</li>
1902 <div align="center">
1903 <strong>2.1</strong><br> 22/8/06
1908 <li>MAFFT Multiple Alignment in default Web Service list</li>
1909 <li>DAS Feature fetching</li>
1910 <li>Hide sequences and columns</li>
1911 <li>Export Annotations and Features</li>
1912 <li>GFF file reading / writing</li>
1913 <li>Associate structures with sequences from local PDB
1915 <li>Add sequences to exisiting alignment</li>
1916 <li>Recently opened files / URL lists</li>
1917 <li>Applet can launch the full application</li>
1918 <li>Applet has transparency for features (Java 1.2
1920 <li>Applet has user defined colours parameter</li>
1921 <li>Applet can load sequences from parameter
1922 "sequence<em>x</em>"
1928 <li>Redundancy Panel reinstalled in the Applet</li>
1929 <li>Monospaced font - EPS / rescaling bug fixed</li>
1930 <li>Annotation files with sequence references bug fixed</li>
1936 <div align="center">
1937 <strong>2.08.1</strong><br> 2/5/06
1942 <li>Change case of selected region from Popup menu</li>
1943 <li>Choose to match case when searching</li>
1944 <li>Middle mouse button and mouse movement can compress /
1945 expand the visible width and height of the alignment</li>
1950 <li>Annotation Panel displays complete JNet results</li>
1956 <div align="center">
1957 <strong>2.08b</strong><br> 18/4/06
1963 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1964 <li>Righthand label on wrapped alignments shows correct
1971 <div align="center">
1972 <strong>2.08</strong><br> 10/4/06
1977 <li>Editing can be locked to the selection area</li>
1978 <li>Keyboard editing</li>
1979 <li>Create sequence features from searches</li>
1980 <li>Precalculated annotations can be loaded onto
1982 <li>Features file allows grouping of features</li>
1983 <li>Annotation Colouring scheme added</li>
1984 <li>Smooth fonts off by default - Faster rendering</li>
1985 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1990 <li>Drag & Drop fixed on Linux</li>
1991 <li>Jalview Archive file faster to load/save, sequence
1992 descriptions saved.</li>
1998 <div align="center">
1999 <strong>2.07</strong><br> 12/12/05
2004 <li>PDB Structure Viewer enhanced</li>
2005 <li>Sequence Feature retrieval and display enhanced</li>
2006 <li>Choose to output sequence start-end after sequence
2007 name for file output</li>
2008 <li>Sequence Fetcher WSDBFetch@EBI</li>
2009 <li>Applet can read feature files, PDB files and can be
2010 used for HTML form input</li>
2015 <li>HTML output writes groups and features</li>
2016 <li>Group editing is Control and mouse click</li>
2017 <li>File IO bugs</li>
2023 <div align="center">
2024 <strong>2.06</strong><br> 28/9/05
2029 <li>View annotations in wrapped mode</li>
2030 <li>More options for PCA viewer</li>
2035 <li>GUI bugs resolved</li>
2036 <li>Runs with -nodisplay from command line</li>
2042 <div align="center">
2043 <strong>2.05b</strong><br> 15/9/05
2048 <li>Choose EPS export as lineart or text</li>
2049 <li>Jar files are executable</li>
2050 <li>Can read in Uracil - maps to unknown residue</li>
2055 <li>Known OutOfMemory errors give warning message</li>
2056 <li>Overview window calculated more efficiently</li>
2057 <li>Several GUI bugs resolved</li>
2063 <div align="center">
2064 <strong>2.05</strong><br> 30/8/05
2069 <li>Edit and annotate in "Wrapped" view</li>
2074 <li>Several GUI bugs resolved</li>
2080 <div align="center">
2081 <strong>2.04</strong><br> 24/8/05
2086 <li>Hold down mouse wheel & scroll to change font
2092 <li>Improved JPred client reliability</li>
2093 <li>Improved loading of Jalview files</li>
2099 <div align="center">
2100 <strong>2.03</strong><br> 18/8/05
2105 <li>Set Proxy server name and port in preferences</li>
2106 <li>Multiple URL links from sequence ids</li>
2107 <li>User Defined Colours can have a scheme name and added
2109 <li>Choose to ignore gaps in consensus calculation</li>
2110 <li>Unix users can set default web browser</li>
2111 <li>Runs without GUI for batch processing</li>
2112 <li>Dynamically generated Web Service Menus</li>
2117 <li>InstallAnywhere download for Sparc Solaris</li>
2123 <div align="center">
2124 <strong>2.02</strong><br> 18/7/05
2130 <li>Copy & Paste order of sequences maintains
2131 alignment order.</li>
2137 <div align="center">
2138 <strong>2.01</strong><br> 12/7/05
2143 <li>Use delete key for deleting selection.</li>
2144 <li>Use Mouse wheel to scroll sequences.</li>
2145 <li>Help file updated to describe how to add alignment
2147 <li>Version and build date written to build properties
2149 <li>InstallAnywhere installation will check for updates
2150 at launch of Jalview.</li>
2155 <li>Delete gaps bug fixed.</li>
2156 <li>FileChooser sorts columns.</li>
2157 <li>Can remove groups one by one.</li>
2158 <li>Filechooser icons installed.</li>
2159 <li>Finder ignores return character when searching.
2160 Return key will initiate a search.<br>
2167 <div align="center">
2168 <strong>2.0</strong><br> 20/6/05
2173 <li>New codebase</li>