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.2.9.1">2.9.1</a><br /> <em>21/6/2016</em></strong>
56 </ul> <em>Application</em>
59 <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
60 <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
61 <li><!-- JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
62 <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
72 <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
73 <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
74 <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
75 <li><!-- JAL-2053-->hidden column markers not always rendered at right of alignment window</li>
76 <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
77 <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
78 <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
79 <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
80 <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
85 <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
86 <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
87 <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
88 <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
89 <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
90 <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
91 <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
101 <td width="60" nowrap>
103 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
104 <em>16/10/2015</em></strong>
109 <li>Time stamps for signed Jalview application and applet
116 <li>Duplicate group consensus and conservation rows
117 shown when tree is partitioned</li>
118 <li>Erratic behaviour when tree partitions made with
119 multiple cDNA/Protein split views</li>
125 <td width="60" nowrap>
127 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
128 <em>8/10/2015</em></strong>
133 <li>Updated Spanish translations of localized text for
135 </ul> <em>Application</em>
137 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
138 <li>Signed OSX InstallAnywhere installer<br></li>
139 <li>Support for per-sequence based annotations in BioJSON</li>
140 </ul> <em>Applet</em>
142 <li>Split frame example added to applet examples page</li>
148 <li>Mapping of cDNA to protein in split frames
149 incorrect when sequence start > 1</li>
150 <li>Broken images in filter column by annotation dialog
152 <li>Feature colours not parsed from features file</li>
153 <li>Exceptions and incomplete link URLs recovered when
154 loading a features file containing HTML tags in feature
160 <li>Annotations corrupted after BioJS export and
162 <li>Incorrect sequence limits after Fetch DB References
163 with 'trim retrieved sequences'</li>
164 <li>Incorrect warning about deleting all data when
165 deleting selected columns</li>
166 <li>Patch to build system for shipping properly signed
167 JNLP templates for webstart launch</li>
168 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
169 unreleased structures for download or viewing</li>
170 <li>Tab/space/return keystroke operation of EMBL-PDBe
171 fetcher/viewer dialogs works correctly</li>
172 <li>Disabled 'minimise' button on Jalview windows
173 running on OSX to workaround redraw hang bug</li>
174 <li>Split cDNA/Protein view position and geometry not
175 recovered from jalview project</li>
176 <li>Initial enabled/disabled state of annotation menu
177 sorter 'show autocalculated first/last' corresponds to
179 <li>Restoring of Clustal, RNA Helices and T-Coffee
180 color schemes from BioJSON</li>
184 <li>Reorder sequences mirrored in cDNA/Protein split
186 <li>Applet with Jmol examples not loading correctly</li>
192 <td><div align="center">
193 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
197 <li>Linked visualisation and analysis of DNA and Protein
200 <li>Translated cDNA alignments shown as split protein
201 and DNA alignment views</li>
202 <li>Codon consensus annotation for linked protein and
203 cDNA alignment views</li>
204 <li>Link cDNA or Protein product sequences by loading
205 them onto Protein or cDNA alignments</li>
206 <li>Reconstruct linked cDNA alignment from aligned
207 protein sequences</li>
210 <li>Jmol integration updated to Jmol v14.2.14</li>
211 <li>Import and export of Jalview alignment views as <a
212 href="features/bioJsonFormat.html">BioJSON</a></li>
213 <li>New alignment annotation file statements for
214 reference sequences and marking hidden columns</li>
215 <li>Reference sequence based alignment shading to
216 highlight variation</li>
217 <li>Select or hide columns according to alignment
219 <li>Find option for locating sequences by description</li>
220 <li>Conserved physicochemical properties shown in amino
221 acid conservation row</li>
222 <li>Alignments can be sorted by number of RNA helices</li>
223 </ul> <em>Application</em>
225 <li>New cDNA/Protein analysis capabilities
227 <li>Get Cross-References should open a Split Frame
228 view with cDNA/Protein</li>
229 <li>Detect when nucleotide sequences and protein
230 sequences are placed in the same alignment</li>
231 <li>Split cDNA/Protein views are saved in Jalview
236 <li>Use REST API to talk to Chimera</li>
237 <li>Selected regions in Chimera are highlighted in linked
240 <li>VARNA RNA viewer updated to v3.93</li>
241 <li>VARNA views are saved in Jalview Projects</li>
242 <li>Pseudoknots displayed as Jalview RNA annotation can
243 be shown in VARNA</li>
245 <li>Make groups for selection uses marked columns as well
246 as the active selected region</li>
248 <li>Calculate UPGMA and NJ trees using sequence feature
250 <li>New Export options
252 <li>New Export Settings dialog to control hidden
253 region export in flat file generation</li>
255 <li>Export alignment views for display with the <a
256 href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
258 <li>Export scrollable SVG in HTML page</li>
259 <li>Optional embedding of BioJSON data when exporting
260 alignment figures to HTML</li>
262 <li>3D structure retrieval and display
264 <li>Free text and structured queries with the PDBe
266 <li>PDBe Search API based discovery and selection of
267 PDB structures for a sequence set</li>
271 <li>JPred4 employed for protein secondary structure
273 <li>Hide Insertions menu option to hide unaligned columns
274 for one or a group of sequences</li>
275 <li>Automatically hide insertions in alignments imported
276 from the JPred4 web server</li>
277 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
278 system on OSX<br />LGPL libraries courtesy of <a
279 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
281 <li>changed 'View nucleotide structure' submenu to 'View
282 VARNA 2D Structure'</li>
283 <li>change "View protein structure" menu option to "3D
286 </ul> <em>Applet</em>
288 <li>New layout for applet example pages</li>
289 <li>New parameters to enable SplitFrame view
290 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
291 <li>New example demonstrating linked viewing of cDNA and
292 Protein alignments</li>
293 </ul> <em>Development and deployment</em>
295 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
296 <li>Include installation type and git revision in build
297 properties and console log output</li>
298 <li>Jalview Github organisation, and new github site for
299 storing BioJsMSA Templates</li>
300 <li>Jalview's unit tests now managed with TestNG</li>
303 <!-- <em>General</em>
305 </ul> --> <!-- issues resolved --> <em>Application</em>
307 <li>Escape should close any open find dialogs</li>
308 <li>Typo in select-by-features status report</li>
309 <li>Consensus RNA secondary secondary structure
310 predictions are not highlighted in amber</li>
311 <li>Missing gap character in v2.7 example file means
312 alignment appears unaligned when pad-gaps is not enabled</li>
313 <li>First switch to RNA Helices colouring doesn't colour
314 associated structure views</li>
315 <li>ID width preference option is greyed out when auto
316 width checkbox not enabled</li>
317 <li>Stopped a warning dialog from being shown when
318 creating user defined colours</li>
319 <li>'View Mapping' in structure viewer shows sequence
320 mappings for just that viewer's sequences</li>
321 <li>Workaround for superposing PDB files containing
322 multiple models in Chimera</li>
323 <li>Report sequence position in status bar when hovering
324 over Jmol structure</li>
325 <li>Cannot output gaps as '.' symbols with Selection ->
326 output to text box</li>
327 <li>Flat file exports of alignments with hidden columns
328 have incorrect sequence start/end</li>
329 <li>'Aligning' a second chain to a Chimera structure from
331 <li>Colour schemes applied to structure viewers don't
332 work for nucleotide</li>
333 <li>Loading/cut'n'pasting an empty or invalid file leads
334 to a grey/invisible alignment window</li>
335 <li>Exported Jpred annotation from a sequence region
336 imports to different position</li>
337 <li>Space at beginning of sequence feature tooltips shown
338 on some platforms</li>
339 <li>Chimera viewer 'View | Show Chain' menu is not
341 <li>'New View' fails with a Null Pointer Exception in
342 console if Chimera has been opened</li>
343 <li>Mouseover to Chimera not working</li>
344 <li>Miscellaneous ENA XML feature qualifiers not
346 <li>NPE in annotation renderer after 'Extract Scores'</li>
347 <li>If two structures in one Chimera window, mouseover of
348 either sequence shows on first structure</li>
349 <li>'Show annotations' options should not make
350 non-positional annotations visible</li>
351 <li>Subsequence secondary structure annotation not shown
352 in right place after 'view flanking regions'</li>
353 <li>File Save As type unset when current file format is
355 <li>Save as '.jar' option removed for saving Jalview
357 <li>Colour by Sequence colouring in Chimera more
359 <li>Cannot 'add reference annotation' for a sequence in
360 several views on same alignment</li>
361 <li>Cannot show linked products for EMBL / ENA records</li>
362 <li>Jalview's tooltip wraps long texts containing no
364 </ul> <em>Applet</em>
366 <li>Jmol to JalviewLite mouseover/link not working</li>
367 <li>JalviewLite can't import sequences with ID
368 descriptions containing angle brackets</li>
369 </ul> <em>General</em>
371 <li>Cannot export and reimport RNA secondary structure
372 via jalview annotation file</li>
373 <li>Random helix colour palette for colour by annotation
374 with RNA secondary structure</li>
375 <li>Mouseover to cDNA from STOP residue in protein
376 translation doesn't work.</li>
377 <li>hints when using the select by annotation dialog box</li>
378 <li>Jmol alignment incorrect if PDB file has alternate CA
380 <li>FontChooser message dialog appears to hang after
381 choosing 1pt font</li>
382 <li>Peptide secondary structure incorrectly imported from
383 annotation file when annotation display text includes 'e' or
385 <li>Cannot set colour of new feature type whilst creating
387 <li>cDNA translation alignment should not be sequence
389 <li>'Show unconserved' doesn't work for lower case
391 <li>Nucleotide ambiguity codes involving R not recognised</li>
392 </ul> <em>Deployment and Documentation</em>
394 <li>Applet example pages appear different to the rest of
396 </ul> <em>Application Known issues</em>
398 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
399 <li>Misleading message appears after trying to delete
401 <li>Jalview icon not shown in dock after InstallAnywhere
402 version launches</li>
403 <li>Fetching EMBL reference for an RNA sequence results
404 fails with a sequence mismatch</li>
405 <li>Corrupted or unreadable alignment display when
406 scrolling alignment to right</li>
407 <li>ArrayIndexOutOfBoundsException thrown when remove
408 empty columns called on alignment with ragged gapped ends</li>
409 <li>auto calculated alignment annotation rows do not get
410 placed above or below non-autocalculated rows</li>
411 <li>Jalview dekstop becomes sluggish at full screen in
412 ultra-high resolution</li>
413 <li>Cannot disable consensus calculation independently of
414 quality and conservation</li>
415 <li>Mouseover highlighting between cDNA and protein can
416 become sluggish with more than one splitframe shown</li>
417 </ul> <em>Applet Known Issues</em>
419 <li>Core PDB parsing code requires Jmol</li>
420 <li>Sequence canvas panel goes white when alignment
421 window is being resized</li>
427 <td><div align="center">
428 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
432 <li>Updated Java code signing certificate donated by
434 <li>Features and annotation preserved when performing
435 pairwise alignment</li>
436 <li>RNA pseudoknot annotation can be
437 imported/exported/displayed</li>
438 <li>'colour by annotation' can colour by RNA and
439 protein secondary structure</li>
440 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
441 post-hoc with 2.9 release</em>)
444 </ul> <em>Application</em>
446 <li>Extract and display secondary structure for sequences
447 with 3D structures</li>
448 <li>Support for parsing RNAML</li>
449 <li>Annotations menu for layout
451 <li>sort sequence annotation rows by alignment</li>
452 <li>place sequence annotation above/below alignment
455 <li>Output in Stockholm format</li>
456 <li>Internationalisation: improved Spanish (es)
458 <li>Structure viewer preferences tab</li>
459 <li>Disorder and Secondary Structure annotation tracks
460 shared between alignments</li>
461 <li>UCSF Chimera launch and linked highlighting from
463 <li>Show/hide all sequence associated annotation rows for
464 all or current selection</li>
465 <li>disorder and secondary structure predictions
466 available as dataset annotation</li>
467 <li>Per-sequence rna helices colouring</li>
470 <li>Sequence database accessions imported when fetching
471 alignments from Rfam</li>
472 <li>update VARNA version to 3.91</li>
474 <li>New groovy scripts for exporting aligned positions,
475 conservation values, and calculating sum of pairs scores.</li>
476 <li>Command line argument to set default JABAWS server</li>
477 <li>include installation type in build properties and
478 console log output</li>
479 <li>Updated Jalview project format to preserve dataset
483 <!-- issues resolved --> <em>Application</em>
485 <li>Distinguish alignment and sequence associated RNA
486 structure in structure->view->VARNA</li>
487 <li>Raise dialog box if user deletes all sequences in an
489 <li>Pressing F1 results in documentation opening twice</li>
490 <li>Sequence feature tooltip is wrapped</li>
491 <li>Double click on sequence associated annotation
492 selects only first column</li>
493 <li>Redundancy removal doesn't result in unlinked
494 leaves shown in tree</li>
495 <li>Undos after several redundancy removals don't undo
497 <li>Hide sequence doesn't hide associated annotation</li>
498 <li>User defined colours dialog box too big to fit on
499 screen and buttons not visible</li>
500 <li>author list isn't updated if already written to
501 Jalview properties</li>
502 <li>Popup menu won't open after retrieving sequence
504 <li>File open window for associate PDB doesn't open</li>
505 <li>Left-then-right click on a sequence id opens a
506 browser search window</li>
507 <li>Cannot open sequence feature shading/sort popup menu
508 in feature settings dialog</li>
509 <li>better tooltip placement for some areas of Jalview
511 <li>Allow addition of JABAWS Server which doesn't
513 <li>Web services parameters dialog box is too large to
515 <li>Muscle nucleotide alignment preset obscured by
517 <li>JABAWS preset submenus don't contain newly
518 defined user preset</li>
519 <li>MSA web services warns user if they were launched
520 with invalid input</li>
521 <li>Jalview cannot contact DAS Registy when running on
524 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
525 'Superpose with' submenu not shown when new view
529 </ul> <!-- <em>Applet</em>
531 </ul> <em>General</em>
533 </ul>--> <em>Deployment and Documentation</em>
535 <li>2G and 1G options in launchApp have no effect on
536 memory allocation</li>
537 <li>launchApp service doesn't automatically open
538 www.jalview.org/examples/exampleFile.jar if no file is given</li>
540 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
541 InstallAnywhere reports cannot find valid JVM when Java
544 </ul> <em>Application Known issues</em>
547 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
548 corrupted or unreadable alignment display when scrolling
552 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
553 retrieval fails but progress bar continues for DAS retrieval
554 with large number of ID
557 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
558 flatfile output of visible region has incorrect sequence
562 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
563 rna structure consensus doesn't update when secondary
564 structure tracks are rearranged
567 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
568 invalid rna structure positional highlighting does not
569 highlight position of invalid base pairs
572 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
573 out of memory errors are not raised when saving Jalview
574 project from alignment window file menu
577 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
578 Switching to RNA Helices colouring doesn't propagate to
582 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
583 colour by RNA Helices not enabled when user created
584 annotation added to alignment
587 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
588 Jalview icon not shown on dock in Mountain Lion/Webstart
590 </ul> <em>Applet Known Issues</em>
593 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
594 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
597 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
598 Jalview and Jmol example not compatible with IE9
601 <li>Sort by annotation score doesn't reverse order
607 <td><div align="center">
608 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
611 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
614 <li>Internationalisation of user interface (usually
615 called i18n support) and translation for Spanish locale</li>
616 <li>Define/Undefine group on current selection with
617 Ctrl-G/Shift Ctrl-G</li>
618 <li>Improved group creation/removal options in
619 alignment/sequence Popup menu</li>
620 <li>Sensible precision for symbol distribution
621 percentages shown in logo tooltip.</li>
622 <li>Annotation panel height set according to amount of
623 annotation when alignment first opened</li>
624 </ul> <em>Application</em>
626 <li>Interactive consensus RNA secondary structure
627 prediction VIENNA RNAAliFold JABA 2.1 service</li>
628 <li>Select columns containing particular features from
629 Feature Settings dialog</li>
630 <li>View all 'representative' PDB structures for selected
632 <li>Update Jalview project format:
634 <li>New file extension for Jalview projects '.jvp'</li>
635 <li>Preserve sequence and annotation dataset (to
636 store secondary structure annotation,etc)</li>
637 <li>Per group and alignment annotation and RNA helix
641 <li>New similarity measures for PCA and Tree calculation
643 <li>Experimental support for retrieval and viewing of
644 flanking regions for an alignment</li>
648 <!-- issues resolved --> <em>Application</em>
650 <li>logo keeps spinning and status remains at queued or
651 running after job is cancelled</li>
652 <li>cannot export features from alignments imported from
653 Jalview/VAMSAS projects</li>
654 <li>Buggy slider for web service parameters that take
656 <li>Newly created RNA secondary structure line doesn't
657 have 'display all symbols' flag set</li>
658 <li>T-COFFEE alignment score shading scheme and other
659 annotation shading not saved in Jalview project</li>
660 <li>Local file cannot be loaded in freshly downloaded
662 <li>Jalview icon not shown on dock in Mountain
664 <li>Load file from desktop file browser fails</li>
665 <li>Occasional NPE thrown when calculating large trees</li>
666 <li>Cannot reorder or slide sequences after dragging an
667 alignment onto desktop</li>
668 <li>Colour by annotation dialog throws NPE after using
669 'extract scores' function</li>
670 <li>Loading/cut'n'pasting an empty file leads to a grey
671 alignment window</li>
672 <li>Disorder thresholds rendered incorrectly after
673 performing IUPred disorder prediction</li>
674 <li>Multiple group annotated consensus rows shown when
675 changing 'normalise logo' display setting</li>
676 <li>Find shows blank dialog after 'finished searching' if
677 nothing matches query</li>
678 <li>Null Pointer Exceptions raised when sorting by
679 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
681 <li>Errors in Jmol console when structures in alignment
682 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
684 <li>Not all working JABAWS services are shown in
686 <li>JAVAWS version of Jalview fails to launch with
687 'invalid literal/length code'</li>
688 <li>Annotation/RNA Helix colourschemes cannot be applied
689 to alignment with groups (actually fixed in 2.8.0b1)</li>
690 <li>RNA Helices and T-Coffee Scores available as default
693 </ul> <em>Applet</em>
695 <li>Remove group option is shown even when selection is
697 <li>Apply to all groups ticked but colourscheme changes
698 don't affect groups</li>
699 <li>Documented RNA Helices and T-Coffee Scores as valid
700 colourscheme name</li>
701 <li>Annotation labels drawn on sequence IDs when
702 Annotation panel is not displayed</li>
703 <li>Increased font size for dropdown menus on OSX and
704 embedded windows</li>
707 <li>Consensus sequence for alignments/groups with a
708 single sequence were not calculated</li>
709 <li>annotation files that contain only groups imported as
710 annotation and junk sequences</li>
711 <li>Fasta files with sequences containing '*' incorrectly
712 recognised as PFAM or BLC</li>
713 <li>conservation/PID slider apply all groups option
714 doesn't affect background (2.8.0b1)
716 <li>redundancy highlighting is erratic at 0% and 100%</li>
717 <li>Remove gapped columns fails for sequences with ragged
719 <li>AMSA annotation row with leading spaces is not
720 registered correctly on import</li>
721 <li>Jalview crashes when selecting PCA analysis for
722 certain alignments</li>
723 <li>Opening the colour by annotation dialog for an
724 existing annotation based 'use original colours'
725 colourscheme loses original colours setting</li>
730 <td><div align="center">
731 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
732 <em>30/1/2014</em></strong>
736 <li>Trusted certificates for JalviewLite applet and
737 Jalview Desktop application<br />Certificate was donated by
738 <a href="https://www.certum.eu">Certum</a> to the Jalview
739 open source project).
741 <li>Jalview SRS links replaced by Uniprot and EBI-search
743 <li>Output in Stockholm format</li>
744 <li>Allow import of data from gzipped files</li>
745 <li>Export/import group and sequence associated line
746 graph thresholds</li>
747 <li>Nucleotide substitution matrix that supports RNA and
749 <li>Allow disorder predictions to be made on the current
750 selection (or visible selection) in the same way that JPred
752 <li>Groovy scripting for headless Jalview operation</li>
753 </ul> <em>Other improvements</em>
755 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
756 <li>COMBINE statement uses current SEQUENCE_REF and
757 GROUP_REF scope to group annotation rows</li>
758 <li>Support '' style escaping of quotes in Newick
760 <li>Group options for JABAWS service by command line name</li>
761 <li>Empty tooltip shown for JABA service options with a
762 link but no description</li>
763 <li>Select primary source when selecting authority in
764 database fetcher GUI</li>
765 <li>Add .mfa to FASTA file extensions recognised by
767 <li>Annotation label tooltip text wrap</li>
772 <li>Slow scrolling when lots of annotation rows are
774 <li>Lots of NPE (and slowness) after creating RNA
775 secondary structure annotation line</li>
776 <li>Sequence database accessions not imported when
777 fetching alignments from Rfam</li>
778 <li>Incorrect SHMR submission for sequences with
780 <li>View all structures does not always superpose
782 <li>Option widgets in service parameters not updated to
783 reflect user or preset settings</li>
784 <li>Null pointer exceptions for some services without
785 presets or adjustable parameters</li>
786 <li>Discover PDB IDs entry in structure menu doesn't
787 discover PDB xRefs</li>
788 <li>Exception encountered while trying to retrieve
789 features with DAS</li>
790 <li>Lowest value in annotation row isn't coloured
791 when colour by annotation (per sequence) is coloured</li>
792 <li>Keyboard mode P jumps to start of gapped region when
793 residue follows a gap</li>
794 <li>Jalview appears to hang importing an alignment with
795 Wrap as default or after enabling Wrap</li>
796 <li>'Right click to add annotations' message
797 shown in wrap mode when no annotations present</li>
798 <li>Disorder predictions fail with NPE if no automatic
799 annotation already exists on alignment</li>
800 <li>oninit javascript function should be called after
801 initialisation completes</li>
802 <li>Remove redundancy after disorder prediction corrupts
803 alignment window display</li>
804 <li>Example annotation file in documentation is invalid</li>
805 <li>Grouped line graph annotation rows are not exported
806 to annotation file</li>
807 <li>Multi-harmony analysis cannot be run when only two
809 <li>Cannot create multiple groups of line graphs with
810 several 'combine' statements in annotation file</li>
811 <li>Pressing return several times causes Number Format
812 exceptions in keyboard mode</li>
813 <li>Multi-harmony (SHMMR) method doesn't submit
814 correct partitions for input data</li>
815 <li>Translation from DNA to Amino Acids fails</li>
816 <li>Jalview fail to load newick tree with quoted label</li>
817 <li>--headless flag isn't understood</li>
818 <li>ClassCastException when generating EPS in headless
820 <li>Adjusting sequence-associated shading threshold only
821 changes one row's threshold</li>
822 <li>Preferences and Feature settings panel panel
823 doesn't open</li>
824 <li>hide consensus histogram also hides conservation and
825 quality histograms</li>
830 <td><div align="center">
831 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
833 <td><em>Application</em>
835 <li>Support for JABAWS 2.0 Services (AACon alignment
836 conservation, protein disorder and Clustal Omega)</li>
837 <li>JABAWS server status indicator in Web Services
839 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
840 in Jalview alignment window</li>
841 <li>Updated Jalview build and deploy framework for OSX
842 mountain lion, windows 7, and 8</li>
843 <li>Nucleotide substitution matrix for PCA that supports
844 RNA and ambiguity codes</li>
846 <li>Improved sequence database retrieval GUI</li>
847 <li>Support fetching and database reference look up
848 against multiple DAS sources (Fetch all from in 'fetch db
850 <li>Jalview project improvements
852 <li>Store and retrieve the 'belowAlignment'
853 flag for annotation</li>
854 <li>calcId attribute to group annotation rows on the
856 <li>Store AACon calculation settings for a view in
861 <li>horizontal scrolling gesture support</li>
862 <li>Visual progress indicator when PCA calculation is
864 <li>Simpler JABA web services menus</li>
865 <li>visual indication that web service results are still
866 being retrieved from server</li>
867 <li>Serialise the dialogs that are shown when Jalview
868 starts up for first time</li>
869 <li>Jalview user agent string for interacting with HTTP
871 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
873 <li>Examples directory and Groovy library included in
874 InstallAnywhere distribution</li>
875 </ul> <em>Applet</em>
877 <li>RNA alignment and secondary structure annotation
878 visualization applet example</li>
879 </ul> <em>General</em>
881 <li>Normalise option for consensus sequence logo</li>
882 <li>Reset button in PCA window to return dimensions to
884 <li>Allow seqspace or Jalview variant of alignment PCA
886 <li>PCA with either nucleic acid and protein substitution
888 <li>Allow windows containing HTML reports to be exported
890 <li>Interactive display and editing of RNA secondary
891 structure contacts</li>
892 <li>RNA Helix Alignment Colouring</li>
893 <li>RNA base pair logo consensus</li>
894 <li>Parse sequence associated secondary structure
895 information in Stockholm files</li>
896 <li>HTML Export database accessions and annotation
897 information presented in tooltip for sequences</li>
898 <li>Import secondary structure from LOCARNA clustalw
899 style RNA alignment files</li>
900 <li>import and visualise T-COFFEE quality scores for an
902 <li>'colour by annotation' per sequence option to
903 shade each sequence according to its associated alignment
905 <li>New Jalview Logo</li>
906 </ul> <em>Documentation and Development</em>
908 <li>documentation for score matrices used in Jalview</li>
909 <li>New Website!</li>
911 <td><em>Application</em>
913 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
914 wsdbfetch REST service</li>
915 <li>Stop windows being moved outside desktop on OSX</li>
916 <li>Filetype associations not installed for webstart
918 <li>Jalview does not always retrieve progress of a JABAWS
919 job execution in full once it is complete</li>
920 <li>revise SHMR RSBS definition to ensure alignment is
921 uploaded via ali_file parameter</li>
922 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
923 <li>View all structures superposed fails with exception</li>
924 <li>Jnet job queues forever if a very short sequence is
925 submitted for prediction</li>
926 <li>Cut and paste menu not opened when mouse clicked on
928 <li>Putting fractional value into integer text box in
929 alignment parameter dialog causes Jalview to hang</li>
930 <li>Structure view highlighting doesn't work on
932 <li>View all structures fails with exception shown in
934 <li>Characters in filename associated with PDBEntry not
935 escaped in a platform independent way</li>
936 <li>Jalview desktop fails to launch with exception when
938 <li>Tree calculation reports 'you must have 2 or more
939 sequences selected' when selection is empty</li>
940 <li>Jalview desktop fails to launch with jar signature
941 failure when java web start temporary file caching is
943 <li>DAS Sequence retrieval with range qualification
944 results in sequence xref which includes range qualification</li>
945 <li>Errors during processing of command line arguments
946 cause progress bar (JAL-898) to be removed</li>
947 <li>Replace comma for semi-colon option not disabled for
948 DAS sources in sequence fetcher</li>
949 <li>Cannot close news reader when JABAWS server warning
951 <li>Option widgets not updated to reflect user settings</li>
952 <li>Edited sequence not submitted to web service</li>
953 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
954 <li>InstallAnywhere installer doesn't unpack and run
955 on OSX Mountain Lion</li>
956 <li>Annotation panel not given a scroll bar when
957 sequences with alignment annotation are pasted into the
959 <li>Sequence associated annotation rows not associated
960 when loaded from Jalview project</li>
961 <li>Browser launch fails with NPE on java 1.7</li>
962 <li>JABAWS alignment marked as finished when job was
963 cancelled or job failed due to invalid input</li>
964 <li>NPE with v2.7 example when clicking on Tree
965 associated with all views</li>
966 <li>Exceptions when copy/paste sequences with grouped
967 annotation rows to new window</li>
968 </ul> <em>Applet</em>
970 <li>Sequence features are momentarily displayed before
971 they are hidden using hidefeaturegroups applet parameter</li>
972 <li>loading features via javascript API automatically
973 enables feature display</li>
974 <li>scrollToColumnIn javascript API method doesn't
976 </ul> <em>General</em>
978 <li>Redundancy removal fails for rna alignment</li>
979 <li>PCA calculation fails when sequence has been selected
980 and then deselected</li>
981 <li>PCA window shows grey box when first opened on OSX</li>
982 <li>Letters coloured pink in sequence logo when alignment
983 coloured with clustalx</li>
984 <li>Choosing fonts without letter symbols defined causes
985 exceptions and redraw errors</li>
986 <li>Initial PCA plot view is not same as manually
987 reconfigured view</li>
988 <li>Grouped annotation graph label has incorrect line
990 <li>Grouped annotation graph label display is corrupted
991 for lots of labels</li>
997 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1000 <td><em>Application</em>
1002 <li>Jalview Desktop News Reader</li>
1003 <li>Tweaked default layout of web services menu</li>
1004 <li>View/alignment association menu to enable user to
1005 easily specify which alignment a multi-structure view takes
1006 its colours/correspondences from</li>
1007 <li>Allow properties file location to be specified as URL</li>
1008 <li>Extend Jalview project to preserve associations
1009 between many alignment views and a single Jmol display</li>
1010 <li>Store annotation row height in Jalview project file</li>
1011 <li>Annotation row column label formatting attributes
1012 stored in project file</li>
1013 <li>Annotation row order for auto-calculated annotation
1014 rows preserved in Jalview project file</li>
1015 <li>Visual progress indication when Jalview state is
1016 saved using Desktop window menu</li>
1017 <li>Visual indication that command line arguments are
1018 still being processed</li>
1019 <li>Groovy script execution from URL</li>
1020 <li>Colour by annotation default min and max colours in
1022 <li>Automatically associate PDB files dragged onto an
1023 alignment with sequences that have high similarity and
1025 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1026 <li>'view structures' option to open many
1027 structures in same window</li>
1028 <li>Sort associated views menu option for tree panel</li>
1029 <li>Group all JABA and non-JABA services for a particular
1030 analysis function in its own submenu</li>
1031 </ul> <em>Applet</em>
1033 <li>Userdefined and autogenerated annotation rows for
1035 <li>Adjustment of alignment annotation pane height</li>
1036 <li>Annotation scrollbar for annotation panel</li>
1037 <li>Drag to reorder annotation rows in annotation panel</li>
1038 <li>'automaticScrolling' parameter</li>
1039 <li>Allow sequences with partial ID string matches to be
1040 annotated from GFF/Jalview features files</li>
1041 <li>Sequence logo annotation row in applet</li>
1042 <li>Absolute paths relative to host server in applet
1043 parameters are treated as such</li>
1044 <li>New in the JalviewLite javascript API:
1046 <li>JalviewLite.js javascript library</li>
1047 <li>Javascript callbacks for
1049 <li>Applet initialisation</li>
1050 <li>Sequence/alignment mouse-overs and selections</li>
1053 <li>scrollTo row and column alignment scrolling
1055 <li>Select sequence/alignment regions from javascript</li>
1056 <li>javascript structure viewer harness to pass
1057 messages between Jmol and Jalview when running as
1058 distinct applets</li>
1059 <li>sortBy method</li>
1060 <li>Set of applet and application examples shipped
1061 with documentation</li>
1062 <li>New example to demonstrate JalviewLite and Jmol
1063 javascript message exchange</li>
1065 </ul> <em>General</em>
1067 <li>Enable Jmol displays to be associated with multiple
1068 multiple alignments</li>
1069 <li>Option to automatically sort alignment with new tree</li>
1070 <li>User configurable link to enable redirects to a
1071 www.Jalview.org mirror</li>
1072 <li>Jmol colours option for Jmol displays</li>
1073 <li>Configurable newline string when writing alignment
1074 and other flat files</li>
1075 <li>Allow alignment annotation description lines to
1076 contain html tags</li>
1077 </ul> <em>Documentation and Development</em>
1079 <li>Add groovy test harness for bulk load testing to
1081 <li>Groovy script to load and align a set of sequences
1082 using a web service before displaying the result in the
1083 Jalview desktop</li>
1084 <li>Restructured javascript and applet api documentation</li>
1085 <li>Ant target to publish example html files with applet
1087 <li>Netbeans project for building Jalview from source</li>
1088 <li>ant task to create online javadoc for Jalview source</li>
1090 <td><em>Application</em>
1092 <li>User defined colourscheme throws exception when
1093 current built in colourscheme is saved as new scheme</li>
1094 <li>AlignFrame->Save in application pops up save
1095 dialog for valid filename/format</li>
1096 <li>Cannot view associated structure for Uniprot sequence</li>
1097 <li>PDB file association breaks for Uniprot sequence
1099 <li>Associate PDB from file dialog does not tell you
1100 which sequence is to be associated with the file</li>
1101 <li>Find All raises null pointer exception when query
1102 only matches sequence IDs</li>
1103 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1104 <li>Jalview project with Jmol views created with Jalview
1105 2.4 cannot be loaded</li>
1106 <li>Filetype associations not installed for webstart
1108 <li>Two or more chains in a single PDB file associated
1109 with sequences in different alignments do not get coloured
1110 by their associated sequence</li>
1111 <li>Visibility status of autocalculated annotation row
1112 not preserved when project is loaded</li>
1113 <li>Annotation row height and visibility attributes not
1114 stored in Jalview project</li>
1115 <li>Tree bootstraps are not preserved when saved as a
1116 Jalview project</li>
1117 <li>Envision2 workflow tooltips are corrupted</li>
1118 <li>Enabling show group conservation also enables colour
1119 by conservation</li>
1120 <li>Duplicate group associated conservation or consensus
1121 created on new view</li>
1122 <li>Annotation scrollbar not displayed after 'show
1123 all hidden annotation rows' option selected</li>
1124 <li>Alignment quality not updated after alignment
1125 annotation row is hidden then shown</li>
1126 <li>Preserve colouring of structures coloured by
1127 sequences in pre Jalview 2.7 projects</li>
1128 <li>Web service job parameter dialog is not laid out
1130 <li>Web services menu not refreshed after 'reset
1131 services' button is pressed in preferences</li>
1132 <li>Annotation off by one in Jalview v2_3 example project</li>
1133 <li>Structures imported from file and saved in project
1134 get name like jalview_pdb1234.txt when reloaded</li>
1135 <li>Jalview does not always retrieve progress of a JABAWS
1136 job execution in full once it is complete</li>
1137 </ul> <em>Applet</em>
1139 <li>Alignment height set incorrectly when lots of
1140 annotation rows are displayed</li>
1141 <li>Relative URLs in feature HTML text not resolved to
1143 <li>View follows highlighting does not work for positions
1145 <li><= shown as = in tooltip</li>
1146 <li>Export features raises exception when no features
1148 <li>Separator string used for serialising lists of IDs
1149 for javascript api is modified when separator string
1150 provided as parameter</li>
1151 <li>Null pointer exception when selecting tree leaves for
1152 alignment with no existing selection</li>
1153 <li>Relative URLs for datasources assumed to be relative
1154 to applet's codebase</li>
1155 <li>Status bar not updated after finished searching and
1156 search wraps around to first result</li>
1157 <li>StructureSelectionManager instance shared between
1158 several Jalview applets causes race conditions and memory
1160 <li>Hover tooltip and mouseover of position on structure
1161 not sent from Jmol in applet</li>
1162 <li>Certain sequences of javascript method calls to
1163 applet API fatally hang browser</li>
1164 </ul> <em>General</em>
1166 <li>View follows structure mouseover scrolls beyond
1167 position with wrapped view and hidden regions</li>
1168 <li>Find sequence position moves to wrong residue
1169 with/without hidden columns</li>
1170 <li>Sequence length given in alignment properties window
1172 <li>InvalidNumberFormat exceptions thrown when trying to
1173 import PDB like structure files</li>
1174 <li>Positional search results are only highlighted
1175 between user-supplied sequence start/end bounds</li>
1176 <li>End attribute of sequence is not validated</li>
1177 <li>Find dialog only finds first sequence containing a
1178 given sequence position</li>
1179 <li>Sequence numbering not preserved in MSF alignment
1181 <li>Jalview PDB file reader does not extract sequence
1182 from nucleotide chains correctly</li>
1183 <li>Structure colours not updated when tree partition
1184 changed in alignment</li>
1185 <li>Sequence associated secondary structure not correctly
1186 parsed in interleaved stockholm</li>
1187 <li>Colour by annotation dialog does not restore current
1189 <li>Hiding (nearly) all sequences doesn't work
1191 <li>Sequences containing lowercase letters are not
1192 properly associated with their pdb files</li>
1193 </ul> <em>Documentation and Development</em>
1195 <li>schemas/JalviewWsParamSet.xsd corrupted by
1196 ApplyCopyright tool</li>
1201 <div align="center">
1202 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1205 <td><em>Application</em>
1207 <li>New warning dialog when the Jalview Desktop cannot
1208 contact web services</li>
1209 <li>JABA service parameters for a preset are shown in
1210 service job window</li>
1211 <li>JABA Service menu entries reworded</li>
1215 <li>Modeller PIR IO broken - cannot correctly import a
1216 pir file emitted by Jalview</li>
1217 <li>Existing feature settings transferred to new
1218 alignment view created from cut'n'paste</li>
1219 <li>Improved test for mixed amino/nucleotide chains when
1220 parsing PDB files</li>
1221 <li>Consensus and conservation annotation rows
1222 occasionally become blank for all new windows</li>
1223 <li>Exception raised when right clicking above sequences
1224 in wrapped view mode</li>
1225 </ul> <em>Application</em>
1227 <li>multiple multiply aligned structure views cause cpu
1228 usage to hit 100% and computer to hang</li>
1229 <li>Web Service parameter layout breaks for long user
1230 parameter names</li>
1231 <li>Jaba service discovery hangs desktop if Jaba server
1238 <div align="center">
1239 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1242 <td><em>Application</em>
1244 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1245 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1248 <li>Web Services preference tab</li>
1249 <li>Analysis parameters dialog box and user defined
1251 <li>Improved speed and layout of Envision2 service menu</li>
1252 <li>Superpose structures using associated sequence
1254 <li>Export coordinates and projection as CSV from PCA
1256 </ul> <em>Applet</em>
1258 <li>enable javascript: execution by the applet via the
1259 link out mechanism</li>
1260 </ul> <em>Other</em>
1262 <li>Updated the Jmol Jalview interface to work with Jmol
1264 <li>The Jalview Desktop and JalviewLite applet now
1265 require Java 1.5</li>
1266 <li>Allow Jalview feature colour specification for GFF
1267 sequence annotation files</li>
1268 <li>New 'colour by label' keword in Jalview feature file
1269 type colour specification</li>
1270 <li>New Jalview Desktop Groovy API method that allows a
1271 script to check if it being run in an interactive session or
1272 in a batch operation from the Jalview command line</li>
1276 <li>clustalx colourscheme colours Ds preferentially when
1277 both D+E are present in over 50% of the column</li>
1278 </ul> <em>Application</em>
1280 <li>typo in AlignmentFrame->View->Hide->all but
1281 selected Regions menu item</li>
1282 <li>sequence fetcher replaces ',' for ';' when the ',' is
1283 part of a valid accession ID</li>
1284 <li>fatal OOM if object retrieved by sequence fetcher
1285 runs out of memory</li>
1286 <li>unhandled Out of Memory Error when viewing pca
1287 analysis results</li>
1288 <li>InstallAnywhere builds fail to launch on OS X java
1289 10.5 update 4 (due to apple Java 1.6 update)</li>
1290 <li>Installanywhere Jalview silently fails to launch</li>
1291 </ul> <em>Applet</em>
1293 <li>Jalview.getFeatureGroups() raises an
1294 ArrayIndexOutOfBoundsException if no feature groups are
1301 <div align="center">
1302 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1308 <li>Alignment prettyprinter doesn't cope with long
1310 <li>clustalx colourscheme colours Ds preferentially when
1311 both D+E are present in over 50% of the column</li>
1312 <li>nucleic acid structures retrieved from PDB do not
1313 import correctly</li>
1314 <li>More columns get selected than were clicked on when a
1315 number of columns are hidden</li>
1316 <li>annotation label popup menu not providing correct
1317 add/hide/show options when rows are hidden or none are
1319 <li>Stockholm format shown in list of readable formats,
1320 and parser copes better with alignments from RFAM.</li>
1321 <li>CSV output of consensus only includes the percentage
1322 of all symbols if sequence logo display is enabled</li>
1324 </ul> <em>Applet</em>
1326 <li>annotation panel disappears when annotation is
1328 </ul> <em>Application</em>
1330 <li>Alignment view not redrawn properly when new
1331 alignment opened where annotation panel is visible but no
1332 annotations are present on alignment</li>
1333 <li>pasted region containing hidden columns is
1334 incorrectly displayed in new alignment window</li>
1335 <li>Jalview slow to complete operations when stdout is
1336 flooded (fix is to close the Jalview console)</li>
1337 <li>typo in AlignmentFrame->View->Hide->all but
1338 selected Rregions menu item.</li>
1339 <li>inconsistent group submenu and Format submenu entry
1340 'Un' or 'Non'conserved</li>
1341 <li>Sequence feature settings are being shared by
1342 multiple distinct alignments</li>
1343 <li>group annotation not recreated when tree partition is
1345 <li>double click on group annotation to select sequences
1346 does not propagate to associated trees</li>
1347 <li>Mac OSX specific issues:
1349 <li>exception raised when mouse clicked on desktop
1350 window background</li>
1351 <li>Desktop menu placed on menu bar and application
1352 name set correctly</li>
1353 <li>sequence feature settings not wide enough for the
1354 save feature colourscheme button</li>
1363 <div align="center">
1364 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1367 <td><em>New Capabilities</em>
1369 <li>URL links generated from description line for
1370 regular-expression based URL links (applet and application)
1373 <li>Non-positional feature URL links are shown in link
1375 <li>Linked viewing of nucleic acid sequences and
1377 <li>Automatic Scrolling option in View menu to display
1378 the currently highlighted region of an alignment.</li>
1379 <li>Order an alignment by sequence length, or using the
1380 average score or total feature count for each sequence.</li>
1381 <li>Shading features by score or associated description</li>
1382 <li>Subdivide alignment and groups based on identity of
1383 selected subsequence (Make Groups from Selection).</li>
1384 <li>New hide/show options including Shift+Control+H to
1385 hide everything but the currently selected region.</li>
1386 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1387 </ul> <em>Application</em>
1389 <li>Fetch DB References capabilities and UI expanded to
1390 support retrieval from DAS sequence sources</li>
1391 <li>Local DAS Sequence sources can be added via the
1392 command line or via the Add local source dialog box.</li>
1393 <li>DAS Dbref and DbxRef feature types are parsed as
1394 database references and protein_name is parsed as
1395 description line (BioSapiens terms).</li>
1396 <li>Enable or disable non-positional feature and database
1397 references in sequence ID tooltip from View menu in
1399 <!-- <li>New hidden columns and rows and representatives capabilities
1400 in annotations file (in progress - not yet fully implemented)</li> -->
1401 <li>Group-associated consensus, sequence logos and
1402 conservation plots</li>
1403 <li>Symbol distributions for each column can be exported
1404 and visualized as sequence logos</li>
1405 <li>Optionally scale multi-character column labels to fit
1406 within each column of annotation row<!-- todo for applet -->
1408 <li>Optional automatic sort of associated alignment view
1409 when a new tree is opened.</li>
1410 <li>Jalview Java Console</li>
1411 <li>Better placement of desktop window when moving
1412 between different screens.</li>
1413 <li>New preference items for sequence ID tooltip and
1414 consensus annotation</li>
1415 <li>Client to submit sequences and IDs to Envision2 Workflows</li>
1416 <li><em>Vamsas Capabilities</em>
1418 <li>Improved VAMSAS synchronization (Jalview archive
1419 used to preserve views, structures, and tree display
1421 <li>Import of vamsas documents from disk or URL via
1423 <li>Sharing of selected regions between views and
1424 with other VAMSAS applications (Experimental feature!)</li>
1425 <li>Updated API to VAMSAS version 0.2</li>
1427 </ul> <em>Applet</em>
1429 <li>Middle button resizes annotation row height</li>
1432 <li>sortByTree (true/false) - automatically sort the
1433 associated alignment view by the tree when a new tree is
1435 <li>showTreeBootstraps (true/false) - show or hide
1436 branch bootstraps (default is to show them if available)</li>
1437 <li>showTreeDistances (true/false) - show or hide
1438 branch lengths (default is to show them if available)</li>
1439 <li>showUnlinkedTreeNodes (true/false) - indicate if
1440 unassociated nodes should be highlighted in the tree
1442 <li>heightScale and widthScale (1.0 or more) -
1443 increase the height or width of a cell in the alignment
1444 grid relative to the current font size.</li>
1447 <li>Non-positional features displayed in sequence ID
1449 </ul> <em>Other</em>
1451 <li>Features format: graduated colour definitions and
1452 specification of feature scores</li>
1453 <li>Alignment Annotations format: new keywords for group
1454 associated annotation (GROUP_REF) and annotation row display
1455 properties (ROW_PROPERTIES)</li>
1456 <li>XML formats extended to support graduated feature
1457 colourschemes, group associated annotation, and profile
1458 visualization settings.</li></td>
1461 <li>Source field in GFF files parsed as feature source
1462 rather than description</li>
1463 <li>Non-positional features are now included in sequence
1464 feature and gff files (controlled via non-positional feature
1465 visibility in tooltip).</li>
1466 <li>URL links generated for all feature links (bugfix)</li>
1467 <li>Added URL embedding instructions to features file
1469 <li>Codons containing ambiguous nucleotides translated as
1470 'X' in peptide product</li>
1471 <li>Match case switch in find dialog box works for both
1472 sequence ID and sequence string and query strings do not
1473 have to be in upper case to match case-insensitively.</li>
1474 <li>AMSA files only contain first column of
1475 multi-character column annotation labels</li>
1476 <li>Jalview Annotation File generation/parsing consistent
1477 with documentation (e.g. Stockholm annotation can be
1478 exported and re-imported)</li>
1479 <li>PDB files without embedded PDB IDs given a friendly
1481 <li>Find incrementally searches ID string matches as well
1482 as subsequence matches, and correctly reports total number
1486 <li>Better handling of exceptions during sequence
1488 <li>Dasobert generated non-positional feature URL
1489 link text excludes the start_end suffix</li>
1490 <li>DAS feature and source retrieval buttons disabled
1491 when fetch or registry operations in progress.</li>
1492 <li>PDB files retrieved from URLs are cached properly</li>
1493 <li>Sequence description lines properly shared via
1495 <li>Sequence fetcher fetches multiple records for all
1497 <li>Ensured that command line das feature retrieval
1498 completes before alignment figures are generated.</li>
1499 <li>Reduced time taken when opening file browser for
1501 <li>isAligned check prior to calculating tree, PCA or
1502 submitting an MSA to JNet now excludes hidden sequences.</li>
1503 <li>User defined group colours properly recovered
1504 from Jalview projects.</li>
1513 <div align="center">
1514 <strong>2.4.0.b2</strong><br> 28/10/2009
1519 <li>Experimental support for google analytics usage
1521 <li>Jalview privacy settings (user preferences and docs).</li>
1526 <li>Race condition in applet preventing startup in
1528 <li>Exception when feature created from selection beyond
1529 length of sequence.</li>
1530 <li>Allow synthetic PDB files to be imported gracefully</li>
1531 <li>Sequence associated annotation rows associate with
1532 all sequences with a given id</li>
1533 <li>Find function matches case-insensitively for sequence
1534 ID string searches</li>
1535 <li>Non-standard characters do not cause pairwise
1536 alignment to fail with exception</li>
1537 </ul> <em>Application Issues</em>
1539 <li>Sequences are now validated against EMBL database</li>
1540 <li>Sequence fetcher fetches multiple records for all
1542 </ul> <em>InstallAnywhere Issues</em>
1544 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1545 issue with installAnywhere mechanism)</li>
1546 <li>Command line launching of JARs from InstallAnywhere
1547 version (java class versioning error fixed)</li>
1554 <div align="center">
1555 <strong>2.4</strong><br> 27/8/2008
1558 <td><em>User Interface</em>
1560 <li>Linked highlighting of codon and amino acid from
1561 translation and protein products</li>
1562 <li>Linked highlighting of structure associated with
1563 residue mapping to codon position</li>
1564 <li>Sequence Fetcher provides example accession numbers
1565 and 'clear' button</li>
1566 <li>MemoryMonitor added as an option under Desktop's
1568 <li>Extract score function to parse whitespace separated
1569 numeric data in description line</li>
1570 <li>Column labels in alignment annotation can be centred.</li>
1571 <li>Tooltip for sequence associated annotation give name
1573 </ul> <em>Web Services and URL fetching</em>
1575 <li>JPred3 web service</li>
1576 <li>Prototype sequence search client (no public services
1578 <li>Fetch either seed alignment or full alignment from
1580 <li>URL Links created for matching database cross
1581 references as well as sequence ID</li>
1582 <li>URL Links can be created using regular-expressions</li>
1583 </ul> <em>Sequence Database Connectivity</em>
1585 <li>Retrieval of cross-referenced sequences from other
1587 <li>Generalised database reference retrieval and
1588 validation to all fetchable databases</li>
1589 <li>Fetch sequences from DAS sources supporting the
1590 sequence command</li>
1591 </ul> <em>Import and Export</em>
1592 <li>export annotation rows as CSV for spreadsheet import</li>
1593 <li>Jalview projects record alignment dataset associations,
1594 EMBL products, and cDNA sequence mappings</li>
1595 <li>Sequence Group colour can be specified in Annotation
1597 <li>Ad-hoc colouring of group in Annotation File using RGB
1598 triplet as name of colourscheme</li>
1599 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1601 <li>treenode binding for VAMSAS tree exchange</li>
1602 <li>local editing and update of sequences in VAMSAS
1603 alignments (experimental)</li>
1604 <li>Create new or select existing session to join</li>
1605 <li>load and save of vamsas documents</li>
1606 </ul> <em>Application command line</em>
1608 <li>-tree parameter to open trees (introduced for passing
1610 <li>-fetchfrom command line argument to specify nicknames
1611 of DAS servers to query for alignment features</li>
1612 <li>-dasserver command line argument to add new servers
1613 that are also automatically queried for features</li>
1614 <li>-groovy command line argument executes a given groovy
1615 script after all input data has been loaded and parsed</li>
1616 </ul> <em>Applet-Application data exchange</em>
1618 <li>Trees passed as applet parameters can be passed to
1619 application (when using "View in full
1620 application")</li>
1621 </ul> <em>Applet Parameters</em>
1623 <li>feature group display control parameter</li>
1624 <li>debug parameter</li>
1625 <li>showbutton parameter</li>
1626 </ul> <em>Applet API methods</em>
1628 <li>newView public method</li>
1629 <li>Window (current view) specific get/set public methods</li>
1630 <li>Feature display control methods</li>
1631 <li>get list of currently selected sequences</li>
1632 </ul> <em>New Jalview distribution features</em>
1634 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1635 <li>RELEASE file gives build properties for the latest
1636 Jalview release.</li>
1637 <li>Java 1.1 Applet build made easier and donotobfuscate
1638 property controls execution of obfuscator</li>
1639 <li>Build target for generating source distribution</li>
1640 <li>Debug flag for javacc</li>
1641 <li>.jalview_properties file is documented (slightly) in
1642 jalview.bin.Cache</li>
1643 <li>Continuous Build Integration for stable and
1644 development version of Application, Applet and source
1649 <li>selected region output includes visible annotations
1650 (for certain formats)</li>
1651 <li>edit label/displaychar contains existing label/char
1653 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1654 <li>shorter peptide product names from EMBL records</li>
1655 <li>Newick string generator makes compact representations</li>
1656 <li>bootstrap values parsed correctly for tree files with
1658 <li>pathological filechooser bug avoided by not allowing
1659 filenames containing a ':'</li>
1660 <li>Fixed exception when parsing GFF files containing
1661 global sequence features</li>
1662 <li>Alignment datasets are finalized only when number of
1663 references from alignment sequences goes to zero</li>
1664 <li>Close of tree branch colour box without colour
1665 selection causes cascading exceptions</li>
1666 <li>occasional negative imgwidth exceptions</li>
1667 <li>better reporting of non-fatal warnings to user when
1668 file parsing fails.</li>
1669 <li>Save works when Jalview project is default format</li>
1670 <li>Save as dialog opened if current alignment format is
1671 not a valid output format</li>
1672 <li>Uniprot canonical names introduced for both das and
1674 <li>Histidine should be midblue (not pink!) in Zappo</li>
1675 <li>error messages passed up and output when data read
1677 <li>edit undo recovers previous dataset sequence when
1678 sequence is edited</li>
1679 <li>allow PDB files without pdb ID HEADER lines (like
1680 those generated by MODELLER) to be read in properly</li>
1681 <li>allow reading of JPred concise files as a normal
1683 <li>Stockholm annotation parsing and alignment properties
1684 import fixed for PFAM records</li>
1685 <li>Structure view windows have correct name in Desktop
1687 <li>annotation consisting of sequence associated scores
1688 can be read and written correctly to annotation file</li>
1689 <li>Aligned cDNA translation to aligned peptide works
1691 <li>Fixed display of hidden sequence markers and
1692 non-italic font for representatives in Applet</li>
1693 <li>Applet Menus are always embedded in applet window on
1695 <li>Newly shown features appear at top of stack (in
1697 <li>Annotations added via parameter not drawn properly
1698 due to null pointer exceptions</li>
1699 <li>Secondary structure lines are drawn starting from
1700 first column of alignment</li>
1701 <li>Uniprot XML import updated for new schema release in
1703 <li>Sequence feature to sequence ID match for Features
1704 file is case-insensitive</li>
1705 <li>Sequence features read from Features file appended to
1706 all sequences with matching IDs</li>
1707 <li>PDB structure coloured correctly for associated views
1708 containing a sub-sequence</li>
1709 <li>PDB files can be retrieved by applet from Jar files</li>
1710 <li>feature and annotation file applet parameters
1711 referring to different directories are retrieved correctly</li>
1712 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1713 <li>Fixed application hang whilst waiting for
1714 splash-screen version check to complete</li>
1715 <li>Applet properly URLencodes input parameter values
1716 when passing them to the launchApp service</li>
1717 <li>display name and local features preserved in results
1718 retrieved from web service</li>
1719 <li>Visual delay indication for sequence retrieval and
1720 sequence fetcher initialisation</li>
1721 <li>updated Application to use DAS 1.53e version of
1722 dasobert DAS client</li>
1723 <li>Re-instated Full AMSA support and .amsa file
1725 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1733 <div align="center">
1734 <strong>2.3</strong><br> 9/5/07
1739 <li>Jmol 11.0.2 integration</li>
1740 <li>PDB views stored in Jalview XML files</li>
1741 <li>Slide sequences</li>
1742 <li>Edit sequence in place</li>
1743 <li>EMBL CDS features</li>
1744 <li>DAS Feature mapping</li>
1745 <li>Feature ordering</li>
1746 <li>Alignment Properties</li>
1747 <li>Annotation Scores</li>
1748 <li>Sort by scores</li>
1749 <li>Feature/annotation editing in applet</li>
1754 <li>Headless state operation in 2.2.1</li>
1755 <li>Incorrect and unstable DNA pairwise alignment</li>
1756 <li>Cut and paste of sequences with annotation</li>
1757 <li>Feature group display state in XML</li>
1758 <li>Feature ordering in XML</li>
1759 <li>blc file iteration selection using filename # suffix</li>
1760 <li>Stockholm alignment properties</li>
1761 <li>Stockhom alignment secondary structure annotation</li>
1762 <li>2.2.1 applet had no feature transparency</li>
1763 <li>Number pad keys can be used in cursor mode</li>
1764 <li>Structure Viewer mirror image resolved</li>
1771 <div align="center">
1772 <strong>2.2.1</strong><br> 12/2/07
1777 <li>Non standard characters can be read and displayed
1778 <li>Annotations/Features can be imported/exported to the
1780 <li>Applet allows editing of sequence/annotation/group
1781 name & description
1782 <li>Preference setting to display sequence name in
1784 <li>Annotation file format extended to allow
1785 Sequence_groups to be defined
1786 <li>Default opening of alignment overview panel can be
1787 specified in preferences
1788 <li>PDB residue numbering annotation added to associated
1794 <li>Applet crash under certain Linux OS with Java 1.6
1796 <li>Annotation file export / import bugs fixed
1797 <li>PNG / EPS image output bugs fixed
1803 <div align="center">
1804 <strong>2.2</strong><br> 27/11/06
1809 <li>Multiple views on alignment
1810 <li>Sequence feature editing
1811 <li>"Reload" alignment
1812 <li>"Save" to current filename
1813 <li>Background dependent text colour
1814 <li>Right align sequence ids
1815 <li>User-defined lower case residue colours
1818 <li>Menu item accelerator keys
1819 <li>Control-V pastes to current alignment
1820 <li>Cancel button for DAS Feature Fetching
1821 <li>PCA and PDB Viewers zoom via mouse roller
1822 <li>User-defined sub-tree colours and sub-tree selection
1825 <li>'New Window' button on the 'Output to Text box'
1830 <li>New memory efficient Undo/Redo System
1831 <li>Optimised symbol lookups and conservation/consensus
1833 <li>Region Conservation/Consensus recalculated after
1835 <li>Fixed Remove Empty Columns Bug (empty columns at end
1837 <li>Slowed DAS Feature Fetching for increased robustness.
1840 <li>Made angle brackets in ASCII feature descriptions
1842 <li>Re-instated Zoom function for PCA
1843 <li>Sequence descriptions conserved in web service
1845 <li>Uniprot ID discoverer uses any word separated by
1847 <li>WsDbFetch query/result association resolved
1848 <li>Tree leaf to sequence mapping improved
1849 <li>Smooth fonts switch moved to FontChooser dialog box.
1857 <div align="center">
1858 <strong>2.1.1</strong><br> 12/9/06
1863 <li>Copy consensus sequence to clipboard</li>
1868 <li>Image output - rightmost residues are rendered if
1869 sequence id panel has been resized</li>
1870 <li>Image output - all offscreen group boundaries are
1872 <li>Annotation files with sequence references - all
1873 elements in file are relative to sequence position</li>
1874 <li>Mac Applet users can use Alt key for group editing</li>
1880 <div align="center">
1881 <strong>2.1</strong><br> 22/8/06
1886 <li>MAFFT Multiple Alignment in default Web Service list</li>
1887 <li>DAS Feature fetching</li>
1888 <li>Hide sequences and columns</li>
1889 <li>Export Annotations and Features</li>
1890 <li>GFF file reading / writing</li>
1891 <li>Associate structures with sequences from local PDB
1893 <li>Add sequences to exisiting alignment</li>
1894 <li>Recently opened files / URL lists</li>
1895 <li>Applet can launch the full application</li>
1896 <li>Applet has transparency for features (Java 1.2
1898 <li>Applet has user defined colours parameter</li>
1899 <li>Applet can load sequences from parameter
1900 "sequence<em>x</em>"
1906 <li>Redundancy Panel reinstalled in the Applet</li>
1907 <li>Monospaced font - EPS / rescaling bug fixed</li>
1908 <li>Annotation files with sequence references bug fixed</li>
1914 <div align="center">
1915 <strong>2.08.1</strong><br> 2/5/06
1920 <li>Change case of selected region from Popup menu</li>
1921 <li>Choose to match case when searching</li>
1922 <li>Middle mouse button and mouse movement can compress /
1923 expand the visible width and height of the alignment</li>
1928 <li>Annotation Panel displays complete JNet results</li>
1934 <div align="center">
1935 <strong>2.08b</strong><br> 18/4/06
1941 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1942 <li>Righthand label on wrapped alignments shows correct
1949 <div align="center">
1950 <strong>2.08</strong><br> 10/4/06
1955 <li>Editing can be locked to the selection area</li>
1956 <li>Keyboard editing</li>
1957 <li>Create sequence features from searches</li>
1958 <li>Precalculated annotations can be loaded onto
1960 <li>Features file allows grouping of features</li>
1961 <li>Annotation Colouring scheme added</li>
1962 <li>Smooth fonts off by default - Faster rendering</li>
1963 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1968 <li>Drag & Drop fixed on Linux</li>
1969 <li>Jalview Archive file faster to load/save, sequence
1970 descriptions saved.</li>
1976 <div align="center">
1977 <strong>2.07</strong><br> 12/12/05
1982 <li>PDB Structure Viewer enhanced</li>
1983 <li>Sequence Feature retrieval and display enhanced</li>
1984 <li>Choose to output sequence start-end after sequence
1985 name for file output</li>
1986 <li>Sequence Fetcher WSDBFetch@EBI</li>
1987 <li>Applet can read feature files, PDB files and can be
1988 used for HTML form input</li>
1993 <li>HTML output writes groups and features</li>
1994 <li>Group editing is Control and mouse click</li>
1995 <li>File IO bugs</li>
2001 <div align="center">
2002 <strong>2.06</strong><br> 28/9/05
2007 <li>View annotations in wrapped mode</li>
2008 <li>More options for PCA viewer</li>
2013 <li>GUI bugs resolved</li>
2014 <li>Runs with -nodisplay from command line</li>
2020 <div align="center">
2021 <strong>2.05b</strong><br> 15/9/05
2026 <li>Choose EPS export as lineart or text</li>
2027 <li>Jar files are executable</li>
2028 <li>Can read in Uracil - maps to unknown residue</li>
2033 <li>Known OutOfMemory errors give warning message</li>
2034 <li>Overview window calculated more efficiently</li>
2035 <li>Several GUI bugs resolved</li>
2041 <div align="center">
2042 <strong>2.05</strong><br> 30/8/05
2047 <li>Edit and annotate in "Wrapped" view</li>
2052 <li>Several GUI bugs resolved</li>
2058 <div align="center">
2059 <strong>2.04</strong><br> 24/8/05
2064 <li>Hold down mouse wheel & scroll to change font
2070 <li>Improved JPred client reliability</li>
2071 <li>Improved loading of Jalview files</li>
2077 <div align="center">
2078 <strong>2.03</strong><br> 18/8/05
2083 <li>Set Proxy server name and port in preferences</li>
2084 <li>Multiple URL links from sequence ids</li>
2085 <li>User Defined Colours can have a scheme name and added
2087 <li>Choose to ignore gaps in consensus calculation</li>
2088 <li>Unix users can set default web browser</li>
2089 <li>Runs without GUI for batch processing</li>
2090 <li>Dynamically generated Web Service Menus</li>
2095 <li>InstallAnywhere download for Sparc Solaris</li>
2101 <div align="center">
2102 <strong>2.02</strong><br> 18/7/05
2108 <li>Copy & Paste order of sequences maintains
2109 alignment order.</li>
2115 <div align="center">
2116 <strong>2.01</strong><br> 12/7/05
2121 <li>Use delete key for deleting selection.</li>
2122 <li>Use Mouse wheel to scroll sequences.</li>
2123 <li>Help file updated to describe how to add alignment
2125 <li>Version and build date written to build properties
2127 <li>InstallAnywhere installation will check for updates
2128 at launch of Jalview.</li>
2133 <li>Delete gaps bug fixed.</li>
2134 <li>FileChooser sorts columns.</li>
2135 <li>Can remove groups one by one.</li>
2136 <li>Filechooser icons installed.</li>
2137 <li>Finder ignores return character when searching.
2138 Return key will initiate a search.<br>
2145 <div align="center">
2146 <strong>2.0</strong><br> 20/6/05
2151 <li>New codebase</li>