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 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
71 <li><!-- JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
72 <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
73 <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
74 <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
75 <li><!-- JAL-2183-->Free-text search client for UniProt using the UniProt web API</li>
86 <li><!-- JAL-2077 -->reinstate CTRL-click for opening pop-up menu on OSX</li>
87 <li><!-- JAL-2018-->Export features in Jalview format (again) includes graduated colourschemes</li>
88 <li><!-- JAL-1722, JAL-2001-->More responsive when working with big alignments and lots of hidden columns</li>
89 <li><!-- JAL-2053-->Hidden column markers not always rendered at right of alignment window</li>
90 <li><!-- JAL-2067, JAL- -->Tidied up links in help file table of contents</li>
91 <li><!-- JAL-2072 -->Feature based tree calculation not shown for DNA alignments</li>
92 <li><!-- JAL-2075 -->Hidden columns ignored during feature based tree calculation</li>
93 <li><!-- JAL-2065 -->Alignment view stops updating when show unconserved enabled for group on alignment</li>
94 <li><!-- JAL-2086 -->Cannot insert gaps into sequence when set as reference</li>
95 <li><!-- JAL-2146 -->Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation</li>
96 <li><!-- JAL-2099 -->Incorrect column numbers in ruler when hidden columns present</li>
101 <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
102 <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
103 <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</li>
104 <li><!-- JAL-2030-->InstallAnywhere distribution fails when launching Chimera</li>
105 <li><!-- JAL-2080-->Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)</li>
106 <li><!-- JAL-2085 -->Cannot save project when view has a reference sequence defined</li>
107 <li><!-- JAL-1011 -->Columns are suddenly selected in other alignments and views when revealing hidden columns</li>
108 <li><!-- JAL-1989 -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
109 <li><!-- JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
110 <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
112 <!-- may exclude, this is an external service stability issue JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
122 <td width="60" nowrap>
124 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
125 <em>16/10/2015</em></strong>
130 <li>Time stamps for signed Jalview application and applet
137 <li>Duplicate group consensus and conservation rows
138 shown when tree is partitioned</li>
139 <li>Erratic behaviour when tree partitions made with
140 multiple cDNA/Protein split views</li>
146 <td width="60" nowrap>
148 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
149 <em>8/10/2015</em></strong>
154 <li>Updated Spanish translations of localized text for
156 </ul> <em>Application</em>
158 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
159 <li>Signed OSX InstallAnywhere installer<br></li>
160 <li>Support for per-sequence based annotations in BioJSON</li>
161 </ul> <em>Applet</em>
163 <li>Split frame example added to applet examples page</li>
169 <li>Mapping of cDNA to protein in split frames
170 incorrect when sequence start > 1</li>
171 <li>Broken images in filter column by annotation dialog
173 <li>Feature colours not parsed from features file</li>
174 <li>Exceptions and incomplete link URLs recovered when
175 loading a features file containing HTML tags in feature
181 <li>Annotations corrupted after BioJS export and
183 <li>Incorrect sequence limits after Fetch DB References
184 with 'trim retrieved sequences'</li>
185 <li>Incorrect warning about deleting all data when
186 deleting selected columns</li>
187 <li>Patch to build system for shipping properly signed
188 JNLP templates for webstart launch</li>
189 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
190 unreleased structures for download or viewing</li>
191 <li>Tab/space/return keystroke operation of EMBL-PDBe
192 fetcher/viewer dialogs works correctly</li>
193 <li>Disabled 'minimise' button on Jalview windows
194 running on OSX to workaround redraw hang bug</li>
195 <li>Split cDNA/Protein view position and geometry not
196 recovered from jalview project</li>
197 <li>Initial enabled/disabled state of annotation menu
198 sorter 'show autocalculated first/last' corresponds to
200 <li>Restoring of Clustal, RNA Helices and T-Coffee
201 color schemes from BioJSON</li>
205 <li>Reorder sequences mirrored in cDNA/Protein split
207 <li>Applet with Jmol examples not loading correctly</li>
213 <td><div align="center">
214 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
218 <li>Linked visualisation and analysis of DNA and Protein
221 <li>Translated cDNA alignments shown as split protein
222 and DNA alignment views</li>
223 <li>Codon consensus annotation for linked protein and
224 cDNA alignment views</li>
225 <li>Link cDNA or Protein product sequences by loading
226 them onto Protein or cDNA alignments</li>
227 <li>Reconstruct linked cDNA alignment from aligned
228 protein sequences</li>
231 <li>Jmol integration updated to Jmol v14.2.14</li>
232 <li>Import and export of Jalview alignment views as <a
233 href="features/bioJsonFormat.html">BioJSON</a></li>
234 <li>New alignment annotation file statements for
235 reference sequences and marking hidden columns</li>
236 <li>Reference sequence based alignment shading to
237 highlight variation</li>
238 <li>Select or hide columns according to alignment
240 <li>Find option for locating sequences by description</li>
241 <li>Conserved physicochemical properties shown in amino
242 acid conservation row</li>
243 <li>Alignments can be sorted by number of RNA helices</li>
244 </ul> <em>Application</em>
246 <li>New cDNA/Protein analysis capabilities
248 <li>Get Cross-References should open a Split Frame
249 view with cDNA/Protein</li>
250 <li>Detect when nucleotide sequences and protein
251 sequences are placed in the same alignment</li>
252 <li>Split cDNA/Protein views are saved in Jalview
257 <li>Use REST API to talk to Chimera</li>
258 <li>Selected regions in Chimera are highlighted in linked
261 <li>VARNA RNA viewer updated to v3.93</li>
262 <li>VARNA views are saved in Jalview Projects</li>
263 <li>Pseudoknots displayed as Jalview RNA annotation can
264 be shown in VARNA</li>
266 <li>Make groups for selection uses marked columns as well
267 as the active selected region</li>
269 <li>Calculate UPGMA and NJ trees using sequence feature
271 <li>New Export options
273 <li>New Export Settings dialog to control hidden
274 region export in flat file generation</li>
276 <li>Export alignment views for display with the <a
277 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
279 <li>Export scrollable SVG in HTML page</li>
280 <li>Optional embedding of BioJSON data when exporting
281 alignment figures to HTML</li>
283 <li>3D structure retrieval and display
285 <li>Free text and structured queries with the PDBe
287 <li>PDBe Search API based discovery and selection of
288 PDB structures for a sequence set</li>
292 <li>JPred4 employed for protein secondary structure
294 <li>Hide Insertions menu option to hide unaligned columns
295 for one or a group of sequences</li>
296 <li>Automatically hide insertions in alignments imported
297 from the JPred4 web server</li>
298 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
299 system on OSX<br />LGPL libraries courtesy of <a
300 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
302 <li>changed 'View nucleotide structure' submenu to 'View
303 VARNA 2D Structure'</li>
304 <li>change "View protein structure" menu option to "3D
307 </ul> <em>Applet</em>
309 <li>New layout for applet example pages</li>
310 <li>New parameters to enable SplitFrame view
311 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
312 <li>New example demonstrating linked viewing of cDNA and
313 Protein alignments</li>
314 </ul> <em>Development and deployment</em>
316 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
317 <li>Include installation type and git revision in build
318 properties and console log output</li>
319 <li>Jalview Github organisation, and new github site for
320 storing BioJsMSA Templates</li>
321 <li>Jalview's unit tests now managed with TestNG</li>
324 <!-- <em>General</em>
326 </ul> --> <!-- issues resolved --> <em>Application</em>
328 <li>Escape should close any open find dialogs</li>
329 <li>Typo in select-by-features status report</li>
330 <li>Consensus RNA secondary secondary structure
331 predictions are not highlighted in amber</li>
332 <li>Missing gap character in v2.7 example file means
333 alignment appears unaligned when pad-gaps is not enabled</li>
334 <li>First switch to RNA Helices colouring doesn't colour
335 associated structure views</li>
336 <li>ID width preference option is greyed out when auto
337 width checkbox not enabled</li>
338 <li>Stopped a warning dialog from being shown when
339 creating user defined colours</li>
340 <li>'View Mapping' in structure viewer shows sequence
341 mappings for just that viewer's sequences</li>
342 <li>Workaround for superposing PDB files containing
343 multiple models in Chimera</li>
344 <li>Report sequence position in status bar when hovering
345 over Jmol structure</li>
346 <li>Cannot output gaps as '.' symbols with Selection ->
347 output to text box</li>
348 <li>Flat file exports of alignments with hidden columns
349 have incorrect sequence start/end</li>
350 <li>'Aligning' a second chain to a Chimera structure from
352 <li>Colour schemes applied to structure viewers don't
353 work for nucleotide</li>
354 <li>Loading/cut'n'pasting an empty or invalid file leads
355 to a grey/invisible alignment window</li>
356 <li>Exported Jpred annotation from a sequence region
357 imports to different position</li>
358 <li>Space at beginning of sequence feature tooltips shown
359 on some platforms</li>
360 <li>Chimera viewer 'View | Show Chain' menu is not
362 <li>'New View' fails with a Null Pointer Exception in
363 console if Chimera has been opened</li>
364 <li>Mouseover to Chimera not working</li>
365 <li>Miscellaneous ENA XML feature qualifiers not
367 <li>NPE in annotation renderer after 'Extract Scores'</li>
368 <li>If two structures in one Chimera window, mouseover of
369 either sequence shows on first structure</li>
370 <li>'Show annotations' options should not make
371 non-positional annotations visible</li>
372 <li>Subsequence secondary structure annotation not shown
373 in right place after 'view flanking regions'</li>
374 <li>File Save As type unset when current file format is
376 <li>Save as '.jar' option removed for saving Jalview
378 <li>Colour by Sequence colouring in Chimera more
380 <li>Cannot 'add reference annotation' for a sequence in
381 several views on same alignment</li>
382 <li>Cannot show linked products for EMBL / ENA records</li>
383 <li>Jalview's tooltip wraps long texts containing no
385 </ul> <em>Applet</em>
387 <li>Jmol to JalviewLite mouseover/link not working</li>
388 <li>JalviewLite can't import sequences with ID
389 descriptions containing angle brackets</li>
390 </ul> <em>General</em>
392 <li>Cannot export and reimport RNA secondary structure
393 via jalview annotation file</li>
394 <li>Random helix colour palette for colour by annotation
395 with RNA secondary structure</li>
396 <li>Mouseover to cDNA from STOP residue in protein
397 translation doesn't work.</li>
398 <li>hints when using the select by annotation dialog box</li>
399 <li>Jmol alignment incorrect if PDB file has alternate CA
401 <li>FontChooser message dialog appears to hang after
402 choosing 1pt font</li>
403 <li>Peptide secondary structure incorrectly imported from
404 annotation file when annotation display text includes 'e' or
406 <li>Cannot set colour of new feature type whilst creating
408 <li>cDNA translation alignment should not be sequence
410 <li>'Show unconserved' doesn't work for lower case
412 <li>Nucleotide ambiguity codes involving R not recognised</li>
413 </ul> <em>Deployment and Documentation</em>
415 <li>Applet example pages appear different to the rest of
417 </ul> <em>Application Known issues</em>
419 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
420 <li>Misleading message appears after trying to delete
422 <li>Jalview icon not shown in dock after InstallAnywhere
423 version launches</li>
424 <li>Fetching EMBL reference for an RNA sequence results
425 fails with a sequence mismatch</li>
426 <li>Corrupted or unreadable alignment display when
427 scrolling alignment to right</li>
428 <li>ArrayIndexOutOfBoundsException thrown when remove
429 empty columns called on alignment with ragged gapped ends</li>
430 <li>auto calculated alignment annotation rows do not get
431 placed above or below non-autocalculated rows</li>
432 <li>Jalview dekstop becomes sluggish at full screen in
433 ultra-high resolution</li>
434 <li>Cannot disable consensus calculation independently of
435 quality and conservation</li>
436 <li>Mouseover highlighting between cDNA and protein can
437 become sluggish with more than one splitframe shown</li>
438 </ul> <em>Applet Known Issues</em>
440 <li>Core PDB parsing code requires Jmol</li>
441 <li>Sequence canvas panel goes white when alignment
442 window is being resized</li>
448 <td><div align="center">
449 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
453 <li>Updated Java code signing certificate donated by
455 <li>Features and annotation preserved when performing
456 pairwise alignment</li>
457 <li>RNA pseudoknot annotation can be
458 imported/exported/displayed</li>
459 <li>'colour by annotation' can colour by RNA and
460 protein secondary structure</li>
461 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
462 post-hoc with 2.9 release</em>)
465 </ul> <em>Application</em>
467 <li>Extract and display secondary structure for sequences
468 with 3D structures</li>
469 <li>Support for parsing RNAML</li>
470 <li>Annotations menu for layout
472 <li>sort sequence annotation rows by alignment</li>
473 <li>place sequence annotation above/below alignment
476 <li>Output in Stockholm format</li>
477 <li>Internationalisation: improved Spanish (es)
479 <li>Structure viewer preferences tab</li>
480 <li>Disorder and Secondary Structure annotation tracks
481 shared between alignments</li>
482 <li>UCSF Chimera launch and linked highlighting from
484 <li>Show/hide all sequence associated annotation rows for
485 all or current selection</li>
486 <li>disorder and secondary structure predictions
487 available as dataset annotation</li>
488 <li>Per-sequence rna helices colouring</li>
491 <li>Sequence database accessions imported when fetching
492 alignments from Rfam</li>
493 <li>update VARNA version to 3.91</li>
495 <li>New groovy scripts for exporting aligned positions,
496 conservation values, and calculating sum of pairs scores.</li>
497 <li>Command line argument to set default JABAWS server</li>
498 <li>include installation type in build properties and
499 console log output</li>
500 <li>Updated Jalview project format to preserve dataset
504 <!-- issues resolved --> <em>Application</em>
506 <li>Distinguish alignment and sequence associated RNA
507 structure in structure->view->VARNA</li>
508 <li>Raise dialog box if user deletes all sequences in an
510 <li>Pressing F1 results in documentation opening twice</li>
511 <li>Sequence feature tooltip is wrapped</li>
512 <li>Double click on sequence associated annotation
513 selects only first column</li>
514 <li>Redundancy removal doesn't result in unlinked
515 leaves shown in tree</li>
516 <li>Undos after several redundancy removals don't undo
518 <li>Hide sequence doesn't hide associated annotation</li>
519 <li>User defined colours dialog box too big to fit on
520 screen and buttons not visible</li>
521 <li>author list isn't updated if already written to
522 Jalview properties</li>
523 <li>Popup menu won't open after retrieving sequence
525 <li>File open window for associate PDB doesn't open</li>
526 <li>Left-then-right click on a sequence id opens a
527 browser search window</li>
528 <li>Cannot open sequence feature shading/sort popup menu
529 in feature settings dialog</li>
530 <li>better tooltip placement for some areas of Jalview
532 <li>Allow addition of JABAWS Server which doesn't
534 <li>Web services parameters dialog box is too large to
536 <li>Muscle nucleotide alignment preset obscured by
538 <li>JABAWS preset submenus don't contain newly
539 defined user preset</li>
540 <li>MSA web services warns user if they were launched
541 with invalid input</li>
542 <li>Jalview cannot contact DAS Registy when running on
545 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
546 'Superpose with' submenu not shown when new view
550 </ul> <!-- <em>Applet</em>
552 </ul> <em>General</em>
554 </ul>--> <em>Deployment and Documentation</em>
556 <li>2G and 1G options in launchApp have no effect on
557 memory allocation</li>
558 <li>launchApp service doesn't automatically open
559 www.jalview.org/examples/exampleFile.jar if no file is given</li>
561 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
562 InstallAnywhere reports cannot find valid JVM when Java
565 </ul> <em>Application Known issues</em>
568 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
569 corrupted or unreadable alignment display when scrolling
573 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
574 retrieval fails but progress bar continues for DAS retrieval
575 with large number of ID
578 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
579 flatfile output of visible region has incorrect sequence
583 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
584 rna structure consensus doesn't update when secondary
585 structure tracks are rearranged
588 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
589 invalid rna structure positional highlighting does not
590 highlight position of invalid base pairs
593 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
594 out of memory errors are not raised when saving Jalview
595 project from alignment window file menu
598 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
599 Switching to RNA Helices colouring doesn't propagate to
603 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
604 colour by RNA Helices not enabled when user created
605 annotation added to alignment
608 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
609 Jalview icon not shown on dock in Mountain Lion/Webstart
611 </ul> <em>Applet Known Issues</em>
614 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
615 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
618 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
619 Jalview and Jmol example not compatible with IE9
622 <li>Sort by annotation score doesn't reverse order
628 <td><div align="center">
629 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
632 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
635 <li>Internationalisation of user interface (usually
636 called i18n support) and translation for Spanish locale</li>
637 <li>Define/Undefine group on current selection with
638 Ctrl-G/Shift Ctrl-G</li>
639 <li>Improved group creation/removal options in
640 alignment/sequence Popup menu</li>
641 <li>Sensible precision for symbol distribution
642 percentages shown in logo tooltip.</li>
643 <li>Annotation panel height set according to amount of
644 annotation when alignment first opened</li>
645 </ul> <em>Application</em>
647 <li>Interactive consensus RNA secondary structure
648 prediction VIENNA RNAAliFold JABA 2.1 service</li>
649 <li>Select columns containing particular features from
650 Feature Settings dialog</li>
651 <li>View all 'representative' PDB structures for selected
653 <li>Update Jalview project format:
655 <li>New file extension for Jalview projects '.jvp'</li>
656 <li>Preserve sequence and annotation dataset (to
657 store secondary structure annotation,etc)</li>
658 <li>Per group and alignment annotation and RNA helix
662 <li>New similarity measures for PCA and Tree calculation
664 <li>Experimental support for retrieval and viewing of
665 flanking regions for an alignment</li>
669 <!-- issues resolved --> <em>Application</em>
671 <li>logo keeps spinning and status remains at queued or
672 running after job is cancelled</li>
673 <li>cannot export features from alignments imported from
674 Jalview/VAMSAS projects</li>
675 <li>Buggy slider for web service parameters that take
677 <li>Newly created RNA secondary structure line doesn't
678 have 'display all symbols' flag set</li>
679 <li>T-COFFEE alignment score shading scheme and other
680 annotation shading not saved in Jalview project</li>
681 <li>Local file cannot be loaded in freshly downloaded
683 <li>Jalview icon not shown on dock in Mountain
685 <li>Load file from desktop file browser fails</li>
686 <li>Occasional NPE thrown when calculating large trees</li>
687 <li>Cannot reorder or slide sequences after dragging an
688 alignment onto desktop</li>
689 <li>Colour by annotation dialog throws NPE after using
690 'extract scores' function</li>
691 <li>Loading/cut'n'pasting an empty file leads to a grey
692 alignment window</li>
693 <li>Disorder thresholds rendered incorrectly after
694 performing IUPred disorder prediction</li>
695 <li>Multiple group annotated consensus rows shown when
696 changing 'normalise logo' display setting</li>
697 <li>Find shows blank dialog after 'finished searching' if
698 nothing matches query</li>
699 <li>Null Pointer Exceptions raised when sorting by
700 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
702 <li>Errors in Jmol console when structures in alignment
703 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
705 <li>Not all working JABAWS services are shown in
707 <li>JAVAWS version of Jalview fails to launch with
708 'invalid literal/length code'</li>
709 <li>Annotation/RNA Helix colourschemes cannot be applied
710 to alignment with groups (actually fixed in 2.8.0b1)</li>
711 <li>RNA Helices and T-Coffee Scores available as default
714 </ul> <em>Applet</em>
716 <li>Remove group option is shown even when selection is
718 <li>Apply to all groups ticked but colourscheme changes
719 don't affect groups</li>
720 <li>Documented RNA Helices and T-Coffee Scores as valid
721 colourscheme name</li>
722 <li>Annotation labels drawn on sequence IDs when
723 Annotation panel is not displayed</li>
724 <li>Increased font size for dropdown menus on OSX and
725 embedded windows</li>
728 <li>Consensus sequence for alignments/groups with a
729 single sequence were not calculated</li>
730 <li>annotation files that contain only groups imported as
731 annotation and junk sequences</li>
732 <li>Fasta files with sequences containing '*' incorrectly
733 recognised as PFAM or BLC</li>
734 <li>conservation/PID slider apply all groups option
735 doesn't affect background (2.8.0b1)
737 <li>redundancy highlighting is erratic at 0% and 100%</li>
738 <li>Remove gapped columns fails for sequences with ragged
740 <li>AMSA annotation row with leading spaces is not
741 registered correctly on import</li>
742 <li>Jalview crashes when selecting PCA analysis for
743 certain alignments</li>
744 <li>Opening the colour by annotation dialog for an
745 existing annotation based 'use original colours'
746 colourscheme loses original colours setting</li>
751 <td><div align="center">
752 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
753 <em>30/1/2014</em></strong>
757 <li>Trusted certificates for JalviewLite applet and
758 Jalview Desktop application<br />Certificate was donated by
759 <a href="https://www.certum.eu">Certum</a> to the Jalview
760 open source project).
762 <li>Jalview SRS links replaced by UniProt and EBI-search
764 <li>Output in Stockholm format</li>
765 <li>Allow import of data from gzipped files</li>
766 <li>Export/import group and sequence associated line
767 graph thresholds</li>
768 <li>Nucleotide substitution matrix that supports RNA and
770 <li>Allow disorder predictions to be made on the current
771 selection (or visible selection) in the same way that JPred
773 <li>Groovy scripting for headless Jalview operation</li>
774 </ul> <em>Other improvements</em>
776 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
777 <li>COMBINE statement uses current SEQUENCE_REF and
778 GROUP_REF scope to group annotation rows</li>
779 <li>Support '' style escaping of quotes in Newick
781 <li>Group options for JABAWS service by command line name</li>
782 <li>Empty tooltip shown for JABA service options with a
783 link but no description</li>
784 <li>Select primary source when selecting authority in
785 database fetcher GUI</li>
786 <li>Add .mfa to FASTA file extensions recognised by
788 <li>Annotation label tooltip text wrap</li>
793 <li>Slow scrolling when lots of annotation rows are
795 <li>Lots of NPE (and slowness) after creating RNA
796 secondary structure annotation line</li>
797 <li>Sequence database accessions not imported when
798 fetching alignments from Rfam</li>
799 <li>Incorrect SHMR submission for sequences with
801 <li>View all structures does not always superpose
803 <li>Option widgets in service parameters not updated to
804 reflect user or preset settings</li>
805 <li>Null pointer exceptions for some services without
806 presets or adjustable parameters</li>
807 <li>Discover PDB IDs entry in structure menu doesn't
808 discover PDB xRefs</li>
809 <li>Exception encountered while trying to retrieve
810 features with DAS</li>
811 <li>Lowest value in annotation row isn't coloured
812 when colour by annotation (per sequence) is coloured</li>
813 <li>Keyboard mode P jumps to start of gapped region when
814 residue follows a gap</li>
815 <li>Jalview appears to hang importing an alignment with
816 Wrap as default or after enabling Wrap</li>
817 <li>'Right click to add annotations' message
818 shown in wrap mode when no annotations present</li>
819 <li>Disorder predictions fail with NPE if no automatic
820 annotation already exists on alignment</li>
821 <li>oninit javascript function should be called after
822 initialisation completes</li>
823 <li>Remove redundancy after disorder prediction corrupts
824 alignment window display</li>
825 <li>Example annotation file in documentation is invalid</li>
826 <li>Grouped line graph annotation rows are not exported
827 to annotation file</li>
828 <li>Multi-harmony analysis cannot be run when only two
830 <li>Cannot create multiple groups of line graphs with
831 several 'combine' statements in annotation file</li>
832 <li>Pressing return several times causes Number Format
833 exceptions in keyboard mode</li>
834 <li>Multi-harmony (SHMMR) method doesn't submit
835 correct partitions for input data</li>
836 <li>Translation from DNA to Amino Acids fails</li>
837 <li>Jalview fail to load newick tree with quoted label</li>
838 <li>--headless flag isn't understood</li>
839 <li>ClassCastException when generating EPS in headless
841 <li>Adjusting sequence-associated shading threshold only
842 changes one row's threshold</li>
843 <li>Preferences and Feature settings panel panel
844 doesn't open</li>
845 <li>hide consensus histogram also hides conservation and
846 quality histograms</li>
851 <td><div align="center">
852 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
854 <td><em>Application</em>
856 <li>Support for JABAWS 2.0 Services (AACon alignment
857 conservation, protein disorder and Clustal Omega)</li>
858 <li>JABAWS server status indicator in Web Services
860 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
861 in Jalview alignment window</li>
862 <li>Updated Jalview build and deploy framework for OSX
863 mountain lion, windows 7, and 8</li>
864 <li>Nucleotide substitution matrix for PCA that supports
865 RNA and ambiguity codes</li>
867 <li>Improved sequence database retrieval GUI</li>
868 <li>Support fetching and database reference look up
869 against multiple DAS sources (Fetch all from in 'fetch db
871 <li>Jalview project improvements
873 <li>Store and retrieve the 'belowAlignment'
874 flag for annotation</li>
875 <li>calcId attribute to group annotation rows on the
877 <li>Store AACon calculation settings for a view in
882 <li>horizontal scrolling gesture support</li>
883 <li>Visual progress indicator when PCA calculation is
885 <li>Simpler JABA web services menus</li>
886 <li>visual indication that web service results are still
887 being retrieved from server</li>
888 <li>Serialise the dialogs that are shown when Jalview
889 starts up for first time</li>
890 <li>Jalview user agent string for interacting with HTTP
892 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
894 <li>Examples directory and Groovy library included in
895 InstallAnywhere distribution</li>
896 </ul> <em>Applet</em>
898 <li>RNA alignment and secondary structure annotation
899 visualization applet example</li>
900 </ul> <em>General</em>
902 <li>Normalise option for consensus sequence logo</li>
903 <li>Reset button in PCA window to return dimensions to
905 <li>Allow seqspace or Jalview variant of alignment PCA
907 <li>PCA with either nucleic acid and protein substitution
909 <li>Allow windows containing HTML reports to be exported
911 <li>Interactive display and editing of RNA secondary
912 structure contacts</li>
913 <li>RNA Helix Alignment Colouring</li>
914 <li>RNA base pair logo consensus</li>
915 <li>Parse sequence associated secondary structure
916 information in Stockholm files</li>
917 <li>HTML Export database accessions and annotation
918 information presented in tooltip for sequences</li>
919 <li>Import secondary structure from LOCARNA clustalw
920 style RNA alignment files</li>
921 <li>import and visualise T-COFFEE quality scores for an
923 <li>'colour by annotation' per sequence option to
924 shade each sequence according to its associated alignment
926 <li>New Jalview Logo</li>
927 </ul> <em>Documentation and Development</em>
929 <li>documentation for score matrices used in Jalview</li>
930 <li>New Website!</li>
932 <td><em>Application</em>
934 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
935 wsdbfetch REST service</li>
936 <li>Stop windows being moved outside desktop on OSX</li>
937 <li>Filetype associations not installed for webstart
939 <li>Jalview does not always retrieve progress of a JABAWS
940 job execution in full once it is complete</li>
941 <li>revise SHMR RSBS definition to ensure alignment is
942 uploaded via ali_file parameter</li>
943 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
944 <li>View all structures superposed fails with exception</li>
945 <li>Jnet job queues forever if a very short sequence is
946 submitted for prediction</li>
947 <li>Cut and paste menu not opened when mouse clicked on
949 <li>Putting fractional value into integer text box in
950 alignment parameter dialog causes Jalview to hang</li>
951 <li>Structure view highlighting doesn't work on
953 <li>View all structures fails with exception shown in
955 <li>Characters in filename associated with PDBEntry not
956 escaped in a platform independent way</li>
957 <li>Jalview desktop fails to launch with exception when
959 <li>Tree calculation reports 'you must have 2 or more
960 sequences selected' when selection is empty</li>
961 <li>Jalview desktop fails to launch with jar signature
962 failure when java web start temporary file caching is
964 <li>DAS Sequence retrieval with range qualification
965 results in sequence xref which includes range qualification</li>
966 <li>Errors during processing of command line arguments
967 cause progress bar (JAL-898) to be removed</li>
968 <li>Replace comma for semi-colon option not disabled for
969 DAS sources in sequence fetcher</li>
970 <li>Cannot close news reader when JABAWS server warning
972 <li>Option widgets not updated to reflect user settings</li>
973 <li>Edited sequence not submitted to web service</li>
974 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
975 <li>InstallAnywhere installer doesn't unpack and run
976 on OSX Mountain Lion</li>
977 <li>Annotation panel not given a scroll bar when
978 sequences with alignment annotation are pasted into the
980 <li>Sequence associated annotation rows not associated
981 when loaded from Jalview project</li>
982 <li>Browser launch fails with NPE on java 1.7</li>
983 <li>JABAWS alignment marked as finished when job was
984 cancelled or job failed due to invalid input</li>
985 <li>NPE with v2.7 example when clicking on Tree
986 associated with all views</li>
987 <li>Exceptions when copy/paste sequences with grouped
988 annotation rows to new window</li>
989 </ul> <em>Applet</em>
991 <li>Sequence features are momentarily displayed before
992 they are hidden using hidefeaturegroups applet parameter</li>
993 <li>loading features via javascript API automatically
994 enables feature display</li>
995 <li>scrollToColumnIn javascript API method doesn't
997 </ul> <em>General</em>
999 <li>Redundancy removal fails for rna alignment</li>
1000 <li>PCA calculation fails when sequence has been selected
1001 and then deselected</li>
1002 <li>PCA window shows grey box when first opened on OSX</li>
1003 <li>Letters coloured pink in sequence logo when alignment
1004 coloured with clustalx</li>
1005 <li>Choosing fonts without letter symbols defined causes
1006 exceptions and redraw errors</li>
1007 <li>Initial PCA plot view is not same as manually
1008 reconfigured view</li>
1009 <li>Grouped annotation graph label has incorrect line
1011 <li>Grouped annotation graph label display is corrupted
1012 for lots of labels</li>
1017 <div align="center">
1018 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
1021 <td><em>Application</em>
1023 <li>Jalview Desktop News Reader</li>
1024 <li>Tweaked default layout of web services menu</li>
1025 <li>View/alignment association menu to enable user to
1026 easily specify which alignment a multi-structure view takes
1027 its colours/correspondences from</li>
1028 <li>Allow properties file location to be specified as URL</li>
1029 <li>Extend Jalview project to preserve associations
1030 between many alignment views and a single Jmol display</li>
1031 <li>Store annotation row height in Jalview project file</li>
1032 <li>Annotation row column label formatting attributes
1033 stored in project file</li>
1034 <li>Annotation row order for auto-calculated annotation
1035 rows preserved in Jalview project file</li>
1036 <li>Visual progress indication when Jalview state is
1037 saved using Desktop window menu</li>
1038 <li>Visual indication that command line arguments are
1039 still being processed</li>
1040 <li>Groovy script execution from URL</li>
1041 <li>Colour by annotation default min and max colours in
1043 <li>Automatically associate PDB files dragged onto an
1044 alignment with sequences that have high similarity and
1046 <li>Update JGoogleAnalytics to latest release (0.3)</li>
1047 <li>'view structures' option to open many
1048 structures in same window</li>
1049 <li>Sort associated views menu option for tree panel</li>
1050 <li>Group all JABA and non-JABA services for a particular
1051 analysis function in its own submenu</li>
1052 </ul> <em>Applet</em>
1054 <li>Userdefined and autogenerated annotation rows for
1056 <li>Adjustment of alignment annotation pane height</li>
1057 <li>Annotation scrollbar for annotation panel</li>
1058 <li>Drag to reorder annotation rows in annotation panel</li>
1059 <li>'automaticScrolling' parameter</li>
1060 <li>Allow sequences with partial ID string matches to be
1061 annotated from GFF/Jalview features files</li>
1062 <li>Sequence logo annotation row in applet</li>
1063 <li>Absolute paths relative to host server in applet
1064 parameters are treated as such</li>
1065 <li>New in the JalviewLite javascript API:
1067 <li>JalviewLite.js javascript library</li>
1068 <li>Javascript callbacks for
1070 <li>Applet initialisation</li>
1071 <li>Sequence/alignment mouse-overs and selections</li>
1074 <li>scrollTo row and column alignment scrolling
1076 <li>Select sequence/alignment regions from javascript</li>
1077 <li>javascript structure viewer harness to pass
1078 messages between Jmol and Jalview when running as
1079 distinct applets</li>
1080 <li>sortBy method</li>
1081 <li>Set of applet and application examples shipped
1082 with documentation</li>
1083 <li>New example to demonstrate JalviewLite and Jmol
1084 javascript message exchange</li>
1086 </ul> <em>General</em>
1088 <li>Enable Jmol displays to be associated with multiple
1089 multiple alignments</li>
1090 <li>Option to automatically sort alignment with new tree</li>
1091 <li>User configurable link to enable redirects to a
1092 www.Jalview.org mirror</li>
1093 <li>Jmol colours option for Jmol displays</li>
1094 <li>Configurable newline string when writing alignment
1095 and other flat files</li>
1096 <li>Allow alignment annotation description lines to
1097 contain html tags</li>
1098 </ul> <em>Documentation and Development</em>
1100 <li>Add groovy test harness for bulk load testing to
1102 <li>Groovy script to load and align a set of sequences
1103 using a web service before displaying the result in the
1104 Jalview desktop</li>
1105 <li>Restructured javascript and applet api documentation</li>
1106 <li>Ant target to publish example html files with applet
1108 <li>Netbeans project for building Jalview from source</li>
1109 <li>ant task to create online javadoc for Jalview source</li>
1111 <td><em>Application</em>
1113 <li>User defined colourscheme throws exception when
1114 current built in colourscheme is saved as new scheme</li>
1115 <li>AlignFrame->Save in application pops up save
1116 dialog for valid filename/format</li>
1117 <li>Cannot view associated structure for UniProt sequence</li>
1118 <li>PDB file association breaks for UniProt sequence
1120 <li>Associate PDB from file dialog does not tell you
1121 which sequence is to be associated with the file</li>
1122 <li>Find All raises null pointer exception when query
1123 only matches sequence IDs</li>
1124 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
1125 <li>Jalview project with Jmol views created with Jalview
1126 2.4 cannot be loaded</li>
1127 <li>Filetype associations not installed for webstart
1129 <li>Two or more chains in a single PDB file associated
1130 with sequences in different alignments do not get coloured
1131 by their associated sequence</li>
1132 <li>Visibility status of autocalculated annotation row
1133 not preserved when project is loaded</li>
1134 <li>Annotation row height and visibility attributes not
1135 stored in Jalview project</li>
1136 <li>Tree bootstraps are not preserved when saved as a
1137 Jalview project</li>
1138 <li>Envision2 workflow tooltips are corrupted</li>
1139 <li>Enabling show group conservation also enables colour
1140 by conservation</li>
1141 <li>Duplicate group associated conservation or consensus
1142 created on new view</li>
1143 <li>Annotation scrollbar not displayed after 'show
1144 all hidden annotation rows' option selected</li>
1145 <li>Alignment quality not updated after alignment
1146 annotation row is hidden then shown</li>
1147 <li>Preserve colouring of structures coloured by
1148 sequences in pre Jalview 2.7 projects</li>
1149 <li>Web service job parameter dialog is not laid out
1151 <li>Web services menu not refreshed after 'reset
1152 services' button is pressed in preferences</li>
1153 <li>Annotation off by one in Jalview v2_3 example project</li>
1154 <li>Structures imported from file and saved in project
1155 get name like jalview_pdb1234.txt when reloaded</li>
1156 <li>Jalview does not always retrieve progress of a JABAWS
1157 job execution in full once it is complete</li>
1158 </ul> <em>Applet</em>
1160 <li>Alignment height set incorrectly when lots of
1161 annotation rows are displayed</li>
1162 <li>Relative URLs in feature HTML text not resolved to
1164 <li>View follows highlighting does not work for positions
1166 <li><= shown as = in tooltip</li>
1167 <li>Export features raises exception when no features
1169 <li>Separator string used for serialising lists of IDs
1170 for javascript api is modified when separator string
1171 provided as parameter</li>
1172 <li>Null pointer exception when selecting tree leaves for
1173 alignment with no existing selection</li>
1174 <li>Relative URLs for datasources assumed to be relative
1175 to applet's codebase</li>
1176 <li>Status bar not updated after finished searching and
1177 search wraps around to first result</li>
1178 <li>StructureSelectionManager instance shared between
1179 several Jalview applets causes race conditions and memory
1181 <li>Hover tooltip and mouseover of position on structure
1182 not sent from Jmol in applet</li>
1183 <li>Certain sequences of javascript method calls to
1184 applet API fatally hang browser</li>
1185 </ul> <em>General</em>
1187 <li>View follows structure mouseover scrolls beyond
1188 position with wrapped view and hidden regions</li>
1189 <li>Find sequence position moves to wrong residue
1190 with/without hidden columns</li>
1191 <li>Sequence length given in alignment properties window
1193 <li>InvalidNumberFormat exceptions thrown when trying to
1194 import PDB like structure files</li>
1195 <li>Positional search results are only highlighted
1196 between user-supplied sequence start/end bounds</li>
1197 <li>End attribute of sequence is not validated</li>
1198 <li>Find dialog only finds first sequence containing a
1199 given sequence position</li>
1200 <li>Sequence numbering not preserved in MSF alignment
1202 <li>Jalview PDB file reader does not extract sequence
1203 from nucleotide chains correctly</li>
1204 <li>Structure colours not updated when tree partition
1205 changed in alignment</li>
1206 <li>Sequence associated secondary structure not correctly
1207 parsed in interleaved stockholm</li>
1208 <li>Colour by annotation dialog does not restore current
1210 <li>Hiding (nearly) all sequences doesn't work
1212 <li>Sequences containing lowercase letters are not
1213 properly associated with their pdb files</li>
1214 </ul> <em>Documentation and Development</em>
1216 <li>schemas/JalviewWsParamSet.xsd corrupted by
1217 ApplyCopyright tool</li>
1222 <div align="center">
1223 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
1226 <td><em>Application</em>
1228 <li>New warning dialog when the Jalview Desktop cannot
1229 contact web services</li>
1230 <li>JABA service parameters for a preset are shown in
1231 service job window</li>
1232 <li>JABA Service menu entries reworded</li>
1236 <li>Modeller PIR IO broken - cannot correctly import a
1237 pir file emitted by Jalview</li>
1238 <li>Existing feature settings transferred to new
1239 alignment view created from cut'n'paste</li>
1240 <li>Improved test for mixed amino/nucleotide chains when
1241 parsing PDB files</li>
1242 <li>Consensus and conservation annotation rows
1243 occasionally become blank for all new windows</li>
1244 <li>Exception raised when right clicking above sequences
1245 in wrapped view mode</li>
1246 </ul> <em>Application</em>
1248 <li>multiple multiply aligned structure views cause cpu
1249 usage to hit 100% and computer to hang</li>
1250 <li>Web Service parameter layout breaks for long user
1251 parameter names</li>
1252 <li>Jaba service discovery hangs desktop if Jaba server
1259 <div align="center">
1260 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
1263 <td><em>Application</em>
1265 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
1266 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
1269 <li>Web Services preference tab</li>
1270 <li>Analysis parameters dialog box and user defined
1272 <li>Improved speed and layout of Envision2 service menu</li>
1273 <li>Superpose structures using associated sequence
1275 <li>Export coordinates and projection as CSV from PCA
1277 </ul> <em>Applet</em>
1279 <li>enable javascript: execution by the applet via the
1280 link out mechanism</li>
1281 </ul> <em>Other</em>
1283 <li>Updated the Jmol Jalview interface to work with Jmol
1285 <li>The Jalview Desktop and JalviewLite applet now
1286 require Java 1.5</li>
1287 <li>Allow Jalview feature colour specification for GFF
1288 sequence annotation files</li>
1289 <li>New 'colour by label' keword in Jalview feature file
1290 type colour specification</li>
1291 <li>New Jalview Desktop Groovy API method that allows a
1292 script to check if it being run in an interactive session or
1293 in a batch operation from the Jalview command line</li>
1297 <li>clustalx colourscheme colours Ds preferentially when
1298 both D+E are present in over 50% of the column</li>
1299 </ul> <em>Application</em>
1301 <li>typo in AlignmentFrame->View->Hide->all but
1302 selected Regions menu item</li>
1303 <li>sequence fetcher replaces ',' for ';' when the ',' is
1304 part of a valid accession ID</li>
1305 <li>fatal OOM if object retrieved by sequence fetcher
1306 runs out of memory</li>
1307 <li>unhandled Out of Memory Error when viewing pca
1308 analysis results</li>
1309 <li>InstallAnywhere builds fail to launch on OS X java
1310 10.5 update 4 (due to apple Java 1.6 update)</li>
1311 <li>Installanywhere Jalview silently fails to launch</li>
1312 </ul> <em>Applet</em>
1314 <li>Jalview.getFeatureGroups() raises an
1315 ArrayIndexOutOfBoundsException if no feature groups are
1322 <div align="center">
1323 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
1329 <li>Alignment prettyprinter doesn't cope with long
1331 <li>clustalx colourscheme colours Ds preferentially when
1332 both D+E are present in over 50% of the column</li>
1333 <li>nucleic acid structures retrieved from PDB do not
1334 import correctly</li>
1335 <li>More columns get selected than were clicked on when a
1336 number of columns are hidden</li>
1337 <li>annotation label popup menu not providing correct
1338 add/hide/show options when rows are hidden or none are
1340 <li>Stockholm format shown in list of readable formats,
1341 and parser copes better with alignments from RFAM.</li>
1342 <li>CSV output of consensus only includes the percentage
1343 of all symbols if sequence logo display is enabled</li>
1345 </ul> <em>Applet</em>
1347 <li>annotation panel disappears when annotation is
1349 </ul> <em>Application</em>
1351 <li>Alignment view not redrawn properly when new
1352 alignment opened where annotation panel is visible but no
1353 annotations are present on alignment</li>
1354 <li>pasted region containing hidden columns is
1355 incorrectly displayed in new alignment window</li>
1356 <li>Jalview slow to complete operations when stdout is
1357 flooded (fix is to close the Jalview console)</li>
1358 <li>typo in AlignmentFrame->View->Hide->all but
1359 selected Rregions menu item.</li>
1360 <li>inconsistent group submenu and Format submenu entry
1361 'Un' or 'Non'conserved</li>
1362 <li>Sequence feature settings are being shared by
1363 multiple distinct alignments</li>
1364 <li>group annotation not recreated when tree partition is
1366 <li>double click on group annotation to select sequences
1367 does not propagate to associated trees</li>
1368 <li>Mac OSX specific issues:
1370 <li>exception raised when mouse clicked on desktop
1371 window background</li>
1372 <li>Desktop menu placed on menu bar and application
1373 name set correctly</li>
1374 <li>sequence feature settings not wide enough for the
1375 save feature colourscheme button</li>
1384 <div align="center">
1385 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
1388 <td><em>New Capabilities</em>
1390 <li>URL links generated from description line for
1391 regular-expression based URL links (applet and application)
1394 <li>Non-positional feature URL links are shown in link
1396 <li>Linked viewing of nucleic acid sequences and
1398 <li>Automatic Scrolling option in View menu to display
1399 the currently highlighted region of an alignment.</li>
1400 <li>Order an alignment by sequence length, or using the
1401 average score or total feature count for each sequence.</li>
1402 <li>Shading features by score or associated description</li>
1403 <li>Subdivide alignment and groups based on identity of
1404 selected subsequence (Make Groups from Selection).</li>
1405 <li>New hide/show options including Shift+Control+H to
1406 hide everything but the currently selected region.</li>
1407 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
1408 </ul> <em>Application</em>
1410 <li>Fetch DB References capabilities and UI expanded to
1411 support retrieval from DAS sequence sources</li>
1412 <li>Local DAS Sequence sources can be added via the
1413 command line or via the Add local source dialog box.</li>
1414 <li>DAS Dbref and DbxRef feature types are parsed as
1415 database references and protein_name is parsed as
1416 description line (BioSapiens terms).</li>
1417 <li>Enable or disable non-positional feature and database
1418 references in sequence ID tooltip from View menu in
1420 <!-- <li>New hidden columns and rows and representatives capabilities
1421 in annotations file (in progress - not yet fully implemented)</li> -->
1422 <li>Group-associated consensus, sequence logos and
1423 conservation plots</li>
1424 <li>Symbol distributions for each column can be exported
1425 and visualized as sequence logos</li>
1426 <li>Optionally scale multi-character column labels to fit
1427 within each column of annotation row<!-- todo for applet -->
1429 <li>Optional automatic sort of associated alignment view
1430 when a new tree is opened.</li>
1431 <li>Jalview Java Console</li>
1432 <li>Better placement of desktop window when moving
1433 between different screens.</li>
1434 <li>New preference items for sequence ID tooltip and
1435 consensus annotation</li>
1436 <li>Client to submit sequences and IDs to Envision2 Workflows</li>
1437 <li><em>Vamsas Capabilities</em>
1439 <li>Improved VAMSAS synchronization (Jalview archive
1440 used to preserve views, structures, and tree display
1442 <li>Import of vamsas documents from disk or URL via
1444 <li>Sharing of selected regions between views and
1445 with other VAMSAS applications (Experimental feature!)</li>
1446 <li>Updated API to VAMSAS version 0.2</li>
1448 </ul> <em>Applet</em>
1450 <li>Middle button resizes annotation row height</li>
1453 <li>sortByTree (true/false) - automatically sort the
1454 associated alignment view by the tree when a new tree is
1456 <li>showTreeBootstraps (true/false) - show or hide
1457 branch bootstraps (default is to show them if available)</li>
1458 <li>showTreeDistances (true/false) - show or hide
1459 branch lengths (default is to show them if available)</li>
1460 <li>showUnlinkedTreeNodes (true/false) - indicate if
1461 unassociated nodes should be highlighted in the tree
1463 <li>heightScale and widthScale (1.0 or more) -
1464 increase the height or width of a cell in the alignment
1465 grid relative to the current font size.</li>
1468 <li>Non-positional features displayed in sequence ID
1470 </ul> <em>Other</em>
1472 <li>Features format: graduated colour definitions and
1473 specification of feature scores</li>
1474 <li>Alignment Annotations format: new keywords for group
1475 associated annotation (GROUP_REF) and annotation row display
1476 properties (ROW_PROPERTIES)</li>
1477 <li>XML formats extended to support graduated feature
1478 colourschemes, group associated annotation, and profile
1479 visualization settings.</li></td>
1482 <li>Source field in GFF files parsed as feature source
1483 rather than description</li>
1484 <li>Non-positional features are now included in sequence
1485 feature and gff files (controlled via non-positional feature
1486 visibility in tooltip).</li>
1487 <li>URL links generated for all feature links (bugfix)</li>
1488 <li>Added URL embedding instructions to features file
1490 <li>Codons containing ambiguous nucleotides translated as
1491 'X' in peptide product</li>
1492 <li>Match case switch in find dialog box works for both
1493 sequence ID and sequence string and query strings do not
1494 have to be in upper case to match case-insensitively.</li>
1495 <li>AMSA files only contain first column of
1496 multi-character column annotation labels</li>
1497 <li>Jalview Annotation File generation/parsing consistent
1498 with documentation (e.g. Stockholm annotation can be
1499 exported and re-imported)</li>
1500 <li>PDB files without embedded PDB IDs given a friendly
1502 <li>Find incrementally searches ID string matches as well
1503 as subsequence matches, and correctly reports total number
1507 <li>Better handling of exceptions during sequence
1509 <li>Dasobert generated non-positional feature URL
1510 link text excludes the start_end suffix</li>
1511 <li>DAS feature and source retrieval buttons disabled
1512 when fetch or registry operations in progress.</li>
1513 <li>PDB files retrieved from URLs are cached properly</li>
1514 <li>Sequence description lines properly shared via
1516 <li>Sequence fetcher fetches multiple records for all
1518 <li>Ensured that command line das feature retrieval
1519 completes before alignment figures are generated.</li>
1520 <li>Reduced time taken when opening file browser for
1522 <li>isAligned check prior to calculating tree, PCA or
1523 submitting an MSA to JNet now excludes hidden sequences.</li>
1524 <li>User defined group colours properly recovered
1525 from Jalview projects.</li>
1534 <div align="center">
1535 <strong>2.4.0.b2</strong><br> 28/10/2009
1540 <li>Experimental support for google analytics usage
1542 <li>Jalview privacy settings (user preferences and docs).</li>
1547 <li>Race condition in applet preventing startup in
1549 <li>Exception when feature created from selection beyond
1550 length of sequence.</li>
1551 <li>Allow synthetic PDB files to be imported gracefully</li>
1552 <li>Sequence associated annotation rows associate with
1553 all sequences with a given id</li>
1554 <li>Find function matches case-insensitively for sequence
1555 ID string searches</li>
1556 <li>Non-standard characters do not cause pairwise
1557 alignment to fail with exception</li>
1558 </ul> <em>Application Issues</em>
1560 <li>Sequences are now validated against EMBL database</li>
1561 <li>Sequence fetcher fetches multiple records for all
1563 </ul> <em>InstallAnywhere Issues</em>
1565 <li>Dock icon works for Mac OS X java (Mac 1.6 update
1566 issue with installAnywhere mechanism)</li>
1567 <li>Command line launching of JARs from InstallAnywhere
1568 version (java class versioning error fixed)</li>
1575 <div align="center">
1576 <strong>2.4</strong><br> 27/8/2008
1579 <td><em>User Interface</em>
1581 <li>Linked highlighting of codon and amino acid from
1582 translation and protein products</li>
1583 <li>Linked highlighting of structure associated with
1584 residue mapping to codon position</li>
1585 <li>Sequence Fetcher provides example accession numbers
1586 and 'clear' button</li>
1587 <li>MemoryMonitor added as an option under Desktop's
1589 <li>Extract score function to parse whitespace separated
1590 numeric data in description line</li>
1591 <li>Column labels in alignment annotation can be centred.</li>
1592 <li>Tooltip for sequence associated annotation give name
1594 </ul> <em>Web Services and URL fetching</em>
1596 <li>JPred3 web service</li>
1597 <li>Prototype sequence search client (no public services
1599 <li>Fetch either seed alignment or full alignment from
1601 <li>URL Links created for matching database cross
1602 references as well as sequence ID</li>
1603 <li>URL Links can be created using regular-expressions</li>
1604 </ul> <em>Sequence Database Connectivity</em>
1606 <li>Retrieval of cross-referenced sequences from other
1608 <li>Generalised database reference retrieval and
1609 validation to all fetchable databases</li>
1610 <li>Fetch sequences from DAS sources supporting the
1611 sequence command</li>
1612 </ul> <em>Import and Export</em>
1613 <li>export annotation rows as CSV for spreadsheet import</li>
1614 <li>Jalview projects record alignment dataset associations,
1615 EMBL products, and cDNA sequence mappings</li>
1616 <li>Sequence Group colour can be specified in Annotation
1618 <li>Ad-hoc colouring of group in Annotation File using RGB
1619 triplet as name of colourscheme</li>
1620 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
1622 <li>treenode binding for VAMSAS tree exchange</li>
1623 <li>local editing and update of sequences in VAMSAS
1624 alignments (experimental)</li>
1625 <li>Create new or select existing session to join</li>
1626 <li>load and save of vamsas documents</li>
1627 </ul> <em>Application command line</em>
1629 <li>-tree parameter to open trees (introduced for passing
1631 <li>-fetchfrom command line argument to specify nicknames
1632 of DAS servers to query for alignment features</li>
1633 <li>-dasserver command line argument to add new servers
1634 that are also automatically queried for features</li>
1635 <li>-groovy command line argument executes a given groovy
1636 script after all input data has been loaded and parsed</li>
1637 </ul> <em>Applet-Application data exchange</em>
1639 <li>Trees passed as applet parameters can be passed to
1640 application (when using "View in full
1641 application")</li>
1642 </ul> <em>Applet Parameters</em>
1644 <li>feature group display control parameter</li>
1645 <li>debug parameter</li>
1646 <li>showbutton parameter</li>
1647 </ul> <em>Applet API methods</em>
1649 <li>newView public method</li>
1650 <li>Window (current view) specific get/set public methods</li>
1651 <li>Feature display control methods</li>
1652 <li>get list of currently selected sequences</li>
1653 </ul> <em>New Jalview distribution features</em>
1655 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
1656 <li>RELEASE file gives build properties for the latest
1657 Jalview release.</li>
1658 <li>Java 1.1 Applet build made easier and donotobfuscate
1659 property controls execution of obfuscator</li>
1660 <li>Build target for generating source distribution</li>
1661 <li>Debug flag for javacc</li>
1662 <li>.jalview_properties file is documented (slightly) in
1663 jalview.bin.Cache</li>
1664 <li>Continuous Build Integration for stable and
1665 development version of Application, Applet and source
1670 <li>selected region output includes visible annotations
1671 (for certain formats)</li>
1672 <li>edit label/displaychar contains existing label/char
1674 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
1675 <li>shorter peptide product names from EMBL records</li>
1676 <li>Newick string generator makes compact representations</li>
1677 <li>bootstrap values parsed correctly for tree files with
1679 <li>pathological filechooser bug avoided by not allowing
1680 filenames containing a ':'</li>
1681 <li>Fixed exception when parsing GFF files containing
1682 global sequence features</li>
1683 <li>Alignment datasets are finalized only when number of
1684 references from alignment sequences goes to zero</li>
1685 <li>Close of tree branch colour box without colour
1686 selection causes cascading exceptions</li>
1687 <li>occasional negative imgwidth exceptions</li>
1688 <li>better reporting of non-fatal warnings to user when
1689 file parsing fails.</li>
1690 <li>Save works when Jalview project is default format</li>
1691 <li>Save as dialog opened if current alignment format is
1692 not a valid output format</li>
1693 <li>UniProt canonical names introduced for both das and
1695 <li>Histidine should be midblue (not pink!) in Zappo</li>
1696 <li>error messages passed up and output when data read
1698 <li>edit undo recovers previous dataset sequence when
1699 sequence is edited</li>
1700 <li>allow PDB files without pdb ID HEADER lines (like
1701 those generated by MODELLER) to be read in properly</li>
1702 <li>allow reading of JPred concise files as a normal
1704 <li>Stockholm annotation parsing and alignment properties
1705 import fixed for PFAM records</li>
1706 <li>Structure view windows have correct name in Desktop
1708 <li>annotation consisting of sequence associated scores
1709 can be read and written correctly to annotation file</li>
1710 <li>Aligned cDNA translation to aligned peptide works
1712 <li>Fixed display of hidden sequence markers and
1713 non-italic font for representatives in Applet</li>
1714 <li>Applet Menus are always embedded in applet window on
1716 <li>Newly shown features appear at top of stack (in
1718 <li>Annotations added via parameter not drawn properly
1719 due to null pointer exceptions</li>
1720 <li>Secondary structure lines are drawn starting from
1721 first column of alignment</li>
1722 <li>UniProt XML import updated for new schema release in
1724 <li>Sequence feature to sequence ID match for Features
1725 file is case-insensitive</li>
1726 <li>Sequence features read from Features file appended to
1727 all sequences with matching IDs</li>
1728 <li>PDB structure coloured correctly for associated views
1729 containing a sub-sequence</li>
1730 <li>PDB files can be retrieved by applet from Jar files</li>
1731 <li>feature and annotation file applet parameters
1732 referring to different directories are retrieved correctly</li>
1733 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
1734 <li>Fixed application hang whilst waiting for
1735 splash-screen version check to complete</li>
1736 <li>Applet properly URLencodes input parameter values
1737 when passing them to the launchApp service</li>
1738 <li>display name and local features preserved in results
1739 retrieved from web service</li>
1740 <li>Visual delay indication for sequence retrieval and
1741 sequence fetcher initialisation</li>
1742 <li>updated Application to use DAS 1.53e version of
1743 dasobert DAS client</li>
1744 <li>Re-instated Full AMSA support and .amsa file
1746 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
1754 <div align="center">
1755 <strong>2.3</strong><br> 9/5/07
1760 <li>Jmol 11.0.2 integration</li>
1761 <li>PDB views stored in Jalview XML files</li>
1762 <li>Slide sequences</li>
1763 <li>Edit sequence in place</li>
1764 <li>EMBL CDS features</li>
1765 <li>DAS Feature mapping</li>
1766 <li>Feature ordering</li>
1767 <li>Alignment Properties</li>
1768 <li>Annotation Scores</li>
1769 <li>Sort by scores</li>
1770 <li>Feature/annotation editing in applet</li>
1775 <li>Headless state operation in 2.2.1</li>
1776 <li>Incorrect and unstable DNA pairwise alignment</li>
1777 <li>Cut and paste of sequences with annotation</li>
1778 <li>Feature group display state in XML</li>
1779 <li>Feature ordering in XML</li>
1780 <li>blc file iteration selection using filename # suffix</li>
1781 <li>Stockholm alignment properties</li>
1782 <li>Stockhom alignment secondary structure annotation</li>
1783 <li>2.2.1 applet had no feature transparency</li>
1784 <li>Number pad keys can be used in cursor mode</li>
1785 <li>Structure Viewer mirror image resolved</li>
1792 <div align="center">
1793 <strong>2.2.1</strong><br> 12/2/07
1798 <li>Non standard characters can be read and displayed
1799 <li>Annotations/Features can be imported/exported to the
1801 <li>Applet allows editing of sequence/annotation/group
1802 name & description
1803 <li>Preference setting to display sequence name in
1805 <li>Annotation file format extended to allow
1806 Sequence_groups to be defined
1807 <li>Default opening of alignment overview panel can be
1808 specified in preferences
1809 <li>PDB residue numbering annotation added to associated
1815 <li>Applet crash under certain Linux OS with Java 1.6
1817 <li>Annotation file export / import bugs fixed
1818 <li>PNG / EPS image output bugs fixed
1824 <div align="center">
1825 <strong>2.2</strong><br> 27/11/06
1830 <li>Multiple views on alignment
1831 <li>Sequence feature editing
1832 <li>"Reload" alignment
1833 <li>"Save" to current filename
1834 <li>Background dependent text colour
1835 <li>Right align sequence ids
1836 <li>User-defined lower case residue colours
1839 <li>Menu item accelerator keys
1840 <li>Control-V pastes to current alignment
1841 <li>Cancel button for DAS Feature Fetching
1842 <li>PCA and PDB Viewers zoom via mouse roller
1843 <li>User-defined sub-tree colours and sub-tree selection
1846 <li>'New Window' button on the 'Output to Text box'
1851 <li>New memory efficient Undo/Redo System
1852 <li>Optimised symbol lookups and conservation/consensus
1854 <li>Region Conservation/Consensus recalculated after
1856 <li>Fixed Remove Empty Columns Bug (empty columns at end
1858 <li>Slowed DAS Feature Fetching for increased robustness.
1861 <li>Made angle brackets in ASCII feature descriptions
1863 <li>Re-instated Zoom function for PCA
1864 <li>Sequence descriptions conserved in web service
1866 <li>UniProt ID discoverer uses any word separated by
1868 <li>WsDbFetch query/result association resolved
1869 <li>Tree leaf to sequence mapping improved
1870 <li>Smooth fonts switch moved to FontChooser dialog box.
1878 <div align="center">
1879 <strong>2.1.1</strong><br> 12/9/06
1884 <li>Copy consensus sequence to clipboard</li>
1889 <li>Image output - rightmost residues are rendered if
1890 sequence id panel has been resized</li>
1891 <li>Image output - all offscreen group boundaries are
1893 <li>Annotation files with sequence references - all
1894 elements in file are relative to sequence position</li>
1895 <li>Mac Applet users can use Alt key for group editing</li>
1901 <div align="center">
1902 <strong>2.1</strong><br> 22/8/06
1907 <li>MAFFT Multiple Alignment in default Web Service list</li>
1908 <li>DAS Feature fetching</li>
1909 <li>Hide sequences and columns</li>
1910 <li>Export Annotations and Features</li>
1911 <li>GFF file reading / writing</li>
1912 <li>Associate structures with sequences from local PDB
1914 <li>Add sequences to exisiting alignment</li>
1915 <li>Recently opened files / URL lists</li>
1916 <li>Applet can launch the full application</li>
1917 <li>Applet has transparency for features (Java 1.2
1919 <li>Applet has user defined colours parameter</li>
1920 <li>Applet can load sequences from parameter
1921 "sequence<em>x</em>"
1927 <li>Redundancy Panel reinstalled in the Applet</li>
1928 <li>Monospaced font - EPS / rescaling bug fixed</li>
1929 <li>Annotation files with sequence references bug fixed</li>
1935 <div align="center">
1936 <strong>2.08.1</strong><br> 2/5/06
1941 <li>Change case of selected region from Popup menu</li>
1942 <li>Choose to match case when searching</li>
1943 <li>Middle mouse button and mouse movement can compress /
1944 expand the visible width and height of the alignment</li>
1949 <li>Annotation Panel displays complete JNet results</li>
1955 <div align="center">
1956 <strong>2.08b</strong><br> 18/4/06
1962 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
1963 <li>Righthand label on wrapped alignments shows correct
1970 <div align="center">
1971 <strong>2.08</strong><br> 10/4/06
1976 <li>Editing can be locked to the selection area</li>
1977 <li>Keyboard editing</li>
1978 <li>Create sequence features from searches</li>
1979 <li>Precalculated annotations can be loaded onto
1981 <li>Features file allows grouping of features</li>
1982 <li>Annotation Colouring scheme added</li>
1983 <li>Smooth fonts off by default - Faster rendering</li>
1984 <li>Choose to toggle Autocalculate Consensus On/Off</li>
1989 <li>Drag & Drop fixed on Linux</li>
1990 <li>Jalview Archive file faster to load/save, sequence
1991 descriptions saved.</li>
1997 <div align="center">
1998 <strong>2.07</strong><br> 12/12/05
2003 <li>PDB Structure Viewer enhanced</li>
2004 <li>Sequence Feature retrieval and display enhanced</li>
2005 <li>Choose to output sequence start-end after sequence
2006 name for file output</li>
2007 <li>Sequence Fetcher WSDBFetch@EBI</li>
2008 <li>Applet can read feature files, PDB files and can be
2009 used for HTML form input</li>
2014 <li>HTML output writes groups and features</li>
2015 <li>Group editing is Control and mouse click</li>
2016 <li>File IO bugs</li>
2022 <div align="center">
2023 <strong>2.06</strong><br> 28/9/05
2028 <li>View annotations in wrapped mode</li>
2029 <li>More options for PCA viewer</li>
2034 <li>GUI bugs resolved</li>
2035 <li>Runs with -nodisplay from command line</li>
2041 <div align="center">
2042 <strong>2.05b</strong><br> 15/9/05
2047 <li>Choose EPS export as lineart or text</li>
2048 <li>Jar files are executable</li>
2049 <li>Can read in Uracil - maps to unknown residue</li>
2054 <li>Known OutOfMemory errors give warning message</li>
2055 <li>Overview window calculated more efficiently</li>
2056 <li>Several GUI bugs resolved</li>
2062 <div align="center">
2063 <strong>2.05</strong><br> 30/8/05
2068 <li>Edit and annotate in "Wrapped" view</li>
2073 <li>Several GUI bugs resolved</li>
2079 <div align="center">
2080 <strong>2.04</strong><br> 24/8/05
2085 <li>Hold down mouse wheel & scroll to change font
2091 <li>Improved JPred client reliability</li>
2092 <li>Improved loading of Jalview files</li>
2098 <div align="center">
2099 <strong>2.03</strong><br> 18/8/05
2104 <li>Set Proxy server name and port in preferences</li>
2105 <li>Multiple URL links from sequence ids</li>
2106 <li>User Defined Colours can have a scheme name and added
2108 <li>Choose to ignore gaps in consensus calculation</li>
2109 <li>Unix users can set default web browser</li>
2110 <li>Runs without GUI for batch processing</li>
2111 <li>Dynamically generated Web Service Menus</li>
2116 <li>InstallAnywhere download for Sparc Solaris</li>
2122 <div align="center">
2123 <strong>2.02</strong><br> 18/7/05
2129 <li>Copy & Paste order of sequences maintains
2130 alignment order.</li>
2136 <div align="center">
2137 <strong>2.01</strong><br> 12/7/05
2142 <li>Use delete key for deleting selection.</li>
2143 <li>Use Mouse wheel to scroll sequences.</li>
2144 <li>Help file updated to describe how to add alignment
2146 <li>Version and build date written to build properties
2148 <li>InstallAnywhere installation will check for updates
2149 at launch of Jalview.</li>
2154 <li>Delete gaps bug fixed.</li>
2155 <li>FileChooser sorts columns.</li>
2156 <li>Can remove groups one by one.</li>
2157 <li>Filechooser icons installed.</li>
2158 <li>Finder ignores return character when searching.
2159 Return key will initiate a search.<br>
2166 <div align="center">
2167 <strong>2.0</strong><br> 20/6/05
2172 <li>New codebase</li>