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>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
99 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
100 <em>Testing and Deployment</em>
101 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
104 <td><div align="left">
107 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
108 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
109 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
110 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
114 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
115 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
117 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
119 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
120 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
121 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
122 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
123 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
124 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
125 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
126 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
127 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
128 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
129 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
130 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
131 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
132 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
133 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
134 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
136 <strong><em>Applet</em></strong><br/>
138 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
144 <td width="60" nowrap>
146 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
147 <em>2/10/2017</em></strong>
150 <td><div align="left">
151 <em>New features in Jalview Desktop</em>
154 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
156 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
160 <td><div align="left">
164 <td width="60" nowrap>
166 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
167 <em>7/9/2017</em></strong>
170 <td><div align="left">
174 <!-- JAL-2588 -->Show gaps in overview window by colouring
175 in grey (sequences used to be coloured grey, and gaps were
179 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
183 <!-- JAL-2587 -->Overview updates immediately on increase
184 in size and progress bar shown as higher resolution
185 overview is recalculated
190 <td><div align="left">
194 <!-- JAL-2664 -->Overview window redraws every hidden
195 column region row by row
198 <!-- JAL-2681 -->duplicate protein sequences shown after
199 retrieving Ensembl crossrefs for sequences from Uniprot
202 <!-- JAL-2603 -->Overview window throws NPE if show boxes
203 format setting is unticked
206 <!-- JAL-2610 -->Groups are coloured wrongly in overview
207 if group has show boxes format setting unticked
210 <!-- JAL-2672,JAL-2665 -->Redraw problems when
211 autoscrolling whilst dragging current selection group to
212 include sequences and columns not currently displayed
215 <!-- JAL-2691 -->Not all chains are mapped when multimeric
216 assemblies are imported via CIF file
219 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
220 displayed when threshold or conservation colouring is also
224 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
228 <!-- JAL-2673 -->Jalview continues to scroll after
229 dragging a selected region off the visible region of the
233 <!-- JAL-2724 -->Cannot apply annotation based
234 colourscheme to all groups in a view
237 <!-- JAL-2511 -->IDs don't line up with sequences
238 initially after font size change using the Font chooser or
245 <td width="60" nowrap>
247 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
250 <td><div align="left">
251 <em>Calculations</em>
255 <!-- JAL-1933 -->Occupancy annotation row shows number of
256 ungapped positions in each column of the alignment.
259 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
260 a calculation dialog box
263 <!-- JAL-2379 -->Revised implementation of PCA for speed
264 and memory efficiency (~30x faster)
267 <!-- JAL-2403 -->Revised implementation of sequence
268 similarity scores as used by Tree, PCA, Shading Consensus
269 and other calculations
272 <!-- JAL-2416 -->Score matrices are stored as resource
273 files within the Jalview codebase
276 <!-- JAL-2500 -->Trees computed on Sequence Feature
277 Similarity may have different topology due to increased
284 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
285 model for alignments and groups
288 <!-- JAL-384 -->Custom shading schemes created via groovy
295 <!-- JAL-2526 -->Efficiency improvements for interacting
296 with alignment and overview windows
299 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
303 <!-- JAL-2388 -->Hidden columns and sequences can be
307 <!-- JAL-2611 -->Click-drag in visible area allows fine
308 adjustment of visible position
312 <em>Data import/export</em>
315 <!-- JAL-2535 -->Posterior probability annotation from
316 Stockholm files imported as sequence associated annotation
319 <!-- JAL-2507 -->More robust per-sequence positional
320 annotation input/output via stockholm flatfile
323 <!-- JAL-2533 -->Sequence names don't include file
324 extension when importing structure files without embedded
325 names or PDB accessions
328 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
329 format sequence substitution matrices
332 <em>User Interface</em>
335 <!-- JAL-2447 --> Experimental Features Checkbox in
336 Desktop's Tools menu to hide or show untested features in
340 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
341 via Overview or sequence motif search operations
344 <!-- JAL-2547 -->Amend sequence features dialog box can be
345 opened by double clicking gaps within sequence feature
349 <!-- JAL-1476 -->Status bar message shown when not enough
350 aligned positions were available to create a 3D structure
354 <em>3D Structure</em>
357 <!-- JAL-2430 -->Hidden regions in alignment views are not
358 coloured in linked structure views
361 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
362 file-based command exchange
365 <!-- JAL-2375 -->Structure chooser automatically shows
366 Cached Structures rather than querying the PDBe if
367 structures are already available for sequences
370 <!-- JAL-2520 -->Structures imported via URL are cached in
371 the Jalview project rather than downloaded again when the
375 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
376 to transfer Chimera's structure attributes as Jalview
377 features, and vice-versa (<strong>Experimental
381 <em>Web Services</em>
384 <!-- JAL-2549 -->Updated JABAWS client to v2.2
387 <!-- JAL-2335 -->Filter non-standard amino acids and
388 nucleotides when submitting to AACon and other MSA
392 <!-- JAL-2316, -->URLs for viewing database
393 cross-references provided by identifiers.org and the
401 <!-- JAL-2344 -->FileFormatI interface for describing and
402 identifying file formats (instead of String constants)
405 <!-- JAL-2228 -->FeatureCounter script refactored for
406 efficiency when counting all displayed features (not
407 backwards compatible with 2.10.1)
410 <em>Example files</em>
413 <!-- JAL-2631 -->Graduated feature colour style example
414 included in the example feature file
417 <em>Documentation</em>
420 <!-- JAL-2339 -->Release notes reformatted for readability
421 with the built-in Java help viewer
424 <!-- JAL-1644 -->Find documentation updated with 'search
425 sequence description' option
431 <!-- JAL-2485, -->External service integration tests for
432 Uniprot REST Free Text Search Client
435 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
438 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
443 <td><div align="left">
444 <em>Calculations</em>
447 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
448 matrix - C->R should be '-3'<br />Old matrix restored
449 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
451 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
452 Jalview's treatment of gaps in PCA and substitution matrix
453 based Tree calculations.<br /> <br />In earlier versions
454 of Jalview, gaps matching gaps were penalised, and gaps
455 matching non-gaps penalised even more. In the PCA
456 calculation, gaps were actually treated as non-gaps - so
457 different costs were applied, which meant Jalview's PCAs
458 were different to those produced by SeqSpace.<br />Jalview
459 now treats gaps in the same way as SeqSpace (ie it scores
460 them as 0). <br /> <br />Enter the following in the
461 Groovy console to restore pre-2.10.2 behaviour:<br />
462 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
463 // for 2.10.1 mode <br />
464 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
465 // to restore 2.10.2 mode <br /> <br /> <em>Note:
466 these settings will affect all subsequent tree and PCA
467 calculations (not recommended)</em></li>
469 <!-- JAL-2424 -->Fixed off-by-one bug that affected
470 scaling of branch lengths for trees computed using
471 Sequence Feature Similarity.
474 <!-- JAL-2377 -->PCA calculation could hang when
475 generating output report when working with highly
479 <!-- JAL-2544 --> Sort by features includes features to
480 right of selected region when gaps present on right-hand
484 <em>User Interface</em>
487 <!-- JAL-2346 -->Reopening Colour by annotation dialog
488 doesn't reselect a specific sequence's associated
489 annotation after it was used for colouring a view
492 <!-- JAL-2419 -->Current selection lost if popup menu
493 opened on a region of alignment without groups
496 <!-- JAL-2374 -->Popup menu not always shown for regions
497 of an alignment with overlapping groups
500 <!-- JAL-2310 -->Finder double counts if both a sequence's
501 name and description match
504 <!-- JAL-2370 -->Hiding column selection containing two
505 hidden regions results in incorrect hidden regions
508 <!-- JAL-2386 -->'Apply to all groups' setting when
509 changing colour does not apply Conservation slider value
513 <!-- JAL-2373 -->Percentage identity and conservation menu
514 items do not show a tick or allow shading to be disabled
517 <!-- JAL-2385 -->Conservation shading or PID threshold
518 lost when base colourscheme changed if slider not visible
521 <!-- JAL-2547 -->Sequence features shown in tooltip for
522 gaps before start of features
525 <!-- JAL-2623 -->Graduated feature colour threshold not
526 restored to UI when feature colour is edited
529 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
530 a time when scrolling vertically in wrapped mode.
533 <!-- JAL-2630 -->Structure and alignment overview update
534 as graduate feature colour settings are modified via the
538 <!-- JAL-2034 -->Overview window doesn't always update
539 when a group defined on the alignment is resized
542 <!-- JAL-2605 -->Mouseovers on left/right scale region in
543 wrapped view result in positional status updates
547 <!-- JAL-2563 -->Status bar doesn't show position for
548 ambiguous amino acid and nucleotide symbols
551 <!-- JAL-2602 -->Copy consensus sequence failed if
552 alignment included gapped columns
555 <!-- JAL-2473 -->Minimum size set for Jalview windows so
556 widgets don't permanently disappear
559 <!-- JAL-2503 -->Cannot select or filter quantitative
560 annotation that are shown only as column labels (e.g.
561 T-Coffee column reliability scores)
564 <!-- JAL-2594 -->Exception thrown if trying to create a
565 sequence feature on gaps only
568 <!-- JAL-2504 -->Features created with 'New feature'
569 button from a Find inherit previously defined feature type
570 rather than the Find query string
573 <!-- JAL-2423 -->incorrect title in output window when
574 exporting tree calculated in Jalview
577 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
578 and then revealing them reorders sequences on the
582 <!-- JAL-964 -->Group panel in sequence feature settings
583 doesn't update to reflect available set of groups after
584 interactively adding or modifying features
587 <!-- JAL-2225 -->Sequence Database chooser unusable on
591 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
592 only excluded gaps in current sequence and ignored
599 <!-- JAL-2421 -->Overview window visible region moves
600 erratically when hidden rows or columns are present
603 <!-- JAL-2362 -->Per-residue colourschemes applied via the
604 Structure Viewer's colour menu don't correspond to
608 <!-- JAL-2405 -->Protein specific colours only offered in
609 colour and group colour menu for protein alignments
612 <!-- JAL-2385 -->Colour threshold slider doesn't update to
613 reflect currently selected view or group's shading
617 <!-- JAL-2624 -->Feature colour thresholds not respected
618 when rendered on overview and structures when opacity at
622 <!-- JAL-2589 -->User defined gap colour not shown in
623 overview when features overlaid on alignment
626 <em>Data import/export</em>
629 <!-- JAL-2576 -->Very large alignments take a long time to
633 <!-- JAL-2507 -->Per-sequence RNA secondary structures
634 added after a sequence was imported are not written to
638 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
639 when importing RNA secondary structure via Stockholm
642 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
643 not shown in correct direction for simple pseudoknots
646 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
647 with lightGray or darkGray via features file (but can
651 <!-- JAL-2383 -->Above PID colour threshold not recovered
652 when alignment view imported from project
655 <!-- JAL-2520,JAL-2465 -->No mappings generated between
656 structure and sequences extracted from structure files
657 imported via URL and viewed in Jmol
660 <!-- JAL-2520 -->Structures loaded via URL are saved in
661 Jalview Projects rather than fetched via URL again when
662 the project is loaded and the structure viewed
665 <em>Web Services</em>
668 <!-- JAL-2519 -->EnsemblGenomes example failing after
669 release of Ensembl v.88
672 <!-- JAL-2366 -->Proxy server address and port always
673 appear enabled in Preferences->Connections
676 <!-- JAL-2461 -->DAS registry not found exceptions
677 removed from console output
680 <!-- JAL-2582 -->Cannot retrieve protein products from
681 Ensembl by Peptide ID
684 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
685 created from SIFTs, and spurious 'Couldn't open structure
686 in Chimera' errors raised after April 2017 update (problem
687 due to 'null' string rather than empty string used for
688 residues with no corresponding PDB mapping).
691 <em>Application UI</em>
694 <!-- JAL-2361 -->User Defined Colours not added to Colour
698 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
699 case' residues (button in colourscheme editor debugged and
700 new documentation and tooltips added)
703 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
704 doesn't restore group-specific text colour thresholds
707 <!-- JAL-2243 -->Feature settings panel does not update as
708 new features are added to alignment
711 <!-- JAL-2532 -->Cancel in feature settings reverts
712 changes to feature colours via the Amend features dialog
715 <!-- JAL-2506 -->Null pointer exception when attempting to
716 edit graduated feature colour via amend features dialog
720 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
721 selection menu changes colours of alignment views
724 <!-- JAL-2426 -->Spurious exceptions in console raised
725 from alignment calculation workers after alignment has
729 <!-- JAL-1608 -->Typo in selection popup menu - Create
730 groups now 'Create Group'
733 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
734 Create/Undefine group doesn't always work
737 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
738 shown again after pressing 'Cancel'
741 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
742 adjusts start position in wrap mode
745 <!-- JAL-2563 -->Status bar doesn't show positions for
746 ambiguous amino acids
749 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
750 CDS/Protein view after CDS sequences added for aligned
754 <!-- JAL-2592 -->User defined colourschemes called 'User
755 Defined' don't appear in Colours menu
761 <!-- JAL-2468 -->Switching between Nucleotide and Protein
762 score models doesn't always result in an updated PCA plot
765 <!-- JAL-2442 -->Features not rendered as transparent on
766 overview or linked structure view
769 <!-- JAL-2372 -->Colour group by conservation doesn't
773 <!-- JAL-2517 -->Hitting Cancel after applying
774 user-defined colourscheme doesn't restore original
781 <!-- JAL-2314 -->Unit test failure:
782 jalview.ws.jabaws.RNAStructExportImport setup fails
785 <!-- JAL-2307 -->Unit test failure:
786 jalview.ws.sifts.SiftsClientTest due to compatibility
787 problems with deep array comparison equality asserts in
788 successive versions of TestNG
791 <!-- JAL-2479 -->Relocated StructureChooserTest and
792 ParameterUtilsTest Unit tests to Network suite
795 <em>New Known Issues</em>
798 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
799 phase after a sequence motif find operation
802 <!-- JAL-2550 -->Importing annotation file with rows
803 containing just upper and lower case letters are
804 interpreted as WUSS RNA secondary structure symbols
807 <!-- JAL-2590 -->Cannot load and display Newick trees
808 reliably from eggnog Ortholog database
811 <!-- JAL-2468 -->Status bar shows 'Marked x columns
812 containing features of type Highlight' when 'B' is pressed
813 to mark columns containing highlighted regions.
816 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
817 doesn't always add secondary structure annotation.
822 <td width="60" nowrap>
824 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
827 <td><div align="left">
831 <!-- JAL-98 -->Improved memory usage: sparse arrays used
832 for all consensus calculations
835 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
838 <li>Updated Jalview's Certum code signing certificate
844 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
845 set of database cross-references, sorted alphabetically
848 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
849 from database cross references. Users with custom links
850 will receive a <a href="webServices/urllinks.html#warning">warning
851 dialog</a> asking them to update their preferences.
854 <!-- JAL-2287-->Cancel button and escape listener on
855 dialog warning user about disconnecting Jalview from a
859 <!-- JAL-2320-->Jalview's Chimera control window closes if
860 the Chimera it is connected to is shut down
863 <!-- JAL-1738-->New keystroke (B) and Select highlighted
864 columns menu item to mark columns containing highlighted
865 regions (e.g. from structure selections or results of a
869 <!-- JAL-2284-->Command line option for batch-generation
870 of HTML pages rendering alignment data with the BioJS
880 <!-- JAL-2286 -->Columns with more than one modal residue
881 are not coloured or thresholded according to percent
882 identity (first observed in Jalview 2.8.2)
885 <!-- JAL-2301 -->Threonine incorrectly reported as not
889 <!-- JAL-2318 -->Updates to documentation pages (above PID
890 threshold, amino acid properties)
893 <!-- JAL-2292 -->Lower case residues in sequences are not
894 reported as mapped to residues in a structure file in the
898 <!--JAL-2324 -->Identical features with non-numeric scores
899 could be added multiple times to a sequence
902 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
903 bond features shown as two highlighted residues rather
904 than a range in linked structure views, and treated
905 correctly when selecting and computing trees from features
908 <!-- JAL-2281-->Custom URL links for database
909 cross-references are matched to database name regardless
917 <!-- JAL-2282-->Custom URL links for specific database
918 names without regular expressions also offer links from
922 <!-- JAL-2315-->Removing a single configured link in the
923 URL links pane in Connections preferences doesn't actually
924 update Jalview configuration
927 <!-- JAL-2272-->CTRL-Click on a selected region to open
928 the alignment area popup menu doesn't work on El-Capitan
931 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
932 files with similarly named sequences if dropped onto the
936 <!-- JAL-2312 -->Additional mappings are shown for PDB
937 entries where more chains exist in the PDB accession than
938 are reported in the SIFTS file
941 <!-- JAL-2317-->Certain structures do not get mapped to
942 the structure view when displayed with Chimera
945 <!-- JAL-2317-->No chains shown in the Chimera view
946 panel's View->Show Chains submenu
949 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
950 work for wrapped alignment views
953 <!--JAL-2197 -->Rename UI components for running JPred
954 predictions from 'JNet' to 'JPred'
957 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
958 corrupted when annotation panel vertical scroll is not at
962 <!--JAL-2332 -->Attempting to view structure for Hen
963 lysozyme results in a PDB Client error dialog box
966 <!-- JAL-2319 -->Structure View's mapping report switched
967 ranges for PDB and sequence for SIFTS
970 SIFTS 'Not_Observed' residues mapped to non-existant
974 <!-- <em>New Known Issues</em>
981 <td width="60" nowrap>
983 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
984 <em>25/10/2016</em></strong>
987 <td><em>Application</em>
989 <li>3D Structure chooser opens with 'Cached structures'
990 view if structures already loaded</li>
991 <li>Progress bar reports models as they are loaded to
998 <li>Colour by conservation always enabled and no tick
999 shown in menu when BLOSUM or PID shading applied</li>
1000 <li>FER1_ARATH and FER2_ARATH labels were switched in
1001 example sequences/projects/trees</li>
1003 <em>Application</em>
1005 <li>Jalview projects with views of local PDB structure
1006 files saved on Windows cannot be opened on OSX</li>
1007 <li>Multiple structure views can be opened and superposed
1008 without timeout for structures with multiple models or
1009 multiple sequences in alignment</li>
1010 <li>Cannot import or associated local PDB files without a
1011 PDB ID HEADER line</li>
1012 <li>RMSD is not output in Jmol console when superposition
1014 <li>Drag and drop of URL from Browser fails for Linux and
1015 OSX versions earlier than El Capitan</li>
1016 <li>ENA client ignores invalid content from ENA server</li>
1017 <li>Exceptions are not raised in console when ENA client
1018 attempts to fetch non-existent IDs via Fetch DB Refs UI
1020 <li>Exceptions are not raised in console when a new view
1021 is created on the alignment</li>
1022 <li>OSX right-click fixed for group selections: CMD-click
1023 to insert/remove gaps in groups and CTRL-click to open group
1026 <em>Build and deployment</em>
1028 <li>URL link checker now copes with multi-line anchor
1031 <em>New Known Issues</em>
1033 <li>Drag and drop from URL links in browsers do not work
1040 <td width="60" nowrap>
1041 <div align="center">
1042 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1045 <td><em>General</em>
1048 <!-- JAL-2124 -->Updated Spanish translations.
1051 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1052 for importing structure data to Jalview. Enables mmCIF and
1056 <!-- JAL-192 --->Alignment ruler shows positions relative to
1060 <!-- JAL-2202 -->Position/residue shown in status bar when
1061 mousing over sequence associated annotation
1064 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1068 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1069 '()', canonical '[]' and invalid '{}' base pair populations
1073 <!-- JAL-2092 -->Feature settings popup menu options for
1074 showing or hiding columns containing a feature
1077 <!-- JAL-1557 -->Edit selected group by double clicking on
1078 group and sequence associated annotation labels
1081 <!-- JAL-2236 -->Sequence name added to annotation label in
1082 select/hide columns by annotation and colour by annotation
1086 </ul> <em>Application</em>
1089 <!-- JAL-2050-->Automatically hide introns when opening a
1090 gene/transcript view
1093 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1097 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1098 structure mappings with the EMBL-EBI PDBe SIFTS database
1101 <!-- JAL-2079 -->Updated download sites used for Rfam and
1102 Pfam sources to xfam.org
1105 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1108 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1109 over sequences in Jalview
1112 <!-- JAL-2027-->Support for reverse-complement coding
1113 regions in ENA and EMBL
1116 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1117 for record retrieval via ENA rest API
1120 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1124 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1125 groovy script execution
1128 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1129 alignment window's Calculate menu
1132 <!-- JAL-1812 -->Allow groovy scripts that call
1133 Jalview.getAlignFrames() to run in headless mode
1136 <!-- JAL-2068 -->Support for creating new alignment
1137 calculation workers from groovy scripts
1140 <!-- JAL-1369 --->Store/restore reference sequence in
1144 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1145 associations are now saved/restored from project
1148 <!-- JAL-1993 -->Database selection dialog always shown
1149 before sequence fetcher is opened
1152 <!-- JAL-2183 -->Double click on an entry in Jalview's
1153 database chooser opens a sequence fetcher
1156 <!-- JAL-1563 -->Free-text search client for UniProt using
1157 the UniProt REST API
1160 <!-- JAL-2168 -->-nonews command line parameter to prevent
1161 the news reader opening
1164 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1165 querying stored in preferences
1168 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1172 <!-- JAL-1977-->Tooltips shown on database chooser
1175 <!-- JAL-391 -->Reverse complement function in calculate
1176 menu for nucleotide sequences
1179 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1180 and feature counts preserves alignment ordering (and
1181 debugged for complex feature sets).
1184 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1185 viewing structures with Jalview 2.10
1188 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1189 genome, transcript CCDS and gene ids via the Ensembl and
1190 Ensembl Genomes REST API
1193 <!-- JAL-2049 -->Protein sequence variant annotation
1194 computed for 'sequence_variant' annotation on CDS regions
1198 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1202 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1203 Ref Fetcher fails to match, or otherwise updates sequence
1204 data from external database records.
1207 <!-- JAL-2154 -->Revised Jalview Project format for
1208 efficient recovery of sequence coding and alignment
1209 annotation relationships.
1211 </ul> <!-- <em>Applet</em>
1222 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1226 <!-- JAL-2018-->Export features in Jalview format (again)
1227 includes graduated colourschemes
1230 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1231 working with big alignments and lots of hidden columns
1234 <!-- JAL-2053-->Hidden column markers not always rendered
1235 at right of alignment window
1238 <!-- JAL-2067 -->Tidied up links in help file table of
1242 <!-- JAL-2072 -->Feature based tree calculation not shown
1246 <!-- JAL-2075 -->Hidden columns ignored during feature
1247 based tree calculation
1250 <!-- JAL-2065 -->Alignment view stops updating when show
1251 unconserved enabled for group on alignment
1254 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1258 <!-- JAL-2146 -->Alignment column in status incorrectly
1259 shown as "Sequence position" when mousing over
1263 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1264 hidden columns present
1267 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1268 user created annotation added to alignment
1271 <!-- JAL-1841 -->RNA Structure consensus only computed for
1272 '()' base pair annotation
1275 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1276 in zero scores for all base pairs in RNA Structure
1280 <!-- JAL-2174-->Extend selection with columns containing
1284 <!-- JAL-2275 -->Pfam format writer puts extra space at
1285 beginning of sequence
1288 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1292 <!-- JAL-2238 -->Cannot create groups on an alignment from
1293 from a tree when t-coffee scores are shown
1296 <!-- JAL-1836,1967 -->Cannot import and view PDB
1297 structures with chains containing negative resnums (4q4h)
1300 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1304 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1305 to Clustal, PIR and PileUp output
1308 <!-- JAL-2008 -->Reordering sequence features that are
1309 not visible causes alignment window to repaint
1312 <!-- JAL-2006 -->Threshold sliders don't work in
1313 graduated colour and colour by annotation row for e-value
1314 scores associated with features and annotation rows
1317 <!-- JAL-1797 -->amino acid physicochemical conservation
1318 calculation should be case independent
1321 <!-- JAL-2173 -->Remove annotation also updates hidden
1325 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1326 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1327 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1330 <!-- JAL-2065 -->Null pointer exceptions and redraw
1331 problems when reference sequence defined and 'show
1332 non-conserved' enabled
1335 <!-- JAL-1306 -->Quality and Conservation are now shown on
1336 load even when Consensus calculation is disabled
1339 <!-- JAL-1932 -->Remove right on penultimate column of
1340 alignment does nothing
1343 <em>Application</em>
1346 <!-- JAL-1552-->URLs and links can't be imported by
1347 drag'n'drop on OSX when launched via webstart (note - not
1348 yet fixed for El Capitan)
1351 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1352 output when running on non-gb/us i18n platforms
1355 <!-- JAL-1944 -->Error thrown when exporting a view with
1356 hidden sequences as flat-file alignment
1359 <!-- JAL-2030-->InstallAnywhere distribution fails when
1363 <!-- JAL-2080-->Jalview very slow to launch via webstart
1364 (also hotfix for 2.9.0b2)
1367 <!-- JAL-2085 -->Cannot save project when view has a
1368 reference sequence defined
1371 <!-- JAL-1011 -->Columns are suddenly selected in other
1372 alignments and views when revealing hidden columns
1375 <!-- JAL-1989 -->Hide columns not mirrored in complement
1376 view in a cDNA/Protein splitframe
1379 <!-- JAL-1369 -->Cannot save/restore representative
1380 sequence from project when only one sequence is
1384 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1385 in Structure Chooser
1388 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1389 structure consensus didn't refresh annotation panel
1392 <!-- JAL-1962 -->View mapping in structure view shows
1393 mappings between sequence and all chains in a PDB file
1396 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1397 dialogs format columns correctly, don't display array
1398 data, sort columns according to type
1401 <!-- JAL-1975 -->Export complete shown after destination
1402 file chooser is cancelled during an image export
1405 <!-- JAL-2025 -->Error when querying PDB Service with
1406 sequence name containing special characters
1409 <!-- JAL-2024 -->Manual PDB structure querying should be
1413 <!-- JAL-2104 -->Large tooltips with broken HTML
1414 formatting don't wrap
1417 <!-- JAL-1128 -->Figures exported from wrapped view are
1418 truncated so L looks like I in consensus annotation
1421 <!-- JAL-2003 -->Export features should only export the
1422 currently displayed features for the current selection or
1426 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1427 after fetching cross-references, and restoring from
1431 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1432 followed in the structure viewer
1435 <!-- JAL-2163 -->Titles for individual alignments in
1436 splitframe not restored from project
1439 <!-- JAL-2145 -->missing autocalculated annotation at
1440 trailing end of protein alignment in transcript/product
1441 splitview when pad-gaps not enabled by default
1444 <!-- JAL-1797 -->amino acid physicochemical conservation
1448 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1449 article has been read (reopened issue due to
1450 internationalisation problems)
1453 <!-- JAL-1960 -->Only offer PDB structures in structure
1454 viewer based on sequence name, PDB and UniProt
1459 <!-- JAL-1976 -->No progress bar shown during export of
1463 <!-- JAL-2213 -->Structures not always superimposed after
1464 multiple structures are shown for one or more sequences.
1467 <!-- JAL-1370 -->Reference sequence characters should not
1468 be replaced with '.' when 'Show unconserved' format option
1472 <!-- JAL-1823 -->Cannot specify chain code when entering
1473 specific PDB id for sequence
1476 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1477 'Export hidden sequences' is enabled, but 'export hidden
1478 columns' is disabled.
1481 <!--JAL-2026-->Best Quality option in structure chooser
1482 selects lowest rather than highest resolution structures
1486 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1487 to sequence mapping in 'View Mappings' report
1490 <!-- JAL-2284 -->Unable to read old Jalview projects that
1491 contain non-XML data added after Jalvew wrote project.
1494 <!-- JAL-2118 -->Newly created annotation row reorders
1495 after clicking on it to create new annotation for a
1499 <!-- JAL-1980 -->Null Pointer Exception raised when
1500 pressing Add on an orphaned cut'n'paste window.
1502 <!-- may exclude, this is an external service stability issue JAL-1941
1503 -- > RNA 3D structure not added via DSSR service</li> -->
1508 <!-- JAL-2151 -->Incorrect columns are selected when
1509 hidden columns present before start of sequence
1512 <!-- JAL-1986 -->Missing dependencies on applet pages
1516 <!-- JAL-1947 -->Overview pixel size changes when
1517 sequences are hidden in applet
1520 <!-- JAL-1996 -->Updated instructions for applet
1521 deployment on examples pages.
1528 <td width="60" nowrap>
1529 <div align="center">
1530 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1531 <em>16/10/2015</em></strong>
1534 <td><em>General</em>
1536 <li>Time stamps for signed Jalview application and applet
1541 <em>Application</em>
1543 <li>Duplicate group consensus and conservation rows
1544 shown when tree is partitioned</li>
1545 <li>Erratic behaviour when tree partitions made with
1546 multiple cDNA/Protein split views</li>
1552 <td width="60" nowrap>
1553 <div align="center">
1554 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1555 <em>8/10/2015</em></strong>
1558 <td><em>General</em>
1560 <li>Updated Spanish translations of localized text for
1562 </ul> <em>Application</em>
1564 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1565 <li>Signed OSX InstallAnywhere installer<br></li>
1566 <li>Support for per-sequence based annotations in BioJSON</li>
1567 </ul> <em>Applet</em>
1569 <li>Split frame example added to applet examples page</li>
1570 </ul> <em>Build and Deployment</em>
1573 <!-- JAL-1888 -->New ant target for running Jalview's test
1581 <li>Mapping of cDNA to protein in split frames
1582 incorrect when sequence start > 1</li>
1583 <li>Broken images in filter column by annotation dialog
1585 <li>Feature colours not parsed from features file</li>
1586 <li>Exceptions and incomplete link URLs recovered when
1587 loading a features file containing HTML tags in feature
1591 <em>Application</em>
1593 <li>Annotations corrupted after BioJS export and
1595 <li>Incorrect sequence limits after Fetch DB References
1596 with 'trim retrieved sequences'</li>
1597 <li>Incorrect warning about deleting all data when
1598 deleting selected columns</li>
1599 <li>Patch to build system for shipping properly signed
1600 JNLP templates for webstart launch</li>
1601 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1602 unreleased structures for download or viewing</li>
1603 <li>Tab/space/return keystroke operation of EMBL-PDBe
1604 fetcher/viewer dialogs works correctly</li>
1605 <li>Disabled 'minimise' button on Jalview windows
1606 running on OSX to workaround redraw hang bug</li>
1607 <li>Split cDNA/Protein view position and geometry not
1608 recovered from jalview project</li>
1609 <li>Initial enabled/disabled state of annotation menu
1610 sorter 'show autocalculated first/last' corresponds to
1612 <li>Restoring of Clustal, RNA Helices and T-Coffee
1613 color schemes from BioJSON</li>
1617 <li>Reorder sequences mirrored in cDNA/Protein split
1619 <li>Applet with Jmol examples not loading correctly</li>
1625 <td><div align="center">
1626 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1628 <td><em>General</em>
1630 <li>Linked visualisation and analysis of DNA and Protein
1633 <li>Translated cDNA alignments shown as split protein
1634 and DNA alignment views</li>
1635 <li>Codon consensus annotation for linked protein and
1636 cDNA alignment views</li>
1637 <li>Link cDNA or Protein product sequences by loading
1638 them onto Protein or cDNA alignments</li>
1639 <li>Reconstruct linked cDNA alignment from aligned
1640 protein sequences</li>
1643 <li>Jmol integration updated to Jmol v14.2.14</li>
1644 <li>Import and export of Jalview alignment views as <a
1645 href="features/bioJsonFormat.html">BioJSON</a></li>
1646 <li>New alignment annotation file statements for
1647 reference sequences and marking hidden columns</li>
1648 <li>Reference sequence based alignment shading to
1649 highlight variation</li>
1650 <li>Select or hide columns according to alignment
1652 <li>Find option for locating sequences by description</li>
1653 <li>Conserved physicochemical properties shown in amino
1654 acid conservation row</li>
1655 <li>Alignments can be sorted by number of RNA helices</li>
1656 </ul> <em>Application</em>
1658 <li>New cDNA/Protein analysis capabilities
1660 <li>Get Cross-References should open a Split Frame
1661 view with cDNA/Protein</li>
1662 <li>Detect when nucleotide sequences and protein
1663 sequences are placed in the same alignment</li>
1664 <li>Split cDNA/Protein views are saved in Jalview
1669 <li>Use REST API to talk to Chimera</li>
1670 <li>Selected regions in Chimera are highlighted in linked
1671 Jalview windows</li>
1673 <li>VARNA RNA viewer updated to v3.93</li>
1674 <li>VARNA views are saved in Jalview Projects</li>
1675 <li>Pseudoknots displayed as Jalview RNA annotation can
1676 be shown in VARNA</li>
1678 <li>Make groups for selection uses marked columns as well
1679 as the active selected region</li>
1681 <li>Calculate UPGMA and NJ trees using sequence feature
1683 <li>New Export options
1685 <li>New Export Settings dialog to control hidden
1686 region export in flat file generation</li>
1688 <li>Export alignment views for display with the <a
1689 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1691 <li>Export scrollable SVG in HTML page</li>
1692 <li>Optional embedding of BioJSON data when exporting
1693 alignment figures to HTML</li>
1695 <li>3D structure retrieval and display
1697 <li>Free text and structured queries with the PDBe
1699 <li>PDBe Search API based discovery and selection of
1700 PDB structures for a sequence set</li>
1704 <li>JPred4 employed for protein secondary structure
1706 <li>Hide Insertions menu option to hide unaligned columns
1707 for one or a group of sequences</li>
1708 <li>Automatically hide insertions in alignments imported
1709 from the JPred4 web server</li>
1710 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1711 system on OSX<br />LGPL libraries courtesy of <a
1712 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1714 <li>changed 'View nucleotide structure' submenu to 'View
1715 VARNA 2D Structure'</li>
1716 <li>change "View protein structure" menu option to "3D
1719 </ul> <em>Applet</em>
1721 <li>New layout for applet example pages</li>
1722 <li>New parameters to enable SplitFrame view
1723 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1724 <li>New example demonstrating linked viewing of cDNA and
1725 Protein alignments</li>
1726 </ul> <em>Development and deployment</em>
1728 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1729 <li>Include installation type and git revision in build
1730 properties and console log output</li>
1731 <li>Jalview Github organisation, and new github site for
1732 storing BioJsMSA Templates</li>
1733 <li>Jalview's unit tests now managed with TestNG</li>
1736 <!-- <em>General</em>
1738 </ul> --> <!-- issues resolved --> <em>Application</em>
1740 <li>Escape should close any open find dialogs</li>
1741 <li>Typo in select-by-features status report</li>
1742 <li>Consensus RNA secondary secondary structure
1743 predictions are not highlighted in amber</li>
1744 <li>Missing gap character in v2.7 example file means
1745 alignment appears unaligned when pad-gaps is not enabled</li>
1746 <li>First switch to RNA Helices colouring doesn't colour
1747 associated structure views</li>
1748 <li>ID width preference option is greyed out when auto
1749 width checkbox not enabled</li>
1750 <li>Stopped a warning dialog from being shown when
1751 creating user defined colours</li>
1752 <li>'View Mapping' in structure viewer shows sequence
1753 mappings for just that viewer's sequences</li>
1754 <li>Workaround for superposing PDB files containing
1755 multiple models in Chimera</li>
1756 <li>Report sequence position in status bar when hovering
1757 over Jmol structure</li>
1758 <li>Cannot output gaps as '.' symbols with Selection ->
1759 output to text box</li>
1760 <li>Flat file exports of alignments with hidden columns
1761 have incorrect sequence start/end</li>
1762 <li>'Aligning' a second chain to a Chimera structure from
1764 <li>Colour schemes applied to structure viewers don't
1765 work for nucleotide</li>
1766 <li>Loading/cut'n'pasting an empty or invalid file leads
1767 to a grey/invisible alignment window</li>
1768 <li>Exported Jpred annotation from a sequence region
1769 imports to different position</li>
1770 <li>Space at beginning of sequence feature tooltips shown
1771 on some platforms</li>
1772 <li>Chimera viewer 'View | Show Chain' menu is not
1774 <li>'New View' fails with a Null Pointer Exception in
1775 console if Chimera has been opened</li>
1776 <li>Mouseover to Chimera not working</li>
1777 <li>Miscellaneous ENA XML feature qualifiers not
1779 <li>NPE in annotation renderer after 'Extract Scores'</li>
1780 <li>If two structures in one Chimera window, mouseover of
1781 either sequence shows on first structure</li>
1782 <li>'Show annotations' options should not make
1783 non-positional annotations visible</li>
1784 <li>Subsequence secondary structure annotation not shown
1785 in right place after 'view flanking regions'</li>
1786 <li>File Save As type unset when current file format is
1788 <li>Save as '.jar' option removed for saving Jalview
1790 <li>Colour by Sequence colouring in Chimera more
1792 <li>Cannot 'add reference annotation' for a sequence in
1793 several views on same alignment</li>
1794 <li>Cannot show linked products for EMBL / ENA records</li>
1795 <li>Jalview's tooltip wraps long texts containing no
1797 </ul> <em>Applet</em>
1799 <li>Jmol to JalviewLite mouseover/link not working</li>
1800 <li>JalviewLite can't import sequences with ID
1801 descriptions containing angle brackets</li>
1802 </ul> <em>General</em>
1804 <li>Cannot export and reimport RNA secondary structure
1805 via jalview annotation file</li>
1806 <li>Random helix colour palette for colour by annotation
1807 with RNA secondary structure</li>
1808 <li>Mouseover to cDNA from STOP residue in protein
1809 translation doesn't work.</li>
1810 <li>hints when using the select by annotation dialog box</li>
1811 <li>Jmol alignment incorrect if PDB file has alternate CA
1813 <li>FontChooser message dialog appears to hang after
1814 choosing 1pt font</li>
1815 <li>Peptide secondary structure incorrectly imported from
1816 annotation file when annotation display text includes 'e' or
1818 <li>Cannot set colour of new feature type whilst creating
1820 <li>cDNA translation alignment should not be sequence
1821 order dependent</li>
1822 <li>'Show unconserved' doesn't work for lower case
1824 <li>Nucleotide ambiguity codes involving R not recognised</li>
1825 </ul> <em>Deployment and Documentation</em>
1827 <li>Applet example pages appear different to the rest of
1828 www.jalview.org</li>
1829 </ul> <em>Application Known issues</em>
1831 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1832 <li>Misleading message appears after trying to delete
1834 <li>Jalview icon not shown in dock after InstallAnywhere
1835 version launches</li>
1836 <li>Fetching EMBL reference for an RNA sequence results
1837 fails with a sequence mismatch</li>
1838 <li>Corrupted or unreadable alignment display when
1839 scrolling alignment to right</li>
1840 <li>ArrayIndexOutOfBoundsException thrown when remove
1841 empty columns called on alignment with ragged gapped ends</li>
1842 <li>auto calculated alignment annotation rows do not get
1843 placed above or below non-autocalculated rows</li>
1844 <li>Jalview dekstop becomes sluggish at full screen in
1845 ultra-high resolution</li>
1846 <li>Cannot disable consensus calculation independently of
1847 quality and conservation</li>
1848 <li>Mouseover highlighting between cDNA and protein can
1849 become sluggish with more than one splitframe shown</li>
1850 </ul> <em>Applet Known Issues</em>
1852 <li>Core PDB parsing code requires Jmol</li>
1853 <li>Sequence canvas panel goes white when alignment
1854 window is being resized</li>
1860 <td><div align="center">
1861 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1863 <td><em>General</em>
1865 <li>Updated Java code signing certificate donated by
1867 <li>Features and annotation preserved when performing
1868 pairwise alignment</li>
1869 <li>RNA pseudoknot annotation can be
1870 imported/exported/displayed</li>
1871 <li>'colour by annotation' can colour by RNA and
1872 protein secondary structure</li>
1873 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1874 post-hoc with 2.9 release</em>)
1877 </ul> <em>Application</em>
1879 <li>Extract and display secondary structure for sequences
1880 with 3D structures</li>
1881 <li>Support for parsing RNAML</li>
1882 <li>Annotations menu for layout
1884 <li>sort sequence annotation rows by alignment</li>
1885 <li>place sequence annotation above/below alignment
1888 <li>Output in Stockholm format</li>
1889 <li>Internationalisation: improved Spanish (es)
1891 <li>Structure viewer preferences tab</li>
1892 <li>Disorder and Secondary Structure annotation tracks
1893 shared between alignments</li>
1894 <li>UCSF Chimera launch and linked highlighting from
1896 <li>Show/hide all sequence associated annotation rows for
1897 all or current selection</li>
1898 <li>disorder and secondary structure predictions
1899 available as dataset annotation</li>
1900 <li>Per-sequence rna helices colouring</li>
1903 <li>Sequence database accessions imported when fetching
1904 alignments from Rfam</li>
1905 <li>update VARNA version to 3.91</li>
1907 <li>New groovy scripts for exporting aligned positions,
1908 conservation values, and calculating sum of pairs scores.</li>
1909 <li>Command line argument to set default JABAWS server</li>
1910 <li>include installation type in build properties and
1911 console log output</li>
1912 <li>Updated Jalview project format to preserve dataset
1916 <!-- issues resolved --> <em>Application</em>
1918 <li>Distinguish alignment and sequence associated RNA
1919 structure in structure->view->VARNA</li>
1920 <li>Raise dialog box if user deletes all sequences in an
1922 <li>Pressing F1 results in documentation opening twice</li>
1923 <li>Sequence feature tooltip is wrapped</li>
1924 <li>Double click on sequence associated annotation
1925 selects only first column</li>
1926 <li>Redundancy removal doesn't result in unlinked
1927 leaves shown in tree</li>
1928 <li>Undos after several redundancy removals don't undo
1930 <li>Hide sequence doesn't hide associated annotation</li>
1931 <li>User defined colours dialog box too big to fit on
1932 screen and buttons not visible</li>
1933 <li>author list isn't updated if already written to
1934 Jalview properties</li>
1935 <li>Popup menu won't open after retrieving sequence
1937 <li>File open window for associate PDB doesn't open</li>
1938 <li>Left-then-right click on a sequence id opens a
1939 browser search window</li>
1940 <li>Cannot open sequence feature shading/sort popup menu
1941 in feature settings dialog</li>
1942 <li>better tooltip placement for some areas of Jalview
1944 <li>Allow addition of JABAWS Server which doesn't
1945 pass validation</li>
1946 <li>Web services parameters dialog box is too large to
1948 <li>Muscle nucleotide alignment preset obscured by
1950 <li>JABAWS preset submenus don't contain newly
1951 defined user preset</li>
1952 <li>MSA web services warns user if they were launched
1953 with invalid input</li>
1954 <li>Jalview cannot contact DAS Registy when running on
1957 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1958 'Superpose with' submenu not shown when new view
1962 </ul> <!-- <em>Applet</em>
1964 </ul> <em>General</em>
1966 </ul>--> <em>Deployment and Documentation</em>
1968 <li>2G and 1G options in launchApp have no effect on
1969 memory allocation</li>
1970 <li>launchApp service doesn't automatically open
1971 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1973 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1974 InstallAnywhere reports cannot find valid JVM when Java
1975 1.7_055 is available
1977 </ul> <em>Application Known issues</em>
1980 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1981 corrupted or unreadable alignment display when scrolling
1985 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1986 retrieval fails but progress bar continues for DAS retrieval
1987 with large number of ID
1990 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1991 flatfile output of visible region has incorrect sequence
1995 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1996 rna structure consensus doesn't update when secondary
1997 structure tracks are rearranged
2000 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2001 invalid rna structure positional highlighting does not
2002 highlight position of invalid base pairs
2005 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2006 out of memory errors are not raised when saving Jalview
2007 project from alignment window file menu
2010 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2011 Switching to RNA Helices colouring doesn't propagate to
2015 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2016 colour by RNA Helices not enabled when user created
2017 annotation added to alignment
2020 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2021 Jalview icon not shown on dock in Mountain Lion/Webstart
2023 </ul> <em>Applet Known Issues</em>
2026 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2027 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2030 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2031 Jalview and Jmol example not compatible with IE9
2034 <li>Sort by annotation score doesn't reverse order
2040 <td><div align="center">
2041 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2044 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2047 <li>Internationalisation of user interface (usually
2048 called i18n support) and translation for Spanish locale</li>
2049 <li>Define/Undefine group on current selection with
2050 Ctrl-G/Shift Ctrl-G</li>
2051 <li>Improved group creation/removal options in
2052 alignment/sequence Popup menu</li>
2053 <li>Sensible precision for symbol distribution
2054 percentages shown in logo tooltip.</li>
2055 <li>Annotation panel height set according to amount of
2056 annotation when alignment first opened</li>
2057 </ul> <em>Application</em>
2059 <li>Interactive consensus RNA secondary structure
2060 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2061 <li>Select columns containing particular features from
2062 Feature Settings dialog</li>
2063 <li>View all 'representative' PDB structures for selected
2065 <li>Update Jalview project format:
2067 <li>New file extension for Jalview projects '.jvp'</li>
2068 <li>Preserve sequence and annotation dataset (to
2069 store secondary structure annotation,etc)</li>
2070 <li>Per group and alignment annotation and RNA helix
2074 <li>New similarity measures for PCA and Tree calculation
2076 <li>Experimental support for retrieval and viewing of
2077 flanking regions for an alignment</li>
2081 <!-- issues resolved --> <em>Application</em>
2083 <li>logo keeps spinning and status remains at queued or
2084 running after job is cancelled</li>
2085 <li>cannot export features from alignments imported from
2086 Jalview/VAMSAS projects</li>
2087 <li>Buggy slider for web service parameters that take
2089 <li>Newly created RNA secondary structure line doesn't
2090 have 'display all symbols' flag set</li>
2091 <li>T-COFFEE alignment score shading scheme and other
2092 annotation shading not saved in Jalview project</li>
2093 <li>Local file cannot be loaded in freshly downloaded
2095 <li>Jalview icon not shown on dock in Mountain
2097 <li>Load file from desktop file browser fails</li>
2098 <li>Occasional NPE thrown when calculating large trees</li>
2099 <li>Cannot reorder or slide sequences after dragging an
2100 alignment onto desktop</li>
2101 <li>Colour by annotation dialog throws NPE after using
2102 'extract scores' function</li>
2103 <li>Loading/cut'n'pasting an empty file leads to a grey
2104 alignment window</li>
2105 <li>Disorder thresholds rendered incorrectly after
2106 performing IUPred disorder prediction</li>
2107 <li>Multiple group annotated consensus rows shown when
2108 changing 'normalise logo' display setting</li>
2109 <li>Find shows blank dialog after 'finished searching' if
2110 nothing matches query</li>
2111 <li>Null Pointer Exceptions raised when sorting by
2112 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2114 <li>Errors in Jmol console when structures in alignment
2115 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2117 <li>Not all working JABAWS services are shown in
2119 <li>JAVAWS version of Jalview fails to launch with
2120 'invalid literal/length code'</li>
2121 <li>Annotation/RNA Helix colourschemes cannot be applied
2122 to alignment with groups (actually fixed in 2.8.0b1)</li>
2123 <li>RNA Helices and T-Coffee Scores available as default
2126 </ul> <em>Applet</em>
2128 <li>Remove group option is shown even when selection is
2130 <li>Apply to all groups ticked but colourscheme changes
2131 don't affect groups</li>
2132 <li>Documented RNA Helices and T-Coffee Scores as valid
2133 colourscheme name</li>
2134 <li>Annotation labels drawn on sequence IDs when
2135 Annotation panel is not displayed</li>
2136 <li>Increased font size for dropdown menus on OSX and
2137 embedded windows</li>
2138 </ul> <em>Other</em>
2140 <li>Consensus sequence for alignments/groups with a
2141 single sequence were not calculated</li>
2142 <li>annotation files that contain only groups imported as
2143 annotation and junk sequences</li>
2144 <li>Fasta files with sequences containing '*' incorrectly
2145 recognised as PFAM or BLC</li>
2146 <li>conservation/PID slider apply all groups option
2147 doesn't affect background (2.8.0b1)
2149 <li>redundancy highlighting is erratic at 0% and 100%</li>
2150 <li>Remove gapped columns fails for sequences with ragged
2152 <li>AMSA annotation row with leading spaces is not
2153 registered correctly on import</li>
2154 <li>Jalview crashes when selecting PCA analysis for
2155 certain alignments</li>
2156 <li>Opening the colour by annotation dialog for an
2157 existing annotation based 'use original colours'
2158 colourscheme loses original colours setting</li>
2163 <td><div align="center">
2164 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2165 <em>30/1/2014</em></strong>
2169 <li>Trusted certificates for JalviewLite applet and
2170 Jalview Desktop application<br />Certificate was donated by
2171 <a href="https://www.certum.eu">Certum</a> to the Jalview
2172 open source project).
2174 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2175 <li>Output in Stockholm format</li>
2176 <li>Allow import of data from gzipped files</li>
2177 <li>Export/import group and sequence associated line
2178 graph thresholds</li>
2179 <li>Nucleotide substitution matrix that supports RNA and
2180 ambiguity codes</li>
2181 <li>Allow disorder predictions to be made on the current
2182 selection (or visible selection) in the same way that JPred
2184 <li>Groovy scripting for headless Jalview operation</li>
2185 </ul> <em>Other improvements</em>
2187 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2188 <li>COMBINE statement uses current SEQUENCE_REF and
2189 GROUP_REF scope to group annotation rows</li>
2190 <li>Support '' style escaping of quotes in Newick
2192 <li>Group options for JABAWS service by command line name</li>
2193 <li>Empty tooltip shown for JABA service options with a
2194 link but no description</li>
2195 <li>Select primary source when selecting authority in
2196 database fetcher GUI</li>
2197 <li>Add .mfa to FASTA file extensions recognised by
2199 <li>Annotation label tooltip text wrap</li>
2204 <li>Slow scrolling when lots of annotation rows are
2206 <li>Lots of NPE (and slowness) after creating RNA
2207 secondary structure annotation line</li>
2208 <li>Sequence database accessions not imported when
2209 fetching alignments from Rfam</li>
2210 <li>Incorrect SHMR submission for sequences with
2212 <li>View all structures does not always superpose
2214 <li>Option widgets in service parameters not updated to
2215 reflect user or preset settings</li>
2216 <li>Null pointer exceptions for some services without
2217 presets or adjustable parameters</li>
2218 <li>Discover PDB IDs entry in structure menu doesn't
2219 discover PDB xRefs</li>
2220 <li>Exception encountered while trying to retrieve
2221 features with DAS</li>
2222 <li>Lowest value in annotation row isn't coloured
2223 when colour by annotation (per sequence) is coloured</li>
2224 <li>Keyboard mode P jumps to start of gapped region when
2225 residue follows a gap</li>
2226 <li>Jalview appears to hang importing an alignment with
2227 Wrap as default or after enabling Wrap</li>
2228 <li>'Right click to add annotations' message
2229 shown in wrap mode when no annotations present</li>
2230 <li>Disorder predictions fail with NPE if no automatic
2231 annotation already exists on alignment</li>
2232 <li>oninit javascript function should be called after
2233 initialisation completes</li>
2234 <li>Remove redundancy after disorder prediction corrupts
2235 alignment window display</li>
2236 <li>Example annotation file in documentation is invalid</li>
2237 <li>Grouped line graph annotation rows are not exported
2238 to annotation file</li>
2239 <li>Multi-harmony analysis cannot be run when only two
2241 <li>Cannot create multiple groups of line graphs with
2242 several 'combine' statements in annotation file</li>
2243 <li>Pressing return several times causes Number Format
2244 exceptions in keyboard mode</li>
2245 <li>Multi-harmony (SHMMR) method doesn't submit
2246 correct partitions for input data</li>
2247 <li>Translation from DNA to Amino Acids fails</li>
2248 <li>Jalview fail to load newick tree with quoted label</li>
2249 <li>--headless flag isn't understood</li>
2250 <li>ClassCastException when generating EPS in headless
2252 <li>Adjusting sequence-associated shading threshold only
2253 changes one row's threshold</li>
2254 <li>Preferences and Feature settings panel panel
2255 doesn't open</li>
2256 <li>hide consensus histogram also hides conservation and
2257 quality histograms</li>
2262 <td><div align="center">
2263 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2265 <td><em>Application</em>
2267 <li>Support for JABAWS 2.0 Services (AACon alignment
2268 conservation, protein disorder and Clustal Omega)</li>
2269 <li>JABAWS server status indicator in Web Services
2271 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2272 in Jalview alignment window</li>
2273 <li>Updated Jalview build and deploy framework for OSX
2274 mountain lion, windows 7, and 8</li>
2275 <li>Nucleotide substitution matrix for PCA that supports
2276 RNA and ambiguity codes</li>
2278 <li>Improved sequence database retrieval GUI</li>
2279 <li>Support fetching and database reference look up
2280 against multiple DAS sources (Fetch all from in 'fetch db
2282 <li>Jalview project improvements
2284 <li>Store and retrieve the 'belowAlignment'
2285 flag for annotation</li>
2286 <li>calcId attribute to group annotation rows on the
2288 <li>Store AACon calculation settings for a view in
2289 Jalview project</li>
2293 <li>horizontal scrolling gesture support</li>
2294 <li>Visual progress indicator when PCA calculation is
2296 <li>Simpler JABA web services menus</li>
2297 <li>visual indication that web service results are still
2298 being retrieved from server</li>
2299 <li>Serialise the dialogs that are shown when Jalview
2300 starts up for first time</li>
2301 <li>Jalview user agent string for interacting with HTTP
2303 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2305 <li>Examples directory and Groovy library included in
2306 InstallAnywhere distribution</li>
2307 </ul> <em>Applet</em>
2309 <li>RNA alignment and secondary structure annotation
2310 visualization applet example</li>
2311 </ul> <em>General</em>
2313 <li>Normalise option for consensus sequence logo</li>
2314 <li>Reset button in PCA window to return dimensions to
2316 <li>Allow seqspace or Jalview variant of alignment PCA
2318 <li>PCA with either nucleic acid and protein substitution
2320 <li>Allow windows containing HTML reports to be exported
2322 <li>Interactive display and editing of RNA secondary
2323 structure contacts</li>
2324 <li>RNA Helix Alignment Colouring</li>
2325 <li>RNA base pair logo consensus</li>
2326 <li>Parse sequence associated secondary structure
2327 information in Stockholm files</li>
2328 <li>HTML Export database accessions and annotation
2329 information presented in tooltip for sequences</li>
2330 <li>Import secondary structure from LOCARNA clustalw
2331 style RNA alignment files</li>
2332 <li>import and visualise T-COFFEE quality scores for an
2334 <li>'colour by annotation' per sequence option to
2335 shade each sequence according to its associated alignment
2337 <li>New Jalview Logo</li>
2338 </ul> <em>Documentation and Development</em>
2340 <li>documentation for score matrices used in Jalview</li>
2341 <li>New Website!</li>
2343 <td><em>Application</em>
2345 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2346 wsdbfetch REST service</li>
2347 <li>Stop windows being moved outside desktop on OSX</li>
2348 <li>Filetype associations not installed for webstart
2350 <li>Jalview does not always retrieve progress of a JABAWS
2351 job execution in full once it is complete</li>
2352 <li>revise SHMR RSBS definition to ensure alignment is
2353 uploaded via ali_file parameter</li>
2354 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2355 <li>View all structures superposed fails with exception</li>
2356 <li>Jnet job queues forever if a very short sequence is
2357 submitted for prediction</li>
2358 <li>Cut and paste menu not opened when mouse clicked on
2360 <li>Putting fractional value into integer text box in
2361 alignment parameter dialog causes Jalview to hang</li>
2362 <li>Structure view highlighting doesn't work on
2364 <li>View all structures fails with exception shown in
2366 <li>Characters in filename associated with PDBEntry not
2367 escaped in a platform independent way</li>
2368 <li>Jalview desktop fails to launch with exception when
2370 <li>Tree calculation reports 'you must have 2 or more
2371 sequences selected' when selection is empty</li>
2372 <li>Jalview desktop fails to launch with jar signature
2373 failure when java web start temporary file caching is
2375 <li>DAS Sequence retrieval with range qualification
2376 results in sequence xref which includes range qualification</li>
2377 <li>Errors during processing of command line arguments
2378 cause progress bar (JAL-898) to be removed</li>
2379 <li>Replace comma for semi-colon option not disabled for
2380 DAS sources in sequence fetcher</li>
2381 <li>Cannot close news reader when JABAWS server warning
2382 dialog is shown</li>
2383 <li>Option widgets not updated to reflect user settings</li>
2384 <li>Edited sequence not submitted to web service</li>
2385 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2386 <li>InstallAnywhere installer doesn't unpack and run
2387 on OSX Mountain Lion</li>
2388 <li>Annotation panel not given a scroll bar when
2389 sequences with alignment annotation are pasted into the
2391 <li>Sequence associated annotation rows not associated
2392 when loaded from Jalview project</li>
2393 <li>Browser launch fails with NPE on java 1.7</li>
2394 <li>JABAWS alignment marked as finished when job was
2395 cancelled or job failed due to invalid input</li>
2396 <li>NPE with v2.7 example when clicking on Tree
2397 associated with all views</li>
2398 <li>Exceptions when copy/paste sequences with grouped
2399 annotation rows to new window</li>
2400 </ul> <em>Applet</em>
2402 <li>Sequence features are momentarily displayed before
2403 they are hidden using hidefeaturegroups applet parameter</li>
2404 <li>loading features via javascript API automatically
2405 enables feature display</li>
2406 <li>scrollToColumnIn javascript API method doesn't
2408 </ul> <em>General</em>
2410 <li>Redundancy removal fails for rna alignment</li>
2411 <li>PCA calculation fails when sequence has been selected
2412 and then deselected</li>
2413 <li>PCA window shows grey box when first opened on OSX</li>
2414 <li>Letters coloured pink in sequence logo when alignment
2415 coloured with clustalx</li>
2416 <li>Choosing fonts without letter symbols defined causes
2417 exceptions and redraw errors</li>
2418 <li>Initial PCA plot view is not same as manually
2419 reconfigured view</li>
2420 <li>Grouped annotation graph label has incorrect line
2422 <li>Grouped annotation graph label display is corrupted
2423 for lots of labels</li>
2428 <div align="center">
2429 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2432 <td><em>Application</em>
2434 <li>Jalview Desktop News Reader</li>
2435 <li>Tweaked default layout of web services menu</li>
2436 <li>View/alignment association menu to enable user to
2437 easily specify which alignment a multi-structure view takes
2438 its colours/correspondences from</li>
2439 <li>Allow properties file location to be specified as URL</li>
2440 <li>Extend Jalview project to preserve associations
2441 between many alignment views and a single Jmol display</li>
2442 <li>Store annotation row height in Jalview project file</li>
2443 <li>Annotation row column label formatting attributes
2444 stored in project file</li>
2445 <li>Annotation row order for auto-calculated annotation
2446 rows preserved in Jalview project file</li>
2447 <li>Visual progress indication when Jalview state is
2448 saved using Desktop window menu</li>
2449 <li>Visual indication that command line arguments are
2450 still being processed</li>
2451 <li>Groovy script execution from URL</li>
2452 <li>Colour by annotation default min and max colours in
2454 <li>Automatically associate PDB files dragged onto an
2455 alignment with sequences that have high similarity and
2457 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2458 <li>'view structures' option to open many
2459 structures in same window</li>
2460 <li>Sort associated views menu option for tree panel</li>
2461 <li>Group all JABA and non-JABA services for a particular
2462 analysis function in its own submenu</li>
2463 </ul> <em>Applet</em>
2465 <li>Userdefined and autogenerated annotation rows for
2467 <li>Adjustment of alignment annotation pane height</li>
2468 <li>Annotation scrollbar for annotation panel</li>
2469 <li>Drag to reorder annotation rows in annotation panel</li>
2470 <li>'automaticScrolling' parameter</li>
2471 <li>Allow sequences with partial ID string matches to be
2472 annotated from GFF/Jalview features files</li>
2473 <li>Sequence logo annotation row in applet</li>
2474 <li>Absolute paths relative to host server in applet
2475 parameters are treated as such</li>
2476 <li>New in the JalviewLite javascript API:
2478 <li>JalviewLite.js javascript library</li>
2479 <li>Javascript callbacks for
2481 <li>Applet initialisation</li>
2482 <li>Sequence/alignment mouse-overs and selections</li>
2485 <li>scrollTo row and column alignment scrolling
2487 <li>Select sequence/alignment regions from javascript</li>
2488 <li>javascript structure viewer harness to pass
2489 messages between Jmol and Jalview when running as
2490 distinct applets</li>
2491 <li>sortBy method</li>
2492 <li>Set of applet and application examples shipped
2493 with documentation</li>
2494 <li>New example to demonstrate JalviewLite and Jmol
2495 javascript message exchange</li>
2497 </ul> <em>General</em>
2499 <li>Enable Jmol displays to be associated with multiple
2500 multiple alignments</li>
2501 <li>Option to automatically sort alignment with new tree</li>
2502 <li>User configurable link to enable redirects to a
2503 www.Jalview.org mirror</li>
2504 <li>Jmol colours option for Jmol displays</li>
2505 <li>Configurable newline string when writing alignment
2506 and other flat files</li>
2507 <li>Allow alignment annotation description lines to
2508 contain html tags</li>
2509 </ul> <em>Documentation and Development</em>
2511 <li>Add groovy test harness for bulk load testing to
2513 <li>Groovy script to load and align a set of sequences
2514 using a web service before displaying the result in the
2515 Jalview desktop</li>
2516 <li>Restructured javascript and applet api documentation</li>
2517 <li>Ant target to publish example html files with applet
2519 <li>Netbeans project for building Jalview from source</li>
2520 <li>ant task to create online javadoc for Jalview source</li>
2522 <td><em>Application</em>
2524 <li>User defined colourscheme throws exception when
2525 current built in colourscheme is saved as new scheme</li>
2526 <li>AlignFrame->Save in application pops up save
2527 dialog for valid filename/format</li>
2528 <li>Cannot view associated structure for UniProt sequence</li>
2529 <li>PDB file association breaks for UniProt sequence
2531 <li>Associate PDB from file dialog does not tell you
2532 which sequence is to be associated with the file</li>
2533 <li>Find All raises null pointer exception when query
2534 only matches sequence IDs</li>
2535 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2536 <li>Jalview project with Jmol views created with Jalview
2537 2.4 cannot be loaded</li>
2538 <li>Filetype associations not installed for webstart
2540 <li>Two or more chains in a single PDB file associated
2541 with sequences in different alignments do not get coloured
2542 by their associated sequence</li>
2543 <li>Visibility status of autocalculated annotation row
2544 not preserved when project is loaded</li>
2545 <li>Annotation row height and visibility attributes not
2546 stored in Jalview project</li>
2547 <li>Tree bootstraps are not preserved when saved as a
2548 Jalview project</li>
2549 <li>Envision2 workflow tooltips are corrupted</li>
2550 <li>Enabling show group conservation also enables colour
2551 by conservation</li>
2552 <li>Duplicate group associated conservation or consensus
2553 created on new view</li>
2554 <li>Annotation scrollbar not displayed after 'show
2555 all hidden annotation rows' option selected</li>
2556 <li>Alignment quality not updated after alignment
2557 annotation row is hidden then shown</li>
2558 <li>Preserve colouring of structures coloured by
2559 sequences in pre Jalview 2.7 projects</li>
2560 <li>Web service job parameter dialog is not laid out
2562 <li>Web services menu not refreshed after 'reset
2563 services' button is pressed in preferences</li>
2564 <li>Annotation off by one in Jalview v2_3 example project</li>
2565 <li>Structures imported from file and saved in project
2566 get name like jalview_pdb1234.txt when reloaded</li>
2567 <li>Jalview does not always retrieve progress of a JABAWS
2568 job execution in full once it is complete</li>
2569 </ul> <em>Applet</em>
2571 <li>Alignment height set incorrectly when lots of
2572 annotation rows are displayed</li>
2573 <li>Relative URLs in feature HTML text not resolved to
2575 <li>View follows highlighting does not work for positions
2577 <li><= shown as = in tooltip</li>
2578 <li>Export features raises exception when no features
2580 <li>Separator string used for serialising lists of IDs
2581 for javascript api is modified when separator string
2582 provided as parameter</li>
2583 <li>Null pointer exception when selecting tree leaves for
2584 alignment with no existing selection</li>
2585 <li>Relative URLs for datasources assumed to be relative
2586 to applet's codebase</li>
2587 <li>Status bar not updated after finished searching and
2588 search wraps around to first result</li>
2589 <li>StructureSelectionManager instance shared between
2590 several Jalview applets causes race conditions and memory
2592 <li>Hover tooltip and mouseover of position on structure
2593 not sent from Jmol in applet</li>
2594 <li>Certain sequences of javascript method calls to
2595 applet API fatally hang browser</li>
2596 </ul> <em>General</em>
2598 <li>View follows structure mouseover scrolls beyond
2599 position with wrapped view and hidden regions</li>
2600 <li>Find sequence position moves to wrong residue
2601 with/without hidden columns</li>
2602 <li>Sequence length given in alignment properties window
2604 <li>InvalidNumberFormat exceptions thrown when trying to
2605 import PDB like structure files</li>
2606 <li>Positional search results are only highlighted
2607 between user-supplied sequence start/end bounds</li>
2608 <li>End attribute of sequence is not validated</li>
2609 <li>Find dialog only finds first sequence containing a
2610 given sequence position</li>
2611 <li>Sequence numbering not preserved in MSF alignment
2613 <li>Jalview PDB file reader does not extract sequence
2614 from nucleotide chains correctly</li>
2615 <li>Structure colours not updated when tree partition
2616 changed in alignment</li>
2617 <li>Sequence associated secondary structure not correctly
2618 parsed in interleaved stockholm</li>
2619 <li>Colour by annotation dialog does not restore current
2621 <li>Hiding (nearly) all sequences doesn't work
2623 <li>Sequences containing lowercase letters are not
2624 properly associated with their pdb files</li>
2625 </ul> <em>Documentation and Development</em>
2627 <li>schemas/JalviewWsParamSet.xsd corrupted by
2628 ApplyCopyright tool</li>
2633 <div align="center">
2634 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2637 <td><em>Application</em>
2639 <li>New warning dialog when the Jalview Desktop cannot
2640 contact web services</li>
2641 <li>JABA service parameters for a preset are shown in
2642 service job window</li>
2643 <li>JABA Service menu entries reworded</li>
2647 <li>Modeller PIR IO broken - cannot correctly import a
2648 pir file emitted by Jalview</li>
2649 <li>Existing feature settings transferred to new
2650 alignment view created from cut'n'paste</li>
2651 <li>Improved test for mixed amino/nucleotide chains when
2652 parsing PDB files</li>
2653 <li>Consensus and conservation annotation rows
2654 occasionally become blank for all new windows</li>
2655 <li>Exception raised when right clicking above sequences
2656 in wrapped view mode</li>
2657 </ul> <em>Application</em>
2659 <li>multiple multiply aligned structure views cause cpu
2660 usage to hit 100% and computer to hang</li>
2661 <li>Web Service parameter layout breaks for long user
2662 parameter names</li>
2663 <li>Jaba service discovery hangs desktop if Jaba server
2670 <div align="center">
2671 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2674 <td><em>Application</em>
2676 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2677 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2680 <li>Web Services preference tab</li>
2681 <li>Analysis parameters dialog box and user defined
2683 <li>Improved speed and layout of Envision2 service menu</li>
2684 <li>Superpose structures using associated sequence
2686 <li>Export coordinates and projection as CSV from PCA
2688 </ul> <em>Applet</em>
2690 <li>enable javascript: execution by the applet via the
2691 link out mechanism</li>
2692 </ul> <em>Other</em>
2694 <li>Updated the Jmol Jalview interface to work with Jmol
2696 <li>The Jalview Desktop and JalviewLite applet now
2697 require Java 1.5</li>
2698 <li>Allow Jalview feature colour specification for GFF
2699 sequence annotation files</li>
2700 <li>New 'colour by label' keword in Jalview feature file
2701 type colour specification</li>
2702 <li>New Jalview Desktop Groovy API method that allows a
2703 script to check if it being run in an interactive session or
2704 in a batch operation from the Jalview command line</li>
2708 <li>clustalx colourscheme colours Ds preferentially when
2709 both D+E are present in over 50% of the column</li>
2710 </ul> <em>Application</em>
2712 <li>typo in AlignmentFrame->View->Hide->all but
2713 selected Regions menu item</li>
2714 <li>sequence fetcher replaces ',' for ';' when the ',' is
2715 part of a valid accession ID</li>
2716 <li>fatal OOM if object retrieved by sequence fetcher
2717 runs out of memory</li>
2718 <li>unhandled Out of Memory Error when viewing pca
2719 analysis results</li>
2720 <li>InstallAnywhere builds fail to launch on OS X java
2721 10.5 update 4 (due to apple Java 1.6 update)</li>
2722 <li>Installanywhere Jalview silently fails to launch</li>
2723 </ul> <em>Applet</em>
2725 <li>Jalview.getFeatureGroups() raises an
2726 ArrayIndexOutOfBoundsException if no feature groups are
2733 <div align="center">
2734 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2740 <li>Alignment prettyprinter doesn't cope with long
2742 <li>clustalx colourscheme colours Ds preferentially when
2743 both D+E are present in over 50% of the column</li>
2744 <li>nucleic acid structures retrieved from PDB do not
2745 import correctly</li>
2746 <li>More columns get selected than were clicked on when a
2747 number of columns are hidden</li>
2748 <li>annotation label popup menu not providing correct
2749 add/hide/show options when rows are hidden or none are
2751 <li>Stockholm format shown in list of readable formats,
2752 and parser copes better with alignments from RFAM.</li>
2753 <li>CSV output of consensus only includes the percentage
2754 of all symbols if sequence logo display is enabled</li>
2756 </ul> <em>Applet</em>
2758 <li>annotation panel disappears when annotation is
2760 </ul> <em>Application</em>
2762 <li>Alignment view not redrawn properly when new
2763 alignment opened where annotation panel is visible but no
2764 annotations are present on alignment</li>
2765 <li>pasted region containing hidden columns is
2766 incorrectly displayed in new alignment window</li>
2767 <li>Jalview slow to complete operations when stdout is
2768 flooded (fix is to close the Jalview console)</li>
2769 <li>typo in AlignmentFrame->View->Hide->all but
2770 selected Rregions menu item.</li>
2771 <li>inconsistent group submenu and Format submenu entry
2772 'Un' or 'Non'conserved</li>
2773 <li>Sequence feature settings are being shared by
2774 multiple distinct alignments</li>
2775 <li>group annotation not recreated when tree partition is
2777 <li>double click on group annotation to select sequences
2778 does not propagate to associated trees</li>
2779 <li>Mac OSX specific issues:
2781 <li>exception raised when mouse clicked on desktop
2782 window background</li>
2783 <li>Desktop menu placed on menu bar and application
2784 name set correctly</li>
2785 <li>sequence feature settings not wide enough for the
2786 save feature colourscheme button</li>
2795 <div align="center">
2796 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2799 <td><em>New Capabilities</em>
2801 <li>URL links generated from description line for
2802 regular-expression based URL links (applet and application)
2804 <li>Non-positional feature URL links are shown in link
2806 <li>Linked viewing of nucleic acid sequences and
2808 <li>Automatic Scrolling option in View menu to display
2809 the currently highlighted region of an alignment.</li>
2810 <li>Order an alignment by sequence length, or using the
2811 average score or total feature count for each sequence.</li>
2812 <li>Shading features by score or associated description</li>
2813 <li>Subdivide alignment and groups based on identity of
2814 selected subsequence (Make Groups from Selection).</li>
2815 <li>New hide/show options including Shift+Control+H to
2816 hide everything but the currently selected region.</li>
2817 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2818 </ul> <em>Application</em>
2820 <li>Fetch DB References capabilities and UI expanded to
2821 support retrieval from DAS sequence sources</li>
2822 <li>Local DAS Sequence sources can be added via the
2823 command line or via the Add local source dialog box.</li>
2824 <li>DAS Dbref and DbxRef feature types are parsed as
2825 database references and protein_name is parsed as
2826 description line (BioSapiens terms).</li>
2827 <li>Enable or disable non-positional feature and database
2828 references in sequence ID tooltip from View menu in
2830 <!-- <li>New hidden columns and rows and representatives capabilities
2831 in annotations file (in progress - not yet fully implemented)</li> -->
2832 <li>Group-associated consensus, sequence logos and
2833 conservation plots</li>
2834 <li>Symbol distributions for each column can be exported
2835 and visualized as sequence logos</li>
2836 <li>Optionally scale multi-character column labels to fit
2837 within each column of annotation row<!-- todo for applet -->
2839 <li>Optional automatic sort of associated alignment view
2840 when a new tree is opened.</li>
2841 <li>Jalview Java Console</li>
2842 <li>Better placement of desktop window when moving
2843 between different screens.</li>
2844 <li>New preference items for sequence ID tooltip and
2845 consensus annotation</li>
2846 <li>Client to submit sequences and IDs to Envision2
2848 <li><em>Vamsas Capabilities</em>
2850 <li>Improved VAMSAS synchronization (Jalview archive
2851 used to preserve views, structures, and tree display
2853 <li>Import of vamsas documents from disk or URL via
2855 <li>Sharing of selected regions between views and
2856 with other VAMSAS applications (Experimental feature!)</li>
2857 <li>Updated API to VAMSAS version 0.2</li>
2859 </ul> <em>Applet</em>
2861 <li>Middle button resizes annotation row height</li>
2864 <li>sortByTree (true/false) - automatically sort the
2865 associated alignment view by the tree when a new tree is
2867 <li>showTreeBootstraps (true/false) - show or hide
2868 branch bootstraps (default is to show them if available)</li>
2869 <li>showTreeDistances (true/false) - show or hide
2870 branch lengths (default is to show them if available)</li>
2871 <li>showUnlinkedTreeNodes (true/false) - indicate if
2872 unassociated nodes should be highlighted in the tree
2874 <li>heightScale and widthScale (1.0 or more) -
2875 increase the height or width of a cell in the alignment
2876 grid relative to the current font size.</li>
2879 <li>Non-positional features displayed in sequence ID
2881 </ul> <em>Other</em>
2883 <li>Features format: graduated colour definitions and
2884 specification of feature scores</li>
2885 <li>Alignment Annotations format: new keywords for group
2886 associated annotation (GROUP_REF) and annotation row display
2887 properties (ROW_PROPERTIES)</li>
2888 <li>XML formats extended to support graduated feature
2889 colourschemes, group associated annotation, and profile
2890 visualization settings.</li></td>
2893 <li>Source field in GFF files parsed as feature source
2894 rather than description</li>
2895 <li>Non-positional features are now included in sequence
2896 feature and gff files (controlled via non-positional feature
2897 visibility in tooltip).</li>
2898 <li>URL links generated for all feature links (bugfix)</li>
2899 <li>Added URL embedding instructions to features file
2901 <li>Codons containing ambiguous nucleotides translated as
2902 'X' in peptide product</li>
2903 <li>Match case switch in find dialog box works for both
2904 sequence ID and sequence string and query strings do not
2905 have to be in upper case to match case-insensitively.</li>
2906 <li>AMSA files only contain first column of
2907 multi-character column annotation labels</li>
2908 <li>Jalview Annotation File generation/parsing consistent
2909 with documentation (e.g. Stockholm annotation can be
2910 exported and re-imported)</li>
2911 <li>PDB files without embedded PDB IDs given a friendly
2913 <li>Find incrementally searches ID string matches as well
2914 as subsequence matches, and correctly reports total number
2918 <li>Better handling of exceptions during sequence
2920 <li>Dasobert generated non-positional feature URL
2921 link text excludes the start_end suffix</li>
2922 <li>DAS feature and source retrieval buttons disabled
2923 when fetch or registry operations in progress.</li>
2924 <li>PDB files retrieved from URLs are cached properly</li>
2925 <li>Sequence description lines properly shared via
2927 <li>Sequence fetcher fetches multiple records for all
2929 <li>Ensured that command line das feature retrieval
2930 completes before alignment figures are generated.</li>
2931 <li>Reduced time taken when opening file browser for
2933 <li>isAligned check prior to calculating tree, PCA or
2934 submitting an MSA to JNet now excludes hidden sequences.</li>
2935 <li>User defined group colours properly recovered
2936 from Jalview projects.</li>
2945 <div align="center">
2946 <strong>2.4.0.b2</strong><br> 28/10/2009
2951 <li>Experimental support for google analytics usage
2953 <li>Jalview privacy settings (user preferences and docs).</li>
2958 <li>Race condition in applet preventing startup in
2960 <li>Exception when feature created from selection beyond
2961 length of sequence.</li>
2962 <li>Allow synthetic PDB files to be imported gracefully</li>
2963 <li>Sequence associated annotation rows associate with
2964 all sequences with a given id</li>
2965 <li>Find function matches case-insensitively for sequence
2966 ID string searches</li>
2967 <li>Non-standard characters do not cause pairwise
2968 alignment to fail with exception</li>
2969 </ul> <em>Application Issues</em>
2971 <li>Sequences are now validated against EMBL database</li>
2972 <li>Sequence fetcher fetches multiple records for all
2974 </ul> <em>InstallAnywhere Issues</em>
2976 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2977 issue with installAnywhere mechanism)</li>
2978 <li>Command line launching of JARs from InstallAnywhere
2979 version (java class versioning error fixed)</li>
2986 <div align="center">
2987 <strong>2.4</strong><br> 27/8/2008
2990 <td><em>User Interface</em>
2992 <li>Linked highlighting of codon and amino acid from
2993 translation and protein products</li>
2994 <li>Linked highlighting of structure associated with
2995 residue mapping to codon position</li>
2996 <li>Sequence Fetcher provides example accession numbers
2997 and 'clear' button</li>
2998 <li>MemoryMonitor added as an option under Desktop's
3000 <li>Extract score function to parse whitespace separated
3001 numeric data in description line</li>
3002 <li>Column labels in alignment annotation can be centred.</li>
3003 <li>Tooltip for sequence associated annotation give name
3005 </ul> <em>Web Services and URL fetching</em>
3007 <li>JPred3 web service</li>
3008 <li>Prototype sequence search client (no public services
3010 <li>Fetch either seed alignment or full alignment from
3012 <li>URL Links created for matching database cross
3013 references as well as sequence ID</li>
3014 <li>URL Links can be created using regular-expressions</li>
3015 </ul> <em>Sequence Database Connectivity</em>
3017 <li>Retrieval of cross-referenced sequences from other
3019 <li>Generalised database reference retrieval and
3020 validation to all fetchable databases</li>
3021 <li>Fetch sequences from DAS sources supporting the
3022 sequence command</li>
3023 </ul> <em>Import and Export</em>
3024 <li>export annotation rows as CSV for spreadsheet import</li>
3025 <li>Jalview projects record alignment dataset associations,
3026 EMBL products, and cDNA sequence mappings</li>
3027 <li>Sequence Group colour can be specified in Annotation
3029 <li>Ad-hoc colouring of group in Annotation File using RGB
3030 triplet as name of colourscheme</li>
3031 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3033 <li>treenode binding for VAMSAS tree exchange</li>
3034 <li>local editing and update of sequences in VAMSAS
3035 alignments (experimental)</li>
3036 <li>Create new or select existing session to join</li>
3037 <li>load and save of vamsas documents</li>
3038 </ul> <em>Application command line</em>
3040 <li>-tree parameter to open trees (introduced for passing
3042 <li>-fetchfrom command line argument to specify nicknames
3043 of DAS servers to query for alignment features</li>
3044 <li>-dasserver command line argument to add new servers
3045 that are also automatically queried for features</li>
3046 <li>-groovy command line argument executes a given groovy
3047 script after all input data has been loaded and parsed</li>
3048 </ul> <em>Applet-Application data exchange</em>
3050 <li>Trees passed as applet parameters can be passed to
3051 application (when using "View in full
3052 application")</li>
3053 </ul> <em>Applet Parameters</em>
3055 <li>feature group display control parameter</li>
3056 <li>debug parameter</li>
3057 <li>showbutton parameter</li>
3058 </ul> <em>Applet API methods</em>
3060 <li>newView public method</li>
3061 <li>Window (current view) specific get/set public methods</li>
3062 <li>Feature display control methods</li>
3063 <li>get list of currently selected sequences</li>
3064 </ul> <em>New Jalview distribution features</em>
3066 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3067 <li>RELEASE file gives build properties for the latest
3068 Jalview release.</li>
3069 <li>Java 1.1 Applet build made easier and donotobfuscate
3070 property controls execution of obfuscator</li>
3071 <li>Build target for generating source distribution</li>
3072 <li>Debug flag for javacc</li>
3073 <li>.jalview_properties file is documented (slightly) in
3074 jalview.bin.Cache</li>
3075 <li>Continuous Build Integration for stable and
3076 development version of Application, Applet and source
3081 <li>selected region output includes visible annotations
3082 (for certain formats)</li>
3083 <li>edit label/displaychar contains existing label/char
3085 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3086 <li>shorter peptide product names from EMBL records</li>
3087 <li>Newick string generator makes compact representations</li>
3088 <li>bootstrap values parsed correctly for tree files with
3090 <li>pathological filechooser bug avoided by not allowing
3091 filenames containing a ':'</li>
3092 <li>Fixed exception when parsing GFF files containing
3093 global sequence features</li>
3094 <li>Alignment datasets are finalized only when number of
3095 references from alignment sequences goes to zero</li>
3096 <li>Close of tree branch colour box without colour
3097 selection causes cascading exceptions</li>
3098 <li>occasional negative imgwidth exceptions</li>
3099 <li>better reporting of non-fatal warnings to user when
3100 file parsing fails.</li>
3101 <li>Save works when Jalview project is default format</li>
3102 <li>Save as dialog opened if current alignment format is
3103 not a valid output format</li>
3104 <li>UniProt canonical names introduced for both das and
3106 <li>Histidine should be midblue (not pink!) in Zappo</li>
3107 <li>error messages passed up and output when data read
3109 <li>edit undo recovers previous dataset sequence when
3110 sequence is edited</li>
3111 <li>allow PDB files without pdb ID HEADER lines (like
3112 those generated by MODELLER) to be read in properly</li>
3113 <li>allow reading of JPred concise files as a normal
3115 <li>Stockholm annotation parsing and alignment properties
3116 import fixed for PFAM records</li>
3117 <li>Structure view windows have correct name in Desktop
3119 <li>annotation consisting of sequence associated scores
3120 can be read and written correctly to annotation file</li>
3121 <li>Aligned cDNA translation to aligned peptide works
3123 <li>Fixed display of hidden sequence markers and
3124 non-italic font for representatives in Applet</li>
3125 <li>Applet Menus are always embedded in applet window on
3127 <li>Newly shown features appear at top of stack (in
3129 <li>Annotations added via parameter not drawn properly
3130 due to null pointer exceptions</li>
3131 <li>Secondary structure lines are drawn starting from
3132 first column of alignment</li>
3133 <li>UniProt XML import updated for new schema release in
3135 <li>Sequence feature to sequence ID match for Features
3136 file is case-insensitive</li>
3137 <li>Sequence features read from Features file appended to
3138 all sequences with matching IDs</li>
3139 <li>PDB structure coloured correctly for associated views
3140 containing a sub-sequence</li>
3141 <li>PDB files can be retrieved by applet from Jar files</li>
3142 <li>feature and annotation file applet parameters
3143 referring to different directories are retrieved correctly</li>
3144 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3145 <li>Fixed application hang whilst waiting for
3146 splash-screen version check to complete</li>
3147 <li>Applet properly URLencodes input parameter values
3148 when passing them to the launchApp service</li>
3149 <li>display name and local features preserved in results
3150 retrieved from web service</li>
3151 <li>Visual delay indication for sequence retrieval and
3152 sequence fetcher initialisation</li>
3153 <li>updated Application to use DAS 1.53e version of
3154 dasobert DAS client</li>
3155 <li>Re-instated Full AMSA support and .amsa file
3157 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3165 <div align="center">
3166 <strong>2.3</strong><br> 9/5/07
3171 <li>Jmol 11.0.2 integration</li>
3172 <li>PDB views stored in Jalview XML files</li>
3173 <li>Slide sequences</li>
3174 <li>Edit sequence in place</li>
3175 <li>EMBL CDS features</li>
3176 <li>DAS Feature mapping</li>
3177 <li>Feature ordering</li>
3178 <li>Alignment Properties</li>
3179 <li>Annotation Scores</li>
3180 <li>Sort by scores</li>
3181 <li>Feature/annotation editing in applet</li>
3186 <li>Headless state operation in 2.2.1</li>
3187 <li>Incorrect and unstable DNA pairwise alignment</li>
3188 <li>Cut and paste of sequences with annotation</li>
3189 <li>Feature group display state in XML</li>
3190 <li>Feature ordering in XML</li>
3191 <li>blc file iteration selection using filename # suffix</li>
3192 <li>Stockholm alignment properties</li>
3193 <li>Stockhom alignment secondary structure annotation</li>
3194 <li>2.2.1 applet had no feature transparency</li>
3195 <li>Number pad keys can be used in cursor mode</li>
3196 <li>Structure Viewer mirror image resolved</li>
3203 <div align="center">
3204 <strong>2.2.1</strong><br> 12/2/07
3209 <li>Non standard characters can be read and displayed
3210 <li>Annotations/Features can be imported/exported to the
3212 <li>Applet allows editing of sequence/annotation/group
3213 name & description
3214 <li>Preference setting to display sequence name in
3216 <li>Annotation file format extended to allow
3217 Sequence_groups to be defined
3218 <li>Default opening of alignment overview panel can be
3219 specified in preferences
3220 <li>PDB residue numbering annotation added to associated
3226 <li>Applet crash under certain Linux OS with Java 1.6
3228 <li>Annotation file export / import bugs fixed
3229 <li>PNG / EPS image output bugs fixed
3235 <div align="center">
3236 <strong>2.2</strong><br> 27/11/06
3241 <li>Multiple views on alignment
3242 <li>Sequence feature editing
3243 <li>"Reload" alignment
3244 <li>"Save" to current filename
3245 <li>Background dependent text colour
3246 <li>Right align sequence ids
3247 <li>User-defined lower case residue colours
3250 <li>Menu item accelerator keys
3251 <li>Control-V pastes to current alignment
3252 <li>Cancel button for DAS Feature Fetching
3253 <li>PCA and PDB Viewers zoom via mouse roller
3254 <li>User-defined sub-tree colours and sub-tree selection
3256 <li>'New Window' button on the 'Output to Text box'
3261 <li>New memory efficient Undo/Redo System
3262 <li>Optimised symbol lookups and conservation/consensus
3264 <li>Region Conservation/Consensus recalculated after
3266 <li>Fixed Remove Empty Columns Bug (empty columns at end
3268 <li>Slowed DAS Feature Fetching for increased robustness.
3270 <li>Made angle brackets in ASCII feature descriptions
3272 <li>Re-instated Zoom function for PCA
3273 <li>Sequence descriptions conserved in web service
3275 <li>UniProt ID discoverer uses any word separated by
3277 <li>WsDbFetch query/result association resolved
3278 <li>Tree leaf to sequence mapping improved
3279 <li>Smooth fonts switch moved to FontChooser dialog box.
3286 <div align="center">
3287 <strong>2.1.1</strong><br> 12/9/06
3292 <li>Copy consensus sequence to clipboard</li>
3297 <li>Image output - rightmost residues are rendered if
3298 sequence id panel has been resized</li>
3299 <li>Image output - all offscreen group boundaries are
3301 <li>Annotation files with sequence references - all
3302 elements in file are relative to sequence position</li>
3303 <li>Mac Applet users can use Alt key for group editing</li>
3309 <div align="center">
3310 <strong>2.1</strong><br> 22/8/06
3315 <li>MAFFT Multiple Alignment in default Web Service list</li>
3316 <li>DAS Feature fetching</li>
3317 <li>Hide sequences and columns</li>
3318 <li>Export Annotations and Features</li>
3319 <li>GFF file reading / writing</li>
3320 <li>Associate structures with sequences from local PDB
3322 <li>Add sequences to exisiting alignment</li>
3323 <li>Recently opened files / URL lists</li>
3324 <li>Applet can launch the full application</li>
3325 <li>Applet has transparency for features (Java 1.2
3327 <li>Applet has user defined colours parameter</li>
3328 <li>Applet can load sequences from parameter
3329 "sequence<em>x</em>"
3335 <li>Redundancy Panel reinstalled in the Applet</li>
3336 <li>Monospaced font - EPS / rescaling bug fixed</li>
3337 <li>Annotation files with sequence references bug fixed</li>
3343 <div align="center">
3344 <strong>2.08.1</strong><br> 2/5/06
3349 <li>Change case of selected region from Popup menu</li>
3350 <li>Choose to match case when searching</li>
3351 <li>Middle mouse button and mouse movement can compress /
3352 expand the visible width and height of the alignment</li>
3357 <li>Annotation Panel displays complete JNet results</li>
3363 <div align="center">
3364 <strong>2.08b</strong><br> 18/4/06
3370 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3371 <li>Righthand label on wrapped alignments shows correct
3378 <div align="center">
3379 <strong>2.08</strong><br> 10/4/06
3384 <li>Editing can be locked to the selection area</li>
3385 <li>Keyboard editing</li>
3386 <li>Create sequence features from searches</li>
3387 <li>Precalculated annotations can be loaded onto
3389 <li>Features file allows grouping of features</li>
3390 <li>Annotation Colouring scheme added</li>
3391 <li>Smooth fonts off by default - Faster rendering</li>
3392 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3397 <li>Drag & Drop fixed on Linux</li>
3398 <li>Jalview Archive file faster to load/save, sequence
3399 descriptions saved.</li>
3405 <div align="center">
3406 <strong>2.07</strong><br> 12/12/05
3411 <li>PDB Structure Viewer enhanced</li>
3412 <li>Sequence Feature retrieval and display enhanced</li>
3413 <li>Choose to output sequence start-end after sequence
3414 name for file output</li>
3415 <li>Sequence Fetcher WSDBFetch@EBI</li>
3416 <li>Applet can read feature files, PDB files and can be
3417 used for HTML form input</li>
3422 <li>HTML output writes groups and features</li>
3423 <li>Group editing is Control and mouse click</li>
3424 <li>File IO bugs</li>
3430 <div align="center">
3431 <strong>2.06</strong><br> 28/9/05
3436 <li>View annotations in wrapped mode</li>
3437 <li>More options for PCA viewer</li>
3442 <li>GUI bugs resolved</li>
3443 <li>Runs with -nodisplay from command line</li>
3449 <div align="center">
3450 <strong>2.05b</strong><br> 15/9/05
3455 <li>Choose EPS export as lineart or text</li>
3456 <li>Jar files are executable</li>
3457 <li>Can read in Uracil - maps to unknown residue</li>
3462 <li>Known OutOfMemory errors give warning message</li>
3463 <li>Overview window calculated more efficiently</li>
3464 <li>Several GUI bugs resolved</li>
3470 <div align="center">
3471 <strong>2.05</strong><br> 30/8/05
3476 <li>Edit and annotate in "Wrapped" view</li>
3481 <li>Several GUI bugs resolved</li>
3487 <div align="center">
3488 <strong>2.04</strong><br> 24/8/05
3493 <li>Hold down mouse wheel & scroll to change font
3499 <li>Improved JPred client reliability</li>
3500 <li>Improved loading of Jalview files</li>
3506 <div align="center">
3507 <strong>2.03</strong><br> 18/8/05
3512 <li>Set Proxy server name and port in preferences</li>
3513 <li>Multiple URL links from sequence ids</li>
3514 <li>User Defined Colours can have a scheme name and added
3516 <li>Choose to ignore gaps in consensus calculation</li>
3517 <li>Unix users can set default web browser</li>
3518 <li>Runs without GUI for batch processing</li>
3519 <li>Dynamically generated Web Service Menus</li>
3524 <li>InstallAnywhere download for Sparc Solaris</li>
3530 <div align="center">
3531 <strong>2.02</strong><br> 18/7/05
3537 <li>Copy & Paste order of sequences maintains
3538 alignment order.</li>
3544 <div align="center">
3545 <strong>2.01</strong><br> 12/7/05
3550 <li>Use delete key for deleting selection.</li>
3551 <li>Use Mouse wheel to scroll sequences.</li>
3552 <li>Help file updated to describe how to add alignment
3554 <li>Version and build date written to build properties
3556 <li>InstallAnywhere installation will check for updates
3557 at launch of Jalview.</li>
3562 <li>Delete gaps bug fixed.</li>
3563 <li>FileChooser sorts columns.</li>
3564 <li>Can remove groups one by one.</li>
3565 <li>Filechooser icons installed.</li>
3566 <li>Finder ignores return character when searching.
3567 Return key will initiate a search.<br>
3574 <div align="center">
3575 <strong>2.0</strong><br> 20/6/05
3580 <li>New codebase</li>