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>
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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>14/11/2017</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>
135 <li><!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in URL links appears when only default EMBL-EBI link is configured (since 2.10.2b2)</li>
136 <li><!-- JAL-2775 -->Overview redraws whole window when box position is adjusted</li>
138 <strong><em>Applet</em></strong><br/>
140 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
142 <strong><em>BioJSON</em></strong><br/>
145 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
152 <td width="60" nowrap>
154 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
155 <em>2/10/2017</em></strong>
158 <td><div align="left">
159 <em>New features in Jalview Desktop</em>
162 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
164 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
168 <td><div align="left">
172 <td width="60" nowrap>
174 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
175 <em>7/9/2017</em></strong>
178 <td><div align="left">
182 <!-- JAL-2588 -->Show gaps in overview window by colouring
183 in grey (sequences used to be coloured grey, and gaps were
187 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
191 <!-- JAL-2587 -->Overview updates immediately on increase
192 in size and progress bar shown as higher resolution
193 overview is recalculated
198 <td><div align="left">
202 <!-- JAL-2664 -->Overview window redraws every hidden
203 column region row by row
206 <!-- JAL-2681 -->duplicate protein sequences shown after
207 retrieving Ensembl crossrefs for sequences from Uniprot
210 <!-- JAL-2603 -->Overview window throws NPE if show boxes
211 format setting is unticked
214 <!-- JAL-2610 -->Groups are coloured wrongly in overview
215 if group has show boxes format setting unticked
218 <!-- JAL-2672,JAL-2665 -->Redraw problems when
219 autoscrolling whilst dragging current selection group to
220 include sequences and columns not currently displayed
223 <!-- JAL-2691 -->Not all chains are mapped when multimeric
224 assemblies are imported via CIF file
227 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
228 displayed when threshold or conservation colouring is also
232 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
236 <!-- JAL-2673 -->Jalview continues to scroll after
237 dragging a selected region off the visible region of the
241 <!-- JAL-2724 -->Cannot apply annotation based
242 colourscheme to all groups in a view
245 <!-- JAL-2511 -->IDs don't line up with sequences
246 initially after font size change using the Font chooser or
253 <td width="60" nowrap>
255 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
258 <td><div align="left">
259 <em>Calculations</em>
263 <!-- JAL-1933 -->Occupancy annotation row shows number of
264 ungapped positions in each column of the alignment.
267 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
268 a calculation dialog box
271 <!-- JAL-2379 -->Revised implementation of PCA for speed
272 and memory efficiency (~30x faster)
275 <!-- JAL-2403 -->Revised implementation of sequence
276 similarity scores as used by Tree, PCA, Shading Consensus
277 and other calculations
280 <!-- JAL-2416 -->Score matrices are stored as resource
281 files within the Jalview codebase
284 <!-- JAL-2500 -->Trees computed on Sequence Feature
285 Similarity may have different topology due to increased
292 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
293 model for alignments and groups
296 <!-- JAL-384 -->Custom shading schemes created via groovy
303 <!-- JAL-2526 -->Efficiency improvements for interacting
304 with alignment and overview windows
307 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
311 <!-- JAL-2388 -->Hidden columns and sequences can be
315 <!-- JAL-2611 -->Click-drag in visible area allows fine
316 adjustment of visible position
320 <em>Data import/export</em>
323 <!-- JAL-2535 -->Posterior probability annotation from
324 Stockholm files imported as sequence associated annotation
327 <!-- JAL-2507 -->More robust per-sequence positional
328 annotation input/output via stockholm flatfile
331 <!-- JAL-2533 -->Sequence names don't include file
332 extension when importing structure files without embedded
333 names or PDB accessions
336 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
337 format sequence substitution matrices
340 <em>User Interface</em>
343 <!-- JAL-2447 --> Experimental Features Checkbox in
344 Desktop's Tools menu to hide or show untested features in
348 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
349 via Overview or sequence motif search operations
352 <!-- JAL-2547 -->Amend sequence features dialog box can be
353 opened by double clicking gaps within sequence feature
357 <!-- JAL-1476 -->Status bar message shown when not enough
358 aligned positions were available to create a 3D structure
362 <em>3D Structure</em>
365 <!-- JAL-2430 -->Hidden regions in alignment views are not
366 coloured in linked structure views
369 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
370 file-based command exchange
373 <!-- JAL-2375 -->Structure chooser automatically shows
374 Cached Structures rather than querying the PDBe if
375 structures are already available for sequences
378 <!-- JAL-2520 -->Structures imported via URL are cached in
379 the Jalview project rather than downloaded again when the
383 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
384 to transfer Chimera's structure attributes as Jalview
385 features, and vice-versa (<strong>Experimental
389 <em>Web Services</em>
392 <!-- JAL-2549 -->Updated JABAWS client to v2.2
395 <!-- JAL-2335 -->Filter non-standard amino acids and
396 nucleotides when submitting to AACon and other MSA
400 <!-- JAL-2316, -->URLs for viewing database
401 cross-references provided by identifiers.org and the
409 <!-- JAL-2344 -->FileFormatI interface for describing and
410 identifying file formats (instead of String constants)
413 <!-- JAL-2228 -->FeatureCounter script refactored for
414 efficiency when counting all displayed features (not
415 backwards compatible with 2.10.1)
418 <em>Example files</em>
421 <!-- JAL-2631 -->Graduated feature colour style example
422 included in the example feature file
425 <em>Documentation</em>
428 <!-- JAL-2339 -->Release notes reformatted for readability
429 with the built-in Java help viewer
432 <!-- JAL-1644 -->Find documentation updated with 'search
433 sequence description' option
439 <!-- JAL-2485, -->External service integration tests for
440 Uniprot REST Free Text Search Client
443 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
446 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
451 <td><div align="left">
452 <em>Calculations</em>
455 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
456 matrix - C->R should be '-3'<br />Old matrix restored
457 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
459 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
460 Jalview's treatment of gaps in PCA and substitution matrix
461 based Tree calculations.<br /> <br />In earlier versions
462 of Jalview, gaps matching gaps were penalised, and gaps
463 matching non-gaps penalised even more. In the PCA
464 calculation, gaps were actually treated as non-gaps - so
465 different costs were applied, which meant Jalview's PCAs
466 were different to those produced by SeqSpace.<br />Jalview
467 now treats gaps in the same way as SeqSpace (ie it scores
468 them as 0). <br /> <br />Enter the following in the
469 Groovy console to restore pre-2.10.2 behaviour:<br />
470 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
471 // for 2.10.1 mode <br />
472 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
473 // to restore 2.10.2 mode <br /> <br /> <em>Note:
474 these settings will affect all subsequent tree and PCA
475 calculations (not recommended)</em></li>
477 <!-- JAL-2424 -->Fixed off-by-one bug that affected
478 scaling of branch lengths for trees computed using
479 Sequence Feature Similarity.
482 <!-- JAL-2377 -->PCA calculation could hang when
483 generating output report when working with highly
487 <!-- JAL-2544 --> Sort by features includes features to
488 right of selected region when gaps present on right-hand
492 <em>User Interface</em>
495 <!-- JAL-2346 -->Reopening Colour by annotation dialog
496 doesn't reselect a specific sequence's associated
497 annotation after it was used for colouring a view
500 <!-- JAL-2419 -->Current selection lost if popup menu
501 opened on a region of alignment without groups
504 <!-- JAL-2374 -->Popup menu not always shown for regions
505 of an alignment with overlapping groups
508 <!-- JAL-2310 -->Finder double counts if both a sequence's
509 name and description match
512 <!-- JAL-2370 -->Hiding column selection containing two
513 hidden regions results in incorrect hidden regions
516 <!-- JAL-2386 -->'Apply to all groups' setting when
517 changing colour does not apply Conservation slider value
521 <!-- JAL-2373 -->Percentage identity and conservation menu
522 items do not show a tick or allow shading to be disabled
525 <!-- JAL-2385 -->Conservation shading or PID threshold
526 lost when base colourscheme changed if slider not visible
529 <!-- JAL-2547 -->Sequence features shown in tooltip for
530 gaps before start of features
533 <!-- JAL-2623 -->Graduated feature colour threshold not
534 restored to UI when feature colour is edited
537 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
538 a time when scrolling vertically in wrapped mode.
541 <!-- JAL-2630 -->Structure and alignment overview update
542 as graduate feature colour settings are modified via the
546 <!-- JAL-2034 -->Overview window doesn't always update
547 when a group defined on the alignment is resized
550 <!-- JAL-2605 -->Mouseovers on left/right scale region in
551 wrapped view result in positional status updates
555 <!-- JAL-2563 -->Status bar doesn't show position for
556 ambiguous amino acid and nucleotide symbols
559 <!-- JAL-2602 -->Copy consensus sequence failed if
560 alignment included gapped columns
563 <!-- JAL-2473 -->Minimum size set for Jalview windows so
564 widgets don't permanently disappear
567 <!-- JAL-2503 -->Cannot select or filter quantitative
568 annotation that are shown only as column labels (e.g.
569 T-Coffee column reliability scores)
572 <!-- JAL-2594 -->Exception thrown if trying to create a
573 sequence feature on gaps only
576 <!-- JAL-2504 -->Features created with 'New feature'
577 button from a Find inherit previously defined feature type
578 rather than the Find query string
581 <!-- JAL-2423 -->incorrect title in output window when
582 exporting tree calculated in Jalview
585 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
586 and then revealing them reorders sequences on the
590 <!-- JAL-964 -->Group panel in sequence feature settings
591 doesn't update to reflect available set of groups after
592 interactively adding or modifying features
595 <!-- JAL-2225 -->Sequence Database chooser unusable on
599 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
600 only excluded gaps in current sequence and ignored
607 <!-- JAL-2421 -->Overview window visible region moves
608 erratically when hidden rows or columns are present
611 <!-- JAL-2362 -->Per-residue colourschemes applied via the
612 Structure Viewer's colour menu don't correspond to
616 <!-- JAL-2405 -->Protein specific colours only offered in
617 colour and group colour menu for protein alignments
620 <!-- JAL-2385 -->Colour threshold slider doesn't update to
621 reflect currently selected view or group's shading
625 <!-- JAL-2624 -->Feature colour thresholds not respected
626 when rendered on overview and structures when opacity at
630 <!-- JAL-2589 -->User defined gap colour not shown in
631 overview when features overlaid on alignment
634 <em>Data import/export</em>
637 <!-- JAL-2576 -->Very large alignments take a long time to
641 <!-- JAL-2507 -->Per-sequence RNA secondary structures
642 added after a sequence was imported are not written to
646 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
647 when importing RNA secondary structure via Stockholm
650 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
651 not shown in correct direction for simple pseudoknots
654 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
655 with lightGray or darkGray via features file (but can
659 <!-- JAL-2383 -->Above PID colour threshold not recovered
660 when alignment view imported from project
663 <!-- JAL-2520,JAL-2465 -->No mappings generated between
664 structure and sequences extracted from structure files
665 imported via URL and viewed in Jmol
668 <!-- JAL-2520 -->Structures loaded via URL are saved in
669 Jalview Projects rather than fetched via URL again when
670 the project is loaded and the structure viewed
673 <em>Web Services</em>
676 <!-- JAL-2519 -->EnsemblGenomes example failing after
677 release of Ensembl v.88
680 <!-- JAL-2366 -->Proxy server address and port always
681 appear enabled in Preferences->Connections
684 <!-- JAL-2461 -->DAS registry not found exceptions
685 removed from console output
688 <!-- JAL-2582 -->Cannot retrieve protein products from
689 Ensembl by Peptide ID
692 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
693 created from SIFTs, and spurious 'Couldn't open structure
694 in Chimera' errors raised after April 2017 update (problem
695 due to 'null' string rather than empty string used for
696 residues with no corresponding PDB mapping).
699 <em>Application UI</em>
702 <!-- JAL-2361 -->User Defined Colours not added to Colour
706 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
707 case' residues (button in colourscheme editor debugged and
708 new documentation and tooltips added)
711 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
712 doesn't restore group-specific text colour thresholds
715 <!-- JAL-2243 -->Feature settings panel does not update as
716 new features are added to alignment
719 <!-- JAL-2532 -->Cancel in feature settings reverts
720 changes to feature colours via the Amend features dialog
723 <!-- JAL-2506 -->Null pointer exception when attempting to
724 edit graduated feature colour via amend features dialog
728 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
729 selection menu changes colours of alignment views
732 <!-- JAL-2426 -->Spurious exceptions in console raised
733 from alignment calculation workers after alignment has
737 <!-- JAL-1608 -->Typo in selection popup menu - Create
738 groups now 'Create Group'
741 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
742 Create/Undefine group doesn't always work
745 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
746 shown again after pressing 'Cancel'
749 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
750 adjusts start position in wrap mode
753 <!-- JAL-2563 -->Status bar doesn't show positions for
754 ambiguous amino acids
757 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
758 CDS/Protein view after CDS sequences added for aligned
762 <!-- JAL-2592 -->User defined colourschemes called 'User
763 Defined' don't appear in Colours menu
769 <!-- JAL-2468 -->Switching between Nucleotide and Protein
770 score models doesn't always result in an updated PCA plot
773 <!-- JAL-2442 -->Features not rendered as transparent on
774 overview or linked structure view
777 <!-- JAL-2372 -->Colour group by conservation doesn't
781 <!-- JAL-2517 -->Hitting Cancel after applying
782 user-defined colourscheme doesn't restore original
789 <!-- JAL-2314 -->Unit test failure:
790 jalview.ws.jabaws.RNAStructExportImport setup fails
793 <!-- JAL-2307 -->Unit test failure:
794 jalview.ws.sifts.SiftsClientTest due to compatibility
795 problems with deep array comparison equality asserts in
796 successive versions of TestNG
799 <!-- JAL-2479 -->Relocated StructureChooserTest and
800 ParameterUtilsTest Unit tests to Network suite
803 <em>New Known Issues</em>
806 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
807 phase after a sequence motif find operation
810 <!-- JAL-2550 -->Importing annotation file with rows
811 containing just upper and lower case letters are
812 interpreted as WUSS RNA secondary structure symbols
815 <!-- JAL-2590 -->Cannot load and display Newick trees
816 reliably from eggnog Ortholog database
819 <!-- JAL-2468 -->Status bar shows 'Marked x columns
820 containing features of type Highlight' when 'B' is pressed
821 to mark columns containing highlighted regions.
824 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
825 doesn't always add secondary structure annotation.
830 <td width="60" nowrap>
832 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
835 <td><div align="left">
839 <!-- JAL-98 -->Improved memory usage: sparse arrays used
840 for all consensus calculations
843 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
846 <li>Updated Jalview's Certum code signing certificate
852 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
853 set of database cross-references, sorted alphabetically
856 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
857 from database cross references. Users with custom links
858 will receive a <a href="webServices/urllinks.html#warning">warning
859 dialog</a> asking them to update their preferences.
862 <!-- JAL-2287-->Cancel button and escape listener on
863 dialog warning user about disconnecting Jalview from a
867 <!-- JAL-2320-->Jalview's Chimera control window closes if
868 the Chimera it is connected to is shut down
871 <!-- JAL-1738-->New keystroke (B) and Select highlighted
872 columns menu item to mark columns containing highlighted
873 regions (e.g. from structure selections or results of a
877 <!-- JAL-2284-->Command line option for batch-generation
878 of HTML pages rendering alignment data with the BioJS
888 <!-- JAL-2286 -->Columns with more than one modal residue
889 are not coloured or thresholded according to percent
890 identity (first observed in Jalview 2.8.2)
893 <!-- JAL-2301 -->Threonine incorrectly reported as not
897 <!-- JAL-2318 -->Updates to documentation pages (above PID
898 threshold, amino acid properties)
901 <!-- JAL-2292 -->Lower case residues in sequences are not
902 reported as mapped to residues in a structure file in the
906 <!--JAL-2324 -->Identical features with non-numeric scores
907 could be added multiple times to a sequence
910 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
911 bond features shown as two highlighted residues rather
912 than a range in linked structure views, and treated
913 correctly when selecting and computing trees from features
916 <!-- JAL-2281-->Custom URL links for database
917 cross-references are matched to database name regardless
925 <!-- JAL-2282-->Custom URL links for specific database
926 names without regular expressions also offer links from
930 <!-- JAL-2315-->Removing a single configured link in the
931 URL links pane in Connections preferences doesn't actually
932 update Jalview configuration
935 <!-- JAL-2272-->CTRL-Click on a selected region to open
936 the alignment area popup menu doesn't work on El-Capitan
939 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
940 files with similarly named sequences if dropped onto the
944 <!-- JAL-2312 -->Additional mappings are shown for PDB
945 entries where more chains exist in the PDB accession than
946 are reported in the SIFTS file
949 <!-- JAL-2317-->Certain structures do not get mapped to
950 the structure view when displayed with Chimera
953 <!-- JAL-2317-->No chains shown in the Chimera view
954 panel's View->Show Chains submenu
957 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
958 work for wrapped alignment views
961 <!--JAL-2197 -->Rename UI components for running JPred
962 predictions from 'JNet' to 'JPred'
965 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
966 corrupted when annotation panel vertical scroll is not at
970 <!--JAL-2332 -->Attempting to view structure for Hen
971 lysozyme results in a PDB Client error dialog box
974 <!-- JAL-2319 -->Structure View's mapping report switched
975 ranges for PDB and sequence for SIFTS
978 SIFTS 'Not_Observed' residues mapped to non-existant
982 <!-- <em>New Known Issues</em>
989 <td width="60" nowrap>
991 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
992 <em>25/10/2016</em></strong>
995 <td><em>Application</em>
997 <li>3D Structure chooser opens with 'Cached structures'
998 view if structures already loaded</li>
999 <li>Progress bar reports models as they are loaded to
1000 structure views</li>
1006 <li>Colour by conservation always enabled and no tick
1007 shown in menu when BLOSUM or PID shading applied</li>
1008 <li>FER1_ARATH and FER2_ARATH labels were switched in
1009 example sequences/projects/trees</li>
1011 <em>Application</em>
1013 <li>Jalview projects with views of local PDB structure
1014 files saved on Windows cannot be opened on OSX</li>
1015 <li>Multiple structure views can be opened and superposed
1016 without timeout for structures with multiple models or
1017 multiple sequences in alignment</li>
1018 <li>Cannot import or associated local PDB files without a
1019 PDB ID HEADER line</li>
1020 <li>RMSD is not output in Jmol console when superposition
1022 <li>Drag and drop of URL from Browser fails for Linux and
1023 OSX versions earlier than El Capitan</li>
1024 <li>ENA client ignores invalid content from ENA server</li>
1025 <li>Exceptions are not raised in console when ENA client
1026 attempts to fetch non-existent IDs via Fetch DB Refs UI
1028 <li>Exceptions are not raised in console when a new view
1029 is created on the alignment</li>
1030 <li>OSX right-click fixed for group selections: CMD-click
1031 to insert/remove gaps in groups and CTRL-click to open group
1034 <em>Build and deployment</em>
1036 <li>URL link checker now copes with multi-line anchor
1039 <em>New Known Issues</em>
1041 <li>Drag and drop from URL links in browsers do not work
1048 <td width="60" nowrap>
1049 <div align="center">
1050 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1053 <td><em>General</em>
1056 <!-- JAL-2124 -->Updated Spanish translations.
1059 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1060 for importing structure data to Jalview. Enables mmCIF and
1064 <!-- JAL-192 --->Alignment ruler shows positions relative to
1068 <!-- JAL-2202 -->Position/residue shown in status bar when
1069 mousing over sequence associated annotation
1072 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1076 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1077 '()', canonical '[]' and invalid '{}' base pair populations
1081 <!-- JAL-2092 -->Feature settings popup menu options for
1082 showing or hiding columns containing a feature
1085 <!-- JAL-1557 -->Edit selected group by double clicking on
1086 group and sequence associated annotation labels
1089 <!-- JAL-2236 -->Sequence name added to annotation label in
1090 select/hide columns by annotation and colour by annotation
1094 </ul> <em>Application</em>
1097 <!-- JAL-2050-->Automatically hide introns when opening a
1098 gene/transcript view
1101 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1105 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1106 structure mappings with the EMBL-EBI PDBe SIFTS database
1109 <!-- JAL-2079 -->Updated download sites used for Rfam and
1110 Pfam sources to xfam.org
1113 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1116 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1117 over sequences in Jalview
1120 <!-- JAL-2027-->Support for reverse-complement coding
1121 regions in ENA and EMBL
1124 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1125 for record retrieval via ENA rest API
1128 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1132 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1133 groovy script execution
1136 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1137 alignment window's Calculate menu
1140 <!-- JAL-1812 -->Allow groovy scripts that call
1141 Jalview.getAlignFrames() to run in headless mode
1144 <!-- JAL-2068 -->Support for creating new alignment
1145 calculation workers from groovy scripts
1148 <!-- JAL-1369 --->Store/restore reference sequence in
1152 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1153 associations are now saved/restored from project
1156 <!-- JAL-1993 -->Database selection dialog always shown
1157 before sequence fetcher is opened
1160 <!-- JAL-2183 -->Double click on an entry in Jalview's
1161 database chooser opens a sequence fetcher
1164 <!-- JAL-1563 -->Free-text search client for UniProt using
1165 the UniProt REST API
1168 <!-- JAL-2168 -->-nonews command line parameter to prevent
1169 the news reader opening
1172 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1173 querying stored in preferences
1176 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1180 <!-- JAL-1977-->Tooltips shown on database chooser
1183 <!-- JAL-391 -->Reverse complement function in calculate
1184 menu for nucleotide sequences
1187 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1188 and feature counts preserves alignment ordering (and
1189 debugged for complex feature sets).
1192 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1193 viewing structures with Jalview 2.10
1196 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1197 genome, transcript CCDS and gene ids via the Ensembl and
1198 Ensembl Genomes REST API
1201 <!-- JAL-2049 -->Protein sequence variant annotation
1202 computed for 'sequence_variant' annotation on CDS regions
1206 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1210 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1211 Ref Fetcher fails to match, or otherwise updates sequence
1212 data from external database records.
1215 <!-- JAL-2154 -->Revised Jalview Project format for
1216 efficient recovery of sequence coding and alignment
1217 annotation relationships.
1219 </ul> <!-- <em>Applet</em>
1230 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1234 <!-- JAL-2018-->Export features in Jalview format (again)
1235 includes graduated colourschemes
1238 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1239 working with big alignments and lots of hidden columns
1242 <!-- JAL-2053-->Hidden column markers not always rendered
1243 at right of alignment window
1246 <!-- JAL-2067 -->Tidied up links in help file table of
1250 <!-- JAL-2072 -->Feature based tree calculation not shown
1254 <!-- JAL-2075 -->Hidden columns ignored during feature
1255 based tree calculation
1258 <!-- JAL-2065 -->Alignment view stops updating when show
1259 unconserved enabled for group on alignment
1262 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1266 <!-- JAL-2146 -->Alignment column in status incorrectly
1267 shown as "Sequence position" when mousing over
1271 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1272 hidden columns present
1275 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1276 user created annotation added to alignment
1279 <!-- JAL-1841 -->RNA Structure consensus only computed for
1280 '()' base pair annotation
1283 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1284 in zero scores for all base pairs in RNA Structure
1288 <!-- JAL-2174-->Extend selection with columns containing
1292 <!-- JAL-2275 -->Pfam format writer puts extra space at
1293 beginning of sequence
1296 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1300 <!-- JAL-2238 -->Cannot create groups on an alignment from
1301 from a tree when t-coffee scores are shown
1304 <!-- JAL-1836,1967 -->Cannot import and view PDB
1305 structures with chains containing negative resnums (4q4h)
1308 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1312 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1313 to Clustal, PIR and PileUp output
1316 <!-- JAL-2008 -->Reordering sequence features that are
1317 not visible causes alignment window to repaint
1320 <!-- JAL-2006 -->Threshold sliders don't work in
1321 graduated colour and colour by annotation row for e-value
1322 scores associated with features and annotation rows
1325 <!-- JAL-1797 -->amino acid physicochemical conservation
1326 calculation should be case independent
1329 <!-- JAL-2173 -->Remove annotation also updates hidden
1333 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1334 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1335 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1338 <!-- JAL-2065 -->Null pointer exceptions and redraw
1339 problems when reference sequence defined and 'show
1340 non-conserved' enabled
1343 <!-- JAL-1306 -->Quality and Conservation are now shown on
1344 load even when Consensus calculation is disabled
1347 <!-- JAL-1932 -->Remove right on penultimate column of
1348 alignment does nothing
1351 <em>Application</em>
1354 <!-- JAL-1552-->URLs and links can't be imported by
1355 drag'n'drop on OSX when launched via webstart (note - not
1356 yet fixed for El Capitan)
1359 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1360 output when running on non-gb/us i18n platforms
1363 <!-- JAL-1944 -->Error thrown when exporting a view with
1364 hidden sequences as flat-file alignment
1367 <!-- JAL-2030-->InstallAnywhere distribution fails when
1371 <!-- JAL-2080-->Jalview very slow to launch via webstart
1372 (also hotfix for 2.9.0b2)
1375 <!-- JAL-2085 -->Cannot save project when view has a
1376 reference sequence defined
1379 <!-- JAL-1011 -->Columns are suddenly selected in other
1380 alignments and views when revealing hidden columns
1383 <!-- JAL-1989 -->Hide columns not mirrored in complement
1384 view in a cDNA/Protein splitframe
1387 <!-- JAL-1369 -->Cannot save/restore representative
1388 sequence from project when only one sequence is
1392 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1393 in Structure Chooser
1396 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1397 structure consensus didn't refresh annotation panel
1400 <!-- JAL-1962 -->View mapping in structure view shows
1401 mappings between sequence and all chains in a PDB file
1404 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1405 dialogs format columns correctly, don't display array
1406 data, sort columns according to type
1409 <!-- JAL-1975 -->Export complete shown after destination
1410 file chooser is cancelled during an image export
1413 <!-- JAL-2025 -->Error when querying PDB Service with
1414 sequence name containing special characters
1417 <!-- JAL-2024 -->Manual PDB structure querying should be
1421 <!-- JAL-2104 -->Large tooltips with broken HTML
1422 formatting don't wrap
1425 <!-- JAL-1128 -->Figures exported from wrapped view are
1426 truncated so L looks like I in consensus annotation
1429 <!-- JAL-2003 -->Export features should only export the
1430 currently displayed features for the current selection or
1434 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1435 after fetching cross-references, and restoring from
1439 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1440 followed in the structure viewer
1443 <!-- JAL-2163 -->Titles for individual alignments in
1444 splitframe not restored from project
1447 <!-- JAL-2145 -->missing autocalculated annotation at
1448 trailing end of protein alignment in transcript/product
1449 splitview when pad-gaps not enabled by default
1452 <!-- JAL-1797 -->amino acid physicochemical conservation
1456 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1457 article has been read (reopened issue due to
1458 internationalisation problems)
1461 <!-- JAL-1960 -->Only offer PDB structures in structure
1462 viewer based on sequence name, PDB and UniProt
1467 <!-- JAL-1976 -->No progress bar shown during export of
1471 <!-- JAL-2213 -->Structures not always superimposed after
1472 multiple structures are shown for one or more sequences.
1475 <!-- JAL-1370 -->Reference sequence characters should not
1476 be replaced with '.' when 'Show unconserved' format option
1480 <!-- JAL-1823 -->Cannot specify chain code when entering
1481 specific PDB id for sequence
1484 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1485 'Export hidden sequences' is enabled, but 'export hidden
1486 columns' is disabled.
1489 <!--JAL-2026-->Best Quality option in structure chooser
1490 selects lowest rather than highest resolution structures
1494 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1495 to sequence mapping in 'View Mappings' report
1498 <!-- JAL-2284 -->Unable to read old Jalview projects that
1499 contain non-XML data added after Jalvew wrote project.
1502 <!-- JAL-2118 -->Newly created annotation row reorders
1503 after clicking on it to create new annotation for a
1507 <!-- JAL-1980 -->Null Pointer Exception raised when
1508 pressing Add on an orphaned cut'n'paste window.
1510 <!-- may exclude, this is an external service stability issue JAL-1941
1511 -- > RNA 3D structure not added via DSSR service</li> -->
1516 <!-- JAL-2151 -->Incorrect columns are selected when
1517 hidden columns present before start of sequence
1520 <!-- JAL-1986 -->Missing dependencies on applet pages
1524 <!-- JAL-1947 -->Overview pixel size changes when
1525 sequences are hidden in applet
1528 <!-- JAL-1996 -->Updated instructions for applet
1529 deployment on examples pages.
1536 <td width="60" nowrap>
1537 <div align="center">
1538 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1539 <em>16/10/2015</em></strong>
1542 <td><em>General</em>
1544 <li>Time stamps for signed Jalview application and applet
1549 <em>Application</em>
1551 <li>Duplicate group consensus and conservation rows
1552 shown when tree is partitioned</li>
1553 <li>Erratic behaviour when tree partitions made with
1554 multiple cDNA/Protein split views</li>
1560 <td width="60" nowrap>
1561 <div align="center">
1562 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1563 <em>8/10/2015</em></strong>
1566 <td><em>General</em>
1568 <li>Updated Spanish translations of localized text for
1570 </ul> <em>Application</em>
1572 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1573 <li>Signed OSX InstallAnywhere installer<br></li>
1574 <li>Support for per-sequence based annotations in BioJSON</li>
1575 </ul> <em>Applet</em>
1577 <li>Split frame example added to applet examples page</li>
1578 </ul> <em>Build and Deployment</em>
1581 <!-- JAL-1888 -->New ant target for running Jalview's test
1589 <li>Mapping of cDNA to protein in split frames
1590 incorrect when sequence start > 1</li>
1591 <li>Broken images in filter column by annotation dialog
1593 <li>Feature colours not parsed from features file</li>
1594 <li>Exceptions and incomplete link URLs recovered when
1595 loading a features file containing HTML tags in feature
1599 <em>Application</em>
1601 <li>Annotations corrupted after BioJS export and
1603 <li>Incorrect sequence limits after Fetch DB References
1604 with 'trim retrieved sequences'</li>
1605 <li>Incorrect warning about deleting all data when
1606 deleting selected columns</li>
1607 <li>Patch to build system for shipping properly signed
1608 JNLP templates for webstart launch</li>
1609 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1610 unreleased structures for download or viewing</li>
1611 <li>Tab/space/return keystroke operation of EMBL-PDBe
1612 fetcher/viewer dialogs works correctly</li>
1613 <li>Disabled 'minimise' button on Jalview windows
1614 running on OSX to workaround redraw hang bug</li>
1615 <li>Split cDNA/Protein view position and geometry not
1616 recovered from jalview project</li>
1617 <li>Initial enabled/disabled state of annotation menu
1618 sorter 'show autocalculated first/last' corresponds to
1620 <li>Restoring of Clustal, RNA Helices and T-Coffee
1621 color schemes from BioJSON</li>
1625 <li>Reorder sequences mirrored in cDNA/Protein split
1627 <li>Applet with Jmol examples not loading correctly</li>
1633 <td><div align="center">
1634 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1636 <td><em>General</em>
1638 <li>Linked visualisation and analysis of DNA and Protein
1641 <li>Translated cDNA alignments shown as split protein
1642 and DNA alignment views</li>
1643 <li>Codon consensus annotation for linked protein and
1644 cDNA alignment views</li>
1645 <li>Link cDNA or Protein product sequences by loading
1646 them onto Protein or cDNA alignments</li>
1647 <li>Reconstruct linked cDNA alignment from aligned
1648 protein sequences</li>
1651 <li>Jmol integration updated to Jmol v14.2.14</li>
1652 <li>Import and export of Jalview alignment views as <a
1653 href="features/bioJsonFormat.html">BioJSON</a></li>
1654 <li>New alignment annotation file statements for
1655 reference sequences and marking hidden columns</li>
1656 <li>Reference sequence based alignment shading to
1657 highlight variation</li>
1658 <li>Select or hide columns according to alignment
1660 <li>Find option for locating sequences by description</li>
1661 <li>Conserved physicochemical properties shown in amino
1662 acid conservation row</li>
1663 <li>Alignments can be sorted by number of RNA helices</li>
1664 </ul> <em>Application</em>
1666 <li>New cDNA/Protein analysis capabilities
1668 <li>Get Cross-References should open a Split Frame
1669 view with cDNA/Protein</li>
1670 <li>Detect when nucleotide sequences and protein
1671 sequences are placed in the same alignment</li>
1672 <li>Split cDNA/Protein views are saved in Jalview
1677 <li>Use REST API to talk to Chimera</li>
1678 <li>Selected regions in Chimera are highlighted in linked
1679 Jalview windows</li>
1681 <li>VARNA RNA viewer updated to v3.93</li>
1682 <li>VARNA views are saved in Jalview Projects</li>
1683 <li>Pseudoknots displayed as Jalview RNA annotation can
1684 be shown in VARNA</li>
1686 <li>Make groups for selection uses marked columns as well
1687 as the active selected region</li>
1689 <li>Calculate UPGMA and NJ trees using sequence feature
1691 <li>New Export options
1693 <li>New Export Settings dialog to control hidden
1694 region export in flat file generation</li>
1696 <li>Export alignment views for display with the <a
1697 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1699 <li>Export scrollable SVG in HTML page</li>
1700 <li>Optional embedding of BioJSON data when exporting
1701 alignment figures to HTML</li>
1703 <li>3D structure retrieval and display
1705 <li>Free text and structured queries with the PDBe
1707 <li>PDBe Search API based discovery and selection of
1708 PDB structures for a sequence set</li>
1712 <li>JPred4 employed for protein secondary structure
1714 <li>Hide Insertions menu option to hide unaligned columns
1715 for one or a group of sequences</li>
1716 <li>Automatically hide insertions in alignments imported
1717 from the JPred4 web server</li>
1718 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1719 system on OSX<br />LGPL libraries courtesy of <a
1720 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1722 <li>changed 'View nucleotide structure' submenu to 'View
1723 VARNA 2D Structure'</li>
1724 <li>change "View protein structure" menu option to "3D
1727 </ul> <em>Applet</em>
1729 <li>New layout for applet example pages</li>
1730 <li>New parameters to enable SplitFrame view
1731 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1732 <li>New example demonstrating linked viewing of cDNA and
1733 Protein alignments</li>
1734 </ul> <em>Development and deployment</em>
1736 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1737 <li>Include installation type and git revision in build
1738 properties and console log output</li>
1739 <li>Jalview Github organisation, and new github site for
1740 storing BioJsMSA Templates</li>
1741 <li>Jalview's unit tests now managed with TestNG</li>
1744 <!-- <em>General</em>
1746 </ul> --> <!-- issues resolved --> <em>Application</em>
1748 <li>Escape should close any open find dialogs</li>
1749 <li>Typo in select-by-features status report</li>
1750 <li>Consensus RNA secondary secondary structure
1751 predictions are not highlighted in amber</li>
1752 <li>Missing gap character in v2.7 example file means
1753 alignment appears unaligned when pad-gaps is not enabled</li>
1754 <li>First switch to RNA Helices colouring doesn't colour
1755 associated structure views</li>
1756 <li>ID width preference option is greyed out when auto
1757 width checkbox not enabled</li>
1758 <li>Stopped a warning dialog from being shown when
1759 creating user defined colours</li>
1760 <li>'View Mapping' in structure viewer shows sequence
1761 mappings for just that viewer's sequences</li>
1762 <li>Workaround for superposing PDB files containing
1763 multiple models in Chimera</li>
1764 <li>Report sequence position in status bar when hovering
1765 over Jmol structure</li>
1766 <li>Cannot output gaps as '.' symbols with Selection ->
1767 output to text box</li>
1768 <li>Flat file exports of alignments with hidden columns
1769 have incorrect sequence start/end</li>
1770 <li>'Aligning' a second chain to a Chimera structure from
1772 <li>Colour schemes applied to structure viewers don't
1773 work for nucleotide</li>
1774 <li>Loading/cut'n'pasting an empty or invalid file leads
1775 to a grey/invisible alignment window</li>
1776 <li>Exported Jpred annotation from a sequence region
1777 imports to different position</li>
1778 <li>Space at beginning of sequence feature tooltips shown
1779 on some platforms</li>
1780 <li>Chimera viewer 'View | Show Chain' menu is not
1782 <li>'New View' fails with a Null Pointer Exception in
1783 console if Chimera has been opened</li>
1784 <li>Mouseover to Chimera not working</li>
1785 <li>Miscellaneous ENA XML feature qualifiers not
1787 <li>NPE in annotation renderer after 'Extract Scores'</li>
1788 <li>If two structures in one Chimera window, mouseover of
1789 either sequence shows on first structure</li>
1790 <li>'Show annotations' options should not make
1791 non-positional annotations visible</li>
1792 <li>Subsequence secondary structure annotation not shown
1793 in right place after 'view flanking regions'</li>
1794 <li>File Save As type unset when current file format is
1796 <li>Save as '.jar' option removed for saving Jalview
1798 <li>Colour by Sequence colouring in Chimera more
1800 <li>Cannot 'add reference annotation' for a sequence in
1801 several views on same alignment</li>
1802 <li>Cannot show linked products for EMBL / ENA records</li>
1803 <li>Jalview's tooltip wraps long texts containing no
1805 </ul> <em>Applet</em>
1807 <li>Jmol to JalviewLite mouseover/link not working</li>
1808 <li>JalviewLite can't import sequences with ID
1809 descriptions containing angle brackets</li>
1810 </ul> <em>General</em>
1812 <li>Cannot export and reimport RNA secondary structure
1813 via jalview annotation file</li>
1814 <li>Random helix colour palette for colour by annotation
1815 with RNA secondary structure</li>
1816 <li>Mouseover to cDNA from STOP residue in protein
1817 translation doesn't work.</li>
1818 <li>hints when using the select by annotation dialog box</li>
1819 <li>Jmol alignment incorrect if PDB file has alternate CA
1821 <li>FontChooser message dialog appears to hang after
1822 choosing 1pt font</li>
1823 <li>Peptide secondary structure incorrectly imported from
1824 annotation file when annotation display text includes 'e' or
1826 <li>Cannot set colour of new feature type whilst creating
1828 <li>cDNA translation alignment should not be sequence
1829 order dependent</li>
1830 <li>'Show unconserved' doesn't work for lower case
1832 <li>Nucleotide ambiguity codes involving R not recognised</li>
1833 </ul> <em>Deployment and Documentation</em>
1835 <li>Applet example pages appear different to the rest of
1836 www.jalview.org</li>
1837 </ul> <em>Application Known issues</em>
1839 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1840 <li>Misleading message appears after trying to delete
1842 <li>Jalview icon not shown in dock after InstallAnywhere
1843 version launches</li>
1844 <li>Fetching EMBL reference for an RNA sequence results
1845 fails with a sequence mismatch</li>
1846 <li>Corrupted or unreadable alignment display when
1847 scrolling alignment to right</li>
1848 <li>ArrayIndexOutOfBoundsException thrown when remove
1849 empty columns called on alignment with ragged gapped ends</li>
1850 <li>auto calculated alignment annotation rows do not get
1851 placed above or below non-autocalculated rows</li>
1852 <li>Jalview dekstop becomes sluggish at full screen in
1853 ultra-high resolution</li>
1854 <li>Cannot disable consensus calculation independently of
1855 quality and conservation</li>
1856 <li>Mouseover highlighting between cDNA and protein can
1857 become sluggish with more than one splitframe shown</li>
1858 </ul> <em>Applet Known Issues</em>
1860 <li>Core PDB parsing code requires Jmol</li>
1861 <li>Sequence canvas panel goes white when alignment
1862 window is being resized</li>
1868 <td><div align="center">
1869 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1871 <td><em>General</em>
1873 <li>Updated Java code signing certificate donated by
1875 <li>Features and annotation preserved when performing
1876 pairwise alignment</li>
1877 <li>RNA pseudoknot annotation can be
1878 imported/exported/displayed</li>
1879 <li>'colour by annotation' can colour by RNA and
1880 protein secondary structure</li>
1881 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1882 post-hoc with 2.9 release</em>)
1885 </ul> <em>Application</em>
1887 <li>Extract and display secondary structure for sequences
1888 with 3D structures</li>
1889 <li>Support for parsing RNAML</li>
1890 <li>Annotations menu for layout
1892 <li>sort sequence annotation rows by alignment</li>
1893 <li>place sequence annotation above/below alignment
1896 <li>Output in Stockholm format</li>
1897 <li>Internationalisation: improved Spanish (es)
1899 <li>Structure viewer preferences tab</li>
1900 <li>Disorder and Secondary Structure annotation tracks
1901 shared between alignments</li>
1902 <li>UCSF Chimera launch and linked highlighting from
1904 <li>Show/hide all sequence associated annotation rows for
1905 all or current selection</li>
1906 <li>disorder and secondary structure predictions
1907 available as dataset annotation</li>
1908 <li>Per-sequence rna helices colouring</li>
1911 <li>Sequence database accessions imported when fetching
1912 alignments from Rfam</li>
1913 <li>update VARNA version to 3.91</li>
1915 <li>New groovy scripts for exporting aligned positions,
1916 conservation values, and calculating sum of pairs scores.</li>
1917 <li>Command line argument to set default JABAWS server</li>
1918 <li>include installation type in build properties and
1919 console log output</li>
1920 <li>Updated Jalview project format to preserve dataset
1924 <!-- issues resolved --> <em>Application</em>
1926 <li>Distinguish alignment and sequence associated RNA
1927 structure in structure->view->VARNA</li>
1928 <li>Raise dialog box if user deletes all sequences in an
1930 <li>Pressing F1 results in documentation opening twice</li>
1931 <li>Sequence feature tooltip is wrapped</li>
1932 <li>Double click on sequence associated annotation
1933 selects only first column</li>
1934 <li>Redundancy removal doesn't result in unlinked
1935 leaves shown in tree</li>
1936 <li>Undos after several redundancy removals don't undo
1938 <li>Hide sequence doesn't hide associated annotation</li>
1939 <li>User defined colours dialog box too big to fit on
1940 screen and buttons not visible</li>
1941 <li>author list isn't updated if already written to
1942 Jalview properties</li>
1943 <li>Popup menu won't open after retrieving sequence
1945 <li>File open window for associate PDB doesn't open</li>
1946 <li>Left-then-right click on a sequence id opens a
1947 browser search window</li>
1948 <li>Cannot open sequence feature shading/sort popup menu
1949 in feature settings dialog</li>
1950 <li>better tooltip placement for some areas of Jalview
1952 <li>Allow addition of JABAWS Server which doesn't
1953 pass validation</li>
1954 <li>Web services parameters dialog box is too large to
1956 <li>Muscle nucleotide alignment preset obscured by
1958 <li>JABAWS preset submenus don't contain newly
1959 defined user preset</li>
1960 <li>MSA web services warns user if they were launched
1961 with invalid input</li>
1962 <li>Jalview cannot contact DAS Registy when running on
1965 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1966 'Superpose with' submenu not shown when new view
1970 </ul> <!-- <em>Applet</em>
1972 </ul> <em>General</em>
1974 </ul>--> <em>Deployment and Documentation</em>
1976 <li>2G and 1G options in launchApp have no effect on
1977 memory allocation</li>
1978 <li>launchApp service doesn't automatically open
1979 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1981 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1982 InstallAnywhere reports cannot find valid JVM when Java
1983 1.7_055 is available
1985 </ul> <em>Application Known issues</em>
1988 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1989 corrupted or unreadable alignment display when scrolling
1993 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1994 retrieval fails but progress bar continues for DAS retrieval
1995 with large number of ID
1998 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1999 flatfile output of visible region has incorrect sequence
2003 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2004 rna structure consensus doesn't update when secondary
2005 structure tracks are rearranged
2008 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2009 invalid rna structure positional highlighting does not
2010 highlight position of invalid base pairs
2013 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2014 out of memory errors are not raised when saving Jalview
2015 project from alignment window file menu
2018 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2019 Switching to RNA Helices colouring doesn't propagate to
2023 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2024 colour by RNA Helices not enabled when user created
2025 annotation added to alignment
2028 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2029 Jalview icon not shown on dock in Mountain Lion/Webstart
2031 </ul> <em>Applet Known Issues</em>
2034 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2035 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2038 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2039 Jalview and Jmol example not compatible with IE9
2042 <li>Sort by annotation score doesn't reverse order
2048 <td><div align="center">
2049 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2052 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2055 <li>Internationalisation of user interface (usually
2056 called i18n support) and translation for Spanish locale</li>
2057 <li>Define/Undefine group on current selection with
2058 Ctrl-G/Shift Ctrl-G</li>
2059 <li>Improved group creation/removal options in
2060 alignment/sequence Popup menu</li>
2061 <li>Sensible precision for symbol distribution
2062 percentages shown in logo tooltip.</li>
2063 <li>Annotation panel height set according to amount of
2064 annotation when alignment first opened</li>
2065 </ul> <em>Application</em>
2067 <li>Interactive consensus RNA secondary structure
2068 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2069 <li>Select columns containing particular features from
2070 Feature Settings dialog</li>
2071 <li>View all 'representative' PDB structures for selected
2073 <li>Update Jalview project format:
2075 <li>New file extension for Jalview projects '.jvp'</li>
2076 <li>Preserve sequence and annotation dataset (to
2077 store secondary structure annotation,etc)</li>
2078 <li>Per group and alignment annotation and RNA helix
2082 <li>New similarity measures for PCA and Tree calculation
2084 <li>Experimental support for retrieval and viewing of
2085 flanking regions for an alignment</li>
2089 <!-- issues resolved --> <em>Application</em>
2091 <li>logo keeps spinning and status remains at queued or
2092 running after job is cancelled</li>
2093 <li>cannot export features from alignments imported from
2094 Jalview/VAMSAS projects</li>
2095 <li>Buggy slider for web service parameters that take
2097 <li>Newly created RNA secondary structure line doesn't
2098 have 'display all symbols' flag set</li>
2099 <li>T-COFFEE alignment score shading scheme and other
2100 annotation shading not saved in Jalview project</li>
2101 <li>Local file cannot be loaded in freshly downloaded
2103 <li>Jalview icon not shown on dock in Mountain
2105 <li>Load file from desktop file browser fails</li>
2106 <li>Occasional NPE thrown when calculating large trees</li>
2107 <li>Cannot reorder or slide sequences after dragging an
2108 alignment onto desktop</li>
2109 <li>Colour by annotation dialog throws NPE after using
2110 'extract scores' function</li>
2111 <li>Loading/cut'n'pasting an empty file leads to a grey
2112 alignment window</li>
2113 <li>Disorder thresholds rendered incorrectly after
2114 performing IUPred disorder prediction</li>
2115 <li>Multiple group annotated consensus rows shown when
2116 changing 'normalise logo' display setting</li>
2117 <li>Find shows blank dialog after 'finished searching' if
2118 nothing matches query</li>
2119 <li>Null Pointer Exceptions raised when sorting by
2120 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2122 <li>Errors in Jmol console when structures in alignment
2123 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2125 <li>Not all working JABAWS services are shown in
2127 <li>JAVAWS version of Jalview fails to launch with
2128 'invalid literal/length code'</li>
2129 <li>Annotation/RNA Helix colourschemes cannot be applied
2130 to alignment with groups (actually fixed in 2.8.0b1)</li>
2131 <li>RNA Helices and T-Coffee Scores available as default
2134 </ul> <em>Applet</em>
2136 <li>Remove group option is shown even when selection is
2138 <li>Apply to all groups ticked but colourscheme changes
2139 don't affect groups</li>
2140 <li>Documented RNA Helices and T-Coffee Scores as valid
2141 colourscheme name</li>
2142 <li>Annotation labels drawn on sequence IDs when
2143 Annotation panel is not displayed</li>
2144 <li>Increased font size for dropdown menus on OSX and
2145 embedded windows</li>
2146 </ul> <em>Other</em>
2148 <li>Consensus sequence for alignments/groups with a
2149 single sequence were not calculated</li>
2150 <li>annotation files that contain only groups imported as
2151 annotation and junk sequences</li>
2152 <li>Fasta files with sequences containing '*' incorrectly
2153 recognised as PFAM or BLC</li>
2154 <li>conservation/PID slider apply all groups option
2155 doesn't affect background (2.8.0b1)
2157 <li>redundancy highlighting is erratic at 0% and 100%</li>
2158 <li>Remove gapped columns fails for sequences with ragged
2160 <li>AMSA annotation row with leading spaces is not
2161 registered correctly on import</li>
2162 <li>Jalview crashes when selecting PCA analysis for
2163 certain alignments</li>
2164 <li>Opening the colour by annotation dialog for an
2165 existing annotation based 'use original colours'
2166 colourscheme loses original colours setting</li>
2171 <td><div align="center">
2172 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2173 <em>30/1/2014</em></strong>
2177 <li>Trusted certificates for JalviewLite applet and
2178 Jalview Desktop application<br />Certificate was donated by
2179 <a href="https://www.certum.eu">Certum</a> to the Jalview
2180 open source project).
2182 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2183 <li>Output in Stockholm format</li>
2184 <li>Allow import of data from gzipped files</li>
2185 <li>Export/import group and sequence associated line
2186 graph thresholds</li>
2187 <li>Nucleotide substitution matrix that supports RNA and
2188 ambiguity codes</li>
2189 <li>Allow disorder predictions to be made on the current
2190 selection (or visible selection) in the same way that JPred
2192 <li>Groovy scripting for headless Jalview operation</li>
2193 </ul> <em>Other improvements</em>
2195 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2196 <li>COMBINE statement uses current SEQUENCE_REF and
2197 GROUP_REF scope to group annotation rows</li>
2198 <li>Support '' style escaping of quotes in Newick
2200 <li>Group options for JABAWS service by command line name</li>
2201 <li>Empty tooltip shown for JABA service options with a
2202 link but no description</li>
2203 <li>Select primary source when selecting authority in
2204 database fetcher GUI</li>
2205 <li>Add .mfa to FASTA file extensions recognised by
2207 <li>Annotation label tooltip text wrap</li>
2212 <li>Slow scrolling when lots of annotation rows are
2214 <li>Lots of NPE (and slowness) after creating RNA
2215 secondary structure annotation line</li>
2216 <li>Sequence database accessions not imported when
2217 fetching alignments from Rfam</li>
2218 <li>Incorrect SHMR submission for sequences with
2220 <li>View all structures does not always superpose
2222 <li>Option widgets in service parameters not updated to
2223 reflect user or preset settings</li>
2224 <li>Null pointer exceptions for some services without
2225 presets or adjustable parameters</li>
2226 <li>Discover PDB IDs entry in structure menu doesn't
2227 discover PDB xRefs</li>
2228 <li>Exception encountered while trying to retrieve
2229 features with DAS</li>
2230 <li>Lowest value in annotation row isn't coloured
2231 when colour by annotation (per sequence) is coloured</li>
2232 <li>Keyboard mode P jumps to start of gapped region when
2233 residue follows a gap</li>
2234 <li>Jalview appears to hang importing an alignment with
2235 Wrap as default or after enabling Wrap</li>
2236 <li>'Right click to add annotations' message
2237 shown in wrap mode when no annotations present</li>
2238 <li>Disorder predictions fail with NPE if no automatic
2239 annotation already exists on alignment</li>
2240 <li>oninit javascript function should be called after
2241 initialisation completes</li>
2242 <li>Remove redundancy after disorder prediction corrupts
2243 alignment window display</li>
2244 <li>Example annotation file in documentation is invalid</li>
2245 <li>Grouped line graph annotation rows are not exported
2246 to annotation file</li>
2247 <li>Multi-harmony analysis cannot be run when only two
2249 <li>Cannot create multiple groups of line graphs with
2250 several 'combine' statements in annotation file</li>
2251 <li>Pressing return several times causes Number Format
2252 exceptions in keyboard mode</li>
2253 <li>Multi-harmony (SHMMR) method doesn't submit
2254 correct partitions for input data</li>
2255 <li>Translation from DNA to Amino Acids fails</li>
2256 <li>Jalview fail to load newick tree with quoted label</li>
2257 <li>--headless flag isn't understood</li>
2258 <li>ClassCastException when generating EPS in headless
2260 <li>Adjusting sequence-associated shading threshold only
2261 changes one row's threshold</li>
2262 <li>Preferences and Feature settings panel panel
2263 doesn't open</li>
2264 <li>hide consensus histogram also hides conservation and
2265 quality histograms</li>
2270 <td><div align="center">
2271 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2273 <td><em>Application</em>
2275 <li>Support for JABAWS 2.0 Services (AACon alignment
2276 conservation, protein disorder and Clustal Omega)</li>
2277 <li>JABAWS server status indicator in Web Services
2279 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2280 in Jalview alignment window</li>
2281 <li>Updated Jalview build and deploy framework for OSX
2282 mountain lion, windows 7, and 8</li>
2283 <li>Nucleotide substitution matrix for PCA that supports
2284 RNA and ambiguity codes</li>
2286 <li>Improved sequence database retrieval GUI</li>
2287 <li>Support fetching and database reference look up
2288 against multiple DAS sources (Fetch all from in 'fetch db
2290 <li>Jalview project improvements
2292 <li>Store and retrieve the 'belowAlignment'
2293 flag for annotation</li>
2294 <li>calcId attribute to group annotation rows on the
2296 <li>Store AACon calculation settings for a view in
2297 Jalview project</li>
2301 <li>horizontal scrolling gesture support</li>
2302 <li>Visual progress indicator when PCA calculation is
2304 <li>Simpler JABA web services menus</li>
2305 <li>visual indication that web service results are still
2306 being retrieved from server</li>
2307 <li>Serialise the dialogs that are shown when Jalview
2308 starts up for first time</li>
2309 <li>Jalview user agent string for interacting with HTTP
2311 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2313 <li>Examples directory and Groovy library included in
2314 InstallAnywhere distribution</li>
2315 </ul> <em>Applet</em>
2317 <li>RNA alignment and secondary structure annotation
2318 visualization applet example</li>
2319 </ul> <em>General</em>
2321 <li>Normalise option for consensus sequence logo</li>
2322 <li>Reset button in PCA window to return dimensions to
2324 <li>Allow seqspace or Jalview variant of alignment PCA
2326 <li>PCA with either nucleic acid and protein substitution
2328 <li>Allow windows containing HTML reports to be exported
2330 <li>Interactive display and editing of RNA secondary
2331 structure contacts</li>
2332 <li>RNA Helix Alignment Colouring</li>
2333 <li>RNA base pair logo consensus</li>
2334 <li>Parse sequence associated secondary structure
2335 information in Stockholm files</li>
2336 <li>HTML Export database accessions and annotation
2337 information presented in tooltip for sequences</li>
2338 <li>Import secondary structure from LOCARNA clustalw
2339 style RNA alignment files</li>
2340 <li>import and visualise T-COFFEE quality scores for an
2342 <li>'colour by annotation' per sequence option to
2343 shade each sequence according to its associated alignment
2345 <li>New Jalview Logo</li>
2346 </ul> <em>Documentation and Development</em>
2348 <li>documentation for score matrices used in Jalview</li>
2349 <li>New Website!</li>
2351 <td><em>Application</em>
2353 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2354 wsdbfetch REST service</li>
2355 <li>Stop windows being moved outside desktop on OSX</li>
2356 <li>Filetype associations not installed for webstart
2358 <li>Jalview does not always retrieve progress of a JABAWS
2359 job execution in full once it is complete</li>
2360 <li>revise SHMR RSBS definition to ensure alignment is
2361 uploaded via ali_file parameter</li>
2362 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2363 <li>View all structures superposed fails with exception</li>
2364 <li>Jnet job queues forever if a very short sequence is
2365 submitted for prediction</li>
2366 <li>Cut and paste menu not opened when mouse clicked on
2368 <li>Putting fractional value into integer text box in
2369 alignment parameter dialog causes Jalview to hang</li>
2370 <li>Structure view highlighting doesn't work on
2372 <li>View all structures fails with exception shown in
2374 <li>Characters in filename associated with PDBEntry not
2375 escaped in a platform independent way</li>
2376 <li>Jalview desktop fails to launch with exception when
2378 <li>Tree calculation reports 'you must have 2 or more
2379 sequences selected' when selection is empty</li>
2380 <li>Jalview desktop fails to launch with jar signature
2381 failure when java web start temporary file caching is
2383 <li>DAS Sequence retrieval with range qualification
2384 results in sequence xref which includes range qualification</li>
2385 <li>Errors during processing of command line arguments
2386 cause progress bar (JAL-898) to be removed</li>
2387 <li>Replace comma for semi-colon option not disabled for
2388 DAS sources in sequence fetcher</li>
2389 <li>Cannot close news reader when JABAWS server warning
2390 dialog is shown</li>
2391 <li>Option widgets not updated to reflect user settings</li>
2392 <li>Edited sequence not submitted to web service</li>
2393 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2394 <li>InstallAnywhere installer doesn't unpack and run
2395 on OSX Mountain Lion</li>
2396 <li>Annotation panel not given a scroll bar when
2397 sequences with alignment annotation are pasted into the
2399 <li>Sequence associated annotation rows not associated
2400 when loaded from Jalview project</li>
2401 <li>Browser launch fails with NPE on java 1.7</li>
2402 <li>JABAWS alignment marked as finished when job was
2403 cancelled or job failed due to invalid input</li>
2404 <li>NPE with v2.7 example when clicking on Tree
2405 associated with all views</li>
2406 <li>Exceptions when copy/paste sequences with grouped
2407 annotation rows to new window</li>
2408 </ul> <em>Applet</em>
2410 <li>Sequence features are momentarily displayed before
2411 they are hidden using hidefeaturegroups applet parameter</li>
2412 <li>loading features via javascript API automatically
2413 enables feature display</li>
2414 <li>scrollToColumnIn javascript API method doesn't
2416 </ul> <em>General</em>
2418 <li>Redundancy removal fails for rna alignment</li>
2419 <li>PCA calculation fails when sequence has been selected
2420 and then deselected</li>
2421 <li>PCA window shows grey box when first opened on OSX</li>
2422 <li>Letters coloured pink in sequence logo when alignment
2423 coloured with clustalx</li>
2424 <li>Choosing fonts without letter symbols defined causes
2425 exceptions and redraw errors</li>
2426 <li>Initial PCA plot view is not same as manually
2427 reconfigured view</li>
2428 <li>Grouped annotation graph label has incorrect line
2430 <li>Grouped annotation graph label display is corrupted
2431 for lots of labels</li>
2436 <div align="center">
2437 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2440 <td><em>Application</em>
2442 <li>Jalview Desktop News Reader</li>
2443 <li>Tweaked default layout of web services menu</li>
2444 <li>View/alignment association menu to enable user to
2445 easily specify which alignment a multi-structure view takes
2446 its colours/correspondences from</li>
2447 <li>Allow properties file location to be specified as URL</li>
2448 <li>Extend Jalview project to preserve associations
2449 between many alignment views and a single Jmol display</li>
2450 <li>Store annotation row height in Jalview project file</li>
2451 <li>Annotation row column label formatting attributes
2452 stored in project file</li>
2453 <li>Annotation row order for auto-calculated annotation
2454 rows preserved in Jalview project file</li>
2455 <li>Visual progress indication when Jalview state is
2456 saved using Desktop window menu</li>
2457 <li>Visual indication that command line arguments are
2458 still being processed</li>
2459 <li>Groovy script execution from URL</li>
2460 <li>Colour by annotation default min and max colours in
2462 <li>Automatically associate PDB files dragged onto an
2463 alignment with sequences that have high similarity and
2465 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2466 <li>'view structures' option to open many
2467 structures in same window</li>
2468 <li>Sort associated views menu option for tree panel</li>
2469 <li>Group all JABA and non-JABA services for a particular
2470 analysis function in its own submenu</li>
2471 </ul> <em>Applet</em>
2473 <li>Userdefined and autogenerated annotation rows for
2475 <li>Adjustment of alignment annotation pane height</li>
2476 <li>Annotation scrollbar for annotation panel</li>
2477 <li>Drag to reorder annotation rows in annotation panel</li>
2478 <li>'automaticScrolling' parameter</li>
2479 <li>Allow sequences with partial ID string matches to be
2480 annotated from GFF/Jalview features files</li>
2481 <li>Sequence logo annotation row in applet</li>
2482 <li>Absolute paths relative to host server in applet
2483 parameters are treated as such</li>
2484 <li>New in the JalviewLite javascript API:
2486 <li>JalviewLite.js javascript library</li>
2487 <li>Javascript callbacks for
2489 <li>Applet initialisation</li>
2490 <li>Sequence/alignment mouse-overs and selections</li>
2493 <li>scrollTo row and column alignment scrolling
2495 <li>Select sequence/alignment regions from javascript</li>
2496 <li>javascript structure viewer harness to pass
2497 messages between Jmol and Jalview when running as
2498 distinct applets</li>
2499 <li>sortBy method</li>
2500 <li>Set of applet and application examples shipped
2501 with documentation</li>
2502 <li>New example to demonstrate JalviewLite and Jmol
2503 javascript message exchange</li>
2505 </ul> <em>General</em>
2507 <li>Enable Jmol displays to be associated with multiple
2508 multiple alignments</li>
2509 <li>Option to automatically sort alignment with new tree</li>
2510 <li>User configurable link to enable redirects to a
2511 www.Jalview.org mirror</li>
2512 <li>Jmol colours option for Jmol displays</li>
2513 <li>Configurable newline string when writing alignment
2514 and other flat files</li>
2515 <li>Allow alignment annotation description lines to
2516 contain html tags</li>
2517 </ul> <em>Documentation and Development</em>
2519 <li>Add groovy test harness for bulk load testing to
2521 <li>Groovy script to load and align a set of sequences
2522 using a web service before displaying the result in the
2523 Jalview desktop</li>
2524 <li>Restructured javascript and applet api documentation</li>
2525 <li>Ant target to publish example html files with applet
2527 <li>Netbeans project for building Jalview from source</li>
2528 <li>ant task to create online javadoc for Jalview source</li>
2530 <td><em>Application</em>
2532 <li>User defined colourscheme throws exception when
2533 current built in colourscheme is saved as new scheme</li>
2534 <li>AlignFrame->Save in application pops up save
2535 dialog for valid filename/format</li>
2536 <li>Cannot view associated structure for UniProt sequence</li>
2537 <li>PDB file association breaks for UniProt sequence
2539 <li>Associate PDB from file dialog does not tell you
2540 which sequence is to be associated with the file</li>
2541 <li>Find All raises null pointer exception when query
2542 only matches sequence IDs</li>
2543 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2544 <li>Jalview project with Jmol views created with Jalview
2545 2.4 cannot be loaded</li>
2546 <li>Filetype associations not installed for webstart
2548 <li>Two or more chains in a single PDB file associated
2549 with sequences in different alignments do not get coloured
2550 by their associated sequence</li>
2551 <li>Visibility status of autocalculated annotation row
2552 not preserved when project is loaded</li>
2553 <li>Annotation row height and visibility attributes not
2554 stored in Jalview project</li>
2555 <li>Tree bootstraps are not preserved when saved as a
2556 Jalview project</li>
2557 <li>Envision2 workflow tooltips are corrupted</li>
2558 <li>Enabling show group conservation also enables colour
2559 by conservation</li>
2560 <li>Duplicate group associated conservation or consensus
2561 created on new view</li>
2562 <li>Annotation scrollbar not displayed after 'show
2563 all hidden annotation rows' option selected</li>
2564 <li>Alignment quality not updated after alignment
2565 annotation row is hidden then shown</li>
2566 <li>Preserve colouring of structures coloured by
2567 sequences in pre Jalview 2.7 projects</li>
2568 <li>Web service job parameter dialog is not laid out
2570 <li>Web services menu not refreshed after 'reset
2571 services' button is pressed in preferences</li>
2572 <li>Annotation off by one in Jalview v2_3 example project</li>
2573 <li>Structures imported from file and saved in project
2574 get name like jalview_pdb1234.txt when reloaded</li>
2575 <li>Jalview does not always retrieve progress of a JABAWS
2576 job execution in full once it is complete</li>
2577 </ul> <em>Applet</em>
2579 <li>Alignment height set incorrectly when lots of
2580 annotation rows are displayed</li>
2581 <li>Relative URLs in feature HTML text not resolved to
2583 <li>View follows highlighting does not work for positions
2585 <li><= shown as = in tooltip</li>
2586 <li>Export features raises exception when no features
2588 <li>Separator string used for serialising lists of IDs
2589 for javascript api is modified when separator string
2590 provided as parameter</li>
2591 <li>Null pointer exception when selecting tree leaves for
2592 alignment with no existing selection</li>
2593 <li>Relative URLs for datasources assumed to be relative
2594 to applet's codebase</li>
2595 <li>Status bar not updated after finished searching and
2596 search wraps around to first result</li>
2597 <li>StructureSelectionManager instance shared between
2598 several Jalview applets causes race conditions and memory
2600 <li>Hover tooltip and mouseover of position on structure
2601 not sent from Jmol in applet</li>
2602 <li>Certain sequences of javascript method calls to
2603 applet API fatally hang browser</li>
2604 </ul> <em>General</em>
2606 <li>View follows structure mouseover scrolls beyond
2607 position with wrapped view and hidden regions</li>
2608 <li>Find sequence position moves to wrong residue
2609 with/without hidden columns</li>
2610 <li>Sequence length given in alignment properties window
2612 <li>InvalidNumberFormat exceptions thrown when trying to
2613 import PDB like structure files</li>
2614 <li>Positional search results are only highlighted
2615 between user-supplied sequence start/end bounds</li>
2616 <li>End attribute of sequence is not validated</li>
2617 <li>Find dialog only finds first sequence containing a
2618 given sequence position</li>
2619 <li>Sequence numbering not preserved in MSF alignment
2621 <li>Jalview PDB file reader does not extract sequence
2622 from nucleotide chains correctly</li>
2623 <li>Structure colours not updated when tree partition
2624 changed in alignment</li>
2625 <li>Sequence associated secondary structure not correctly
2626 parsed in interleaved stockholm</li>
2627 <li>Colour by annotation dialog does not restore current
2629 <li>Hiding (nearly) all sequences doesn't work
2631 <li>Sequences containing lowercase letters are not
2632 properly associated with their pdb files</li>
2633 </ul> <em>Documentation and Development</em>
2635 <li>schemas/JalviewWsParamSet.xsd corrupted by
2636 ApplyCopyright tool</li>
2641 <div align="center">
2642 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2645 <td><em>Application</em>
2647 <li>New warning dialog when the Jalview Desktop cannot
2648 contact web services</li>
2649 <li>JABA service parameters for a preset are shown in
2650 service job window</li>
2651 <li>JABA Service menu entries reworded</li>
2655 <li>Modeller PIR IO broken - cannot correctly import a
2656 pir file emitted by Jalview</li>
2657 <li>Existing feature settings transferred to new
2658 alignment view created from cut'n'paste</li>
2659 <li>Improved test for mixed amino/nucleotide chains when
2660 parsing PDB files</li>
2661 <li>Consensus and conservation annotation rows
2662 occasionally become blank for all new windows</li>
2663 <li>Exception raised when right clicking above sequences
2664 in wrapped view mode</li>
2665 </ul> <em>Application</em>
2667 <li>multiple multiply aligned structure views cause cpu
2668 usage to hit 100% and computer to hang</li>
2669 <li>Web Service parameter layout breaks for long user
2670 parameter names</li>
2671 <li>Jaba service discovery hangs desktop if Jaba server
2678 <div align="center">
2679 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2682 <td><em>Application</em>
2684 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2685 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2688 <li>Web Services preference tab</li>
2689 <li>Analysis parameters dialog box and user defined
2691 <li>Improved speed and layout of Envision2 service menu</li>
2692 <li>Superpose structures using associated sequence
2694 <li>Export coordinates and projection as CSV from PCA
2696 </ul> <em>Applet</em>
2698 <li>enable javascript: execution by the applet via the
2699 link out mechanism</li>
2700 </ul> <em>Other</em>
2702 <li>Updated the Jmol Jalview interface to work with Jmol
2704 <li>The Jalview Desktop and JalviewLite applet now
2705 require Java 1.5</li>
2706 <li>Allow Jalview feature colour specification for GFF
2707 sequence annotation files</li>
2708 <li>New 'colour by label' keword in Jalview feature file
2709 type colour specification</li>
2710 <li>New Jalview Desktop Groovy API method that allows a
2711 script to check if it being run in an interactive session or
2712 in a batch operation from the Jalview command line</li>
2716 <li>clustalx colourscheme colours Ds preferentially when
2717 both D+E are present in over 50% of the column</li>
2718 </ul> <em>Application</em>
2720 <li>typo in AlignmentFrame->View->Hide->all but
2721 selected Regions menu item</li>
2722 <li>sequence fetcher replaces ',' for ';' when the ',' is
2723 part of a valid accession ID</li>
2724 <li>fatal OOM if object retrieved by sequence fetcher
2725 runs out of memory</li>
2726 <li>unhandled Out of Memory Error when viewing pca
2727 analysis results</li>
2728 <li>InstallAnywhere builds fail to launch on OS X java
2729 10.5 update 4 (due to apple Java 1.6 update)</li>
2730 <li>Installanywhere Jalview silently fails to launch</li>
2731 </ul> <em>Applet</em>
2733 <li>Jalview.getFeatureGroups() raises an
2734 ArrayIndexOutOfBoundsException if no feature groups are
2741 <div align="center">
2742 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2748 <li>Alignment prettyprinter doesn't cope with long
2750 <li>clustalx colourscheme colours Ds preferentially when
2751 both D+E are present in over 50% of the column</li>
2752 <li>nucleic acid structures retrieved from PDB do not
2753 import correctly</li>
2754 <li>More columns get selected than were clicked on when a
2755 number of columns are hidden</li>
2756 <li>annotation label popup menu not providing correct
2757 add/hide/show options when rows are hidden or none are
2759 <li>Stockholm format shown in list of readable formats,
2760 and parser copes better with alignments from RFAM.</li>
2761 <li>CSV output of consensus only includes the percentage
2762 of all symbols if sequence logo display is enabled</li>
2764 </ul> <em>Applet</em>
2766 <li>annotation panel disappears when annotation is
2768 </ul> <em>Application</em>
2770 <li>Alignment view not redrawn properly when new
2771 alignment opened where annotation panel is visible but no
2772 annotations are present on alignment</li>
2773 <li>pasted region containing hidden columns is
2774 incorrectly displayed in new alignment window</li>
2775 <li>Jalview slow to complete operations when stdout is
2776 flooded (fix is to close the Jalview console)</li>
2777 <li>typo in AlignmentFrame->View->Hide->all but
2778 selected Rregions menu item.</li>
2779 <li>inconsistent group submenu and Format submenu entry
2780 'Un' or 'Non'conserved</li>
2781 <li>Sequence feature settings are being shared by
2782 multiple distinct alignments</li>
2783 <li>group annotation not recreated when tree partition is
2785 <li>double click on group annotation to select sequences
2786 does not propagate to associated trees</li>
2787 <li>Mac OSX specific issues:
2789 <li>exception raised when mouse clicked on desktop
2790 window background</li>
2791 <li>Desktop menu placed on menu bar and application
2792 name set correctly</li>
2793 <li>sequence feature settings not wide enough for the
2794 save feature colourscheme button</li>
2803 <div align="center">
2804 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2807 <td><em>New Capabilities</em>
2809 <li>URL links generated from description line for
2810 regular-expression based URL links (applet and application)
2812 <li>Non-positional feature URL links are shown in link
2814 <li>Linked viewing of nucleic acid sequences and
2816 <li>Automatic Scrolling option in View menu to display
2817 the currently highlighted region of an alignment.</li>
2818 <li>Order an alignment by sequence length, or using the
2819 average score or total feature count for each sequence.</li>
2820 <li>Shading features by score or associated description</li>
2821 <li>Subdivide alignment and groups based on identity of
2822 selected subsequence (Make Groups from Selection).</li>
2823 <li>New hide/show options including Shift+Control+H to
2824 hide everything but the currently selected region.</li>
2825 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2826 </ul> <em>Application</em>
2828 <li>Fetch DB References capabilities and UI expanded to
2829 support retrieval from DAS sequence sources</li>
2830 <li>Local DAS Sequence sources can be added via the
2831 command line or via the Add local source dialog box.</li>
2832 <li>DAS Dbref and DbxRef feature types are parsed as
2833 database references and protein_name is parsed as
2834 description line (BioSapiens terms).</li>
2835 <li>Enable or disable non-positional feature and database
2836 references in sequence ID tooltip from View menu in
2838 <!-- <li>New hidden columns and rows and representatives capabilities
2839 in annotations file (in progress - not yet fully implemented)</li> -->
2840 <li>Group-associated consensus, sequence logos and
2841 conservation plots</li>
2842 <li>Symbol distributions for each column can be exported
2843 and visualized as sequence logos</li>
2844 <li>Optionally scale multi-character column labels to fit
2845 within each column of annotation row<!-- todo for applet -->
2847 <li>Optional automatic sort of associated alignment view
2848 when a new tree is opened.</li>
2849 <li>Jalview Java Console</li>
2850 <li>Better placement of desktop window when moving
2851 between different screens.</li>
2852 <li>New preference items for sequence ID tooltip and
2853 consensus annotation</li>
2854 <li>Client to submit sequences and IDs to Envision2
2856 <li><em>Vamsas Capabilities</em>
2858 <li>Improved VAMSAS synchronization (Jalview archive
2859 used to preserve views, structures, and tree display
2861 <li>Import of vamsas documents from disk or URL via
2863 <li>Sharing of selected regions between views and
2864 with other VAMSAS applications (Experimental feature!)</li>
2865 <li>Updated API to VAMSAS version 0.2</li>
2867 </ul> <em>Applet</em>
2869 <li>Middle button resizes annotation row height</li>
2872 <li>sortByTree (true/false) - automatically sort the
2873 associated alignment view by the tree when a new tree is
2875 <li>showTreeBootstraps (true/false) - show or hide
2876 branch bootstraps (default is to show them if available)</li>
2877 <li>showTreeDistances (true/false) - show or hide
2878 branch lengths (default is to show them if available)</li>
2879 <li>showUnlinkedTreeNodes (true/false) - indicate if
2880 unassociated nodes should be highlighted in the tree
2882 <li>heightScale and widthScale (1.0 or more) -
2883 increase the height or width of a cell in the alignment
2884 grid relative to the current font size.</li>
2887 <li>Non-positional features displayed in sequence ID
2889 </ul> <em>Other</em>
2891 <li>Features format: graduated colour definitions and
2892 specification of feature scores</li>
2893 <li>Alignment Annotations format: new keywords for group
2894 associated annotation (GROUP_REF) and annotation row display
2895 properties (ROW_PROPERTIES)</li>
2896 <li>XML formats extended to support graduated feature
2897 colourschemes, group associated annotation, and profile
2898 visualization settings.</li></td>
2901 <li>Source field in GFF files parsed as feature source
2902 rather than description</li>
2903 <li>Non-positional features are now included in sequence
2904 feature and gff files (controlled via non-positional feature
2905 visibility in tooltip).</li>
2906 <li>URL links generated for all feature links (bugfix)</li>
2907 <li>Added URL embedding instructions to features file
2909 <li>Codons containing ambiguous nucleotides translated as
2910 'X' in peptide product</li>
2911 <li>Match case switch in find dialog box works for both
2912 sequence ID and sequence string and query strings do not
2913 have to be in upper case to match case-insensitively.</li>
2914 <li>AMSA files only contain first column of
2915 multi-character column annotation labels</li>
2916 <li>Jalview Annotation File generation/parsing consistent
2917 with documentation (e.g. Stockholm annotation can be
2918 exported and re-imported)</li>
2919 <li>PDB files without embedded PDB IDs given a friendly
2921 <li>Find incrementally searches ID string matches as well
2922 as subsequence matches, and correctly reports total number
2926 <li>Better handling of exceptions during sequence
2928 <li>Dasobert generated non-positional feature URL
2929 link text excludes the start_end suffix</li>
2930 <li>DAS feature and source retrieval buttons disabled
2931 when fetch or registry operations in progress.</li>
2932 <li>PDB files retrieved from URLs are cached properly</li>
2933 <li>Sequence description lines properly shared via
2935 <li>Sequence fetcher fetches multiple records for all
2937 <li>Ensured that command line das feature retrieval
2938 completes before alignment figures are generated.</li>
2939 <li>Reduced time taken when opening file browser for
2941 <li>isAligned check prior to calculating tree, PCA or
2942 submitting an MSA to JNet now excludes hidden sequences.</li>
2943 <li>User defined group colours properly recovered
2944 from Jalview projects.</li>
2953 <div align="center">
2954 <strong>2.4.0.b2</strong><br> 28/10/2009
2959 <li>Experimental support for google analytics usage
2961 <li>Jalview privacy settings (user preferences and docs).</li>
2966 <li>Race condition in applet preventing startup in
2968 <li>Exception when feature created from selection beyond
2969 length of sequence.</li>
2970 <li>Allow synthetic PDB files to be imported gracefully</li>
2971 <li>Sequence associated annotation rows associate with
2972 all sequences with a given id</li>
2973 <li>Find function matches case-insensitively for sequence
2974 ID string searches</li>
2975 <li>Non-standard characters do not cause pairwise
2976 alignment to fail with exception</li>
2977 </ul> <em>Application Issues</em>
2979 <li>Sequences are now validated against EMBL database</li>
2980 <li>Sequence fetcher fetches multiple records for all
2982 </ul> <em>InstallAnywhere Issues</em>
2984 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2985 issue with installAnywhere mechanism)</li>
2986 <li>Command line launching of JARs from InstallAnywhere
2987 version (java class versioning error fixed)</li>
2994 <div align="center">
2995 <strong>2.4</strong><br> 27/8/2008
2998 <td><em>User Interface</em>
3000 <li>Linked highlighting of codon and amino acid from
3001 translation and protein products</li>
3002 <li>Linked highlighting of structure associated with
3003 residue mapping to codon position</li>
3004 <li>Sequence Fetcher provides example accession numbers
3005 and 'clear' button</li>
3006 <li>MemoryMonitor added as an option under Desktop's
3008 <li>Extract score function to parse whitespace separated
3009 numeric data in description line</li>
3010 <li>Column labels in alignment annotation can be centred.</li>
3011 <li>Tooltip for sequence associated annotation give name
3013 </ul> <em>Web Services and URL fetching</em>
3015 <li>JPred3 web service</li>
3016 <li>Prototype sequence search client (no public services
3018 <li>Fetch either seed alignment or full alignment from
3020 <li>URL Links created for matching database cross
3021 references as well as sequence ID</li>
3022 <li>URL Links can be created using regular-expressions</li>
3023 </ul> <em>Sequence Database Connectivity</em>
3025 <li>Retrieval of cross-referenced sequences from other
3027 <li>Generalised database reference retrieval and
3028 validation to all fetchable databases</li>
3029 <li>Fetch sequences from DAS sources supporting the
3030 sequence command</li>
3031 </ul> <em>Import and Export</em>
3032 <li>export annotation rows as CSV for spreadsheet import</li>
3033 <li>Jalview projects record alignment dataset associations,
3034 EMBL products, and cDNA sequence mappings</li>
3035 <li>Sequence Group colour can be specified in Annotation
3037 <li>Ad-hoc colouring of group in Annotation File using RGB
3038 triplet as name of colourscheme</li>
3039 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3041 <li>treenode binding for VAMSAS tree exchange</li>
3042 <li>local editing and update of sequences in VAMSAS
3043 alignments (experimental)</li>
3044 <li>Create new or select existing session to join</li>
3045 <li>load and save of vamsas documents</li>
3046 </ul> <em>Application command line</em>
3048 <li>-tree parameter to open trees (introduced for passing
3050 <li>-fetchfrom command line argument to specify nicknames
3051 of DAS servers to query for alignment features</li>
3052 <li>-dasserver command line argument to add new servers
3053 that are also automatically queried for features</li>
3054 <li>-groovy command line argument executes a given groovy
3055 script after all input data has been loaded and parsed</li>
3056 </ul> <em>Applet-Application data exchange</em>
3058 <li>Trees passed as applet parameters can be passed to
3059 application (when using "View in full
3060 application")</li>
3061 </ul> <em>Applet Parameters</em>
3063 <li>feature group display control parameter</li>
3064 <li>debug parameter</li>
3065 <li>showbutton parameter</li>
3066 </ul> <em>Applet API methods</em>
3068 <li>newView public method</li>
3069 <li>Window (current view) specific get/set public methods</li>
3070 <li>Feature display control methods</li>
3071 <li>get list of currently selected sequences</li>
3072 </ul> <em>New Jalview distribution features</em>
3074 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3075 <li>RELEASE file gives build properties for the latest
3076 Jalview release.</li>
3077 <li>Java 1.1 Applet build made easier and donotobfuscate
3078 property controls execution of obfuscator</li>
3079 <li>Build target for generating source distribution</li>
3080 <li>Debug flag for javacc</li>
3081 <li>.jalview_properties file is documented (slightly) in
3082 jalview.bin.Cache</li>
3083 <li>Continuous Build Integration for stable and
3084 development version of Application, Applet and source
3089 <li>selected region output includes visible annotations
3090 (for certain formats)</li>
3091 <li>edit label/displaychar contains existing label/char
3093 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3094 <li>shorter peptide product names from EMBL records</li>
3095 <li>Newick string generator makes compact representations</li>
3096 <li>bootstrap values parsed correctly for tree files with
3098 <li>pathological filechooser bug avoided by not allowing
3099 filenames containing a ':'</li>
3100 <li>Fixed exception when parsing GFF files containing
3101 global sequence features</li>
3102 <li>Alignment datasets are finalized only when number of
3103 references from alignment sequences goes to zero</li>
3104 <li>Close of tree branch colour box without colour
3105 selection causes cascading exceptions</li>
3106 <li>occasional negative imgwidth exceptions</li>
3107 <li>better reporting of non-fatal warnings to user when
3108 file parsing fails.</li>
3109 <li>Save works when Jalview project is default format</li>
3110 <li>Save as dialog opened if current alignment format is
3111 not a valid output format</li>
3112 <li>UniProt canonical names introduced for both das and
3114 <li>Histidine should be midblue (not pink!) in Zappo</li>
3115 <li>error messages passed up and output when data read
3117 <li>edit undo recovers previous dataset sequence when
3118 sequence is edited</li>
3119 <li>allow PDB files without pdb ID HEADER lines (like
3120 those generated by MODELLER) to be read in properly</li>
3121 <li>allow reading of JPred concise files as a normal
3123 <li>Stockholm annotation parsing and alignment properties
3124 import fixed for PFAM records</li>
3125 <li>Structure view windows have correct name in Desktop
3127 <li>annotation consisting of sequence associated scores
3128 can be read and written correctly to annotation file</li>
3129 <li>Aligned cDNA translation to aligned peptide works
3131 <li>Fixed display of hidden sequence markers and
3132 non-italic font for representatives in Applet</li>
3133 <li>Applet Menus are always embedded in applet window on
3135 <li>Newly shown features appear at top of stack (in
3137 <li>Annotations added via parameter not drawn properly
3138 due to null pointer exceptions</li>
3139 <li>Secondary structure lines are drawn starting from
3140 first column of alignment</li>
3141 <li>UniProt XML import updated for new schema release in
3143 <li>Sequence feature to sequence ID match for Features
3144 file is case-insensitive</li>
3145 <li>Sequence features read from Features file appended to
3146 all sequences with matching IDs</li>
3147 <li>PDB structure coloured correctly for associated views
3148 containing a sub-sequence</li>
3149 <li>PDB files can be retrieved by applet from Jar files</li>
3150 <li>feature and annotation file applet parameters
3151 referring to different directories are retrieved correctly</li>
3152 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3153 <li>Fixed application hang whilst waiting for
3154 splash-screen version check to complete</li>
3155 <li>Applet properly URLencodes input parameter values
3156 when passing them to the launchApp service</li>
3157 <li>display name and local features preserved in results
3158 retrieved from web service</li>
3159 <li>Visual delay indication for sequence retrieval and
3160 sequence fetcher initialisation</li>
3161 <li>updated Application to use DAS 1.53e version of
3162 dasobert DAS client</li>
3163 <li>Re-instated Full AMSA support and .amsa file
3165 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3173 <div align="center">
3174 <strong>2.3</strong><br> 9/5/07
3179 <li>Jmol 11.0.2 integration</li>
3180 <li>PDB views stored in Jalview XML files</li>
3181 <li>Slide sequences</li>
3182 <li>Edit sequence in place</li>
3183 <li>EMBL CDS features</li>
3184 <li>DAS Feature mapping</li>
3185 <li>Feature ordering</li>
3186 <li>Alignment Properties</li>
3187 <li>Annotation Scores</li>
3188 <li>Sort by scores</li>
3189 <li>Feature/annotation editing in applet</li>
3194 <li>Headless state operation in 2.2.1</li>
3195 <li>Incorrect and unstable DNA pairwise alignment</li>
3196 <li>Cut and paste of sequences with annotation</li>
3197 <li>Feature group display state in XML</li>
3198 <li>Feature ordering in XML</li>
3199 <li>blc file iteration selection using filename # suffix</li>
3200 <li>Stockholm alignment properties</li>
3201 <li>Stockhom alignment secondary structure annotation</li>
3202 <li>2.2.1 applet had no feature transparency</li>
3203 <li>Number pad keys can be used in cursor mode</li>
3204 <li>Structure Viewer mirror image resolved</li>
3211 <div align="center">
3212 <strong>2.2.1</strong><br> 12/2/07
3217 <li>Non standard characters can be read and displayed
3218 <li>Annotations/Features can be imported/exported to the
3220 <li>Applet allows editing of sequence/annotation/group
3221 name & description
3222 <li>Preference setting to display sequence name in
3224 <li>Annotation file format extended to allow
3225 Sequence_groups to be defined
3226 <li>Default opening of alignment overview panel can be
3227 specified in preferences
3228 <li>PDB residue numbering annotation added to associated
3234 <li>Applet crash under certain Linux OS with Java 1.6
3236 <li>Annotation file export / import bugs fixed
3237 <li>PNG / EPS image output bugs fixed
3243 <div align="center">
3244 <strong>2.2</strong><br> 27/11/06
3249 <li>Multiple views on alignment
3250 <li>Sequence feature editing
3251 <li>"Reload" alignment
3252 <li>"Save" to current filename
3253 <li>Background dependent text colour
3254 <li>Right align sequence ids
3255 <li>User-defined lower case residue colours
3258 <li>Menu item accelerator keys
3259 <li>Control-V pastes to current alignment
3260 <li>Cancel button for DAS Feature Fetching
3261 <li>PCA and PDB Viewers zoom via mouse roller
3262 <li>User-defined sub-tree colours and sub-tree selection
3264 <li>'New Window' button on the 'Output to Text box'
3269 <li>New memory efficient Undo/Redo System
3270 <li>Optimised symbol lookups and conservation/consensus
3272 <li>Region Conservation/Consensus recalculated after
3274 <li>Fixed Remove Empty Columns Bug (empty columns at end
3276 <li>Slowed DAS Feature Fetching for increased robustness.
3278 <li>Made angle brackets in ASCII feature descriptions
3280 <li>Re-instated Zoom function for PCA
3281 <li>Sequence descriptions conserved in web service
3283 <li>UniProt ID discoverer uses any word separated by
3285 <li>WsDbFetch query/result association resolved
3286 <li>Tree leaf to sequence mapping improved
3287 <li>Smooth fonts switch moved to FontChooser dialog box.
3294 <div align="center">
3295 <strong>2.1.1</strong><br> 12/9/06
3300 <li>Copy consensus sequence to clipboard</li>
3305 <li>Image output - rightmost residues are rendered if
3306 sequence id panel has been resized</li>
3307 <li>Image output - all offscreen group boundaries are
3309 <li>Annotation files with sequence references - all
3310 elements in file are relative to sequence position</li>
3311 <li>Mac Applet users can use Alt key for group editing</li>
3317 <div align="center">
3318 <strong>2.1</strong><br> 22/8/06
3323 <li>MAFFT Multiple Alignment in default Web Service list</li>
3324 <li>DAS Feature fetching</li>
3325 <li>Hide sequences and columns</li>
3326 <li>Export Annotations and Features</li>
3327 <li>GFF file reading / writing</li>
3328 <li>Associate structures with sequences from local PDB
3330 <li>Add sequences to exisiting alignment</li>
3331 <li>Recently opened files / URL lists</li>
3332 <li>Applet can launch the full application</li>
3333 <li>Applet has transparency for features (Java 1.2
3335 <li>Applet has user defined colours parameter</li>
3336 <li>Applet can load sequences from parameter
3337 "sequence<em>x</em>"
3343 <li>Redundancy Panel reinstalled in the Applet</li>
3344 <li>Monospaced font - EPS / rescaling bug fixed</li>
3345 <li>Annotation files with sequence references bug fixed</li>
3351 <div align="center">
3352 <strong>2.08.1</strong><br> 2/5/06
3357 <li>Change case of selected region from Popup menu</li>
3358 <li>Choose to match case when searching</li>
3359 <li>Middle mouse button and mouse movement can compress /
3360 expand the visible width and height of the alignment</li>
3365 <li>Annotation Panel displays complete JNet results</li>
3371 <div align="center">
3372 <strong>2.08b</strong><br> 18/4/06
3378 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3379 <li>Righthand label on wrapped alignments shows correct
3386 <div align="center">
3387 <strong>2.08</strong><br> 10/4/06
3392 <li>Editing can be locked to the selection area</li>
3393 <li>Keyboard editing</li>
3394 <li>Create sequence features from searches</li>
3395 <li>Precalculated annotations can be loaded onto
3397 <li>Features file allows grouping of features</li>
3398 <li>Annotation Colouring scheme added</li>
3399 <li>Smooth fonts off by default - Faster rendering</li>
3400 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3405 <li>Drag & Drop fixed on Linux</li>
3406 <li>Jalview Archive file faster to load/save, sequence
3407 descriptions saved.</li>
3413 <div align="center">
3414 <strong>2.07</strong><br> 12/12/05
3419 <li>PDB Structure Viewer enhanced</li>
3420 <li>Sequence Feature retrieval and display enhanced</li>
3421 <li>Choose to output sequence start-end after sequence
3422 name for file output</li>
3423 <li>Sequence Fetcher WSDBFetch@EBI</li>
3424 <li>Applet can read feature files, PDB files and can be
3425 used for HTML form input</li>
3430 <li>HTML output writes groups and features</li>
3431 <li>Group editing is Control and mouse click</li>
3432 <li>File IO bugs</li>
3438 <div align="center">
3439 <strong>2.06</strong><br> 28/9/05
3444 <li>View annotations in wrapped mode</li>
3445 <li>More options for PCA viewer</li>
3450 <li>GUI bugs resolved</li>
3451 <li>Runs with -nodisplay from command line</li>
3457 <div align="center">
3458 <strong>2.05b</strong><br> 15/9/05
3463 <li>Choose EPS export as lineart or text</li>
3464 <li>Jar files are executable</li>
3465 <li>Can read in Uracil - maps to unknown residue</li>
3470 <li>Known OutOfMemory errors give warning message</li>
3471 <li>Overview window calculated more efficiently</li>
3472 <li>Several GUI bugs resolved</li>
3478 <div align="center">
3479 <strong>2.05</strong><br> 30/8/05
3484 <li>Edit and annotate in "Wrapped" view</li>
3489 <li>Several GUI bugs resolved</li>
3495 <div align="center">
3496 <strong>2.04</strong><br> 24/8/05
3501 <li>Hold down mouse wheel & scroll to change font
3507 <li>Improved JPred client reliability</li>
3508 <li>Improved loading of Jalview files</li>
3514 <div align="center">
3515 <strong>2.03</strong><br> 18/8/05
3520 <li>Set Proxy server name and port in preferences</li>
3521 <li>Multiple URL links from sequence ids</li>
3522 <li>User Defined Colours can have a scheme name and added
3524 <li>Choose to ignore gaps in consensus calculation</li>
3525 <li>Unix users can set default web browser</li>
3526 <li>Runs without GUI for batch processing</li>
3527 <li>Dynamically generated Web Service Menus</li>
3532 <li>InstallAnywhere download for Sparc Solaris</li>
3538 <div align="center">
3539 <strong>2.02</strong><br> 18/7/05
3545 <li>Copy & Paste order of sequences maintains
3546 alignment order.</li>
3552 <div align="center">
3553 <strong>2.01</strong><br> 12/7/05
3558 <li>Use delete key for deleting selection.</li>
3559 <li>Use Mouse wheel to scroll sequences.</li>
3560 <li>Help file updated to describe how to add alignment
3562 <li>Version and build date written to build properties
3564 <li>InstallAnywhere installation will check for updates
3565 at launch of Jalview.</li>
3570 <li>Delete gaps bug fixed.</li>
3571 <li>FileChooser sorts columns.</li>
3572 <li>Can remove groups one by one.</li>
3573 <li>Filechooser icons installed.</li>
3574 <li>Finder ignores return character when searching.
3575 Return key will initiate a search.<br>
3582 <div align="center">
3583 <strong>2.0</strong><br> 20/6/05
3588 <li>New codebase</li>