3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
99 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
100 <em>Testing and Deployment</em>
101 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
104 <td><div align="left">
107 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
108 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
109 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
110 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
114 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
115 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
117 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
119 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
120 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
121 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
122 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
123 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
124 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
125 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
126 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
127 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
128 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
129 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
130 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
131 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
132 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
133 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
134 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
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>
137 <strong><em>Applet</em></strong><br/>
139 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
141 <strong><em>BioJSON</em></strong><br/>
144 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
151 <td width="60" nowrap>
153 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
154 <em>2/10/2017</em></strong>
157 <td><div align="left">
158 <em>New features in Jalview Desktop</em>
161 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
163 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
167 <td><div align="left">
171 <td width="60" nowrap>
173 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
174 <em>7/9/2017</em></strong>
177 <td><div align="left">
181 <!-- JAL-2588 -->Show gaps in overview window by colouring
182 in grey (sequences used to be coloured grey, and gaps were
186 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
190 <!-- JAL-2587 -->Overview updates immediately on increase
191 in size and progress bar shown as higher resolution
192 overview is recalculated
197 <td><div align="left">
201 <!-- JAL-2664 -->Overview window redraws every hidden
202 column region row by row
205 <!-- JAL-2681 -->duplicate protein sequences shown after
206 retrieving Ensembl crossrefs for sequences from Uniprot
209 <!-- JAL-2603 -->Overview window throws NPE if show boxes
210 format setting is unticked
213 <!-- JAL-2610 -->Groups are coloured wrongly in overview
214 if group has show boxes format setting unticked
217 <!-- JAL-2672,JAL-2665 -->Redraw problems when
218 autoscrolling whilst dragging current selection group to
219 include sequences and columns not currently displayed
222 <!-- JAL-2691 -->Not all chains are mapped when multimeric
223 assemblies are imported via CIF file
226 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
227 displayed when threshold or conservation colouring is also
231 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
235 <!-- JAL-2673 -->Jalview continues to scroll after
236 dragging a selected region off the visible region of the
240 <!-- JAL-2724 -->Cannot apply annotation based
241 colourscheme to all groups in a view
244 <!-- JAL-2511 -->IDs don't line up with sequences
245 initially after font size change using the Font chooser or
252 <td width="60" nowrap>
254 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
257 <td><div align="left">
258 <em>Calculations</em>
262 <!-- JAL-1933 -->Occupancy annotation row shows number of
263 ungapped positions in each column of the alignment.
266 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
267 a calculation dialog box
270 <!-- JAL-2379 -->Revised implementation of PCA for speed
271 and memory efficiency (~30x faster)
274 <!-- JAL-2403 -->Revised implementation of sequence
275 similarity scores as used by Tree, PCA, Shading Consensus
276 and other calculations
279 <!-- JAL-2416 -->Score matrices are stored as resource
280 files within the Jalview codebase
283 <!-- JAL-2500 -->Trees computed on Sequence Feature
284 Similarity may have different topology due to increased
291 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
292 model for alignments and groups
295 <!-- JAL-384 -->Custom shading schemes created via groovy
302 <!-- JAL-2526 -->Efficiency improvements for interacting
303 with alignment and overview windows
306 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
310 <!-- JAL-2388 -->Hidden columns and sequences can be
314 <!-- JAL-2611 -->Click-drag in visible area allows fine
315 adjustment of visible position
319 <em>Data import/export</em>
322 <!-- JAL-2535 -->Posterior probability annotation from
323 Stockholm files imported as sequence associated annotation
326 <!-- JAL-2507 -->More robust per-sequence positional
327 annotation input/output via stockholm flatfile
330 <!-- JAL-2533 -->Sequence names don't include file
331 extension when importing structure files without embedded
332 names or PDB accessions
335 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
336 format sequence substitution matrices
339 <em>User Interface</em>
342 <!-- JAL-2447 --> Experimental Features Checkbox in
343 Desktop's Tools menu to hide or show untested features in
347 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
348 via Overview or sequence motif search operations
351 <!-- JAL-2547 -->Amend sequence features dialog box can be
352 opened by double clicking gaps within sequence feature
356 <!-- JAL-1476 -->Status bar message shown when not enough
357 aligned positions were available to create a 3D structure
361 <em>3D Structure</em>
364 <!-- JAL-2430 -->Hidden regions in alignment views are not
365 coloured in linked structure views
368 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
369 file-based command exchange
372 <!-- JAL-2375 -->Structure chooser automatically shows
373 Cached Structures rather than querying the PDBe if
374 structures are already available for sequences
377 <!-- JAL-2520 -->Structures imported via URL are cached in
378 the Jalview project rather than downloaded again when the
382 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
383 to transfer Chimera's structure attributes as Jalview
384 features, and vice-versa (<strong>Experimental
388 <em>Web Services</em>
391 <!-- JAL-2549 -->Updated JABAWS client to v2.2
394 <!-- JAL-2335 -->Filter non-standard amino acids and
395 nucleotides when submitting to AACon and other MSA
399 <!-- JAL-2316, -->URLs for viewing database
400 cross-references provided by identifiers.org and the
408 <!-- JAL-2344 -->FileFormatI interface for describing and
409 identifying file formats (instead of String constants)
412 <!-- JAL-2228 -->FeatureCounter script refactored for
413 efficiency when counting all displayed features (not
414 backwards compatible with 2.10.1)
417 <em>Example files</em>
420 <!-- JAL-2631 -->Graduated feature colour style example
421 included in the example feature file
424 <em>Documentation</em>
427 <!-- JAL-2339 -->Release notes reformatted for readability
428 with the built-in Java help viewer
431 <!-- JAL-1644 -->Find documentation updated with 'search
432 sequence description' option
438 <!-- JAL-2485, -->External service integration tests for
439 Uniprot REST Free Text Search Client
442 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
445 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
450 <td><div align="left">
451 <em>Calculations</em>
454 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
455 matrix - C->R should be '-3'<br />Old matrix restored
456 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
458 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
459 Jalview's treatment of gaps in PCA and substitution matrix
460 based Tree calculations.<br /> <br />In earlier versions
461 of Jalview, gaps matching gaps were penalised, and gaps
462 matching non-gaps penalised even more. In the PCA
463 calculation, gaps were actually treated as non-gaps - so
464 different costs were applied, which meant Jalview's PCAs
465 were different to those produced by SeqSpace.<br />Jalview
466 now treats gaps in the same way as SeqSpace (ie it scores
467 them as 0). <br /> <br />Enter the following in the
468 Groovy console to restore pre-2.10.2 behaviour:<br />
469 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
470 // for 2.10.1 mode <br />
471 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
472 // to restore 2.10.2 mode <br /> <br /> <em>Note:
473 these settings will affect all subsequent tree and PCA
474 calculations (not recommended)</em></li>
476 <!-- JAL-2424 -->Fixed off-by-one bug that affected
477 scaling of branch lengths for trees computed using
478 Sequence Feature Similarity.
481 <!-- JAL-2377 -->PCA calculation could hang when
482 generating output report when working with highly
486 <!-- JAL-2544 --> Sort by features includes features to
487 right of selected region when gaps present on right-hand
491 <em>User Interface</em>
494 <!-- JAL-2346 -->Reopening Colour by annotation dialog
495 doesn't reselect a specific sequence's associated
496 annotation after it was used for colouring a view
499 <!-- JAL-2419 -->Current selection lost if popup menu
500 opened on a region of alignment without groups
503 <!-- JAL-2374 -->Popup menu not always shown for regions
504 of an alignment with overlapping groups
507 <!-- JAL-2310 -->Finder double counts if both a sequence's
508 name and description match
511 <!-- JAL-2370 -->Hiding column selection containing two
512 hidden regions results in incorrect hidden regions
515 <!-- JAL-2386 -->'Apply to all groups' setting when
516 changing colour does not apply Conservation slider value
520 <!-- JAL-2373 -->Percentage identity and conservation menu
521 items do not show a tick or allow shading to be disabled
524 <!-- JAL-2385 -->Conservation shading or PID threshold
525 lost when base colourscheme changed if slider not visible
528 <!-- JAL-2547 -->Sequence features shown in tooltip for
529 gaps before start of features
532 <!-- JAL-2623 -->Graduated feature colour threshold not
533 restored to UI when feature colour is edited
536 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
537 a time when scrolling vertically in wrapped mode.
540 <!-- JAL-2630 -->Structure and alignment overview update
541 as graduate feature colour settings are modified via the
545 <!-- JAL-2034 -->Overview window doesn't always update
546 when a group defined on the alignment is resized
549 <!-- JAL-2605 -->Mouseovers on left/right scale region in
550 wrapped view result in positional status updates
554 <!-- JAL-2563 -->Status bar doesn't show position for
555 ambiguous amino acid and nucleotide symbols
558 <!-- JAL-2602 -->Copy consensus sequence failed if
559 alignment included gapped columns
562 <!-- JAL-2473 -->Minimum size set for Jalview windows so
563 widgets don't permanently disappear
566 <!-- JAL-2503 -->Cannot select or filter quantitative
567 annotation that are shown only as column labels (e.g.
568 T-Coffee column reliability scores)
571 <!-- JAL-2594 -->Exception thrown if trying to create a
572 sequence feature on gaps only
575 <!-- JAL-2504 -->Features created with 'New feature'
576 button from a Find inherit previously defined feature type
577 rather than the Find query string
580 <!-- JAL-2423 -->incorrect title in output window when
581 exporting tree calculated in Jalview
584 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
585 and then revealing them reorders sequences on the
589 <!-- JAL-964 -->Group panel in sequence feature settings
590 doesn't update to reflect available set of groups after
591 interactively adding or modifying features
594 <!-- JAL-2225 -->Sequence Database chooser unusable on
598 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
599 only excluded gaps in current sequence and ignored
606 <!-- JAL-2421 -->Overview window visible region moves
607 erratically when hidden rows or columns are present
610 <!-- JAL-2362 -->Per-residue colourschemes applied via the
611 Structure Viewer's colour menu don't correspond to
615 <!-- JAL-2405 -->Protein specific colours only offered in
616 colour and group colour menu for protein alignments
619 <!-- JAL-2385 -->Colour threshold slider doesn't update to
620 reflect currently selected view or group's shading
624 <!-- JAL-2624 -->Feature colour thresholds not respected
625 when rendered on overview and structures when opacity at
629 <!-- JAL-2589 -->User defined gap colour not shown in
630 overview when features overlaid on alignment
633 <em>Data import/export</em>
636 <!-- JAL-2576 -->Very large alignments take a long time to
640 <!-- JAL-2507 -->Per-sequence RNA secondary structures
641 added after a sequence was imported are not written to
645 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
646 when importing RNA secondary structure via Stockholm
649 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
650 not shown in correct direction for simple pseudoknots
653 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
654 with lightGray or darkGray via features file (but can
658 <!-- JAL-2383 -->Above PID colour threshold not recovered
659 when alignment view imported from project
662 <!-- JAL-2520,JAL-2465 -->No mappings generated between
663 structure and sequences extracted from structure files
664 imported via URL and viewed in Jmol
667 <!-- JAL-2520 -->Structures loaded via URL are saved in
668 Jalview Projects rather than fetched via URL again when
669 the project is loaded and the structure viewed
672 <em>Web Services</em>
675 <!-- JAL-2519 -->EnsemblGenomes example failing after
676 release of Ensembl v.88
679 <!-- JAL-2366 -->Proxy server address and port always
680 appear enabled in Preferences->Connections
683 <!-- JAL-2461 -->DAS registry not found exceptions
684 removed from console output
687 <!-- JAL-2582 -->Cannot retrieve protein products from
688 Ensembl by Peptide ID
691 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
692 created from SIFTs, and spurious 'Couldn't open structure
693 in Chimera' errors raised after April 2017 update (problem
694 due to 'null' string rather than empty string used for
695 residues with no corresponding PDB mapping).
698 <em>Application UI</em>
701 <!-- JAL-2361 -->User Defined Colours not added to Colour
705 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
706 case' residues (button in colourscheme editor debugged and
707 new documentation and tooltips added)
710 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
711 doesn't restore group-specific text colour thresholds
714 <!-- JAL-2243 -->Feature settings panel does not update as
715 new features are added to alignment
718 <!-- JAL-2532 -->Cancel in feature settings reverts
719 changes to feature colours via the Amend features dialog
722 <!-- JAL-2506 -->Null pointer exception when attempting to
723 edit graduated feature colour via amend features dialog
727 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
728 selection menu changes colours of alignment views
731 <!-- JAL-2426 -->Spurious exceptions in console raised
732 from alignment calculation workers after alignment has
736 <!-- JAL-1608 -->Typo in selection popup menu - Create
737 groups now 'Create Group'
740 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
741 Create/Undefine group doesn't always work
744 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
745 shown again after pressing 'Cancel'
748 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
749 adjusts start position in wrap mode
752 <!-- JAL-2563 -->Status bar doesn't show positions for
753 ambiguous amino acids
756 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
757 CDS/Protein view after CDS sequences added for aligned
761 <!-- JAL-2592 -->User defined colourschemes called 'User
762 Defined' don't appear in Colours menu
768 <!-- JAL-2468 -->Switching between Nucleotide and Protein
769 score models doesn't always result in an updated PCA plot
772 <!-- JAL-2442 -->Features not rendered as transparent on
773 overview or linked structure view
776 <!-- JAL-2372 -->Colour group by conservation doesn't
780 <!-- JAL-2517 -->Hitting Cancel after applying
781 user-defined colourscheme doesn't restore original
788 <!-- JAL-2314 -->Unit test failure:
789 jalview.ws.jabaws.RNAStructExportImport setup fails
792 <!-- JAL-2307 -->Unit test failure:
793 jalview.ws.sifts.SiftsClientTest due to compatibility
794 problems with deep array comparison equality asserts in
795 successive versions of TestNG
798 <!-- JAL-2479 -->Relocated StructureChooserTest and
799 ParameterUtilsTest Unit tests to Network suite
802 <em>New Known Issues</em>
805 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
806 phase after a sequence motif find operation
809 <!-- JAL-2550 -->Importing annotation file with rows
810 containing just upper and lower case letters are
811 interpreted as WUSS RNA secondary structure symbols
814 <!-- JAL-2590 -->Cannot load and display Newick trees
815 reliably from eggnog Ortholog database
818 <!-- JAL-2468 -->Status bar shows 'Marked x columns
819 containing features of type Highlight' when 'B' is pressed
820 to mark columns containing highlighted regions.
823 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
824 doesn't always add secondary structure annotation.
829 <td width="60" nowrap>
831 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
834 <td><div align="left">
838 <!-- JAL-98 -->Improved memory usage: sparse arrays used
839 for all consensus calculations
842 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
845 <li>Updated Jalview's Certum code signing certificate
851 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
852 set of database cross-references, sorted alphabetically
855 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
856 from database cross references. Users with custom links
857 will receive a <a href="webServices/urllinks.html#warning">warning
858 dialog</a> asking them to update their preferences.
861 <!-- JAL-2287-->Cancel button and escape listener on
862 dialog warning user about disconnecting Jalview from a
866 <!-- JAL-2320-->Jalview's Chimera control window closes if
867 the Chimera it is connected to is shut down
870 <!-- JAL-1738-->New keystroke (B) and Select highlighted
871 columns menu item to mark columns containing highlighted
872 regions (e.g. from structure selections or results of a
876 <!-- JAL-2284-->Command line option for batch-generation
877 of HTML pages rendering alignment data with the BioJS
887 <!-- JAL-2286 -->Columns with more than one modal residue
888 are not coloured or thresholded according to percent
889 identity (first observed in Jalview 2.8.2)
892 <!-- JAL-2301 -->Threonine incorrectly reported as not
896 <!-- JAL-2318 -->Updates to documentation pages (above PID
897 threshold, amino acid properties)
900 <!-- JAL-2292 -->Lower case residues in sequences are not
901 reported as mapped to residues in a structure file in the
905 <!--JAL-2324 -->Identical features with non-numeric scores
906 could be added multiple times to a sequence
909 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
910 bond features shown as two highlighted residues rather
911 than a range in linked structure views, and treated
912 correctly when selecting and computing trees from features
915 <!-- JAL-2281-->Custom URL links for database
916 cross-references are matched to database name regardless
924 <!-- JAL-2282-->Custom URL links for specific database
925 names without regular expressions also offer links from
929 <!-- JAL-2315-->Removing a single configured link in the
930 URL links pane in Connections preferences doesn't actually
931 update Jalview configuration
934 <!-- JAL-2272-->CTRL-Click on a selected region to open
935 the alignment area popup menu doesn't work on El-Capitan
938 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
939 files with similarly named sequences if dropped onto the
943 <!-- JAL-2312 -->Additional mappings are shown for PDB
944 entries where more chains exist in the PDB accession than
945 are reported in the SIFTS file
948 <!-- JAL-2317-->Certain structures do not get mapped to
949 the structure view when displayed with Chimera
952 <!-- JAL-2317-->No chains shown in the Chimera view
953 panel's View->Show Chains submenu
956 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
957 work for wrapped alignment views
960 <!--JAL-2197 -->Rename UI components for running JPred
961 predictions from 'JNet' to 'JPred'
964 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
965 corrupted when annotation panel vertical scroll is not at
969 <!--JAL-2332 -->Attempting to view structure for Hen
970 lysozyme results in a PDB Client error dialog box
973 <!-- JAL-2319 -->Structure View's mapping report switched
974 ranges for PDB and sequence for SIFTS
977 SIFTS 'Not_Observed' residues mapped to non-existant
981 <!-- <em>New Known Issues</em>
988 <td width="60" nowrap>
990 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
991 <em>25/10/2016</em></strong>
994 <td><em>Application</em>
996 <li>3D Structure chooser opens with 'Cached structures'
997 view if structures already loaded</li>
998 <li>Progress bar reports models as they are loaded to
1005 <li>Colour by conservation always enabled and no tick
1006 shown in menu when BLOSUM or PID shading applied</li>
1007 <li>FER1_ARATH and FER2_ARATH labels were switched in
1008 example sequences/projects/trees</li>
1010 <em>Application</em>
1012 <li>Jalview projects with views of local PDB structure
1013 files saved on Windows cannot be opened on OSX</li>
1014 <li>Multiple structure views can be opened and superposed
1015 without timeout for structures with multiple models or
1016 multiple sequences in alignment</li>
1017 <li>Cannot import or associated local PDB files without a
1018 PDB ID HEADER line</li>
1019 <li>RMSD is not output in Jmol console when superposition
1021 <li>Drag and drop of URL from Browser fails for Linux and
1022 OSX versions earlier than El Capitan</li>
1023 <li>ENA client ignores invalid content from ENA server</li>
1024 <li>Exceptions are not raised in console when ENA client
1025 attempts to fetch non-existent IDs via Fetch DB Refs UI
1027 <li>Exceptions are not raised in console when a new view
1028 is created on the alignment</li>
1029 <li>OSX right-click fixed for group selections: CMD-click
1030 to insert/remove gaps in groups and CTRL-click to open group
1033 <em>Build and deployment</em>
1035 <li>URL link checker now copes with multi-line anchor
1038 <em>New Known Issues</em>
1040 <li>Drag and drop from URL links in browsers do not work
1047 <td width="60" nowrap>
1048 <div align="center">
1049 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1052 <td><em>General</em>
1055 <!-- JAL-2124 -->Updated Spanish translations.
1058 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1059 for importing structure data to Jalview. Enables mmCIF and
1063 <!-- JAL-192 --->Alignment ruler shows positions relative to
1067 <!-- JAL-2202 -->Position/residue shown in status bar when
1068 mousing over sequence associated annotation
1071 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1075 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1076 '()', canonical '[]' and invalid '{}' base pair populations
1080 <!-- JAL-2092 -->Feature settings popup menu options for
1081 showing or hiding columns containing a feature
1084 <!-- JAL-1557 -->Edit selected group by double clicking on
1085 group and sequence associated annotation labels
1088 <!-- JAL-2236 -->Sequence name added to annotation label in
1089 select/hide columns by annotation and colour by annotation
1093 </ul> <em>Application</em>
1096 <!-- JAL-2050-->Automatically hide introns when opening a
1097 gene/transcript view
1100 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1104 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1105 structure mappings with the EMBL-EBI PDBe SIFTS database
1108 <!-- JAL-2079 -->Updated download sites used for Rfam and
1109 Pfam sources to xfam.org
1112 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1115 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1116 over sequences in Jalview
1119 <!-- JAL-2027-->Support for reverse-complement coding
1120 regions in ENA and EMBL
1123 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1124 for record retrieval via ENA rest API
1127 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1131 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1132 groovy script execution
1135 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1136 alignment window's Calculate menu
1139 <!-- JAL-1812 -->Allow groovy scripts that call
1140 Jalview.getAlignFrames() to run in headless mode
1143 <!-- JAL-2068 -->Support for creating new alignment
1144 calculation workers from groovy scripts
1147 <!-- JAL-1369 --->Store/restore reference sequence in
1151 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1152 associations are now saved/restored from project
1155 <!-- JAL-1993 -->Database selection dialog always shown
1156 before sequence fetcher is opened
1159 <!-- JAL-2183 -->Double click on an entry in Jalview's
1160 database chooser opens a sequence fetcher
1163 <!-- JAL-1563 -->Free-text search client for UniProt using
1164 the UniProt REST API
1167 <!-- JAL-2168 -->-nonews command line parameter to prevent
1168 the news reader opening
1171 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1172 querying stored in preferences
1175 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1179 <!-- JAL-1977-->Tooltips shown on database chooser
1182 <!-- JAL-391 -->Reverse complement function in calculate
1183 menu for nucleotide sequences
1186 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1187 and feature counts preserves alignment ordering (and
1188 debugged for complex feature sets).
1191 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1192 viewing structures with Jalview 2.10
1195 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1196 genome, transcript CCDS and gene ids via the Ensembl and
1197 Ensembl Genomes REST API
1200 <!-- JAL-2049 -->Protein sequence variant annotation
1201 computed for 'sequence_variant' annotation on CDS regions
1205 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1209 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1210 Ref Fetcher fails to match, or otherwise updates sequence
1211 data from external database records.
1214 <!-- JAL-2154 -->Revised Jalview Project format for
1215 efficient recovery of sequence coding and alignment
1216 annotation relationships.
1218 </ul> <!-- <em>Applet</em>
1229 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1233 <!-- JAL-2018-->Export features in Jalview format (again)
1234 includes graduated colourschemes
1237 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1238 working with big alignments and lots of hidden columns
1241 <!-- JAL-2053-->Hidden column markers not always rendered
1242 at right of alignment window
1245 <!-- JAL-2067 -->Tidied up links in help file table of
1249 <!-- JAL-2072 -->Feature based tree calculation not shown
1253 <!-- JAL-2075 -->Hidden columns ignored during feature
1254 based tree calculation
1257 <!-- JAL-2065 -->Alignment view stops updating when show
1258 unconserved enabled for group on alignment
1261 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1265 <!-- JAL-2146 -->Alignment column in status incorrectly
1266 shown as "Sequence position" when mousing over
1270 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1271 hidden columns present
1274 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1275 user created annotation added to alignment
1278 <!-- JAL-1841 -->RNA Structure consensus only computed for
1279 '()' base pair annotation
1282 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1283 in zero scores for all base pairs in RNA Structure
1287 <!-- JAL-2174-->Extend selection with columns containing
1291 <!-- JAL-2275 -->Pfam format writer puts extra space at
1292 beginning of sequence
1295 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1299 <!-- JAL-2238 -->Cannot create groups on an alignment from
1300 from a tree when t-coffee scores are shown
1303 <!-- JAL-1836,1967 -->Cannot import and view PDB
1304 structures with chains containing negative resnums (4q4h)
1307 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1311 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1312 to Clustal, PIR and PileUp output
1315 <!-- JAL-2008 -->Reordering sequence features that are
1316 not visible causes alignment window to repaint
1319 <!-- JAL-2006 -->Threshold sliders don't work in
1320 graduated colour and colour by annotation row for e-value
1321 scores associated with features and annotation rows
1324 <!-- JAL-1797 -->amino acid physicochemical conservation
1325 calculation should be case independent
1328 <!-- JAL-2173 -->Remove annotation also updates hidden
1332 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1333 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1334 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1337 <!-- JAL-2065 -->Null pointer exceptions and redraw
1338 problems when reference sequence defined and 'show
1339 non-conserved' enabled
1342 <!-- JAL-1306 -->Quality and Conservation are now shown on
1343 load even when Consensus calculation is disabled
1346 <!-- JAL-1932 -->Remove right on penultimate column of
1347 alignment does nothing
1350 <em>Application</em>
1353 <!-- JAL-1552-->URLs and links can't be imported by
1354 drag'n'drop on OSX when launched via webstart (note - not
1355 yet fixed for El Capitan)
1358 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1359 output when running on non-gb/us i18n platforms
1362 <!-- JAL-1944 -->Error thrown when exporting a view with
1363 hidden sequences as flat-file alignment
1366 <!-- JAL-2030-->InstallAnywhere distribution fails when
1370 <!-- JAL-2080-->Jalview very slow to launch via webstart
1371 (also hotfix for 2.9.0b2)
1374 <!-- JAL-2085 -->Cannot save project when view has a
1375 reference sequence defined
1378 <!-- JAL-1011 -->Columns are suddenly selected in other
1379 alignments and views when revealing hidden columns
1382 <!-- JAL-1989 -->Hide columns not mirrored in complement
1383 view in a cDNA/Protein splitframe
1386 <!-- JAL-1369 -->Cannot save/restore representative
1387 sequence from project when only one sequence is
1391 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1392 in Structure Chooser
1395 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1396 structure consensus didn't refresh annotation panel
1399 <!-- JAL-1962 -->View mapping in structure view shows
1400 mappings between sequence and all chains in a PDB file
1403 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1404 dialogs format columns correctly, don't display array
1405 data, sort columns according to type
1408 <!-- JAL-1975 -->Export complete shown after destination
1409 file chooser is cancelled during an image export
1412 <!-- JAL-2025 -->Error when querying PDB Service with
1413 sequence name containing special characters
1416 <!-- JAL-2024 -->Manual PDB structure querying should be
1420 <!-- JAL-2104 -->Large tooltips with broken HTML
1421 formatting don't wrap
1424 <!-- JAL-1128 -->Figures exported from wrapped view are
1425 truncated so L looks like I in consensus annotation
1428 <!-- JAL-2003 -->Export features should only export the
1429 currently displayed features for the current selection or
1433 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1434 after fetching cross-references, and restoring from
1438 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1439 followed in the structure viewer
1442 <!-- JAL-2163 -->Titles for individual alignments in
1443 splitframe not restored from project
1446 <!-- JAL-2145 -->missing autocalculated annotation at
1447 trailing end of protein alignment in transcript/product
1448 splitview when pad-gaps not enabled by default
1451 <!-- JAL-1797 -->amino acid physicochemical conservation
1455 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1456 article has been read (reopened issue due to
1457 internationalisation problems)
1460 <!-- JAL-1960 -->Only offer PDB structures in structure
1461 viewer based on sequence name, PDB and UniProt
1466 <!-- JAL-1976 -->No progress bar shown during export of
1470 <!-- JAL-2213 -->Structures not always superimposed after
1471 multiple structures are shown for one or more sequences.
1474 <!-- JAL-1370 -->Reference sequence characters should not
1475 be replaced with '.' when 'Show unconserved' format option
1479 <!-- JAL-1823 -->Cannot specify chain code when entering
1480 specific PDB id for sequence
1483 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1484 'Export hidden sequences' is enabled, but 'export hidden
1485 columns' is disabled.
1488 <!--JAL-2026-->Best Quality option in structure chooser
1489 selects lowest rather than highest resolution structures
1493 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1494 to sequence mapping in 'View Mappings' report
1497 <!-- JAL-2284 -->Unable to read old Jalview projects that
1498 contain non-XML data added after Jalvew wrote project.
1501 <!-- JAL-2118 -->Newly created annotation row reorders
1502 after clicking on it to create new annotation for a
1506 <!-- JAL-1980 -->Null Pointer Exception raised when
1507 pressing Add on an orphaned cut'n'paste window.
1509 <!-- may exclude, this is an external service stability issue JAL-1941
1510 -- > RNA 3D structure not added via DSSR service</li> -->
1515 <!-- JAL-2151 -->Incorrect columns are selected when
1516 hidden columns present before start of sequence
1519 <!-- JAL-1986 -->Missing dependencies on applet pages
1523 <!-- JAL-1947 -->Overview pixel size changes when
1524 sequences are hidden in applet
1527 <!-- JAL-1996 -->Updated instructions for applet
1528 deployment on examples pages.
1535 <td width="60" nowrap>
1536 <div align="center">
1537 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1538 <em>16/10/2015</em></strong>
1541 <td><em>General</em>
1543 <li>Time stamps for signed Jalview application and applet
1548 <em>Application</em>
1550 <li>Duplicate group consensus and conservation rows
1551 shown when tree is partitioned</li>
1552 <li>Erratic behaviour when tree partitions made with
1553 multiple cDNA/Protein split views</li>
1559 <td width="60" nowrap>
1560 <div align="center">
1561 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1562 <em>8/10/2015</em></strong>
1565 <td><em>General</em>
1567 <li>Updated Spanish translations of localized text for
1569 </ul> <em>Application</em>
1571 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1572 <li>Signed OSX InstallAnywhere installer<br></li>
1573 <li>Support for per-sequence based annotations in BioJSON</li>
1574 </ul> <em>Applet</em>
1576 <li>Split frame example added to applet examples page</li>
1577 </ul> <em>Build and Deployment</em>
1580 <!-- JAL-1888 -->New ant target for running Jalview's test
1588 <li>Mapping of cDNA to protein in split frames
1589 incorrect when sequence start > 1</li>
1590 <li>Broken images in filter column by annotation dialog
1592 <li>Feature colours not parsed from features file</li>
1593 <li>Exceptions and incomplete link URLs recovered when
1594 loading a features file containing HTML tags in feature
1598 <em>Application</em>
1600 <li>Annotations corrupted after BioJS export and
1602 <li>Incorrect sequence limits after Fetch DB References
1603 with 'trim retrieved sequences'</li>
1604 <li>Incorrect warning about deleting all data when
1605 deleting selected columns</li>
1606 <li>Patch to build system for shipping properly signed
1607 JNLP templates for webstart launch</li>
1608 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1609 unreleased structures for download or viewing</li>
1610 <li>Tab/space/return keystroke operation of EMBL-PDBe
1611 fetcher/viewer dialogs works correctly</li>
1612 <li>Disabled 'minimise' button on Jalview windows
1613 running on OSX to workaround redraw hang bug</li>
1614 <li>Split cDNA/Protein view position and geometry not
1615 recovered from jalview project</li>
1616 <li>Initial enabled/disabled state of annotation menu
1617 sorter 'show autocalculated first/last' corresponds to
1619 <li>Restoring of Clustal, RNA Helices and T-Coffee
1620 color schemes from BioJSON</li>
1624 <li>Reorder sequences mirrored in cDNA/Protein split
1626 <li>Applet with Jmol examples not loading correctly</li>
1632 <td><div align="center">
1633 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1635 <td><em>General</em>
1637 <li>Linked visualisation and analysis of DNA and Protein
1640 <li>Translated cDNA alignments shown as split protein
1641 and DNA alignment views</li>
1642 <li>Codon consensus annotation for linked protein and
1643 cDNA alignment views</li>
1644 <li>Link cDNA or Protein product sequences by loading
1645 them onto Protein or cDNA alignments</li>
1646 <li>Reconstruct linked cDNA alignment from aligned
1647 protein sequences</li>
1650 <li>Jmol integration updated to Jmol v14.2.14</li>
1651 <li>Import and export of Jalview alignment views as <a
1652 href="features/bioJsonFormat.html">BioJSON</a></li>
1653 <li>New alignment annotation file statements for
1654 reference sequences and marking hidden columns</li>
1655 <li>Reference sequence based alignment shading to
1656 highlight variation</li>
1657 <li>Select or hide columns according to alignment
1659 <li>Find option for locating sequences by description</li>
1660 <li>Conserved physicochemical properties shown in amino
1661 acid conservation row</li>
1662 <li>Alignments can be sorted by number of RNA helices</li>
1663 </ul> <em>Application</em>
1665 <li>New cDNA/Protein analysis capabilities
1667 <li>Get Cross-References should open a Split Frame
1668 view with cDNA/Protein</li>
1669 <li>Detect when nucleotide sequences and protein
1670 sequences are placed in the same alignment</li>
1671 <li>Split cDNA/Protein views are saved in Jalview
1676 <li>Use REST API to talk to Chimera</li>
1677 <li>Selected regions in Chimera are highlighted in linked
1678 Jalview windows</li>
1680 <li>VARNA RNA viewer updated to v3.93</li>
1681 <li>VARNA views are saved in Jalview Projects</li>
1682 <li>Pseudoknots displayed as Jalview RNA annotation can
1683 be shown in VARNA</li>
1685 <li>Make groups for selection uses marked columns as well
1686 as the active selected region</li>
1688 <li>Calculate UPGMA and NJ trees using sequence feature
1690 <li>New Export options
1692 <li>New Export Settings dialog to control hidden
1693 region export in flat file generation</li>
1695 <li>Export alignment views for display with the <a
1696 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1698 <li>Export scrollable SVG in HTML page</li>
1699 <li>Optional embedding of BioJSON data when exporting
1700 alignment figures to HTML</li>
1702 <li>3D structure retrieval and display
1704 <li>Free text and structured queries with the PDBe
1706 <li>PDBe Search API based discovery and selection of
1707 PDB structures for a sequence set</li>
1711 <li>JPred4 employed for protein secondary structure
1713 <li>Hide Insertions menu option to hide unaligned columns
1714 for one or a group of sequences</li>
1715 <li>Automatically hide insertions in alignments imported
1716 from the JPred4 web server</li>
1717 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1718 system on OSX<br />LGPL libraries courtesy of <a
1719 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1721 <li>changed 'View nucleotide structure' submenu to 'View
1722 VARNA 2D Structure'</li>
1723 <li>change "View protein structure" menu option to "3D
1726 </ul> <em>Applet</em>
1728 <li>New layout for applet example pages</li>
1729 <li>New parameters to enable SplitFrame view
1730 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1731 <li>New example demonstrating linked viewing of cDNA and
1732 Protein alignments</li>
1733 </ul> <em>Development and deployment</em>
1735 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1736 <li>Include installation type and git revision in build
1737 properties and console log output</li>
1738 <li>Jalview Github organisation, and new github site for
1739 storing BioJsMSA Templates</li>
1740 <li>Jalview's unit tests now managed with TestNG</li>
1743 <!-- <em>General</em>
1745 </ul> --> <!-- issues resolved --> <em>Application</em>
1747 <li>Escape should close any open find dialogs</li>
1748 <li>Typo in select-by-features status report</li>
1749 <li>Consensus RNA secondary secondary structure
1750 predictions are not highlighted in amber</li>
1751 <li>Missing gap character in v2.7 example file means
1752 alignment appears unaligned when pad-gaps is not enabled</li>
1753 <li>First switch to RNA Helices colouring doesn't colour
1754 associated structure views</li>
1755 <li>ID width preference option is greyed out when auto
1756 width checkbox not enabled</li>
1757 <li>Stopped a warning dialog from being shown when
1758 creating user defined colours</li>
1759 <li>'View Mapping' in structure viewer shows sequence
1760 mappings for just that viewer's sequences</li>
1761 <li>Workaround for superposing PDB files containing
1762 multiple models in Chimera</li>
1763 <li>Report sequence position in status bar when hovering
1764 over Jmol structure</li>
1765 <li>Cannot output gaps as '.' symbols with Selection ->
1766 output to text box</li>
1767 <li>Flat file exports of alignments with hidden columns
1768 have incorrect sequence start/end</li>
1769 <li>'Aligning' a second chain to a Chimera structure from
1771 <li>Colour schemes applied to structure viewers don't
1772 work for nucleotide</li>
1773 <li>Loading/cut'n'pasting an empty or invalid file leads
1774 to a grey/invisible alignment window</li>
1775 <li>Exported Jpred annotation from a sequence region
1776 imports to different position</li>
1777 <li>Space at beginning of sequence feature tooltips shown
1778 on some platforms</li>
1779 <li>Chimera viewer 'View | Show Chain' menu is not
1781 <li>'New View' fails with a Null Pointer Exception in
1782 console if Chimera has been opened</li>
1783 <li>Mouseover to Chimera not working</li>
1784 <li>Miscellaneous ENA XML feature qualifiers not
1786 <li>NPE in annotation renderer after 'Extract Scores'</li>
1787 <li>If two structures in one Chimera window, mouseover of
1788 either sequence shows on first structure</li>
1789 <li>'Show annotations' options should not make
1790 non-positional annotations visible</li>
1791 <li>Subsequence secondary structure annotation not shown
1792 in right place after 'view flanking regions'</li>
1793 <li>File Save As type unset when current file format is
1795 <li>Save as '.jar' option removed for saving Jalview
1797 <li>Colour by Sequence colouring in Chimera more
1799 <li>Cannot 'add reference annotation' for a sequence in
1800 several views on same alignment</li>
1801 <li>Cannot show linked products for EMBL / ENA records</li>
1802 <li>Jalview's tooltip wraps long texts containing no
1804 </ul> <em>Applet</em>
1806 <li>Jmol to JalviewLite mouseover/link not working</li>
1807 <li>JalviewLite can't import sequences with ID
1808 descriptions containing angle brackets</li>
1809 </ul> <em>General</em>
1811 <li>Cannot export and reimport RNA secondary structure
1812 via jalview annotation file</li>
1813 <li>Random helix colour palette for colour by annotation
1814 with RNA secondary structure</li>
1815 <li>Mouseover to cDNA from STOP residue in protein
1816 translation doesn't work.</li>
1817 <li>hints when using the select by annotation dialog box</li>
1818 <li>Jmol alignment incorrect if PDB file has alternate CA
1820 <li>FontChooser message dialog appears to hang after
1821 choosing 1pt font</li>
1822 <li>Peptide secondary structure incorrectly imported from
1823 annotation file when annotation display text includes 'e' or
1825 <li>Cannot set colour of new feature type whilst creating
1827 <li>cDNA translation alignment should not be sequence
1828 order dependent</li>
1829 <li>'Show unconserved' doesn't work for lower case
1831 <li>Nucleotide ambiguity codes involving R not recognised</li>
1832 </ul> <em>Deployment and Documentation</em>
1834 <li>Applet example pages appear different to the rest of
1835 www.jalview.org</li>
1836 </ul> <em>Application Known issues</em>
1838 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1839 <li>Misleading message appears after trying to delete
1841 <li>Jalview icon not shown in dock after InstallAnywhere
1842 version launches</li>
1843 <li>Fetching EMBL reference for an RNA sequence results
1844 fails with a sequence mismatch</li>
1845 <li>Corrupted or unreadable alignment display when
1846 scrolling alignment to right</li>
1847 <li>ArrayIndexOutOfBoundsException thrown when remove
1848 empty columns called on alignment with ragged gapped ends</li>
1849 <li>auto calculated alignment annotation rows do not get
1850 placed above or below non-autocalculated rows</li>
1851 <li>Jalview dekstop becomes sluggish at full screen in
1852 ultra-high resolution</li>
1853 <li>Cannot disable consensus calculation independently of
1854 quality and conservation</li>
1855 <li>Mouseover highlighting between cDNA and protein can
1856 become sluggish with more than one splitframe shown</li>
1857 </ul> <em>Applet Known Issues</em>
1859 <li>Core PDB parsing code requires Jmol</li>
1860 <li>Sequence canvas panel goes white when alignment
1861 window is being resized</li>
1867 <td><div align="center">
1868 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1870 <td><em>General</em>
1872 <li>Updated Java code signing certificate donated by
1874 <li>Features and annotation preserved when performing
1875 pairwise alignment</li>
1876 <li>RNA pseudoknot annotation can be
1877 imported/exported/displayed</li>
1878 <li>'colour by annotation' can colour by RNA and
1879 protein secondary structure</li>
1880 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1881 post-hoc with 2.9 release</em>)
1884 </ul> <em>Application</em>
1886 <li>Extract and display secondary structure for sequences
1887 with 3D structures</li>
1888 <li>Support for parsing RNAML</li>
1889 <li>Annotations menu for layout
1891 <li>sort sequence annotation rows by alignment</li>
1892 <li>place sequence annotation above/below alignment
1895 <li>Output in Stockholm format</li>
1896 <li>Internationalisation: improved Spanish (es)
1898 <li>Structure viewer preferences tab</li>
1899 <li>Disorder and Secondary Structure annotation tracks
1900 shared between alignments</li>
1901 <li>UCSF Chimera launch and linked highlighting from
1903 <li>Show/hide all sequence associated annotation rows for
1904 all or current selection</li>
1905 <li>disorder and secondary structure predictions
1906 available as dataset annotation</li>
1907 <li>Per-sequence rna helices colouring</li>
1910 <li>Sequence database accessions imported when fetching
1911 alignments from Rfam</li>
1912 <li>update VARNA version to 3.91</li>
1914 <li>New groovy scripts for exporting aligned positions,
1915 conservation values, and calculating sum of pairs scores.</li>
1916 <li>Command line argument to set default JABAWS server</li>
1917 <li>include installation type in build properties and
1918 console log output</li>
1919 <li>Updated Jalview project format to preserve dataset
1923 <!-- issues resolved --> <em>Application</em>
1925 <li>Distinguish alignment and sequence associated RNA
1926 structure in structure->view->VARNA</li>
1927 <li>Raise dialog box if user deletes all sequences in an
1929 <li>Pressing F1 results in documentation opening twice</li>
1930 <li>Sequence feature tooltip is wrapped</li>
1931 <li>Double click on sequence associated annotation
1932 selects only first column</li>
1933 <li>Redundancy removal doesn't result in unlinked
1934 leaves shown in tree</li>
1935 <li>Undos after several redundancy removals don't undo
1937 <li>Hide sequence doesn't hide associated annotation</li>
1938 <li>User defined colours dialog box too big to fit on
1939 screen and buttons not visible</li>
1940 <li>author list isn't updated if already written to
1941 Jalview properties</li>
1942 <li>Popup menu won't open after retrieving sequence
1944 <li>File open window for associate PDB doesn't open</li>
1945 <li>Left-then-right click on a sequence id opens a
1946 browser search window</li>
1947 <li>Cannot open sequence feature shading/sort popup menu
1948 in feature settings dialog</li>
1949 <li>better tooltip placement for some areas of Jalview
1951 <li>Allow addition of JABAWS Server which doesn't
1952 pass validation</li>
1953 <li>Web services parameters dialog box is too large to
1955 <li>Muscle nucleotide alignment preset obscured by
1957 <li>JABAWS preset submenus don't contain newly
1958 defined user preset</li>
1959 <li>MSA web services warns user if they were launched
1960 with invalid input</li>
1961 <li>Jalview cannot contact DAS Registy when running on
1964 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1965 'Superpose with' submenu not shown when new view
1969 </ul> <!-- <em>Applet</em>
1971 </ul> <em>General</em>
1973 </ul>--> <em>Deployment and Documentation</em>
1975 <li>2G and 1G options in launchApp have no effect on
1976 memory allocation</li>
1977 <li>launchApp service doesn't automatically open
1978 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1980 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1981 InstallAnywhere reports cannot find valid JVM when Java
1982 1.7_055 is available
1984 </ul> <em>Application Known issues</em>
1987 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1988 corrupted or unreadable alignment display when scrolling
1992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1993 retrieval fails but progress bar continues for DAS retrieval
1994 with large number of ID
1997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1998 flatfile output of visible region has incorrect sequence
2002 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2003 rna structure consensus doesn't update when secondary
2004 structure tracks are rearranged
2007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2008 invalid rna structure positional highlighting does not
2009 highlight position of invalid base pairs
2012 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2013 out of memory errors are not raised when saving Jalview
2014 project from alignment window file menu
2017 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2018 Switching to RNA Helices colouring doesn't propagate to
2022 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2023 colour by RNA Helices not enabled when user created
2024 annotation added to alignment
2027 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2028 Jalview icon not shown on dock in Mountain Lion/Webstart
2030 </ul> <em>Applet Known Issues</em>
2033 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2034 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2037 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2038 Jalview and Jmol example not compatible with IE9
2041 <li>Sort by annotation score doesn't reverse order
2047 <td><div align="center">
2048 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2051 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2054 <li>Internationalisation of user interface (usually
2055 called i18n support) and translation for Spanish locale</li>
2056 <li>Define/Undefine group on current selection with
2057 Ctrl-G/Shift Ctrl-G</li>
2058 <li>Improved group creation/removal options in
2059 alignment/sequence Popup menu</li>
2060 <li>Sensible precision for symbol distribution
2061 percentages shown in logo tooltip.</li>
2062 <li>Annotation panel height set according to amount of
2063 annotation when alignment first opened</li>
2064 </ul> <em>Application</em>
2066 <li>Interactive consensus RNA secondary structure
2067 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2068 <li>Select columns containing particular features from
2069 Feature Settings dialog</li>
2070 <li>View all 'representative' PDB structures for selected
2072 <li>Update Jalview project format:
2074 <li>New file extension for Jalview projects '.jvp'</li>
2075 <li>Preserve sequence and annotation dataset (to
2076 store secondary structure annotation,etc)</li>
2077 <li>Per group and alignment annotation and RNA helix
2081 <li>New similarity measures for PCA and Tree calculation
2083 <li>Experimental support for retrieval and viewing of
2084 flanking regions for an alignment</li>
2088 <!-- issues resolved --> <em>Application</em>
2090 <li>logo keeps spinning and status remains at queued or
2091 running after job is cancelled</li>
2092 <li>cannot export features from alignments imported from
2093 Jalview/VAMSAS projects</li>
2094 <li>Buggy slider for web service parameters that take
2096 <li>Newly created RNA secondary structure line doesn't
2097 have 'display all symbols' flag set</li>
2098 <li>T-COFFEE alignment score shading scheme and other
2099 annotation shading not saved in Jalview project</li>
2100 <li>Local file cannot be loaded in freshly downloaded
2102 <li>Jalview icon not shown on dock in Mountain
2104 <li>Load file from desktop file browser fails</li>
2105 <li>Occasional NPE thrown when calculating large trees</li>
2106 <li>Cannot reorder or slide sequences after dragging an
2107 alignment onto desktop</li>
2108 <li>Colour by annotation dialog throws NPE after using
2109 'extract scores' function</li>
2110 <li>Loading/cut'n'pasting an empty file leads to a grey
2111 alignment window</li>
2112 <li>Disorder thresholds rendered incorrectly after
2113 performing IUPred disorder prediction</li>
2114 <li>Multiple group annotated consensus rows shown when
2115 changing 'normalise logo' display setting</li>
2116 <li>Find shows blank dialog after 'finished searching' if
2117 nothing matches query</li>
2118 <li>Null Pointer Exceptions raised when sorting by
2119 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2121 <li>Errors in Jmol console when structures in alignment
2122 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2124 <li>Not all working JABAWS services are shown in
2126 <li>JAVAWS version of Jalview fails to launch with
2127 'invalid literal/length code'</li>
2128 <li>Annotation/RNA Helix colourschemes cannot be applied
2129 to alignment with groups (actually fixed in 2.8.0b1)</li>
2130 <li>RNA Helices and T-Coffee Scores available as default
2133 </ul> <em>Applet</em>
2135 <li>Remove group option is shown even when selection is
2137 <li>Apply to all groups ticked but colourscheme changes
2138 don't affect groups</li>
2139 <li>Documented RNA Helices and T-Coffee Scores as valid
2140 colourscheme name</li>
2141 <li>Annotation labels drawn on sequence IDs when
2142 Annotation panel is not displayed</li>
2143 <li>Increased font size for dropdown menus on OSX and
2144 embedded windows</li>
2145 </ul> <em>Other</em>
2147 <li>Consensus sequence for alignments/groups with a
2148 single sequence were not calculated</li>
2149 <li>annotation files that contain only groups imported as
2150 annotation and junk sequences</li>
2151 <li>Fasta files with sequences containing '*' incorrectly
2152 recognised as PFAM or BLC</li>
2153 <li>conservation/PID slider apply all groups option
2154 doesn't affect background (2.8.0b1)
2156 <li>redundancy highlighting is erratic at 0% and 100%</li>
2157 <li>Remove gapped columns fails for sequences with ragged
2159 <li>AMSA annotation row with leading spaces is not
2160 registered correctly on import</li>
2161 <li>Jalview crashes when selecting PCA analysis for
2162 certain alignments</li>
2163 <li>Opening the colour by annotation dialog for an
2164 existing annotation based 'use original colours'
2165 colourscheme loses original colours setting</li>
2170 <td><div align="center">
2171 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2172 <em>30/1/2014</em></strong>
2176 <li>Trusted certificates for JalviewLite applet and
2177 Jalview Desktop application<br />Certificate was donated by
2178 <a href="https://www.certum.eu">Certum</a> to the Jalview
2179 open source project).
2181 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2182 <li>Output in Stockholm format</li>
2183 <li>Allow import of data from gzipped files</li>
2184 <li>Export/import group and sequence associated line
2185 graph thresholds</li>
2186 <li>Nucleotide substitution matrix that supports RNA and
2187 ambiguity codes</li>
2188 <li>Allow disorder predictions to be made on the current
2189 selection (or visible selection) in the same way that JPred
2191 <li>Groovy scripting for headless Jalview operation</li>
2192 </ul> <em>Other improvements</em>
2194 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2195 <li>COMBINE statement uses current SEQUENCE_REF and
2196 GROUP_REF scope to group annotation rows</li>
2197 <li>Support '' style escaping of quotes in Newick
2199 <li>Group options for JABAWS service by command line name</li>
2200 <li>Empty tooltip shown for JABA service options with a
2201 link but no description</li>
2202 <li>Select primary source when selecting authority in
2203 database fetcher GUI</li>
2204 <li>Add .mfa to FASTA file extensions recognised by
2206 <li>Annotation label tooltip text wrap</li>
2211 <li>Slow scrolling when lots of annotation rows are
2213 <li>Lots of NPE (and slowness) after creating RNA
2214 secondary structure annotation line</li>
2215 <li>Sequence database accessions not imported when
2216 fetching alignments from Rfam</li>
2217 <li>Incorrect SHMR submission for sequences with
2219 <li>View all structures does not always superpose
2221 <li>Option widgets in service parameters not updated to
2222 reflect user or preset settings</li>
2223 <li>Null pointer exceptions for some services without
2224 presets or adjustable parameters</li>
2225 <li>Discover PDB IDs entry in structure menu doesn't
2226 discover PDB xRefs</li>
2227 <li>Exception encountered while trying to retrieve
2228 features with DAS</li>
2229 <li>Lowest value in annotation row isn't coloured
2230 when colour by annotation (per sequence) is coloured</li>
2231 <li>Keyboard mode P jumps to start of gapped region when
2232 residue follows a gap</li>
2233 <li>Jalview appears to hang importing an alignment with
2234 Wrap as default or after enabling Wrap</li>
2235 <li>'Right click to add annotations' message
2236 shown in wrap mode when no annotations present</li>
2237 <li>Disorder predictions fail with NPE if no automatic
2238 annotation already exists on alignment</li>
2239 <li>oninit javascript function should be called after
2240 initialisation completes</li>
2241 <li>Remove redundancy after disorder prediction corrupts
2242 alignment window display</li>
2243 <li>Example annotation file in documentation is invalid</li>
2244 <li>Grouped line graph annotation rows are not exported
2245 to annotation file</li>
2246 <li>Multi-harmony analysis cannot be run when only two
2248 <li>Cannot create multiple groups of line graphs with
2249 several 'combine' statements in annotation file</li>
2250 <li>Pressing return several times causes Number Format
2251 exceptions in keyboard mode</li>
2252 <li>Multi-harmony (SHMMR) method doesn't submit
2253 correct partitions for input data</li>
2254 <li>Translation from DNA to Amino Acids fails</li>
2255 <li>Jalview fail to load newick tree with quoted label</li>
2256 <li>--headless flag isn't understood</li>
2257 <li>ClassCastException when generating EPS in headless
2259 <li>Adjusting sequence-associated shading threshold only
2260 changes one row's threshold</li>
2261 <li>Preferences and Feature settings panel panel
2262 doesn't open</li>
2263 <li>hide consensus histogram also hides conservation and
2264 quality histograms</li>
2269 <td><div align="center">
2270 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2272 <td><em>Application</em>
2274 <li>Support for JABAWS 2.0 Services (AACon alignment
2275 conservation, protein disorder and Clustal Omega)</li>
2276 <li>JABAWS server status indicator in Web Services
2278 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2279 in Jalview alignment window</li>
2280 <li>Updated Jalview build and deploy framework for OSX
2281 mountain lion, windows 7, and 8</li>
2282 <li>Nucleotide substitution matrix for PCA that supports
2283 RNA and ambiguity codes</li>
2285 <li>Improved sequence database retrieval GUI</li>
2286 <li>Support fetching and database reference look up
2287 against multiple DAS sources (Fetch all from in 'fetch db
2289 <li>Jalview project improvements
2291 <li>Store and retrieve the 'belowAlignment'
2292 flag for annotation</li>
2293 <li>calcId attribute to group annotation rows on the
2295 <li>Store AACon calculation settings for a view in
2296 Jalview project</li>
2300 <li>horizontal scrolling gesture support</li>
2301 <li>Visual progress indicator when PCA calculation is
2303 <li>Simpler JABA web services menus</li>
2304 <li>visual indication that web service results are still
2305 being retrieved from server</li>
2306 <li>Serialise the dialogs that are shown when Jalview
2307 starts up for first time</li>
2308 <li>Jalview user agent string for interacting with HTTP
2310 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2312 <li>Examples directory and Groovy library included in
2313 InstallAnywhere distribution</li>
2314 </ul> <em>Applet</em>
2316 <li>RNA alignment and secondary structure annotation
2317 visualization applet example</li>
2318 </ul> <em>General</em>
2320 <li>Normalise option for consensus sequence logo</li>
2321 <li>Reset button in PCA window to return dimensions to
2323 <li>Allow seqspace or Jalview variant of alignment PCA
2325 <li>PCA with either nucleic acid and protein substitution
2327 <li>Allow windows containing HTML reports to be exported
2329 <li>Interactive display and editing of RNA secondary
2330 structure contacts</li>
2331 <li>RNA Helix Alignment Colouring</li>
2332 <li>RNA base pair logo consensus</li>
2333 <li>Parse sequence associated secondary structure
2334 information in Stockholm files</li>
2335 <li>HTML Export database accessions and annotation
2336 information presented in tooltip for sequences</li>
2337 <li>Import secondary structure from LOCARNA clustalw
2338 style RNA alignment files</li>
2339 <li>import and visualise T-COFFEE quality scores for an
2341 <li>'colour by annotation' per sequence option to
2342 shade each sequence according to its associated alignment
2344 <li>New Jalview Logo</li>
2345 </ul> <em>Documentation and Development</em>
2347 <li>documentation for score matrices used in Jalview</li>
2348 <li>New Website!</li>
2350 <td><em>Application</em>
2352 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2353 wsdbfetch REST service</li>
2354 <li>Stop windows being moved outside desktop on OSX</li>
2355 <li>Filetype associations not installed for webstart
2357 <li>Jalview does not always retrieve progress of a JABAWS
2358 job execution in full once it is complete</li>
2359 <li>revise SHMR RSBS definition to ensure alignment is
2360 uploaded via ali_file parameter</li>
2361 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2362 <li>View all structures superposed fails with exception</li>
2363 <li>Jnet job queues forever if a very short sequence is
2364 submitted for prediction</li>
2365 <li>Cut and paste menu not opened when mouse clicked on
2367 <li>Putting fractional value into integer text box in
2368 alignment parameter dialog causes Jalview to hang</li>
2369 <li>Structure view highlighting doesn't work on
2371 <li>View all structures fails with exception shown in
2373 <li>Characters in filename associated with PDBEntry not
2374 escaped in a platform independent way</li>
2375 <li>Jalview desktop fails to launch with exception when
2377 <li>Tree calculation reports 'you must have 2 or more
2378 sequences selected' when selection is empty</li>
2379 <li>Jalview desktop fails to launch with jar signature
2380 failure when java web start temporary file caching is
2382 <li>DAS Sequence retrieval with range qualification
2383 results in sequence xref which includes range qualification</li>
2384 <li>Errors during processing of command line arguments
2385 cause progress bar (JAL-898) to be removed</li>
2386 <li>Replace comma for semi-colon option not disabled for
2387 DAS sources in sequence fetcher</li>
2388 <li>Cannot close news reader when JABAWS server warning
2389 dialog is shown</li>
2390 <li>Option widgets not updated to reflect user settings</li>
2391 <li>Edited sequence not submitted to web service</li>
2392 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2393 <li>InstallAnywhere installer doesn't unpack and run
2394 on OSX Mountain Lion</li>
2395 <li>Annotation panel not given a scroll bar when
2396 sequences with alignment annotation are pasted into the
2398 <li>Sequence associated annotation rows not associated
2399 when loaded from Jalview project</li>
2400 <li>Browser launch fails with NPE on java 1.7</li>
2401 <li>JABAWS alignment marked as finished when job was
2402 cancelled or job failed due to invalid input</li>
2403 <li>NPE with v2.7 example when clicking on Tree
2404 associated with all views</li>
2405 <li>Exceptions when copy/paste sequences with grouped
2406 annotation rows to new window</li>
2407 </ul> <em>Applet</em>
2409 <li>Sequence features are momentarily displayed before
2410 they are hidden using hidefeaturegroups applet parameter</li>
2411 <li>loading features via javascript API automatically
2412 enables feature display</li>
2413 <li>scrollToColumnIn javascript API method doesn't
2415 </ul> <em>General</em>
2417 <li>Redundancy removal fails for rna alignment</li>
2418 <li>PCA calculation fails when sequence has been selected
2419 and then deselected</li>
2420 <li>PCA window shows grey box when first opened on OSX</li>
2421 <li>Letters coloured pink in sequence logo when alignment
2422 coloured with clustalx</li>
2423 <li>Choosing fonts without letter symbols defined causes
2424 exceptions and redraw errors</li>
2425 <li>Initial PCA plot view is not same as manually
2426 reconfigured view</li>
2427 <li>Grouped annotation graph label has incorrect line
2429 <li>Grouped annotation graph label display is corrupted
2430 for lots of labels</li>
2435 <div align="center">
2436 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2439 <td><em>Application</em>
2441 <li>Jalview Desktop News Reader</li>
2442 <li>Tweaked default layout of web services menu</li>
2443 <li>View/alignment association menu to enable user to
2444 easily specify which alignment a multi-structure view takes
2445 its colours/correspondences from</li>
2446 <li>Allow properties file location to be specified as URL</li>
2447 <li>Extend Jalview project to preserve associations
2448 between many alignment views and a single Jmol display</li>
2449 <li>Store annotation row height in Jalview project file</li>
2450 <li>Annotation row column label formatting attributes
2451 stored in project file</li>
2452 <li>Annotation row order for auto-calculated annotation
2453 rows preserved in Jalview project file</li>
2454 <li>Visual progress indication when Jalview state is
2455 saved using Desktop window menu</li>
2456 <li>Visual indication that command line arguments are
2457 still being processed</li>
2458 <li>Groovy script execution from URL</li>
2459 <li>Colour by annotation default min and max colours in
2461 <li>Automatically associate PDB files dragged onto an
2462 alignment with sequences that have high similarity and
2464 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2465 <li>'view structures' option to open many
2466 structures in same window</li>
2467 <li>Sort associated views menu option for tree panel</li>
2468 <li>Group all JABA and non-JABA services for a particular
2469 analysis function in its own submenu</li>
2470 </ul> <em>Applet</em>
2472 <li>Userdefined and autogenerated annotation rows for
2474 <li>Adjustment of alignment annotation pane height</li>
2475 <li>Annotation scrollbar for annotation panel</li>
2476 <li>Drag to reorder annotation rows in annotation panel</li>
2477 <li>'automaticScrolling' parameter</li>
2478 <li>Allow sequences with partial ID string matches to be
2479 annotated from GFF/Jalview features files</li>
2480 <li>Sequence logo annotation row in applet</li>
2481 <li>Absolute paths relative to host server in applet
2482 parameters are treated as such</li>
2483 <li>New in the JalviewLite javascript API:
2485 <li>JalviewLite.js javascript library</li>
2486 <li>Javascript callbacks for
2488 <li>Applet initialisation</li>
2489 <li>Sequence/alignment mouse-overs and selections</li>
2492 <li>scrollTo row and column alignment scrolling
2494 <li>Select sequence/alignment regions from javascript</li>
2495 <li>javascript structure viewer harness to pass
2496 messages between Jmol and Jalview when running as
2497 distinct applets</li>
2498 <li>sortBy method</li>
2499 <li>Set of applet and application examples shipped
2500 with documentation</li>
2501 <li>New example to demonstrate JalviewLite and Jmol
2502 javascript message exchange</li>
2504 </ul> <em>General</em>
2506 <li>Enable Jmol displays to be associated with multiple
2507 multiple alignments</li>
2508 <li>Option to automatically sort alignment with new tree</li>
2509 <li>User configurable link to enable redirects to a
2510 www.Jalview.org mirror</li>
2511 <li>Jmol colours option for Jmol displays</li>
2512 <li>Configurable newline string when writing alignment
2513 and other flat files</li>
2514 <li>Allow alignment annotation description lines to
2515 contain html tags</li>
2516 </ul> <em>Documentation and Development</em>
2518 <li>Add groovy test harness for bulk load testing to
2520 <li>Groovy script to load and align a set of sequences
2521 using a web service before displaying the result in the
2522 Jalview desktop</li>
2523 <li>Restructured javascript and applet api documentation</li>
2524 <li>Ant target to publish example html files with applet
2526 <li>Netbeans project for building Jalview from source</li>
2527 <li>ant task to create online javadoc for Jalview source</li>
2529 <td><em>Application</em>
2531 <li>User defined colourscheme throws exception when
2532 current built in colourscheme is saved as new scheme</li>
2533 <li>AlignFrame->Save in application pops up save
2534 dialog for valid filename/format</li>
2535 <li>Cannot view associated structure for UniProt sequence</li>
2536 <li>PDB file association breaks for UniProt sequence
2538 <li>Associate PDB from file dialog does not tell you
2539 which sequence is to be associated with the file</li>
2540 <li>Find All raises null pointer exception when query
2541 only matches sequence IDs</li>
2542 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2543 <li>Jalview project with Jmol views created with Jalview
2544 2.4 cannot be loaded</li>
2545 <li>Filetype associations not installed for webstart
2547 <li>Two or more chains in a single PDB file associated
2548 with sequences in different alignments do not get coloured
2549 by their associated sequence</li>
2550 <li>Visibility status of autocalculated annotation row
2551 not preserved when project is loaded</li>
2552 <li>Annotation row height and visibility attributes not
2553 stored in Jalview project</li>
2554 <li>Tree bootstraps are not preserved when saved as a
2555 Jalview project</li>
2556 <li>Envision2 workflow tooltips are corrupted</li>
2557 <li>Enabling show group conservation also enables colour
2558 by conservation</li>
2559 <li>Duplicate group associated conservation or consensus
2560 created on new view</li>
2561 <li>Annotation scrollbar not displayed after 'show
2562 all hidden annotation rows' option selected</li>
2563 <li>Alignment quality not updated after alignment
2564 annotation row is hidden then shown</li>
2565 <li>Preserve colouring of structures coloured by
2566 sequences in pre Jalview 2.7 projects</li>
2567 <li>Web service job parameter dialog is not laid out
2569 <li>Web services menu not refreshed after 'reset
2570 services' button is pressed in preferences</li>
2571 <li>Annotation off by one in Jalview v2_3 example project</li>
2572 <li>Structures imported from file and saved in project
2573 get name like jalview_pdb1234.txt when reloaded</li>
2574 <li>Jalview does not always retrieve progress of a JABAWS
2575 job execution in full once it is complete</li>
2576 </ul> <em>Applet</em>
2578 <li>Alignment height set incorrectly when lots of
2579 annotation rows are displayed</li>
2580 <li>Relative URLs in feature HTML text not resolved to
2582 <li>View follows highlighting does not work for positions
2584 <li><= shown as = in tooltip</li>
2585 <li>Export features raises exception when no features
2587 <li>Separator string used for serialising lists of IDs
2588 for javascript api is modified when separator string
2589 provided as parameter</li>
2590 <li>Null pointer exception when selecting tree leaves for
2591 alignment with no existing selection</li>
2592 <li>Relative URLs for datasources assumed to be relative
2593 to applet's codebase</li>
2594 <li>Status bar not updated after finished searching and
2595 search wraps around to first result</li>
2596 <li>StructureSelectionManager instance shared between
2597 several Jalview applets causes race conditions and memory
2599 <li>Hover tooltip and mouseover of position on structure
2600 not sent from Jmol in applet</li>
2601 <li>Certain sequences of javascript method calls to
2602 applet API fatally hang browser</li>
2603 </ul> <em>General</em>
2605 <li>View follows structure mouseover scrolls beyond
2606 position with wrapped view and hidden regions</li>
2607 <li>Find sequence position moves to wrong residue
2608 with/without hidden columns</li>
2609 <li>Sequence length given in alignment properties window
2611 <li>InvalidNumberFormat exceptions thrown when trying to
2612 import PDB like structure files</li>
2613 <li>Positional search results are only highlighted
2614 between user-supplied sequence start/end bounds</li>
2615 <li>End attribute of sequence is not validated</li>
2616 <li>Find dialog only finds first sequence containing a
2617 given sequence position</li>
2618 <li>Sequence numbering not preserved in MSF alignment
2620 <li>Jalview PDB file reader does not extract sequence
2621 from nucleotide chains correctly</li>
2622 <li>Structure colours not updated when tree partition
2623 changed in alignment</li>
2624 <li>Sequence associated secondary structure not correctly
2625 parsed in interleaved stockholm</li>
2626 <li>Colour by annotation dialog does not restore current
2628 <li>Hiding (nearly) all sequences doesn't work
2630 <li>Sequences containing lowercase letters are not
2631 properly associated with their pdb files</li>
2632 </ul> <em>Documentation and Development</em>
2634 <li>schemas/JalviewWsParamSet.xsd corrupted by
2635 ApplyCopyright tool</li>
2640 <div align="center">
2641 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2644 <td><em>Application</em>
2646 <li>New warning dialog when the Jalview Desktop cannot
2647 contact web services</li>
2648 <li>JABA service parameters for a preset are shown in
2649 service job window</li>
2650 <li>JABA Service menu entries reworded</li>
2654 <li>Modeller PIR IO broken - cannot correctly import a
2655 pir file emitted by Jalview</li>
2656 <li>Existing feature settings transferred to new
2657 alignment view created from cut'n'paste</li>
2658 <li>Improved test for mixed amino/nucleotide chains when
2659 parsing PDB files</li>
2660 <li>Consensus and conservation annotation rows
2661 occasionally become blank for all new windows</li>
2662 <li>Exception raised when right clicking above sequences
2663 in wrapped view mode</li>
2664 </ul> <em>Application</em>
2666 <li>multiple multiply aligned structure views cause cpu
2667 usage to hit 100% and computer to hang</li>
2668 <li>Web Service parameter layout breaks for long user
2669 parameter names</li>
2670 <li>Jaba service discovery hangs desktop if Jaba server
2677 <div align="center">
2678 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2681 <td><em>Application</em>
2683 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2684 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2687 <li>Web Services preference tab</li>
2688 <li>Analysis parameters dialog box and user defined
2690 <li>Improved speed and layout of Envision2 service menu</li>
2691 <li>Superpose structures using associated sequence
2693 <li>Export coordinates and projection as CSV from PCA
2695 </ul> <em>Applet</em>
2697 <li>enable javascript: execution by the applet via the
2698 link out mechanism</li>
2699 </ul> <em>Other</em>
2701 <li>Updated the Jmol Jalview interface to work with Jmol
2703 <li>The Jalview Desktop and JalviewLite applet now
2704 require Java 1.5</li>
2705 <li>Allow Jalview feature colour specification for GFF
2706 sequence annotation files</li>
2707 <li>New 'colour by label' keword in Jalview feature file
2708 type colour specification</li>
2709 <li>New Jalview Desktop Groovy API method that allows a
2710 script to check if it being run in an interactive session or
2711 in a batch operation from the Jalview command line</li>
2715 <li>clustalx colourscheme colours Ds preferentially when
2716 both D+E are present in over 50% of the column</li>
2717 </ul> <em>Application</em>
2719 <li>typo in AlignmentFrame->View->Hide->all but
2720 selected Regions menu item</li>
2721 <li>sequence fetcher replaces ',' for ';' when the ',' is
2722 part of a valid accession ID</li>
2723 <li>fatal OOM if object retrieved by sequence fetcher
2724 runs out of memory</li>
2725 <li>unhandled Out of Memory Error when viewing pca
2726 analysis results</li>
2727 <li>InstallAnywhere builds fail to launch on OS X java
2728 10.5 update 4 (due to apple Java 1.6 update)</li>
2729 <li>Installanywhere Jalview silently fails to launch</li>
2730 </ul> <em>Applet</em>
2732 <li>Jalview.getFeatureGroups() raises an
2733 ArrayIndexOutOfBoundsException if no feature groups are
2740 <div align="center">
2741 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2747 <li>Alignment prettyprinter doesn't cope with long
2749 <li>clustalx colourscheme colours Ds preferentially when
2750 both D+E are present in over 50% of the column</li>
2751 <li>nucleic acid structures retrieved from PDB do not
2752 import correctly</li>
2753 <li>More columns get selected than were clicked on when a
2754 number of columns are hidden</li>
2755 <li>annotation label popup menu not providing correct
2756 add/hide/show options when rows are hidden or none are
2758 <li>Stockholm format shown in list of readable formats,
2759 and parser copes better with alignments from RFAM.</li>
2760 <li>CSV output of consensus only includes the percentage
2761 of all symbols if sequence logo display is enabled</li>
2763 </ul> <em>Applet</em>
2765 <li>annotation panel disappears when annotation is
2767 </ul> <em>Application</em>
2769 <li>Alignment view not redrawn properly when new
2770 alignment opened where annotation panel is visible but no
2771 annotations are present on alignment</li>
2772 <li>pasted region containing hidden columns is
2773 incorrectly displayed in new alignment window</li>
2774 <li>Jalview slow to complete operations when stdout is
2775 flooded (fix is to close the Jalview console)</li>
2776 <li>typo in AlignmentFrame->View->Hide->all but
2777 selected Rregions menu item.</li>
2778 <li>inconsistent group submenu and Format submenu entry
2779 'Un' or 'Non'conserved</li>
2780 <li>Sequence feature settings are being shared by
2781 multiple distinct alignments</li>
2782 <li>group annotation not recreated when tree partition is
2784 <li>double click on group annotation to select sequences
2785 does not propagate to associated trees</li>
2786 <li>Mac OSX specific issues:
2788 <li>exception raised when mouse clicked on desktop
2789 window background</li>
2790 <li>Desktop menu placed on menu bar and application
2791 name set correctly</li>
2792 <li>sequence feature settings not wide enough for the
2793 save feature colourscheme button</li>
2802 <div align="center">
2803 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2806 <td><em>New Capabilities</em>
2808 <li>URL links generated from description line for
2809 regular-expression based URL links (applet and application)
2811 <li>Non-positional feature URL links are shown in link
2813 <li>Linked viewing of nucleic acid sequences and
2815 <li>Automatic Scrolling option in View menu to display
2816 the currently highlighted region of an alignment.</li>
2817 <li>Order an alignment by sequence length, or using the
2818 average score or total feature count for each sequence.</li>
2819 <li>Shading features by score or associated description</li>
2820 <li>Subdivide alignment and groups based on identity of
2821 selected subsequence (Make Groups from Selection).</li>
2822 <li>New hide/show options including Shift+Control+H to
2823 hide everything but the currently selected region.</li>
2824 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2825 </ul> <em>Application</em>
2827 <li>Fetch DB References capabilities and UI expanded to
2828 support retrieval from DAS sequence sources</li>
2829 <li>Local DAS Sequence sources can be added via the
2830 command line or via the Add local source dialog box.</li>
2831 <li>DAS Dbref and DbxRef feature types are parsed as
2832 database references and protein_name is parsed as
2833 description line (BioSapiens terms).</li>
2834 <li>Enable or disable non-positional feature and database
2835 references in sequence ID tooltip from View menu in
2837 <!-- <li>New hidden columns and rows and representatives capabilities
2838 in annotations file (in progress - not yet fully implemented)</li> -->
2839 <li>Group-associated consensus, sequence logos and
2840 conservation plots</li>
2841 <li>Symbol distributions for each column can be exported
2842 and visualized as sequence logos</li>
2843 <li>Optionally scale multi-character column labels to fit
2844 within each column of annotation row<!-- todo for applet -->
2846 <li>Optional automatic sort of associated alignment view
2847 when a new tree is opened.</li>
2848 <li>Jalview Java Console</li>
2849 <li>Better placement of desktop window when moving
2850 between different screens.</li>
2851 <li>New preference items for sequence ID tooltip and
2852 consensus annotation</li>
2853 <li>Client to submit sequences and IDs to Envision2
2855 <li><em>Vamsas Capabilities</em>
2857 <li>Improved VAMSAS synchronization (Jalview archive
2858 used to preserve views, structures, and tree display
2860 <li>Import of vamsas documents from disk or URL via
2862 <li>Sharing of selected regions between views and
2863 with other VAMSAS applications (Experimental feature!)</li>
2864 <li>Updated API to VAMSAS version 0.2</li>
2866 </ul> <em>Applet</em>
2868 <li>Middle button resizes annotation row height</li>
2871 <li>sortByTree (true/false) - automatically sort the
2872 associated alignment view by the tree when a new tree is
2874 <li>showTreeBootstraps (true/false) - show or hide
2875 branch bootstraps (default is to show them if available)</li>
2876 <li>showTreeDistances (true/false) - show or hide
2877 branch lengths (default is to show them if available)</li>
2878 <li>showUnlinkedTreeNodes (true/false) - indicate if
2879 unassociated nodes should be highlighted in the tree
2881 <li>heightScale and widthScale (1.0 or more) -
2882 increase the height or width of a cell in the alignment
2883 grid relative to the current font size.</li>
2886 <li>Non-positional features displayed in sequence ID
2888 </ul> <em>Other</em>
2890 <li>Features format: graduated colour definitions and
2891 specification of feature scores</li>
2892 <li>Alignment Annotations format: new keywords for group
2893 associated annotation (GROUP_REF) and annotation row display
2894 properties (ROW_PROPERTIES)</li>
2895 <li>XML formats extended to support graduated feature
2896 colourschemes, group associated annotation, and profile
2897 visualization settings.</li></td>
2900 <li>Source field in GFF files parsed as feature source
2901 rather than description</li>
2902 <li>Non-positional features are now included in sequence
2903 feature and gff files (controlled via non-positional feature
2904 visibility in tooltip).</li>
2905 <li>URL links generated for all feature links (bugfix)</li>
2906 <li>Added URL embedding instructions to features file
2908 <li>Codons containing ambiguous nucleotides translated as
2909 'X' in peptide product</li>
2910 <li>Match case switch in find dialog box works for both
2911 sequence ID and sequence string and query strings do not
2912 have to be in upper case to match case-insensitively.</li>
2913 <li>AMSA files only contain first column of
2914 multi-character column annotation labels</li>
2915 <li>Jalview Annotation File generation/parsing consistent
2916 with documentation (e.g. Stockholm annotation can be
2917 exported and re-imported)</li>
2918 <li>PDB files without embedded PDB IDs given a friendly
2920 <li>Find incrementally searches ID string matches as well
2921 as subsequence matches, and correctly reports total number
2925 <li>Better handling of exceptions during sequence
2927 <li>Dasobert generated non-positional feature URL
2928 link text excludes the start_end suffix</li>
2929 <li>DAS feature and source retrieval buttons disabled
2930 when fetch or registry operations in progress.</li>
2931 <li>PDB files retrieved from URLs are cached properly</li>
2932 <li>Sequence description lines properly shared via
2934 <li>Sequence fetcher fetches multiple records for all
2936 <li>Ensured that command line das feature retrieval
2937 completes before alignment figures are generated.</li>
2938 <li>Reduced time taken when opening file browser for
2940 <li>isAligned check prior to calculating tree, PCA or
2941 submitting an MSA to JNet now excludes hidden sequences.</li>
2942 <li>User defined group colours properly recovered
2943 from Jalview projects.</li>
2952 <div align="center">
2953 <strong>2.4.0.b2</strong><br> 28/10/2009
2958 <li>Experimental support for google analytics usage
2960 <li>Jalview privacy settings (user preferences and docs).</li>
2965 <li>Race condition in applet preventing startup in
2967 <li>Exception when feature created from selection beyond
2968 length of sequence.</li>
2969 <li>Allow synthetic PDB files to be imported gracefully</li>
2970 <li>Sequence associated annotation rows associate with
2971 all sequences with a given id</li>
2972 <li>Find function matches case-insensitively for sequence
2973 ID string searches</li>
2974 <li>Non-standard characters do not cause pairwise
2975 alignment to fail with exception</li>
2976 </ul> <em>Application Issues</em>
2978 <li>Sequences are now validated against EMBL database</li>
2979 <li>Sequence fetcher fetches multiple records for all
2981 </ul> <em>InstallAnywhere Issues</em>
2983 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2984 issue with installAnywhere mechanism)</li>
2985 <li>Command line launching of JARs from InstallAnywhere
2986 version (java class versioning error fixed)</li>
2993 <div align="center">
2994 <strong>2.4</strong><br> 27/8/2008
2997 <td><em>User Interface</em>
2999 <li>Linked highlighting of codon and amino acid from
3000 translation and protein products</li>
3001 <li>Linked highlighting of structure associated with
3002 residue mapping to codon position</li>
3003 <li>Sequence Fetcher provides example accession numbers
3004 and 'clear' button</li>
3005 <li>MemoryMonitor added as an option under Desktop's
3007 <li>Extract score function to parse whitespace separated
3008 numeric data in description line</li>
3009 <li>Column labels in alignment annotation can be centred.</li>
3010 <li>Tooltip for sequence associated annotation give name
3012 </ul> <em>Web Services and URL fetching</em>
3014 <li>JPred3 web service</li>
3015 <li>Prototype sequence search client (no public services
3017 <li>Fetch either seed alignment or full alignment from
3019 <li>URL Links created for matching database cross
3020 references as well as sequence ID</li>
3021 <li>URL Links can be created using regular-expressions</li>
3022 </ul> <em>Sequence Database Connectivity</em>
3024 <li>Retrieval of cross-referenced sequences from other
3026 <li>Generalised database reference retrieval and
3027 validation to all fetchable databases</li>
3028 <li>Fetch sequences from DAS sources supporting the
3029 sequence command</li>
3030 </ul> <em>Import and Export</em>
3031 <li>export annotation rows as CSV for spreadsheet import</li>
3032 <li>Jalview projects record alignment dataset associations,
3033 EMBL products, and cDNA sequence mappings</li>
3034 <li>Sequence Group colour can be specified in Annotation
3036 <li>Ad-hoc colouring of group in Annotation File using RGB
3037 triplet as name of colourscheme</li>
3038 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3040 <li>treenode binding for VAMSAS tree exchange</li>
3041 <li>local editing and update of sequences in VAMSAS
3042 alignments (experimental)</li>
3043 <li>Create new or select existing session to join</li>
3044 <li>load and save of vamsas documents</li>
3045 </ul> <em>Application command line</em>
3047 <li>-tree parameter to open trees (introduced for passing
3049 <li>-fetchfrom command line argument to specify nicknames
3050 of DAS servers to query for alignment features</li>
3051 <li>-dasserver command line argument to add new servers
3052 that are also automatically queried for features</li>
3053 <li>-groovy command line argument executes a given groovy
3054 script after all input data has been loaded and parsed</li>
3055 </ul> <em>Applet-Application data exchange</em>
3057 <li>Trees passed as applet parameters can be passed to
3058 application (when using "View in full
3059 application")</li>
3060 </ul> <em>Applet Parameters</em>
3062 <li>feature group display control parameter</li>
3063 <li>debug parameter</li>
3064 <li>showbutton parameter</li>
3065 </ul> <em>Applet API methods</em>
3067 <li>newView public method</li>
3068 <li>Window (current view) specific get/set public methods</li>
3069 <li>Feature display control methods</li>
3070 <li>get list of currently selected sequences</li>
3071 </ul> <em>New Jalview distribution features</em>
3073 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3074 <li>RELEASE file gives build properties for the latest
3075 Jalview release.</li>
3076 <li>Java 1.1 Applet build made easier and donotobfuscate
3077 property controls execution of obfuscator</li>
3078 <li>Build target for generating source distribution</li>
3079 <li>Debug flag for javacc</li>
3080 <li>.jalview_properties file is documented (slightly) in
3081 jalview.bin.Cache</li>
3082 <li>Continuous Build Integration for stable and
3083 development version of Application, Applet and source
3088 <li>selected region output includes visible annotations
3089 (for certain formats)</li>
3090 <li>edit label/displaychar contains existing label/char
3092 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3093 <li>shorter peptide product names from EMBL records</li>
3094 <li>Newick string generator makes compact representations</li>
3095 <li>bootstrap values parsed correctly for tree files with
3097 <li>pathological filechooser bug avoided by not allowing
3098 filenames containing a ':'</li>
3099 <li>Fixed exception when parsing GFF files containing
3100 global sequence features</li>
3101 <li>Alignment datasets are finalized only when number of
3102 references from alignment sequences goes to zero</li>
3103 <li>Close of tree branch colour box without colour
3104 selection causes cascading exceptions</li>
3105 <li>occasional negative imgwidth exceptions</li>
3106 <li>better reporting of non-fatal warnings to user when
3107 file parsing fails.</li>
3108 <li>Save works when Jalview project is default format</li>
3109 <li>Save as dialog opened if current alignment format is
3110 not a valid output format</li>
3111 <li>UniProt canonical names introduced for both das and
3113 <li>Histidine should be midblue (not pink!) in Zappo</li>
3114 <li>error messages passed up and output when data read
3116 <li>edit undo recovers previous dataset sequence when
3117 sequence is edited</li>
3118 <li>allow PDB files without pdb ID HEADER lines (like
3119 those generated by MODELLER) to be read in properly</li>
3120 <li>allow reading of JPred concise files as a normal
3122 <li>Stockholm annotation parsing and alignment properties
3123 import fixed for PFAM records</li>
3124 <li>Structure view windows have correct name in Desktop
3126 <li>annotation consisting of sequence associated scores
3127 can be read and written correctly to annotation file</li>
3128 <li>Aligned cDNA translation to aligned peptide works
3130 <li>Fixed display of hidden sequence markers and
3131 non-italic font for representatives in Applet</li>
3132 <li>Applet Menus are always embedded in applet window on
3134 <li>Newly shown features appear at top of stack (in
3136 <li>Annotations added via parameter not drawn properly
3137 due to null pointer exceptions</li>
3138 <li>Secondary structure lines are drawn starting from
3139 first column of alignment</li>
3140 <li>UniProt XML import updated for new schema release in
3142 <li>Sequence feature to sequence ID match for Features
3143 file is case-insensitive</li>
3144 <li>Sequence features read from Features file appended to
3145 all sequences with matching IDs</li>
3146 <li>PDB structure coloured correctly for associated views
3147 containing a sub-sequence</li>
3148 <li>PDB files can be retrieved by applet from Jar files</li>
3149 <li>feature and annotation file applet parameters
3150 referring to different directories are retrieved correctly</li>
3151 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3152 <li>Fixed application hang whilst waiting for
3153 splash-screen version check to complete</li>
3154 <li>Applet properly URLencodes input parameter values
3155 when passing them to the launchApp service</li>
3156 <li>display name and local features preserved in results
3157 retrieved from web service</li>
3158 <li>Visual delay indication for sequence retrieval and
3159 sequence fetcher initialisation</li>
3160 <li>updated Application to use DAS 1.53e version of
3161 dasobert DAS client</li>
3162 <li>Re-instated Full AMSA support and .amsa file
3164 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3172 <div align="center">
3173 <strong>2.3</strong><br> 9/5/07
3178 <li>Jmol 11.0.2 integration</li>
3179 <li>PDB views stored in Jalview XML files</li>
3180 <li>Slide sequences</li>
3181 <li>Edit sequence in place</li>
3182 <li>EMBL CDS features</li>
3183 <li>DAS Feature mapping</li>
3184 <li>Feature ordering</li>
3185 <li>Alignment Properties</li>
3186 <li>Annotation Scores</li>
3187 <li>Sort by scores</li>
3188 <li>Feature/annotation editing in applet</li>
3193 <li>Headless state operation in 2.2.1</li>
3194 <li>Incorrect and unstable DNA pairwise alignment</li>
3195 <li>Cut and paste of sequences with annotation</li>
3196 <li>Feature group display state in XML</li>
3197 <li>Feature ordering in XML</li>
3198 <li>blc file iteration selection using filename # suffix</li>
3199 <li>Stockholm alignment properties</li>
3200 <li>Stockhom alignment secondary structure annotation</li>
3201 <li>2.2.1 applet had no feature transparency</li>
3202 <li>Number pad keys can be used in cursor mode</li>
3203 <li>Structure Viewer mirror image resolved</li>
3210 <div align="center">
3211 <strong>2.2.1</strong><br> 12/2/07
3216 <li>Non standard characters can be read and displayed
3217 <li>Annotations/Features can be imported/exported to the
3219 <li>Applet allows editing of sequence/annotation/group
3220 name & description
3221 <li>Preference setting to display sequence name in
3223 <li>Annotation file format extended to allow
3224 Sequence_groups to be defined
3225 <li>Default opening of alignment overview panel can be
3226 specified in preferences
3227 <li>PDB residue numbering annotation added to associated
3233 <li>Applet crash under certain Linux OS with Java 1.6
3235 <li>Annotation file export / import bugs fixed
3236 <li>PNG / EPS image output bugs fixed
3242 <div align="center">
3243 <strong>2.2</strong><br> 27/11/06
3248 <li>Multiple views on alignment
3249 <li>Sequence feature editing
3250 <li>"Reload" alignment
3251 <li>"Save" to current filename
3252 <li>Background dependent text colour
3253 <li>Right align sequence ids
3254 <li>User-defined lower case residue colours
3257 <li>Menu item accelerator keys
3258 <li>Control-V pastes to current alignment
3259 <li>Cancel button for DAS Feature Fetching
3260 <li>PCA and PDB Viewers zoom via mouse roller
3261 <li>User-defined sub-tree colours and sub-tree selection
3263 <li>'New Window' button on the 'Output to Text box'
3268 <li>New memory efficient Undo/Redo System
3269 <li>Optimised symbol lookups and conservation/consensus
3271 <li>Region Conservation/Consensus recalculated after
3273 <li>Fixed Remove Empty Columns Bug (empty columns at end
3275 <li>Slowed DAS Feature Fetching for increased robustness.
3277 <li>Made angle brackets in ASCII feature descriptions
3279 <li>Re-instated Zoom function for PCA
3280 <li>Sequence descriptions conserved in web service
3282 <li>UniProt ID discoverer uses any word separated by
3284 <li>WsDbFetch query/result association resolved
3285 <li>Tree leaf to sequence mapping improved
3286 <li>Smooth fonts switch moved to FontChooser dialog box.
3293 <div align="center">
3294 <strong>2.1.1</strong><br> 12/9/06
3299 <li>Copy consensus sequence to clipboard</li>
3304 <li>Image output - rightmost residues are rendered if
3305 sequence id panel has been resized</li>
3306 <li>Image output - all offscreen group boundaries are
3308 <li>Annotation files with sequence references - all
3309 elements in file are relative to sequence position</li>
3310 <li>Mac Applet users can use Alt key for group editing</li>
3316 <div align="center">
3317 <strong>2.1</strong><br> 22/8/06
3322 <li>MAFFT Multiple Alignment in default Web Service list</li>
3323 <li>DAS Feature fetching</li>
3324 <li>Hide sequences and columns</li>
3325 <li>Export Annotations and Features</li>
3326 <li>GFF file reading / writing</li>
3327 <li>Associate structures with sequences from local PDB
3329 <li>Add sequences to exisiting alignment</li>
3330 <li>Recently opened files / URL lists</li>
3331 <li>Applet can launch the full application</li>
3332 <li>Applet has transparency for features (Java 1.2
3334 <li>Applet has user defined colours parameter</li>
3335 <li>Applet can load sequences from parameter
3336 "sequence<em>x</em>"
3342 <li>Redundancy Panel reinstalled in the Applet</li>
3343 <li>Monospaced font - EPS / rescaling bug fixed</li>
3344 <li>Annotation files with sequence references bug fixed</li>
3350 <div align="center">
3351 <strong>2.08.1</strong><br> 2/5/06
3356 <li>Change case of selected region from Popup menu</li>
3357 <li>Choose to match case when searching</li>
3358 <li>Middle mouse button and mouse movement can compress /
3359 expand the visible width and height of the alignment</li>
3364 <li>Annotation Panel displays complete JNet results</li>
3370 <div align="center">
3371 <strong>2.08b</strong><br> 18/4/06
3377 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3378 <li>Righthand label on wrapped alignments shows correct
3385 <div align="center">
3386 <strong>2.08</strong><br> 10/4/06
3391 <li>Editing can be locked to the selection area</li>
3392 <li>Keyboard editing</li>
3393 <li>Create sequence features from searches</li>
3394 <li>Precalculated annotations can be loaded onto
3396 <li>Features file allows grouping of features</li>
3397 <li>Annotation Colouring scheme added</li>
3398 <li>Smooth fonts off by default - Faster rendering</li>
3399 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3404 <li>Drag & Drop fixed on Linux</li>
3405 <li>Jalview Archive file faster to load/save, sequence
3406 descriptions saved.</li>
3412 <div align="center">
3413 <strong>2.07</strong><br> 12/12/05
3418 <li>PDB Structure Viewer enhanced</li>
3419 <li>Sequence Feature retrieval and display enhanced</li>
3420 <li>Choose to output sequence start-end after sequence
3421 name for file output</li>
3422 <li>Sequence Fetcher WSDBFetch@EBI</li>
3423 <li>Applet can read feature files, PDB files and can be
3424 used for HTML form input</li>
3429 <li>HTML output writes groups and features</li>
3430 <li>Group editing is Control and mouse click</li>
3431 <li>File IO bugs</li>
3437 <div align="center">
3438 <strong>2.06</strong><br> 28/9/05
3443 <li>View annotations in wrapped mode</li>
3444 <li>More options for PCA viewer</li>
3449 <li>GUI bugs resolved</li>
3450 <li>Runs with -nodisplay from command line</li>
3456 <div align="center">
3457 <strong>2.05b</strong><br> 15/9/05
3462 <li>Choose EPS export as lineart or text</li>
3463 <li>Jar files are executable</li>
3464 <li>Can read in Uracil - maps to unknown residue</li>
3469 <li>Known OutOfMemory errors give warning message</li>
3470 <li>Overview window calculated more efficiently</li>
3471 <li>Several GUI bugs resolved</li>
3477 <div align="center">
3478 <strong>2.05</strong><br> 30/8/05
3483 <li>Edit and annotate in "Wrapped" view</li>
3488 <li>Several GUI bugs resolved</li>
3494 <div align="center">
3495 <strong>2.04</strong><br> 24/8/05
3500 <li>Hold down mouse wheel & scroll to change font
3506 <li>Improved JPred client reliability</li>
3507 <li>Improved loading of Jalview files</li>
3513 <div align="center">
3514 <strong>2.03</strong><br> 18/8/05
3519 <li>Set Proxy server name and port in preferences</li>
3520 <li>Multiple URL links from sequence ids</li>
3521 <li>User Defined Colours can have a scheme name and added
3523 <li>Choose to ignore gaps in consensus calculation</li>
3524 <li>Unix users can set default web browser</li>
3525 <li>Runs without GUI for batch processing</li>
3526 <li>Dynamically generated Web Service Menus</li>
3531 <li>InstallAnywhere download for Sparc Solaris</li>
3537 <div align="center">
3538 <strong>2.02</strong><br> 18/7/05
3544 <li>Copy & Paste order of sequences maintains
3545 alignment order.</li>
3551 <div align="center">
3552 <strong>2.01</strong><br> 12/7/05
3557 <li>Use delete key for deleting selection.</li>
3558 <li>Use Mouse wheel to scroll sequences.</li>
3559 <li>Help file updated to describe how to add alignment
3561 <li>Version and build date written to build properties
3563 <li>InstallAnywhere installation will check for updates
3564 at launch of Jalview.</li>
3569 <li>Delete gaps bug fixed.</li>
3570 <li>FileChooser sorts columns.</li>
3571 <li>Can remove groups one by one.</li>
3572 <li>Filechooser icons installed.</li>
3573 <li>Finder ignores return character when searching.
3574 Return key will initiate a search.<br>
3581 <div align="center">
3582 <strong>2.0</strong><br> 20/6/05
3587 <li>New codebase</li>