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-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
121 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
122 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
123 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
124 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
125 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
126 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
127 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
128 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
129 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
130 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
131 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
133 <strong><em>Applet</em></strong><br/>
135 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
141 <td width="60" nowrap>
143 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
144 <em>2/10/2017</em></strong>
147 <td><div align="left">
148 <em>New features in Jalview Desktop</em>
151 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
153 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
157 <td><div align="left">
161 <td width="60" nowrap>
163 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
164 <em>7/9/2017</em></strong>
167 <td><div align="left">
171 <!-- JAL-2588 -->Show gaps in overview window by colouring
172 in grey (sequences used to be coloured grey, and gaps were
176 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
180 <!-- JAL-2587 -->Overview updates immediately on increase
181 in size and progress bar shown as higher resolution
182 overview is recalculated
187 <td><div align="left">
191 <!-- JAL-2664 -->Overview window redraws every hidden
192 column region row by row
195 <!-- JAL-2681 -->duplicate protein sequences shown after
196 retrieving Ensembl crossrefs for sequences from Uniprot
199 <!-- JAL-2603 -->Overview window throws NPE if show boxes
200 format setting is unticked
203 <!-- JAL-2610 -->Groups are coloured wrongly in overview
204 if group has show boxes format setting unticked
207 <!-- JAL-2672,JAL-2665 -->Redraw problems when
208 autoscrolling whilst dragging current selection group to
209 include sequences and columns not currently displayed
212 <!-- JAL-2691 -->Not all chains are mapped when multimeric
213 assemblies are imported via CIF file
216 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
217 displayed when threshold or conservation colouring is also
221 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
225 <!-- JAL-2673 -->Jalview continues to scroll after
226 dragging a selected region off the visible region of the
230 <!-- JAL-2724 -->Cannot apply annotation based
231 colourscheme to all groups in a view
234 <!-- JAL-2511 -->IDs don't line up with sequences
235 initially after font size change using the Font chooser or
242 <td width="60" nowrap>
244 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
247 <td><div align="left">
248 <em>Calculations</em>
252 <!-- JAL-1933 -->Occupancy annotation row shows number of
253 ungapped positions in each column of the alignment.
256 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
257 a calculation dialog box
260 <!-- JAL-2379 -->Revised implementation of PCA for speed
261 and memory efficiency (~30x faster)
264 <!-- JAL-2403 -->Revised implementation of sequence
265 similarity scores as used by Tree, PCA, Shading Consensus
266 and other calculations
269 <!-- JAL-2416 -->Score matrices are stored as resource
270 files within the Jalview codebase
273 <!-- JAL-2500 -->Trees computed on Sequence Feature
274 Similarity may have different topology due to increased
281 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
282 model for alignments and groups
285 <!-- JAL-384 -->Custom shading schemes created via groovy
292 <!-- JAL-2526 -->Efficiency improvements for interacting
293 with alignment and overview windows
296 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
300 <!-- JAL-2388 -->Hidden columns and sequences can be
304 <!-- JAL-2611 -->Click-drag in visible area allows fine
305 adjustment of visible position
309 <em>Data import/export</em>
312 <!-- JAL-2535 -->Posterior probability annotation from
313 Stockholm files imported as sequence associated annotation
316 <!-- JAL-2507 -->More robust per-sequence positional
317 annotation input/output via stockholm flatfile
320 <!-- JAL-2533 -->Sequence names don't include file
321 extension when importing structure files without embedded
322 names or PDB accessions
325 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
326 format sequence substitution matrices
329 <em>User Interface</em>
332 <!-- JAL-2447 --> Experimental Features Checkbox in
333 Desktop's Tools menu to hide or show untested features in
337 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
338 via Overview or sequence motif search operations
341 <!-- JAL-2547 -->Amend sequence features dialog box can be
342 opened by double clicking gaps within sequence feature
346 <!-- JAL-1476 -->Status bar message shown when not enough
347 aligned positions were available to create a 3D structure
351 <em>3D Structure</em>
354 <!-- JAL-2430 -->Hidden regions in alignment views are not
355 coloured in linked structure views
358 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
359 file-based command exchange
362 <!-- JAL-2375 -->Structure chooser automatically shows
363 Cached Structures rather than querying the PDBe if
364 structures are already available for sequences
367 <!-- JAL-2520 -->Structures imported via URL are cached in
368 the Jalview project rather than downloaded again when the
372 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
373 to transfer Chimera's structure attributes as Jalview
374 features, and vice-versa (<strong>Experimental
378 <em>Web Services</em>
381 <!-- JAL-2549 -->Updated JABAWS client to v2.2
384 <!-- JAL-2335 -->Filter non-standard amino acids and
385 nucleotides when submitting to AACon and other MSA
389 <!-- JAL-2316, -->URLs for viewing database
390 cross-references provided by identifiers.org and the
398 <!-- JAL-2344 -->FileFormatI interface for describing and
399 identifying file formats (instead of String constants)
402 <!-- JAL-2228 -->FeatureCounter script refactored for
403 efficiency when counting all displayed features (not
404 backwards compatible with 2.10.1)
407 <em>Example files</em>
410 <!-- JAL-2631 -->Graduated feature colour style example
411 included in the example feature file
414 <em>Documentation</em>
417 <!-- JAL-2339 -->Release notes reformatted for readability
418 with the built-in Java help viewer
421 <!-- JAL-1644 -->Find documentation updated with 'search
422 sequence description' option
428 <!-- JAL-2485, -->External service integration tests for
429 Uniprot REST Free Text Search Client
432 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
435 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
440 <td><div align="left">
441 <em>Calculations</em>
444 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
445 matrix - C->R should be '-3'<br />Old matrix restored
446 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
448 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
449 Jalview's treatment of gaps in PCA and substitution matrix
450 based Tree calculations.<br /> <br />In earlier versions
451 of Jalview, gaps matching gaps were penalised, and gaps
452 matching non-gaps penalised even more. In the PCA
453 calculation, gaps were actually treated as non-gaps - so
454 different costs were applied, which meant Jalview's PCAs
455 were different to those produced by SeqSpace.<br />Jalview
456 now treats gaps in the same way as SeqSpace (ie it scores
457 them as 0). <br /> <br />Enter the following in the
458 Groovy console to restore pre-2.10.2 behaviour:<br />
459 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
460 // for 2.10.1 mode <br />
461 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
462 // to restore 2.10.2 mode <br /> <br /> <em>Note:
463 these settings will affect all subsequent tree and PCA
464 calculations (not recommended)</em></li>
466 <!-- JAL-2424 -->Fixed off-by-one bug that affected
467 scaling of branch lengths for trees computed using
468 Sequence Feature Similarity.
471 <!-- JAL-2377 -->PCA calculation could hang when
472 generating output report when working with highly
476 <!-- JAL-2544 --> Sort by features includes features to
477 right of selected region when gaps present on right-hand
481 <em>User Interface</em>
484 <!-- JAL-2346 -->Reopening Colour by annotation dialog
485 doesn't reselect a specific sequence's associated
486 annotation after it was used for colouring a view
489 <!-- JAL-2419 -->Current selection lost if popup menu
490 opened on a region of alignment without groups
493 <!-- JAL-2374 -->Popup menu not always shown for regions
494 of an alignment with overlapping groups
497 <!-- JAL-2310 -->Finder double counts if both a sequence's
498 name and description match
501 <!-- JAL-2370 -->Hiding column selection containing two
502 hidden regions results in incorrect hidden regions
505 <!-- JAL-2386 -->'Apply to all groups' setting when
506 changing colour does not apply Conservation slider value
510 <!-- JAL-2373 -->Percentage identity and conservation menu
511 items do not show a tick or allow shading to be disabled
514 <!-- JAL-2385 -->Conservation shading or PID threshold
515 lost when base colourscheme changed if slider not visible
518 <!-- JAL-2547 -->Sequence features shown in tooltip for
519 gaps before start of features
522 <!-- JAL-2623 -->Graduated feature colour threshold not
523 restored to UI when feature colour is edited
526 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
527 a time when scrolling vertically in wrapped mode.
530 <!-- JAL-2630 -->Structure and alignment overview update
531 as graduate feature colour settings are modified via the
535 <!-- JAL-2034 -->Overview window doesn't always update
536 when a group defined on the alignment is resized
539 <!-- JAL-2605 -->Mouseovers on left/right scale region in
540 wrapped view result in positional status updates
544 <!-- JAL-2563 -->Status bar doesn't show position for
545 ambiguous amino acid and nucleotide symbols
548 <!-- JAL-2602 -->Copy consensus sequence failed if
549 alignment included gapped columns
552 <!-- JAL-2473 -->Minimum size set for Jalview windows so
553 widgets don't permanently disappear
556 <!-- JAL-2503 -->Cannot select or filter quantitative
557 annotation that are shown only as column labels (e.g.
558 T-Coffee column reliability scores)
561 <!-- JAL-2594 -->Exception thrown if trying to create a
562 sequence feature on gaps only
565 <!-- JAL-2504 -->Features created with 'New feature'
566 button from a Find inherit previously defined feature type
567 rather than the Find query string
570 <!-- JAL-2423 -->incorrect title in output window when
571 exporting tree calculated in Jalview
574 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
575 and then revealing them reorders sequences on the
579 <!-- JAL-964 -->Group panel in sequence feature settings
580 doesn't update to reflect available set of groups after
581 interactively adding or modifying features
584 <!-- JAL-2225 -->Sequence Database chooser unusable on
588 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
589 only excluded gaps in current sequence and ignored
596 <!-- JAL-2421 -->Overview window visible region moves
597 erratically when hidden rows or columns are present
600 <!-- JAL-2362 -->Per-residue colourschemes applied via the
601 Structure Viewer's colour menu don't correspond to
605 <!-- JAL-2405 -->Protein specific colours only offered in
606 colour and group colour menu for protein alignments
609 <!-- JAL-2385 -->Colour threshold slider doesn't update to
610 reflect currently selected view or group's shading
614 <!-- JAL-2624 -->Feature colour thresholds not respected
615 when rendered on overview and structures when opacity at
619 <!-- JAL-2589 -->User defined gap colour not shown in
620 overview when features overlaid on alignment
623 <em>Data import/export</em>
626 <!-- JAL-2576 -->Very large alignments take a long time to
630 <!-- JAL-2507 -->Per-sequence RNA secondary structures
631 added after a sequence was imported are not written to
635 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
636 when importing RNA secondary structure via Stockholm
639 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
640 not shown in correct direction for simple pseudoknots
643 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
644 with lightGray or darkGray via features file (but can
648 <!-- JAL-2383 -->Above PID colour threshold not recovered
649 when alignment view imported from project
652 <!-- JAL-2520,JAL-2465 -->No mappings generated between
653 structure and sequences extracted from structure files
654 imported via URL and viewed in Jmol
657 <!-- JAL-2520 -->Structures loaded via URL are saved in
658 Jalview Projects rather than fetched via URL again when
659 the project is loaded and the structure viewed
662 <em>Web Services</em>
665 <!-- JAL-2519 -->EnsemblGenomes example failing after
666 release of Ensembl v.88
669 <!-- JAL-2366 -->Proxy server address and port always
670 appear enabled in Preferences->Connections
673 <!-- JAL-2461 -->DAS registry not found exceptions
674 removed from console output
677 <!-- JAL-2582 -->Cannot retrieve protein products from
678 Ensembl by Peptide ID
681 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
682 created from SIFTs, and spurious 'Couldn't open structure
683 in Chimera' errors raised after April 2017 update (problem
684 due to 'null' string rather than empty string used for
685 residues with no corresponding PDB mapping).
688 <em>Application UI</em>
691 <!-- JAL-2361 -->User Defined Colours not added to Colour
695 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
696 case' residues (button in colourscheme editor debugged and
697 new documentation and tooltips added)
700 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
701 doesn't restore group-specific text colour thresholds
704 <!-- JAL-2243 -->Feature settings panel does not update as
705 new features are added to alignment
708 <!-- JAL-2532 -->Cancel in feature settings reverts
709 changes to feature colours via the Amend features dialog
712 <!-- JAL-2506 -->Null pointer exception when attempting to
713 edit graduated feature colour via amend features dialog
717 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
718 selection menu changes colours of alignment views
721 <!-- JAL-2426 -->Spurious exceptions in console raised
722 from alignment calculation workers after alignment has
726 <!-- JAL-1608 -->Typo in selection popup menu - Create
727 groups now 'Create Group'
730 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
731 Create/Undefine group doesn't always work
734 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
735 shown again after pressing 'Cancel'
738 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
739 adjusts start position in wrap mode
742 <!-- JAL-2563 -->Status bar doesn't show positions for
743 ambiguous amino acids
746 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
747 CDS/Protein view after CDS sequences added for aligned
751 <!-- JAL-2592 -->User defined colourschemes called 'User
752 Defined' don't appear in Colours menu
758 <!-- JAL-2468 -->Switching between Nucleotide and Protein
759 score models doesn't always result in an updated PCA plot
762 <!-- JAL-2442 -->Features not rendered as transparent on
763 overview or linked structure view
766 <!-- JAL-2372 -->Colour group by conservation doesn't
770 <!-- JAL-2517 -->Hitting Cancel after applying
771 user-defined colourscheme doesn't restore original
778 <!-- JAL-2314 -->Unit test failure:
779 jalview.ws.jabaws.RNAStructExportImport setup fails
782 <!-- JAL-2307 -->Unit test failure:
783 jalview.ws.sifts.SiftsClientTest due to compatibility
784 problems with deep array comparison equality asserts in
785 successive versions of TestNG
788 <!-- JAL-2479 -->Relocated StructureChooserTest and
789 ParameterUtilsTest Unit tests to Network suite
792 <em>New Known Issues</em>
795 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
796 phase after a sequence motif find operation
799 <!-- JAL-2550 -->Importing annotation file with rows
800 containing just upper and lower case letters are
801 interpreted as WUSS RNA secondary structure symbols
804 <!-- JAL-2590 -->Cannot load and display Newick trees
805 reliably from eggnog Ortholog database
808 <!-- JAL-2468 -->Status bar shows 'Marked x columns
809 containing features of type Highlight' when 'B' is pressed
810 to mark columns containing highlighted regions.
813 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
814 doesn't always add secondary structure annotation.
819 <td width="60" nowrap>
821 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
824 <td><div align="left">
828 <!-- JAL-98 -->Improved memory usage: sparse arrays used
829 for all consensus calculations
832 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
835 <li>Updated Jalview's Certum code signing certificate
841 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
842 set of database cross-references, sorted alphabetically
845 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
846 from database cross references. Users with custom links
847 will receive a <a href="webServices/urllinks.html#warning">warning
848 dialog</a> asking them to update their preferences.
851 <!-- JAL-2287-->Cancel button and escape listener on
852 dialog warning user about disconnecting Jalview from a
856 <!-- JAL-2320-->Jalview's Chimera control window closes if
857 the Chimera it is connected to is shut down
860 <!-- JAL-1738-->New keystroke (B) and Select highlighted
861 columns menu item to mark columns containing highlighted
862 regions (e.g. from structure selections or results of a
866 <!-- JAL-2284-->Command line option for batch-generation
867 of HTML pages rendering alignment data with the BioJS
877 <!-- JAL-2286 -->Columns with more than one modal residue
878 are not coloured or thresholded according to percent
879 identity (first observed in Jalview 2.8.2)
882 <!-- JAL-2301 -->Threonine incorrectly reported as not
886 <!-- JAL-2318 -->Updates to documentation pages (above PID
887 threshold, amino acid properties)
890 <!-- JAL-2292 -->Lower case residues in sequences are not
891 reported as mapped to residues in a structure file in the
895 <!--JAL-2324 -->Identical features with non-numeric scores
896 could be added multiple times to a sequence
899 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
900 bond features shown as two highlighted residues rather
901 than a range in linked structure views, and treated
902 correctly when selecting and computing trees from features
905 <!-- JAL-2281-->Custom URL links for database
906 cross-references are matched to database name regardless
914 <!-- JAL-2282-->Custom URL links for specific database
915 names without regular expressions also offer links from
919 <!-- JAL-2315-->Removing a single configured link in the
920 URL links pane in Connections preferences doesn't actually
921 update Jalview configuration
924 <!-- JAL-2272-->CTRL-Click on a selected region to open
925 the alignment area popup menu doesn't work on El-Capitan
928 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
929 files with similarly named sequences if dropped onto the
933 <!-- JAL-2312 -->Additional mappings are shown for PDB
934 entries where more chains exist in the PDB accession than
935 are reported in the SIFTS file
938 <!-- JAL-2317-->Certain structures do not get mapped to
939 the structure view when displayed with Chimera
942 <!-- JAL-2317-->No chains shown in the Chimera view
943 panel's View->Show Chains submenu
946 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
947 work for wrapped alignment views
950 <!--JAL-2197 -->Rename UI components for running JPred
951 predictions from 'JNet' to 'JPred'
954 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
955 corrupted when annotation panel vertical scroll is not at
959 <!--JAL-2332 -->Attempting to view structure for Hen
960 lysozyme results in a PDB Client error dialog box
963 <!-- JAL-2319 -->Structure View's mapping report switched
964 ranges for PDB and sequence for SIFTS
967 SIFTS 'Not_Observed' residues mapped to non-existant
971 <!-- <em>New Known Issues</em>
978 <td width="60" nowrap>
980 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
981 <em>25/10/2016</em></strong>
984 <td><em>Application</em>
986 <li>3D Structure chooser opens with 'Cached structures'
987 view if structures already loaded</li>
988 <li>Progress bar reports models as they are loaded to
995 <li>Colour by conservation always enabled and no tick
996 shown in menu when BLOSUM or PID shading applied</li>
997 <li>FER1_ARATH and FER2_ARATH labels were switched in
998 example sequences/projects/trees</li>
1000 <em>Application</em>
1002 <li>Jalview projects with views of local PDB structure
1003 files saved on Windows cannot be opened on OSX</li>
1004 <li>Multiple structure views can be opened and superposed
1005 without timeout for structures with multiple models or
1006 multiple sequences in alignment</li>
1007 <li>Cannot import or associated local PDB files without a
1008 PDB ID HEADER line</li>
1009 <li>RMSD is not output in Jmol console when superposition
1011 <li>Drag and drop of URL from Browser fails for Linux and
1012 OSX versions earlier than El Capitan</li>
1013 <li>ENA client ignores invalid content from ENA server</li>
1014 <li>Exceptions are not raised in console when ENA client
1015 attempts to fetch non-existent IDs via Fetch DB Refs UI
1017 <li>Exceptions are not raised in console when a new view
1018 is created on the alignment</li>
1019 <li>OSX right-click fixed for group selections: CMD-click
1020 to insert/remove gaps in groups and CTRL-click to open group
1023 <em>Build and deployment</em>
1025 <li>URL link checker now copes with multi-line anchor
1028 <em>New Known Issues</em>
1030 <li>Drag and drop from URL links in browsers do not work
1037 <td width="60" nowrap>
1038 <div align="center">
1039 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1042 <td><em>General</em>
1045 <!-- JAL-2124 -->Updated Spanish translations.
1048 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1049 for importing structure data to Jalview. Enables mmCIF and
1053 <!-- JAL-192 --->Alignment ruler shows positions relative to
1057 <!-- JAL-2202 -->Position/residue shown in status bar when
1058 mousing over sequence associated annotation
1061 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1065 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1066 '()', canonical '[]' and invalid '{}' base pair populations
1070 <!-- JAL-2092 -->Feature settings popup menu options for
1071 showing or hiding columns containing a feature
1074 <!-- JAL-1557 -->Edit selected group by double clicking on
1075 group and sequence associated annotation labels
1078 <!-- JAL-2236 -->Sequence name added to annotation label in
1079 select/hide columns by annotation and colour by annotation
1083 </ul> <em>Application</em>
1086 <!-- JAL-2050-->Automatically hide introns when opening a
1087 gene/transcript view
1090 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1094 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1095 structure mappings with the EMBL-EBI PDBe SIFTS database
1098 <!-- JAL-2079 -->Updated download sites used for Rfam and
1099 Pfam sources to xfam.org
1102 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1105 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1106 over sequences in Jalview
1109 <!-- JAL-2027-->Support for reverse-complement coding
1110 regions in ENA and EMBL
1113 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1114 for record retrieval via ENA rest API
1117 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1121 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1122 groovy script execution
1125 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1126 alignment window's Calculate menu
1129 <!-- JAL-1812 -->Allow groovy scripts that call
1130 Jalview.getAlignFrames() to run in headless mode
1133 <!-- JAL-2068 -->Support for creating new alignment
1134 calculation workers from groovy scripts
1137 <!-- JAL-1369 --->Store/restore reference sequence in
1141 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1142 associations are now saved/restored from project
1145 <!-- JAL-1993 -->Database selection dialog always shown
1146 before sequence fetcher is opened
1149 <!-- JAL-2183 -->Double click on an entry in Jalview's
1150 database chooser opens a sequence fetcher
1153 <!-- JAL-1563 -->Free-text search client for UniProt using
1154 the UniProt REST API
1157 <!-- JAL-2168 -->-nonews command line parameter to prevent
1158 the news reader opening
1161 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1162 querying stored in preferences
1165 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1169 <!-- JAL-1977-->Tooltips shown on database chooser
1172 <!-- JAL-391 -->Reverse complement function in calculate
1173 menu for nucleotide sequences
1176 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1177 and feature counts preserves alignment ordering (and
1178 debugged for complex feature sets).
1181 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1182 viewing structures with Jalview 2.10
1185 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1186 genome, transcript CCDS and gene ids via the Ensembl and
1187 Ensembl Genomes REST API
1190 <!-- JAL-2049 -->Protein sequence variant annotation
1191 computed for 'sequence_variant' annotation on CDS regions
1195 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1199 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1200 Ref Fetcher fails to match, or otherwise updates sequence
1201 data from external database records.
1204 <!-- JAL-2154 -->Revised Jalview Project format for
1205 efficient recovery of sequence coding and alignment
1206 annotation relationships.
1208 </ul> <!-- <em>Applet</em>
1219 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1223 <!-- JAL-2018-->Export features in Jalview format (again)
1224 includes graduated colourschemes
1227 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1228 working with big alignments and lots of hidden columns
1231 <!-- JAL-2053-->Hidden column markers not always rendered
1232 at right of alignment window
1235 <!-- JAL-2067 -->Tidied up links in help file table of
1239 <!-- JAL-2072 -->Feature based tree calculation not shown
1243 <!-- JAL-2075 -->Hidden columns ignored during feature
1244 based tree calculation
1247 <!-- JAL-2065 -->Alignment view stops updating when show
1248 unconserved enabled for group on alignment
1251 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1255 <!-- JAL-2146 -->Alignment column in status incorrectly
1256 shown as "Sequence position" when mousing over
1260 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1261 hidden columns present
1264 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1265 user created annotation added to alignment
1268 <!-- JAL-1841 -->RNA Structure consensus only computed for
1269 '()' base pair annotation
1272 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1273 in zero scores for all base pairs in RNA Structure
1277 <!-- JAL-2174-->Extend selection with columns containing
1281 <!-- JAL-2275 -->Pfam format writer puts extra space at
1282 beginning of sequence
1285 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1289 <!-- JAL-2238 -->Cannot create groups on an alignment from
1290 from a tree when t-coffee scores are shown
1293 <!-- JAL-1836,1967 -->Cannot import and view PDB
1294 structures with chains containing negative resnums (4q4h)
1297 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1301 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1302 to Clustal, PIR and PileUp output
1305 <!-- JAL-2008 -->Reordering sequence features that are
1306 not visible causes alignment window to repaint
1309 <!-- JAL-2006 -->Threshold sliders don't work in
1310 graduated colour and colour by annotation row for e-value
1311 scores associated with features and annotation rows
1314 <!-- JAL-1797 -->amino acid physicochemical conservation
1315 calculation should be case independent
1318 <!-- JAL-2173 -->Remove annotation also updates hidden
1322 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1323 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1324 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1327 <!-- JAL-2065 -->Null pointer exceptions and redraw
1328 problems when reference sequence defined and 'show
1329 non-conserved' enabled
1332 <!-- JAL-1306 -->Quality and Conservation are now shown on
1333 load even when Consensus calculation is disabled
1336 <!-- JAL-1932 -->Remove right on penultimate column of
1337 alignment does nothing
1340 <em>Application</em>
1343 <!-- JAL-1552-->URLs and links can't be imported by
1344 drag'n'drop on OSX when launched via webstart (note - not
1345 yet fixed for El Capitan)
1348 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1349 output when running on non-gb/us i18n platforms
1352 <!-- JAL-1944 -->Error thrown when exporting a view with
1353 hidden sequences as flat-file alignment
1356 <!-- JAL-2030-->InstallAnywhere distribution fails when
1360 <!-- JAL-2080-->Jalview very slow to launch via webstart
1361 (also hotfix for 2.9.0b2)
1364 <!-- JAL-2085 -->Cannot save project when view has a
1365 reference sequence defined
1368 <!-- JAL-1011 -->Columns are suddenly selected in other
1369 alignments and views when revealing hidden columns
1372 <!-- JAL-1989 -->Hide columns not mirrored in complement
1373 view in a cDNA/Protein splitframe
1376 <!-- JAL-1369 -->Cannot save/restore representative
1377 sequence from project when only one sequence is
1381 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1382 in Structure Chooser
1385 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1386 structure consensus didn't refresh annotation panel
1389 <!-- JAL-1962 -->View mapping in structure view shows
1390 mappings between sequence and all chains in a PDB file
1393 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1394 dialogs format columns correctly, don't display array
1395 data, sort columns according to type
1398 <!-- JAL-1975 -->Export complete shown after destination
1399 file chooser is cancelled during an image export
1402 <!-- JAL-2025 -->Error when querying PDB Service with
1403 sequence name containing special characters
1406 <!-- JAL-2024 -->Manual PDB structure querying should be
1410 <!-- JAL-2104 -->Large tooltips with broken HTML
1411 formatting don't wrap
1414 <!-- JAL-1128 -->Figures exported from wrapped view are
1415 truncated so L looks like I in consensus annotation
1418 <!-- JAL-2003 -->Export features should only export the
1419 currently displayed features for the current selection or
1423 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1424 after fetching cross-references, and restoring from
1428 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1429 followed in the structure viewer
1432 <!-- JAL-2163 -->Titles for individual alignments in
1433 splitframe not restored from project
1436 <!-- JAL-2145 -->missing autocalculated annotation at
1437 trailing end of protein alignment in transcript/product
1438 splitview when pad-gaps not enabled by default
1441 <!-- JAL-1797 -->amino acid physicochemical conservation
1445 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1446 article has been read (reopened issue due to
1447 internationalisation problems)
1450 <!-- JAL-1960 -->Only offer PDB structures in structure
1451 viewer based on sequence name, PDB and UniProt
1456 <!-- JAL-1976 -->No progress bar shown during export of
1460 <!-- JAL-2213 -->Structures not always superimposed after
1461 multiple structures are shown for one or more sequences.
1464 <!-- JAL-1370 -->Reference sequence characters should not
1465 be replaced with '.' when 'Show unconserved' format option
1469 <!-- JAL-1823 -->Cannot specify chain code when entering
1470 specific PDB id for sequence
1473 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1474 'Export hidden sequences' is enabled, but 'export hidden
1475 columns' is disabled.
1478 <!--JAL-2026-->Best Quality option in structure chooser
1479 selects lowest rather than highest resolution structures
1483 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1484 to sequence mapping in 'View Mappings' report
1487 <!-- JAL-2284 -->Unable to read old Jalview projects that
1488 contain non-XML data added after Jalvew wrote project.
1491 <!-- JAL-2118 -->Newly created annotation row reorders
1492 after clicking on it to create new annotation for a
1496 <!-- JAL-1980 -->Null Pointer Exception raised when
1497 pressing Add on an orphaned cut'n'paste window.
1499 <!-- may exclude, this is an external service stability issue JAL-1941
1500 -- > RNA 3D structure not added via DSSR service</li> -->
1505 <!-- JAL-2151 -->Incorrect columns are selected when
1506 hidden columns present before start of sequence
1509 <!-- JAL-1986 -->Missing dependencies on applet pages
1513 <!-- JAL-1947 -->Overview pixel size changes when
1514 sequences are hidden in applet
1517 <!-- JAL-1996 -->Updated instructions for applet
1518 deployment on examples pages.
1525 <td width="60" nowrap>
1526 <div align="center">
1527 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1528 <em>16/10/2015</em></strong>
1531 <td><em>General</em>
1533 <li>Time stamps for signed Jalview application and applet
1538 <em>Application</em>
1540 <li>Duplicate group consensus and conservation rows
1541 shown when tree is partitioned</li>
1542 <li>Erratic behaviour when tree partitions made with
1543 multiple cDNA/Protein split views</li>
1549 <td width="60" nowrap>
1550 <div align="center">
1551 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1552 <em>8/10/2015</em></strong>
1555 <td><em>General</em>
1557 <li>Updated Spanish translations of localized text for
1559 </ul> <em>Application</em>
1561 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1562 <li>Signed OSX InstallAnywhere installer<br></li>
1563 <li>Support for per-sequence based annotations in BioJSON</li>
1564 </ul> <em>Applet</em>
1566 <li>Split frame example added to applet examples page</li>
1567 </ul> <em>Build and Deployment</em>
1570 <!-- JAL-1888 -->New ant target for running Jalview's test
1578 <li>Mapping of cDNA to protein in split frames
1579 incorrect when sequence start > 1</li>
1580 <li>Broken images in filter column by annotation dialog
1582 <li>Feature colours not parsed from features file</li>
1583 <li>Exceptions and incomplete link URLs recovered when
1584 loading a features file containing HTML tags in feature
1588 <em>Application</em>
1590 <li>Annotations corrupted after BioJS export and
1592 <li>Incorrect sequence limits after Fetch DB References
1593 with 'trim retrieved sequences'</li>
1594 <li>Incorrect warning about deleting all data when
1595 deleting selected columns</li>
1596 <li>Patch to build system for shipping properly signed
1597 JNLP templates for webstart launch</li>
1598 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1599 unreleased structures for download or viewing</li>
1600 <li>Tab/space/return keystroke operation of EMBL-PDBe
1601 fetcher/viewer dialogs works correctly</li>
1602 <li>Disabled 'minimise' button on Jalview windows
1603 running on OSX to workaround redraw hang bug</li>
1604 <li>Split cDNA/Protein view position and geometry not
1605 recovered from jalview project</li>
1606 <li>Initial enabled/disabled state of annotation menu
1607 sorter 'show autocalculated first/last' corresponds to
1609 <li>Restoring of Clustal, RNA Helices and T-Coffee
1610 color schemes from BioJSON</li>
1614 <li>Reorder sequences mirrored in cDNA/Protein split
1616 <li>Applet with Jmol examples not loading correctly</li>
1622 <td><div align="center">
1623 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1625 <td><em>General</em>
1627 <li>Linked visualisation and analysis of DNA and Protein
1630 <li>Translated cDNA alignments shown as split protein
1631 and DNA alignment views</li>
1632 <li>Codon consensus annotation for linked protein and
1633 cDNA alignment views</li>
1634 <li>Link cDNA or Protein product sequences by loading
1635 them onto Protein or cDNA alignments</li>
1636 <li>Reconstruct linked cDNA alignment from aligned
1637 protein sequences</li>
1640 <li>Jmol integration updated to Jmol v14.2.14</li>
1641 <li>Import and export of Jalview alignment views as <a
1642 href="features/bioJsonFormat.html">BioJSON</a></li>
1643 <li>New alignment annotation file statements for
1644 reference sequences and marking hidden columns</li>
1645 <li>Reference sequence based alignment shading to
1646 highlight variation</li>
1647 <li>Select or hide columns according to alignment
1649 <li>Find option for locating sequences by description</li>
1650 <li>Conserved physicochemical properties shown in amino
1651 acid conservation row</li>
1652 <li>Alignments can be sorted by number of RNA helices</li>
1653 </ul> <em>Application</em>
1655 <li>New cDNA/Protein analysis capabilities
1657 <li>Get Cross-References should open a Split Frame
1658 view with cDNA/Protein</li>
1659 <li>Detect when nucleotide sequences and protein
1660 sequences are placed in the same alignment</li>
1661 <li>Split cDNA/Protein views are saved in Jalview
1666 <li>Use REST API to talk to Chimera</li>
1667 <li>Selected regions in Chimera are highlighted in linked
1668 Jalview windows</li>
1670 <li>VARNA RNA viewer updated to v3.93</li>
1671 <li>VARNA views are saved in Jalview Projects</li>
1672 <li>Pseudoknots displayed as Jalview RNA annotation can
1673 be shown in VARNA</li>
1675 <li>Make groups for selection uses marked columns as well
1676 as the active selected region</li>
1678 <li>Calculate UPGMA and NJ trees using sequence feature
1680 <li>New Export options
1682 <li>New Export Settings dialog to control hidden
1683 region export in flat file generation</li>
1685 <li>Export alignment views for display with the <a
1686 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1688 <li>Export scrollable SVG in HTML page</li>
1689 <li>Optional embedding of BioJSON data when exporting
1690 alignment figures to HTML</li>
1692 <li>3D structure retrieval and display
1694 <li>Free text and structured queries with the PDBe
1696 <li>PDBe Search API based discovery and selection of
1697 PDB structures for a sequence set</li>
1701 <li>JPred4 employed for protein secondary structure
1703 <li>Hide Insertions menu option to hide unaligned columns
1704 for one or a group of sequences</li>
1705 <li>Automatically hide insertions in alignments imported
1706 from the JPred4 web server</li>
1707 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1708 system on OSX<br />LGPL libraries courtesy of <a
1709 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1711 <li>changed 'View nucleotide structure' submenu to 'View
1712 VARNA 2D Structure'</li>
1713 <li>change "View protein structure" menu option to "3D
1716 </ul> <em>Applet</em>
1718 <li>New layout for applet example pages</li>
1719 <li>New parameters to enable SplitFrame view
1720 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1721 <li>New example demonstrating linked viewing of cDNA and
1722 Protein alignments</li>
1723 </ul> <em>Development and deployment</em>
1725 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1726 <li>Include installation type and git revision in build
1727 properties and console log output</li>
1728 <li>Jalview Github organisation, and new github site for
1729 storing BioJsMSA Templates</li>
1730 <li>Jalview's unit tests now managed with TestNG</li>
1733 <!-- <em>General</em>
1735 </ul> --> <!-- issues resolved --> <em>Application</em>
1737 <li>Escape should close any open find dialogs</li>
1738 <li>Typo in select-by-features status report</li>
1739 <li>Consensus RNA secondary secondary structure
1740 predictions are not highlighted in amber</li>
1741 <li>Missing gap character in v2.7 example file means
1742 alignment appears unaligned when pad-gaps is not enabled</li>
1743 <li>First switch to RNA Helices colouring doesn't colour
1744 associated structure views</li>
1745 <li>ID width preference option is greyed out when auto
1746 width checkbox not enabled</li>
1747 <li>Stopped a warning dialog from being shown when
1748 creating user defined colours</li>
1749 <li>'View Mapping' in structure viewer shows sequence
1750 mappings for just that viewer's sequences</li>
1751 <li>Workaround for superposing PDB files containing
1752 multiple models in Chimera</li>
1753 <li>Report sequence position in status bar when hovering
1754 over Jmol structure</li>
1755 <li>Cannot output gaps as '.' symbols with Selection ->
1756 output to text box</li>
1757 <li>Flat file exports of alignments with hidden columns
1758 have incorrect sequence start/end</li>
1759 <li>'Aligning' a second chain to a Chimera structure from
1761 <li>Colour schemes applied to structure viewers don't
1762 work for nucleotide</li>
1763 <li>Loading/cut'n'pasting an empty or invalid file leads
1764 to a grey/invisible alignment window</li>
1765 <li>Exported Jpred annotation from a sequence region
1766 imports to different position</li>
1767 <li>Space at beginning of sequence feature tooltips shown
1768 on some platforms</li>
1769 <li>Chimera viewer 'View | Show Chain' menu is not
1771 <li>'New View' fails with a Null Pointer Exception in
1772 console if Chimera has been opened</li>
1773 <li>Mouseover to Chimera not working</li>
1774 <li>Miscellaneous ENA XML feature qualifiers not
1776 <li>NPE in annotation renderer after 'Extract Scores'</li>
1777 <li>If two structures in one Chimera window, mouseover of
1778 either sequence shows on first structure</li>
1779 <li>'Show annotations' options should not make
1780 non-positional annotations visible</li>
1781 <li>Subsequence secondary structure annotation not shown
1782 in right place after 'view flanking regions'</li>
1783 <li>File Save As type unset when current file format is
1785 <li>Save as '.jar' option removed for saving Jalview
1787 <li>Colour by Sequence colouring in Chimera more
1789 <li>Cannot 'add reference annotation' for a sequence in
1790 several views on same alignment</li>
1791 <li>Cannot show linked products for EMBL / ENA records</li>
1792 <li>Jalview's tooltip wraps long texts containing no
1794 </ul> <em>Applet</em>
1796 <li>Jmol to JalviewLite mouseover/link not working</li>
1797 <li>JalviewLite can't import sequences with ID
1798 descriptions containing angle brackets</li>
1799 </ul> <em>General</em>
1801 <li>Cannot export and reimport RNA secondary structure
1802 via jalview annotation file</li>
1803 <li>Random helix colour palette for colour by annotation
1804 with RNA secondary structure</li>
1805 <li>Mouseover to cDNA from STOP residue in protein
1806 translation doesn't work.</li>
1807 <li>hints when using the select by annotation dialog box</li>
1808 <li>Jmol alignment incorrect if PDB file has alternate CA
1810 <li>FontChooser message dialog appears to hang after
1811 choosing 1pt font</li>
1812 <li>Peptide secondary structure incorrectly imported from
1813 annotation file when annotation display text includes 'e' or
1815 <li>Cannot set colour of new feature type whilst creating
1817 <li>cDNA translation alignment should not be sequence
1818 order dependent</li>
1819 <li>'Show unconserved' doesn't work for lower case
1821 <li>Nucleotide ambiguity codes involving R not recognised</li>
1822 </ul> <em>Deployment and Documentation</em>
1824 <li>Applet example pages appear different to the rest of
1825 www.jalview.org</li>
1826 </ul> <em>Application Known issues</em>
1828 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1829 <li>Misleading message appears after trying to delete
1831 <li>Jalview icon not shown in dock after InstallAnywhere
1832 version launches</li>
1833 <li>Fetching EMBL reference for an RNA sequence results
1834 fails with a sequence mismatch</li>
1835 <li>Corrupted or unreadable alignment display when
1836 scrolling alignment to right</li>
1837 <li>ArrayIndexOutOfBoundsException thrown when remove
1838 empty columns called on alignment with ragged gapped ends</li>
1839 <li>auto calculated alignment annotation rows do not get
1840 placed above or below non-autocalculated rows</li>
1841 <li>Jalview dekstop becomes sluggish at full screen in
1842 ultra-high resolution</li>
1843 <li>Cannot disable consensus calculation independently of
1844 quality and conservation</li>
1845 <li>Mouseover highlighting between cDNA and protein can
1846 become sluggish with more than one splitframe shown</li>
1847 </ul> <em>Applet Known Issues</em>
1849 <li>Core PDB parsing code requires Jmol</li>
1850 <li>Sequence canvas panel goes white when alignment
1851 window is being resized</li>
1857 <td><div align="center">
1858 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1860 <td><em>General</em>
1862 <li>Updated Java code signing certificate donated by
1864 <li>Features and annotation preserved when performing
1865 pairwise alignment</li>
1866 <li>RNA pseudoknot annotation can be
1867 imported/exported/displayed</li>
1868 <li>'colour by annotation' can colour by RNA and
1869 protein secondary structure</li>
1870 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1871 post-hoc with 2.9 release</em>)
1874 </ul> <em>Application</em>
1876 <li>Extract and display secondary structure for sequences
1877 with 3D structures</li>
1878 <li>Support for parsing RNAML</li>
1879 <li>Annotations menu for layout
1881 <li>sort sequence annotation rows by alignment</li>
1882 <li>place sequence annotation above/below alignment
1885 <li>Output in Stockholm format</li>
1886 <li>Internationalisation: improved Spanish (es)
1888 <li>Structure viewer preferences tab</li>
1889 <li>Disorder and Secondary Structure annotation tracks
1890 shared between alignments</li>
1891 <li>UCSF Chimera launch and linked highlighting from
1893 <li>Show/hide all sequence associated annotation rows for
1894 all or current selection</li>
1895 <li>disorder and secondary structure predictions
1896 available as dataset annotation</li>
1897 <li>Per-sequence rna helices colouring</li>
1900 <li>Sequence database accessions imported when fetching
1901 alignments from Rfam</li>
1902 <li>update VARNA version to 3.91</li>
1904 <li>New groovy scripts for exporting aligned positions,
1905 conservation values, and calculating sum of pairs scores.</li>
1906 <li>Command line argument to set default JABAWS server</li>
1907 <li>include installation type in build properties and
1908 console log output</li>
1909 <li>Updated Jalview project format to preserve dataset
1913 <!-- issues resolved --> <em>Application</em>
1915 <li>Distinguish alignment and sequence associated RNA
1916 structure in structure->view->VARNA</li>
1917 <li>Raise dialog box if user deletes all sequences in an
1919 <li>Pressing F1 results in documentation opening twice</li>
1920 <li>Sequence feature tooltip is wrapped</li>
1921 <li>Double click on sequence associated annotation
1922 selects only first column</li>
1923 <li>Redundancy removal doesn't result in unlinked
1924 leaves shown in tree</li>
1925 <li>Undos after several redundancy removals don't undo
1927 <li>Hide sequence doesn't hide associated annotation</li>
1928 <li>User defined colours dialog box too big to fit on
1929 screen and buttons not visible</li>
1930 <li>author list isn't updated if already written to
1931 Jalview properties</li>
1932 <li>Popup menu won't open after retrieving sequence
1934 <li>File open window for associate PDB doesn't open</li>
1935 <li>Left-then-right click on a sequence id opens a
1936 browser search window</li>
1937 <li>Cannot open sequence feature shading/sort popup menu
1938 in feature settings dialog</li>
1939 <li>better tooltip placement for some areas of Jalview
1941 <li>Allow addition of JABAWS Server which doesn't
1942 pass validation</li>
1943 <li>Web services parameters dialog box is too large to
1945 <li>Muscle nucleotide alignment preset obscured by
1947 <li>JABAWS preset submenus don't contain newly
1948 defined user preset</li>
1949 <li>MSA web services warns user if they were launched
1950 with invalid input</li>
1951 <li>Jalview cannot contact DAS Registy when running on
1954 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1955 'Superpose with' submenu not shown when new view
1959 </ul> <!-- <em>Applet</em>
1961 </ul> <em>General</em>
1963 </ul>--> <em>Deployment and Documentation</em>
1965 <li>2G and 1G options in launchApp have no effect on
1966 memory allocation</li>
1967 <li>launchApp service doesn't automatically open
1968 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1970 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1971 InstallAnywhere reports cannot find valid JVM when Java
1972 1.7_055 is available
1974 </ul> <em>Application Known issues</em>
1977 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1978 corrupted or unreadable alignment display when scrolling
1982 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1983 retrieval fails but progress bar continues for DAS retrieval
1984 with large number of ID
1987 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1988 flatfile output of visible region has incorrect sequence
1992 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1993 rna structure consensus doesn't update when secondary
1994 structure tracks are rearranged
1997 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1998 invalid rna structure positional highlighting does not
1999 highlight position of invalid base pairs
2002 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2003 out of memory errors are not raised when saving Jalview
2004 project from alignment window file menu
2007 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2008 Switching to RNA Helices colouring doesn't propagate to
2012 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2013 colour by RNA Helices not enabled when user created
2014 annotation added to alignment
2017 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2018 Jalview icon not shown on dock in Mountain Lion/Webstart
2020 </ul> <em>Applet Known Issues</em>
2023 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2024 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2027 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2028 Jalview and Jmol example not compatible with IE9
2031 <li>Sort by annotation score doesn't reverse order
2037 <td><div align="center">
2038 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2041 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2044 <li>Internationalisation of user interface (usually
2045 called i18n support) and translation for Spanish locale</li>
2046 <li>Define/Undefine group on current selection with
2047 Ctrl-G/Shift Ctrl-G</li>
2048 <li>Improved group creation/removal options in
2049 alignment/sequence Popup menu</li>
2050 <li>Sensible precision for symbol distribution
2051 percentages shown in logo tooltip.</li>
2052 <li>Annotation panel height set according to amount of
2053 annotation when alignment first opened</li>
2054 </ul> <em>Application</em>
2056 <li>Interactive consensus RNA secondary structure
2057 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2058 <li>Select columns containing particular features from
2059 Feature Settings dialog</li>
2060 <li>View all 'representative' PDB structures for selected
2062 <li>Update Jalview project format:
2064 <li>New file extension for Jalview projects '.jvp'</li>
2065 <li>Preserve sequence and annotation dataset (to
2066 store secondary structure annotation,etc)</li>
2067 <li>Per group and alignment annotation and RNA helix
2071 <li>New similarity measures for PCA and Tree calculation
2073 <li>Experimental support for retrieval and viewing of
2074 flanking regions for an alignment</li>
2078 <!-- issues resolved --> <em>Application</em>
2080 <li>logo keeps spinning and status remains at queued or
2081 running after job is cancelled</li>
2082 <li>cannot export features from alignments imported from
2083 Jalview/VAMSAS projects</li>
2084 <li>Buggy slider for web service parameters that take
2086 <li>Newly created RNA secondary structure line doesn't
2087 have 'display all symbols' flag set</li>
2088 <li>T-COFFEE alignment score shading scheme and other
2089 annotation shading not saved in Jalview project</li>
2090 <li>Local file cannot be loaded in freshly downloaded
2092 <li>Jalview icon not shown on dock in Mountain
2094 <li>Load file from desktop file browser fails</li>
2095 <li>Occasional NPE thrown when calculating large trees</li>
2096 <li>Cannot reorder or slide sequences after dragging an
2097 alignment onto desktop</li>
2098 <li>Colour by annotation dialog throws NPE after using
2099 'extract scores' function</li>
2100 <li>Loading/cut'n'pasting an empty file leads to a grey
2101 alignment window</li>
2102 <li>Disorder thresholds rendered incorrectly after
2103 performing IUPred disorder prediction</li>
2104 <li>Multiple group annotated consensus rows shown when
2105 changing 'normalise logo' display setting</li>
2106 <li>Find shows blank dialog after 'finished searching' if
2107 nothing matches query</li>
2108 <li>Null Pointer Exceptions raised when sorting by
2109 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2111 <li>Errors in Jmol console when structures in alignment
2112 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2114 <li>Not all working JABAWS services are shown in
2116 <li>JAVAWS version of Jalview fails to launch with
2117 'invalid literal/length code'</li>
2118 <li>Annotation/RNA Helix colourschemes cannot be applied
2119 to alignment with groups (actually fixed in 2.8.0b1)</li>
2120 <li>RNA Helices and T-Coffee Scores available as default
2123 </ul> <em>Applet</em>
2125 <li>Remove group option is shown even when selection is
2127 <li>Apply to all groups ticked but colourscheme changes
2128 don't affect groups</li>
2129 <li>Documented RNA Helices and T-Coffee Scores as valid
2130 colourscheme name</li>
2131 <li>Annotation labels drawn on sequence IDs when
2132 Annotation panel is not displayed</li>
2133 <li>Increased font size for dropdown menus on OSX and
2134 embedded windows</li>
2135 </ul> <em>Other</em>
2137 <li>Consensus sequence for alignments/groups with a
2138 single sequence were not calculated</li>
2139 <li>annotation files that contain only groups imported as
2140 annotation and junk sequences</li>
2141 <li>Fasta files with sequences containing '*' incorrectly
2142 recognised as PFAM or BLC</li>
2143 <li>conservation/PID slider apply all groups option
2144 doesn't affect background (2.8.0b1)
2146 <li>redundancy highlighting is erratic at 0% and 100%</li>
2147 <li>Remove gapped columns fails for sequences with ragged
2149 <li>AMSA annotation row with leading spaces is not
2150 registered correctly on import</li>
2151 <li>Jalview crashes when selecting PCA analysis for
2152 certain alignments</li>
2153 <li>Opening the colour by annotation dialog for an
2154 existing annotation based 'use original colours'
2155 colourscheme loses original colours setting</li>
2160 <td><div align="center">
2161 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2162 <em>30/1/2014</em></strong>
2166 <li>Trusted certificates for JalviewLite applet and
2167 Jalview Desktop application<br />Certificate was donated by
2168 <a href="https://www.certum.eu">Certum</a> to the Jalview
2169 open source project).
2171 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2172 <li>Output in Stockholm format</li>
2173 <li>Allow import of data from gzipped files</li>
2174 <li>Export/import group and sequence associated line
2175 graph thresholds</li>
2176 <li>Nucleotide substitution matrix that supports RNA and
2177 ambiguity codes</li>
2178 <li>Allow disorder predictions to be made on the current
2179 selection (or visible selection) in the same way that JPred
2181 <li>Groovy scripting for headless Jalview operation</li>
2182 </ul> <em>Other improvements</em>
2184 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2185 <li>COMBINE statement uses current SEQUENCE_REF and
2186 GROUP_REF scope to group annotation rows</li>
2187 <li>Support '' style escaping of quotes in Newick
2189 <li>Group options for JABAWS service by command line name</li>
2190 <li>Empty tooltip shown for JABA service options with a
2191 link but no description</li>
2192 <li>Select primary source when selecting authority in
2193 database fetcher GUI</li>
2194 <li>Add .mfa to FASTA file extensions recognised by
2196 <li>Annotation label tooltip text wrap</li>
2201 <li>Slow scrolling when lots of annotation rows are
2203 <li>Lots of NPE (and slowness) after creating RNA
2204 secondary structure annotation line</li>
2205 <li>Sequence database accessions not imported when
2206 fetching alignments from Rfam</li>
2207 <li>Incorrect SHMR submission for sequences with
2209 <li>View all structures does not always superpose
2211 <li>Option widgets in service parameters not updated to
2212 reflect user or preset settings</li>
2213 <li>Null pointer exceptions for some services without
2214 presets or adjustable parameters</li>
2215 <li>Discover PDB IDs entry in structure menu doesn't
2216 discover PDB xRefs</li>
2217 <li>Exception encountered while trying to retrieve
2218 features with DAS</li>
2219 <li>Lowest value in annotation row isn't coloured
2220 when colour by annotation (per sequence) is coloured</li>
2221 <li>Keyboard mode P jumps to start of gapped region when
2222 residue follows a gap</li>
2223 <li>Jalview appears to hang importing an alignment with
2224 Wrap as default or after enabling Wrap</li>
2225 <li>'Right click to add annotations' message
2226 shown in wrap mode when no annotations present</li>
2227 <li>Disorder predictions fail with NPE if no automatic
2228 annotation already exists on alignment</li>
2229 <li>oninit javascript function should be called after
2230 initialisation completes</li>
2231 <li>Remove redundancy after disorder prediction corrupts
2232 alignment window display</li>
2233 <li>Example annotation file in documentation is invalid</li>
2234 <li>Grouped line graph annotation rows are not exported
2235 to annotation file</li>
2236 <li>Multi-harmony analysis cannot be run when only two
2238 <li>Cannot create multiple groups of line graphs with
2239 several 'combine' statements in annotation file</li>
2240 <li>Pressing return several times causes Number Format
2241 exceptions in keyboard mode</li>
2242 <li>Multi-harmony (SHMMR) method doesn't submit
2243 correct partitions for input data</li>
2244 <li>Translation from DNA to Amino Acids fails</li>
2245 <li>Jalview fail to load newick tree with quoted label</li>
2246 <li>--headless flag isn't understood</li>
2247 <li>ClassCastException when generating EPS in headless
2249 <li>Adjusting sequence-associated shading threshold only
2250 changes one row's threshold</li>
2251 <li>Preferences and Feature settings panel panel
2252 doesn't open</li>
2253 <li>hide consensus histogram also hides conservation and
2254 quality histograms</li>
2259 <td><div align="center">
2260 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2262 <td><em>Application</em>
2264 <li>Support for JABAWS 2.0 Services (AACon alignment
2265 conservation, protein disorder and Clustal Omega)</li>
2266 <li>JABAWS server status indicator in Web Services
2268 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2269 in Jalview alignment window</li>
2270 <li>Updated Jalview build and deploy framework for OSX
2271 mountain lion, windows 7, and 8</li>
2272 <li>Nucleotide substitution matrix for PCA that supports
2273 RNA and ambiguity codes</li>
2275 <li>Improved sequence database retrieval GUI</li>
2276 <li>Support fetching and database reference look up
2277 against multiple DAS sources (Fetch all from in 'fetch db
2279 <li>Jalview project improvements
2281 <li>Store and retrieve the 'belowAlignment'
2282 flag for annotation</li>
2283 <li>calcId attribute to group annotation rows on the
2285 <li>Store AACon calculation settings for a view in
2286 Jalview project</li>
2290 <li>horizontal scrolling gesture support</li>
2291 <li>Visual progress indicator when PCA calculation is
2293 <li>Simpler JABA web services menus</li>
2294 <li>visual indication that web service results are still
2295 being retrieved from server</li>
2296 <li>Serialise the dialogs that are shown when Jalview
2297 starts up for first time</li>
2298 <li>Jalview user agent string for interacting with HTTP
2300 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2302 <li>Examples directory and Groovy library included in
2303 InstallAnywhere distribution</li>
2304 </ul> <em>Applet</em>
2306 <li>RNA alignment and secondary structure annotation
2307 visualization applet example</li>
2308 </ul> <em>General</em>
2310 <li>Normalise option for consensus sequence logo</li>
2311 <li>Reset button in PCA window to return dimensions to
2313 <li>Allow seqspace or Jalview variant of alignment PCA
2315 <li>PCA with either nucleic acid and protein substitution
2317 <li>Allow windows containing HTML reports to be exported
2319 <li>Interactive display and editing of RNA secondary
2320 structure contacts</li>
2321 <li>RNA Helix Alignment Colouring</li>
2322 <li>RNA base pair logo consensus</li>
2323 <li>Parse sequence associated secondary structure
2324 information in Stockholm files</li>
2325 <li>HTML Export database accessions and annotation
2326 information presented in tooltip for sequences</li>
2327 <li>Import secondary structure from LOCARNA clustalw
2328 style RNA alignment files</li>
2329 <li>import and visualise T-COFFEE quality scores for an
2331 <li>'colour by annotation' per sequence option to
2332 shade each sequence according to its associated alignment
2334 <li>New Jalview Logo</li>
2335 </ul> <em>Documentation and Development</em>
2337 <li>documentation for score matrices used in Jalview</li>
2338 <li>New Website!</li>
2340 <td><em>Application</em>
2342 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2343 wsdbfetch REST service</li>
2344 <li>Stop windows being moved outside desktop on OSX</li>
2345 <li>Filetype associations not installed for webstart
2347 <li>Jalview does not always retrieve progress of a JABAWS
2348 job execution in full once it is complete</li>
2349 <li>revise SHMR RSBS definition to ensure alignment is
2350 uploaded via ali_file parameter</li>
2351 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2352 <li>View all structures superposed fails with exception</li>
2353 <li>Jnet job queues forever if a very short sequence is
2354 submitted for prediction</li>
2355 <li>Cut and paste menu not opened when mouse clicked on
2357 <li>Putting fractional value into integer text box in
2358 alignment parameter dialog causes Jalview to hang</li>
2359 <li>Structure view highlighting doesn't work on
2361 <li>View all structures fails with exception shown in
2363 <li>Characters in filename associated with PDBEntry not
2364 escaped in a platform independent way</li>
2365 <li>Jalview desktop fails to launch with exception when
2367 <li>Tree calculation reports 'you must have 2 or more
2368 sequences selected' when selection is empty</li>
2369 <li>Jalview desktop fails to launch with jar signature
2370 failure when java web start temporary file caching is
2372 <li>DAS Sequence retrieval with range qualification
2373 results in sequence xref which includes range qualification</li>
2374 <li>Errors during processing of command line arguments
2375 cause progress bar (JAL-898) to be removed</li>
2376 <li>Replace comma for semi-colon option not disabled for
2377 DAS sources in sequence fetcher</li>
2378 <li>Cannot close news reader when JABAWS server warning
2379 dialog is shown</li>
2380 <li>Option widgets not updated to reflect user settings</li>
2381 <li>Edited sequence not submitted to web service</li>
2382 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2383 <li>InstallAnywhere installer doesn't unpack and run
2384 on OSX Mountain Lion</li>
2385 <li>Annotation panel not given a scroll bar when
2386 sequences with alignment annotation are pasted into the
2388 <li>Sequence associated annotation rows not associated
2389 when loaded from Jalview project</li>
2390 <li>Browser launch fails with NPE on java 1.7</li>
2391 <li>JABAWS alignment marked as finished when job was
2392 cancelled or job failed due to invalid input</li>
2393 <li>NPE with v2.7 example when clicking on Tree
2394 associated with all views</li>
2395 <li>Exceptions when copy/paste sequences with grouped
2396 annotation rows to new window</li>
2397 </ul> <em>Applet</em>
2399 <li>Sequence features are momentarily displayed before
2400 they are hidden using hidefeaturegroups applet parameter</li>
2401 <li>loading features via javascript API automatically
2402 enables feature display</li>
2403 <li>scrollToColumnIn javascript API method doesn't
2405 </ul> <em>General</em>
2407 <li>Redundancy removal fails for rna alignment</li>
2408 <li>PCA calculation fails when sequence has been selected
2409 and then deselected</li>
2410 <li>PCA window shows grey box when first opened on OSX</li>
2411 <li>Letters coloured pink in sequence logo when alignment
2412 coloured with clustalx</li>
2413 <li>Choosing fonts without letter symbols defined causes
2414 exceptions and redraw errors</li>
2415 <li>Initial PCA plot view is not same as manually
2416 reconfigured view</li>
2417 <li>Grouped annotation graph label has incorrect line
2419 <li>Grouped annotation graph label display is corrupted
2420 for lots of labels</li>
2425 <div align="center">
2426 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2429 <td><em>Application</em>
2431 <li>Jalview Desktop News Reader</li>
2432 <li>Tweaked default layout of web services menu</li>
2433 <li>View/alignment association menu to enable user to
2434 easily specify which alignment a multi-structure view takes
2435 its colours/correspondences from</li>
2436 <li>Allow properties file location to be specified as URL</li>
2437 <li>Extend Jalview project to preserve associations
2438 between many alignment views and a single Jmol display</li>
2439 <li>Store annotation row height in Jalview project file</li>
2440 <li>Annotation row column label formatting attributes
2441 stored in project file</li>
2442 <li>Annotation row order for auto-calculated annotation
2443 rows preserved in Jalview project file</li>
2444 <li>Visual progress indication when Jalview state is
2445 saved using Desktop window menu</li>
2446 <li>Visual indication that command line arguments are
2447 still being processed</li>
2448 <li>Groovy script execution from URL</li>
2449 <li>Colour by annotation default min and max colours in
2451 <li>Automatically associate PDB files dragged onto an
2452 alignment with sequences that have high similarity and
2454 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2455 <li>'view structures' option to open many
2456 structures in same window</li>
2457 <li>Sort associated views menu option for tree panel</li>
2458 <li>Group all JABA and non-JABA services for a particular
2459 analysis function in its own submenu</li>
2460 </ul> <em>Applet</em>
2462 <li>Userdefined and autogenerated annotation rows for
2464 <li>Adjustment of alignment annotation pane height</li>
2465 <li>Annotation scrollbar for annotation panel</li>
2466 <li>Drag to reorder annotation rows in annotation panel</li>
2467 <li>'automaticScrolling' parameter</li>
2468 <li>Allow sequences with partial ID string matches to be
2469 annotated from GFF/Jalview features files</li>
2470 <li>Sequence logo annotation row in applet</li>
2471 <li>Absolute paths relative to host server in applet
2472 parameters are treated as such</li>
2473 <li>New in the JalviewLite javascript API:
2475 <li>JalviewLite.js javascript library</li>
2476 <li>Javascript callbacks for
2478 <li>Applet initialisation</li>
2479 <li>Sequence/alignment mouse-overs and selections</li>
2482 <li>scrollTo row and column alignment scrolling
2484 <li>Select sequence/alignment regions from javascript</li>
2485 <li>javascript structure viewer harness to pass
2486 messages between Jmol and Jalview when running as
2487 distinct applets</li>
2488 <li>sortBy method</li>
2489 <li>Set of applet and application examples shipped
2490 with documentation</li>
2491 <li>New example to demonstrate JalviewLite and Jmol
2492 javascript message exchange</li>
2494 </ul> <em>General</em>
2496 <li>Enable Jmol displays to be associated with multiple
2497 multiple alignments</li>
2498 <li>Option to automatically sort alignment with new tree</li>
2499 <li>User configurable link to enable redirects to a
2500 www.Jalview.org mirror</li>
2501 <li>Jmol colours option for Jmol displays</li>
2502 <li>Configurable newline string when writing alignment
2503 and other flat files</li>
2504 <li>Allow alignment annotation description lines to
2505 contain html tags</li>
2506 </ul> <em>Documentation and Development</em>
2508 <li>Add groovy test harness for bulk load testing to
2510 <li>Groovy script to load and align a set of sequences
2511 using a web service before displaying the result in the
2512 Jalview desktop</li>
2513 <li>Restructured javascript and applet api documentation</li>
2514 <li>Ant target to publish example html files with applet
2516 <li>Netbeans project for building Jalview from source</li>
2517 <li>ant task to create online javadoc for Jalview source</li>
2519 <td><em>Application</em>
2521 <li>User defined colourscheme throws exception when
2522 current built in colourscheme is saved as new scheme</li>
2523 <li>AlignFrame->Save in application pops up save
2524 dialog for valid filename/format</li>
2525 <li>Cannot view associated structure for UniProt sequence</li>
2526 <li>PDB file association breaks for UniProt sequence
2528 <li>Associate PDB from file dialog does not tell you
2529 which sequence is to be associated with the file</li>
2530 <li>Find All raises null pointer exception when query
2531 only matches sequence IDs</li>
2532 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2533 <li>Jalview project with Jmol views created with Jalview
2534 2.4 cannot be loaded</li>
2535 <li>Filetype associations not installed for webstart
2537 <li>Two or more chains in a single PDB file associated
2538 with sequences in different alignments do not get coloured
2539 by their associated sequence</li>
2540 <li>Visibility status of autocalculated annotation row
2541 not preserved when project is loaded</li>
2542 <li>Annotation row height and visibility attributes not
2543 stored in Jalview project</li>
2544 <li>Tree bootstraps are not preserved when saved as a
2545 Jalview project</li>
2546 <li>Envision2 workflow tooltips are corrupted</li>
2547 <li>Enabling show group conservation also enables colour
2548 by conservation</li>
2549 <li>Duplicate group associated conservation or consensus
2550 created on new view</li>
2551 <li>Annotation scrollbar not displayed after 'show
2552 all hidden annotation rows' option selected</li>
2553 <li>Alignment quality not updated after alignment
2554 annotation row is hidden then shown</li>
2555 <li>Preserve colouring of structures coloured by
2556 sequences in pre Jalview 2.7 projects</li>
2557 <li>Web service job parameter dialog is not laid out
2559 <li>Web services menu not refreshed after 'reset
2560 services' button is pressed in preferences</li>
2561 <li>Annotation off by one in Jalview v2_3 example project</li>
2562 <li>Structures imported from file and saved in project
2563 get name like jalview_pdb1234.txt when reloaded</li>
2564 <li>Jalview does not always retrieve progress of a JABAWS
2565 job execution in full once it is complete</li>
2566 </ul> <em>Applet</em>
2568 <li>Alignment height set incorrectly when lots of
2569 annotation rows are displayed</li>
2570 <li>Relative URLs in feature HTML text not resolved to
2572 <li>View follows highlighting does not work for positions
2574 <li><= shown as = in tooltip</li>
2575 <li>Export features raises exception when no features
2577 <li>Separator string used for serialising lists of IDs
2578 for javascript api is modified when separator string
2579 provided as parameter</li>
2580 <li>Null pointer exception when selecting tree leaves for
2581 alignment with no existing selection</li>
2582 <li>Relative URLs for datasources assumed to be relative
2583 to applet's codebase</li>
2584 <li>Status bar not updated after finished searching and
2585 search wraps around to first result</li>
2586 <li>StructureSelectionManager instance shared between
2587 several Jalview applets causes race conditions and memory
2589 <li>Hover tooltip and mouseover of position on structure
2590 not sent from Jmol in applet</li>
2591 <li>Certain sequences of javascript method calls to
2592 applet API fatally hang browser</li>
2593 </ul> <em>General</em>
2595 <li>View follows structure mouseover scrolls beyond
2596 position with wrapped view and hidden regions</li>
2597 <li>Find sequence position moves to wrong residue
2598 with/without hidden columns</li>
2599 <li>Sequence length given in alignment properties window
2601 <li>InvalidNumberFormat exceptions thrown when trying to
2602 import PDB like structure files</li>
2603 <li>Positional search results are only highlighted
2604 between user-supplied sequence start/end bounds</li>
2605 <li>End attribute of sequence is not validated</li>
2606 <li>Find dialog only finds first sequence containing a
2607 given sequence position</li>
2608 <li>Sequence numbering not preserved in MSF alignment
2610 <li>Jalview PDB file reader does not extract sequence
2611 from nucleotide chains correctly</li>
2612 <li>Structure colours not updated when tree partition
2613 changed in alignment</li>
2614 <li>Sequence associated secondary structure not correctly
2615 parsed in interleaved stockholm</li>
2616 <li>Colour by annotation dialog does not restore current
2618 <li>Hiding (nearly) all sequences doesn't work
2620 <li>Sequences containing lowercase letters are not
2621 properly associated with their pdb files</li>
2622 </ul> <em>Documentation and Development</em>
2624 <li>schemas/JalviewWsParamSet.xsd corrupted by
2625 ApplyCopyright tool</li>
2630 <div align="center">
2631 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2634 <td><em>Application</em>
2636 <li>New warning dialog when the Jalview Desktop cannot
2637 contact web services</li>
2638 <li>JABA service parameters for a preset are shown in
2639 service job window</li>
2640 <li>JABA Service menu entries reworded</li>
2644 <li>Modeller PIR IO broken - cannot correctly import a
2645 pir file emitted by Jalview</li>
2646 <li>Existing feature settings transferred to new
2647 alignment view created from cut'n'paste</li>
2648 <li>Improved test for mixed amino/nucleotide chains when
2649 parsing PDB files</li>
2650 <li>Consensus and conservation annotation rows
2651 occasionally become blank for all new windows</li>
2652 <li>Exception raised when right clicking above sequences
2653 in wrapped view mode</li>
2654 </ul> <em>Application</em>
2656 <li>multiple multiply aligned structure views cause cpu
2657 usage to hit 100% and computer to hang</li>
2658 <li>Web Service parameter layout breaks for long user
2659 parameter names</li>
2660 <li>Jaba service discovery hangs desktop if Jaba server
2667 <div align="center">
2668 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2671 <td><em>Application</em>
2673 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2674 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2677 <li>Web Services preference tab</li>
2678 <li>Analysis parameters dialog box and user defined
2680 <li>Improved speed and layout of Envision2 service menu</li>
2681 <li>Superpose structures using associated sequence
2683 <li>Export coordinates and projection as CSV from PCA
2685 </ul> <em>Applet</em>
2687 <li>enable javascript: execution by the applet via the
2688 link out mechanism</li>
2689 </ul> <em>Other</em>
2691 <li>Updated the Jmol Jalview interface to work with Jmol
2693 <li>The Jalview Desktop and JalviewLite applet now
2694 require Java 1.5</li>
2695 <li>Allow Jalview feature colour specification for GFF
2696 sequence annotation files</li>
2697 <li>New 'colour by label' keword in Jalview feature file
2698 type colour specification</li>
2699 <li>New Jalview Desktop Groovy API method that allows a
2700 script to check if it being run in an interactive session or
2701 in a batch operation from the Jalview command line</li>
2705 <li>clustalx colourscheme colours Ds preferentially when
2706 both D+E are present in over 50% of the column</li>
2707 </ul> <em>Application</em>
2709 <li>typo in AlignmentFrame->View->Hide->all but
2710 selected Regions menu item</li>
2711 <li>sequence fetcher replaces ',' for ';' when the ',' is
2712 part of a valid accession ID</li>
2713 <li>fatal OOM if object retrieved by sequence fetcher
2714 runs out of memory</li>
2715 <li>unhandled Out of Memory Error when viewing pca
2716 analysis results</li>
2717 <li>InstallAnywhere builds fail to launch on OS X java
2718 10.5 update 4 (due to apple Java 1.6 update)</li>
2719 <li>Installanywhere Jalview silently fails to launch</li>
2720 </ul> <em>Applet</em>
2722 <li>Jalview.getFeatureGroups() raises an
2723 ArrayIndexOutOfBoundsException if no feature groups are
2730 <div align="center">
2731 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2737 <li>Alignment prettyprinter doesn't cope with long
2739 <li>clustalx colourscheme colours Ds preferentially when
2740 both D+E are present in over 50% of the column</li>
2741 <li>nucleic acid structures retrieved from PDB do not
2742 import correctly</li>
2743 <li>More columns get selected than were clicked on when a
2744 number of columns are hidden</li>
2745 <li>annotation label popup menu not providing correct
2746 add/hide/show options when rows are hidden or none are
2748 <li>Stockholm format shown in list of readable formats,
2749 and parser copes better with alignments from RFAM.</li>
2750 <li>CSV output of consensus only includes the percentage
2751 of all symbols if sequence logo display is enabled</li>
2753 </ul> <em>Applet</em>
2755 <li>annotation panel disappears when annotation is
2757 </ul> <em>Application</em>
2759 <li>Alignment view not redrawn properly when new
2760 alignment opened where annotation panel is visible but no
2761 annotations are present on alignment</li>
2762 <li>pasted region containing hidden columns is
2763 incorrectly displayed in new alignment window</li>
2764 <li>Jalview slow to complete operations when stdout is
2765 flooded (fix is to close the Jalview console)</li>
2766 <li>typo in AlignmentFrame->View->Hide->all but
2767 selected Rregions menu item.</li>
2768 <li>inconsistent group submenu and Format submenu entry
2769 'Un' or 'Non'conserved</li>
2770 <li>Sequence feature settings are being shared by
2771 multiple distinct alignments</li>
2772 <li>group annotation not recreated when tree partition is
2774 <li>double click on group annotation to select sequences
2775 does not propagate to associated trees</li>
2776 <li>Mac OSX specific issues:
2778 <li>exception raised when mouse clicked on desktop
2779 window background</li>
2780 <li>Desktop menu placed on menu bar and application
2781 name set correctly</li>
2782 <li>sequence feature settings not wide enough for the
2783 save feature colourscheme button</li>
2792 <div align="center">
2793 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2796 <td><em>New Capabilities</em>
2798 <li>URL links generated from description line for
2799 regular-expression based URL links (applet and application)
2801 <li>Non-positional feature URL links are shown in link
2803 <li>Linked viewing of nucleic acid sequences and
2805 <li>Automatic Scrolling option in View menu to display
2806 the currently highlighted region of an alignment.</li>
2807 <li>Order an alignment by sequence length, or using the
2808 average score or total feature count for each sequence.</li>
2809 <li>Shading features by score or associated description</li>
2810 <li>Subdivide alignment and groups based on identity of
2811 selected subsequence (Make Groups from Selection).</li>
2812 <li>New hide/show options including Shift+Control+H to
2813 hide everything but the currently selected region.</li>
2814 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2815 </ul> <em>Application</em>
2817 <li>Fetch DB References capabilities and UI expanded to
2818 support retrieval from DAS sequence sources</li>
2819 <li>Local DAS Sequence sources can be added via the
2820 command line or via the Add local source dialog box.</li>
2821 <li>DAS Dbref and DbxRef feature types are parsed as
2822 database references and protein_name is parsed as
2823 description line (BioSapiens terms).</li>
2824 <li>Enable or disable non-positional feature and database
2825 references in sequence ID tooltip from View menu in
2827 <!-- <li>New hidden columns and rows and representatives capabilities
2828 in annotations file (in progress - not yet fully implemented)</li> -->
2829 <li>Group-associated consensus, sequence logos and
2830 conservation plots</li>
2831 <li>Symbol distributions for each column can be exported
2832 and visualized as sequence logos</li>
2833 <li>Optionally scale multi-character column labels to fit
2834 within each column of annotation row<!-- todo for applet -->
2836 <li>Optional automatic sort of associated alignment view
2837 when a new tree is opened.</li>
2838 <li>Jalview Java Console</li>
2839 <li>Better placement of desktop window when moving
2840 between different screens.</li>
2841 <li>New preference items for sequence ID tooltip and
2842 consensus annotation</li>
2843 <li>Client to submit sequences and IDs to Envision2
2845 <li><em>Vamsas Capabilities</em>
2847 <li>Improved VAMSAS synchronization (Jalview archive
2848 used to preserve views, structures, and tree display
2850 <li>Import of vamsas documents from disk or URL via
2852 <li>Sharing of selected regions between views and
2853 with other VAMSAS applications (Experimental feature!)</li>
2854 <li>Updated API to VAMSAS version 0.2</li>
2856 </ul> <em>Applet</em>
2858 <li>Middle button resizes annotation row height</li>
2861 <li>sortByTree (true/false) - automatically sort the
2862 associated alignment view by the tree when a new tree is
2864 <li>showTreeBootstraps (true/false) - show or hide
2865 branch bootstraps (default is to show them if available)</li>
2866 <li>showTreeDistances (true/false) - show or hide
2867 branch lengths (default is to show them if available)</li>
2868 <li>showUnlinkedTreeNodes (true/false) - indicate if
2869 unassociated nodes should be highlighted in the tree
2871 <li>heightScale and widthScale (1.0 or more) -
2872 increase the height or width of a cell in the alignment
2873 grid relative to the current font size.</li>
2876 <li>Non-positional features displayed in sequence ID
2878 </ul> <em>Other</em>
2880 <li>Features format: graduated colour definitions and
2881 specification of feature scores</li>
2882 <li>Alignment Annotations format: new keywords for group
2883 associated annotation (GROUP_REF) and annotation row display
2884 properties (ROW_PROPERTIES)</li>
2885 <li>XML formats extended to support graduated feature
2886 colourschemes, group associated annotation, and profile
2887 visualization settings.</li></td>
2890 <li>Source field in GFF files parsed as feature source
2891 rather than description</li>
2892 <li>Non-positional features are now included in sequence
2893 feature and gff files (controlled via non-positional feature
2894 visibility in tooltip).</li>
2895 <li>URL links generated for all feature links (bugfix)</li>
2896 <li>Added URL embedding instructions to features file
2898 <li>Codons containing ambiguous nucleotides translated as
2899 'X' in peptide product</li>
2900 <li>Match case switch in find dialog box works for both
2901 sequence ID and sequence string and query strings do not
2902 have to be in upper case to match case-insensitively.</li>
2903 <li>AMSA files only contain first column of
2904 multi-character column annotation labels</li>
2905 <li>Jalview Annotation File generation/parsing consistent
2906 with documentation (e.g. Stockholm annotation can be
2907 exported and re-imported)</li>
2908 <li>PDB files without embedded PDB IDs given a friendly
2910 <li>Find incrementally searches ID string matches as well
2911 as subsequence matches, and correctly reports total number
2915 <li>Better handling of exceptions during sequence
2917 <li>Dasobert generated non-positional feature URL
2918 link text excludes the start_end suffix</li>
2919 <li>DAS feature and source retrieval buttons disabled
2920 when fetch or registry operations in progress.</li>
2921 <li>PDB files retrieved from URLs are cached properly</li>
2922 <li>Sequence description lines properly shared via
2924 <li>Sequence fetcher fetches multiple records for all
2926 <li>Ensured that command line das feature retrieval
2927 completes before alignment figures are generated.</li>
2928 <li>Reduced time taken when opening file browser for
2930 <li>isAligned check prior to calculating tree, PCA or
2931 submitting an MSA to JNet now excludes hidden sequences.</li>
2932 <li>User defined group colours properly recovered
2933 from Jalview projects.</li>
2942 <div align="center">
2943 <strong>2.4.0.b2</strong><br> 28/10/2009
2948 <li>Experimental support for google analytics usage
2950 <li>Jalview privacy settings (user preferences and docs).</li>
2955 <li>Race condition in applet preventing startup in
2957 <li>Exception when feature created from selection beyond
2958 length of sequence.</li>
2959 <li>Allow synthetic PDB files to be imported gracefully</li>
2960 <li>Sequence associated annotation rows associate with
2961 all sequences with a given id</li>
2962 <li>Find function matches case-insensitively for sequence
2963 ID string searches</li>
2964 <li>Non-standard characters do not cause pairwise
2965 alignment to fail with exception</li>
2966 </ul> <em>Application Issues</em>
2968 <li>Sequences are now validated against EMBL database</li>
2969 <li>Sequence fetcher fetches multiple records for all
2971 </ul> <em>InstallAnywhere Issues</em>
2973 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2974 issue with installAnywhere mechanism)</li>
2975 <li>Command line launching of JARs from InstallAnywhere
2976 version (java class versioning error fixed)</li>
2983 <div align="center">
2984 <strong>2.4</strong><br> 27/8/2008
2987 <td><em>User Interface</em>
2989 <li>Linked highlighting of codon and amino acid from
2990 translation and protein products</li>
2991 <li>Linked highlighting of structure associated with
2992 residue mapping to codon position</li>
2993 <li>Sequence Fetcher provides example accession numbers
2994 and 'clear' button</li>
2995 <li>MemoryMonitor added as an option under Desktop's
2997 <li>Extract score function to parse whitespace separated
2998 numeric data in description line</li>
2999 <li>Column labels in alignment annotation can be centred.</li>
3000 <li>Tooltip for sequence associated annotation give name
3002 </ul> <em>Web Services and URL fetching</em>
3004 <li>JPred3 web service</li>
3005 <li>Prototype sequence search client (no public services
3007 <li>Fetch either seed alignment or full alignment from
3009 <li>URL Links created for matching database cross
3010 references as well as sequence ID</li>
3011 <li>URL Links can be created using regular-expressions</li>
3012 </ul> <em>Sequence Database Connectivity</em>
3014 <li>Retrieval of cross-referenced sequences from other
3016 <li>Generalised database reference retrieval and
3017 validation to all fetchable databases</li>
3018 <li>Fetch sequences from DAS sources supporting the
3019 sequence command</li>
3020 </ul> <em>Import and Export</em>
3021 <li>export annotation rows as CSV for spreadsheet import</li>
3022 <li>Jalview projects record alignment dataset associations,
3023 EMBL products, and cDNA sequence mappings</li>
3024 <li>Sequence Group colour can be specified in Annotation
3026 <li>Ad-hoc colouring of group in Annotation File using RGB
3027 triplet as name of colourscheme</li>
3028 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3030 <li>treenode binding for VAMSAS tree exchange</li>
3031 <li>local editing and update of sequences in VAMSAS
3032 alignments (experimental)</li>
3033 <li>Create new or select existing session to join</li>
3034 <li>load and save of vamsas documents</li>
3035 </ul> <em>Application command line</em>
3037 <li>-tree parameter to open trees (introduced for passing
3039 <li>-fetchfrom command line argument to specify nicknames
3040 of DAS servers to query for alignment features</li>
3041 <li>-dasserver command line argument to add new servers
3042 that are also automatically queried for features</li>
3043 <li>-groovy command line argument executes a given groovy
3044 script after all input data has been loaded and parsed</li>
3045 </ul> <em>Applet-Application data exchange</em>
3047 <li>Trees passed as applet parameters can be passed to
3048 application (when using "View in full
3049 application")</li>
3050 </ul> <em>Applet Parameters</em>
3052 <li>feature group display control parameter</li>
3053 <li>debug parameter</li>
3054 <li>showbutton parameter</li>
3055 </ul> <em>Applet API methods</em>
3057 <li>newView public method</li>
3058 <li>Window (current view) specific get/set public methods</li>
3059 <li>Feature display control methods</li>
3060 <li>get list of currently selected sequences</li>
3061 </ul> <em>New Jalview distribution features</em>
3063 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3064 <li>RELEASE file gives build properties for the latest
3065 Jalview release.</li>
3066 <li>Java 1.1 Applet build made easier and donotobfuscate
3067 property controls execution of obfuscator</li>
3068 <li>Build target for generating source distribution</li>
3069 <li>Debug flag for javacc</li>
3070 <li>.jalview_properties file is documented (slightly) in
3071 jalview.bin.Cache</li>
3072 <li>Continuous Build Integration for stable and
3073 development version of Application, Applet and source
3078 <li>selected region output includes visible annotations
3079 (for certain formats)</li>
3080 <li>edit label/displaychar contains existing label/char
3082 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3083 <li>shorter peptide product names from EMBL records</li>
3084 <li>Newick string generator makes compact representations</li>
3085 <li>bootstrap values parsed correctly for tree files with
3087 <li>pathological filechooser bug avoided by not allowing
3088 filenames containing a ':'</li>
3089 <li>Fixed exception when parsing GFF files containing
3090 global sequence features</li>
3091 <li>Alignment datasets are finalized only when number of
3092 references from alignment sequences goes to zero</li>
3093 <li>Close of tree branch colour box without colour
3094 selection causes cascading exceptions</li>
3095 <li>occasional negative imgwidth exceptions</li>
3096 <li>better reporting of non-fatal warnings to user when
3097 file parsing fails.</li>
3098 <li>Save works when Jalview project is default format</li>
3099 <li>Save as dialog opened if current alignment format is
3100 not a valid output format</li>
3101 <li>UniProt canonical names introduced for both das and
3103 <li>Histidine should be midblue (not pink!) in Zappo</li>
3104 <li>error messages passed up and output when data read
3106 <li>edit undo recovers previous dataset sequence when
3107 sequence is edited</li>
3108 <li>allow PDB files without pdb ID HEADER lines (like
3109 those generated by MODELLER) to be read in properly</li>
3110 <li>allow reading of JPred concise files as a normal
3112 <li>Stockholm annotation parsing and alignment properties
3113 import fixed for PFAM records</li>
3114 <li>Structure view windows have correct name in Desktop
3116 <li>annotation consisting of sequence associated scores
3117 can be read and written correctly to annotation file</li>
3118 <li>Aligned cDNA translation to aligned peptide works
3120 <li>Fixed display of hidden sequence markers and
3121 non-italic font for representatives in Applet</li>
3122 <li>Applet Menus are always embedded in applet window on
3124 <li>Newly shown features appear at top of stack (in
3126 <li>Annotations added via parameter not drawn properly
3127 due to null pointer exceptions</li>
3128 <li>Secondary structure lines are drawn starting from
3129 first column of alignment</li>
3130 <li>UniProt XML import updated for new schema release in
3132 <li>Sequence feature to sequence ID match for Features
3133 file is case-insensitive</li>
3134 <li>Sequence features read from Features file appended to
3135 all sequences with matching IDs</li>
3136 <li>PDB structure coloured correctly for associated views
3137 containing a sub-sequence</li>
3138 <li>PDB files can be retrieved by applet from Jar files</li>
3139 <li>feature and annotation file applet parameters
3140 referring to different directories are retrieved correctly</li>
3141 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3142 <li>Fixed application hang whilst waiting for
3143 splash-screen version check to complete</li>
3144 <li>Applet properly URLencodes input parameter values
3145 when passing them to the launchApp service</li>
3146 <li>display name and local features preserved in results
3147 retrieved from web service</li>
3148 <li>Visual delay indication for sequence retrieval and
3149 sequence fetcher initialisation</li>
3150 <li>updated Application to use DAS 1.53e version of
3151 dasobert DAS client</li>
3152 <li>Re-instated Full AMSA support and .amsa file
3154 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3162 <div align="center">
3163 <strong>2.3</strong><br> 9/5/07
3168 <li>Jmol 11.0.2 integration</li>
3169 <li>PDB views stored in Jalview XML files</li>
3170 <li>Slide sequences</li>
3171 <li>Edit sequence in place</li>
3172 <li>EMBL CDS features</li>
3173 <li>DAS Feature mapping</li>
3174 <li>Feature ordering</li>
3175 <li>Alignment Properties</li>
3176 <li>Annotation Scores</li>
3177 <li>Sort by scores</li>
3178 <li>Feature/annotation editing in applet</li>
3183 <li>Headless state operation in 2.2.1</li>
3184 <li>Incorrect and unstable DNA pairwise alignment</li>
3185 <li>Cut and paste of sequences with annotation</li>
3186 <li>Feature group display state in XML</li>
3187 <li>Feature ordering in XML</li>
3188 <li>blc file iteration selection using filename # suffix</li>
3189 <li>Stockholm alignment properties</li>
3190 <li>Stockhom alignment secondary structure annotation</li>
3191 <li>2.2.1 applet had no feature transparency</li>
3192 <li>Number pad keys can be used in cursor mode</li>
3193 <li>Structure Viewer mirror image resolved</li>
3200 <div align="center">
3201 <strong>2.2.1</strong><br> 12/2/07
3206 <li>Non standard characters can be read and displayed
3207 <li>Annotations/Features can be imported/exported to the
3209 <li>Applet allows editing of sequence/annotation/group
3210 name & description
3211 <li>Preference setting to display sequence name in
3213 <li>Annotation file format extended to allow
3214 Sequence_groups to be defined
3215 <li>Default opening of alignment overview panel can be
3216 specified in preferences
3217 <li>PDB residue numbering annotation added to associated
3223 <li>Applet crash under certain Linux OS with Java 1.6
3225 <li>Annotation file export / import bugs fixed
3226 <li>PNG / EPS image output bugs fixed
3232 <div align="center">
3233 <strong>2.2</strong><br> 27/11/06
3238 <li>Multiple views on alignment
3239 <li>Sequence feature editing
3240 <li>"Reload" alignment
3241 <li>"Save" to current filename
3242 <li>Background dependent text colour
3243 <li>Right align sequence ids
3244 <li>User-defined lower case residue colours
3247 <li>Menu item accelerator keys
3248 <li>Control-V pastes to current alignment
3249 <li>Cancel button for DAS Feature Fetching
3250 <li>PCA and PDB Viewers zoom via mouse roller
3251 <li>User-defined sub-tree colours and sub-tree selection
3253 <li>'New Window' button on the 'Output to Text box'
3258 <li>New memory efficient Undo/Redo System
3259 <li>Optimised symbol lookups and conservation/consensus
3261 <li>Region Conservation/Consensus recalculated after
3263 <li>Fixed Remove Empty Columns Bug (empty columns at end
3265 <li>Slowed DAS Feature Fetching for increased robustness.
3267 <li>Made angle brackets in ASCII feature descriptions
3269 <li>Re-instated Zoom function for PCA
3270 <li>Sequence descriptions conserved in web service
3272 <li>UniProt ID discoverer uses any word separated by
3274 <li>WsDbFetch query/result association resolved
3275 <li>Tree leaf to sequence mapping improved
3276 <li>Smooth fonts switch moved to FontChooser dialog box.
3283 <div align="center">
3284 <strong>2.1.1</strong><br> 12/9/06
3289 <li>Copy consensus sequence to clipboard</li>
3294 <li>Image output - rightmost residues are rendered if
3295 sequence id panel has been resized</li>
3296 <li>Image output - all offscreen group boundaries are
3298 <li>Annotation files with sequence references - all
3299 elements in file are relative to sequence position</li>
3300 <li>Mac Applet users can use Alt key for group editing</li>
3306 <div align="center">
3307 <strong>2.1</strong><br> 22/8/06
3312 <li>MAFFT Multiple Alignment in default Web Service list</li>
3313 <li>DAS Feature fetching</li>
3314 <li>Hide sequences and columns</li>
3315 <li>Export Annotations and Features</li>
3316 <li>GFF file reading / writing</li>
3317 <li>Associate structures with sequences from local PDB
3319 <li>Add sequences to exisiting alignment</li>
3320 <li>Recently opened files / URL lists</li>
3321 <li>Applet can launch the full application</li>
3322 <li>Applet has transparency for features (Java 1.2
3324 <li>Applet has user defined colours parameter</li>
3325 <li>Applet can load sequences from parameter
3326 "sequence<em>x</em>"
3332 <li>Redundancy Panel reinstalled in the Applet</li>
3333 <li>Monospaced font - EPS / rescaling bug fixed</li>
3334 <li>Annotation files with sequence references bug fixed</li>
3340 <div align="center">
3341 <strong>2.08.1</strong><br> 2/5/06
3346 <li>Change case of selected region from Popup menu</li>
3347 <li>Choose to match case when searching</li>
3348 <li>Middle mouse button and mouse movement can compress /
3349 expand the visible width and height of the alignment</li>
3354 <li>Annotation Panel displays complete JNet results</li>
3360 <div align="center">
3361 <strong>2.08b</strong><br> 18/4/06
3367 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3368 <li>Righthand label on wrapped alignments shows correct
3375 <div align="center">
3376 <strong>2.08</strong><br> 10/4/06
3381 <li>Editing can be locked to the selection area</li>
3382 <li>Keyboard editing</li>
3383 <li>Create sequence features from searches</li>
3384 <li>Precalculated annotations can be loaded onto
3386 <li>Features file allows grouping of features</li>
3387 <li>Annotation Colouring scheme added</li>
3388 <li>Smooth fonts off by default - Faster rendering</li>
3389 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3394 <li>Drag & Drop fixed on Linux</li>
3395 <li>Jalview Archive file faster to load/save, sequence
3396 descriptions saved.</li>
3402 <div align="center">
3403 <strong>2.07</strong><br> 12/12/05
3408 <li>PDB Structure Viewer enhanced</li>
3409 <li>Sequence Feature retrieval and display enhanced</li>
3410 <li>Choose to output sequence start-end after sequence
3411 name for file output</li>
3412 <li>Sequence Fetcher WSDBFetch@EBI</li>
3413 <li>Applet can read feature files, PDB files and can be
3414 used for HTML form input</li>
3419 <li>HTML output writes groups and features</li>
3420 <li>Group editing is Control and mouse click</li>
3421 <li>File IO bugs</li>
3427 <div align="center">
3428 <strong>2.06</strong><br> 28/9/05
3433 <li>View annotations in wrapped mode</li>
3434 <li>More options for PCA viewer</li>
3439 <li>GUI bugs resolved</li>
3440 <li>Runs with -nodisplay from command line</li>
3446 <div align="center">
3447 <strong>2.05b</strong><br> 15/9/05
3452 <li>Choose EPS export as lineart or text</li>
3453 <li>Jar files are executable</li>
3454 <li>Can read in Uracil - maps to unknown residue</li>
3459 <li>Known OutOfMemory errors give warning message</li>
3460 <li>Overview window calculated more efficiently</li>
3461 <li>Several GUI bugs resolved</li>
3467 <div align="center">
3468 <strong>2.05</strong><br> 30/8/05
3473 <li>Edit and annotate in "Wrapped" view</li>
3478 <li>Several GUI bugs resolved</li>
3484 <div align="center">
3485 <strong>2.04</strong><br> 24/8/05
3490 <li>Hold down mouse wheel & scroll to change font
3496 <li>Improved JPred client reliability</li>
3497 <li>Improved loading of Jalview files</li>
3503 <div align="center">
3504 <strong>2.03</strong><br> 18/8/05
3509 <li>Set Proxy server name and port in preferences</li>
3510 <li>Multiple URL links from sequence ids</li>
3511 <li>User Defined Colours can have a scheme name and added
3513 <li>Choose to ignore gaps in consensus calculation</li>
3514 <li>Unix users can set default web browser</li>
3515 <li>Runs without GUI for batch processing</li>
3516 <li>Dynamically generated Web Service Menus</li>
3521 <li>InstallAnywhere download for Sparc Solaris</li>
3527 <div align="center">
3528 <strong>2.02</strong><br> 18/7/05
3534 <li>Copy & Paste order of sequences maintains
3535 alignment order.</li>
3541 <div align="center">
3542 <strong>2.01</strong><br> 12/7/05
3547 <li>Use delete key for deleting selection.</li>
3548 <li>Use Mouse wheel to scroll sequences.</li>
3549 <li>Help file updated to describe how to add alignment
3551 <li>Version and build date written to build properties
3553 <li>InstallAnywhere installation will check for updates
3554 at launch of Jalview.</li>
3559 <li>Delete gaps bug fixed.</li>
3560 <li>FileChooser sorts columns.</li>
3561 <li>Can remove groups one by one.</li>
3562 <li>Filechooser icons installed.</li>
3563 <li>Finder ignores return character when searching.
3564 Return key will initiate a search.<br>
3571 <div align="center">
3572 <strong>2.0</strong><br> 20/6/05
3577 <li>New codebase</li>