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;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
85 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
86 429 rate limit request hander
89 <!-- JAL-2773 -->Structure views don't get updated unless
90 their colours have changed
92 <li><!-- JAL-2495 -->All linked sequences are highlighted for a structure mousover (Jmol) or selection (Chimera)</li>
93 <li><!-- JAL-2790 -->'Cancel' button in progress bar for JABAWS AACon, RNAAliFold and Disorder prediction jobs
96 <li><!-- JAL-2617 -->Stop codons are excluded in CDS/Protein view from Ensembl locus cross-references</li>
97 <li><!-- JAL-2685 -->Start/End limits are shown in Pairwise Alignment report</li>
99 <ul><li>Example groovy script for generating a matrix of percent identity scores for current alignment.</li></ul>
100 <em>Testing and Deployment</em>
101 <ul><li><!-- JAL-2727 -->Test to catch memory leaks in Jalview UI</li></ul>
104 <td><div align="left">
107 <li><!-- JAL-2643 -->Pressing tab after updating the colour threshold text field doesn't trigger an update to the alignment view</li>
108 <li><!-- JAL-2682 -->Race condition when parsing sequence ID strings in parallel</li>
109 <li><!-- JAL-2608 -->Overview windows are also closed when alignment window is closed</li>
110 <li><!-- JAL-2548 -->Export of features doesn't always respect group visibility</li>
114 <li><!-- JAL-2777 -->Structures with whitespace chainCode cannot be viewed in Chimera</li>
115 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
117 <li><!-- JAL-2757 -->Can't edit the query after the server error warning icon is shown in Uniprot and PDB Free Text Search Dialogs
119 <li><!-- JAL-2253 -->Slow EnsemblGenome ID lookup</li>
120 <li><!-- JAL-2529 -->Revised Ensembl REST API CDNA query</li>
121 <li><!-- JAL-2739 -->Hidden column marker in last column not rendered when switching back from Wrapped to normal view</li>
122 <li><!-- JAL-2768 -->Annotation display corrupted when scrolling right in unwapped alignment view</li>
123 <li><!-- JAL-2542 -->Existing features on subsequence incorrectly relocated when full sequence retrieved from database</li>
124 <li><!-- JAL-2733 -->Last reported memory still shown when Desktop->Show Memory is unticked (OSX only)</li>
125 <li><!-- JAL-2658 -->Amend Features dialog doesn't allow features of same type and group to be selected for amending</li>
126 <li><!-- JAL-2524 -->Jalview becomes sluggish in wide alignments when hidden columns are present</li>
127 <li><!-- JAL-2392 -->Jalview freezes when loading and displaying several structures</li>
128 <li><!-- JAL-2732 -->Black outlines left after resizing or moving a window</li>
129 <li><!-- JAL-1900,JAL-1625 -->Unable to minimise windows within the Jalview desktop on OSX</li>
130 <li><!-- JAL-2667 -->Mouse wheel doesn't scroll vertically when in wrapped alignment mode</li>
131 <li><!-- JAL-2636 -->Scale mark not shown when close to right hand end of alignment</li>
132 <li><!-- JAL-2684 -->Pairwise alignment only aligns selected regions of each selected sequence</li>
133 <li><!-- JAL-2973 -->Alignment ruler height set incorrectly after canceling the Alignment Window's Font dialog</li>
134 <li><!-- JAL-2036 -->Show cross-references not enabled after restoring project until a new view is created</li>
136 <strong><em>Applet</em></strong><br/>
138 <li><!-- JAL-2687 -->Concurrent modification exception when closing alignment panel</li>
140 <strong><em>BioJSON</em></strong><br/>
143 <!-- JAL-2546 -->BioJSON export does not preserve non-positional features
150 <td width="60" nowrap>
152 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
153 <em>2/10/2017</em></strong>
156 <td><div align="left">
157 <em>New features in Jalview Desktop</em>
160 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
162 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
166 <td><div align="left">
170 <td width="60" nowrap>
172 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
173 <em>7/9/2017</em></strong>
176 <td><div align="left">
180 <!-- JAL-2588 -->Show gaps in overview window by colouring
181 in grey (sequences used to be coloured grey, and gaps were
185 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
189 <!-- JAL-2587 -->Overview updates immediately on increase
190 in size and progress bar shown as higher resolution
191 overview is recalculated
196 <td><div align="left">
200 <!-- JAL-2664 -->Overview window redraws every hidden
201 column region row by row
204 <!-- JAL-2681 -->duplicate protein sequences shown after
205 retrieving Ensembl crossrefs for sequences from Uniprot
208 <!-- JAL-2603 -->Overview window throws NPE if show boxes
209 format setting is unticked
212 <!-- JAL-2610 -->Groups are coloured wrongly in overview
213 if group has show boxes format setting unticked
216 <!-- JAL-2672,JAL-2665 -->Redraw problems when
217 autoscrolling whilst dragging current selection group to
218 include sequences and columns not currently displayed
221 <!-- JAL-2691 -->Not all chains are mapped when multimeric
222 assemblies are imported via CIF file
225 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
226 displayed when threshold or conservation colouring is also
230 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
234 <!-- JAL-2673 -->Jalview continues to scroll after
235 dragging a selected region off the visible region of the
239 <!-- JAL-2724 -->Cannot apply annotation based
240 colourscheme to all groups in a view
243 <!-- JAL-2511 -->IDs don't line up with sequences
244 initially after font size change using the Font chooser or
251 <td width="60" nowrap>
253 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
256 <td><div align="left">
257 <em>Calculations</em>
261 <!-- JAL-1933 -->Occupancy annotation row shows number of
262 ungapped positions in each column of the alignment.
265 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
266 a calculation dialog box
269 <!-- JAL-2379 -->Revised implementation of PCA for speed
270 and memory efficiency (~30x faster)
273 <!-- JAL-2403 -->Revised implementation of sequence
274 similarity scores as used by Tree, PCA, Shading Consensus
275 and other calculations
278 <!-- JAL-2416 -->Score matrices are stored as resource
279 files within the Jalview codebase
282 <!-- JAL-2500 -->Trees computed on Sequence Feature
283 Similarity may have different topology due to increased
290 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
291 model for alignments and groups
294 <!-- JAL-384 -->Custom shading schemes created via groovy
301 <!-- JAL-2526 -->Efficiency improvements for interacting
302 with alignment and overview windows
305 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
309 <!-- JAL-2388 -->Hidden columns and sequences can be
313 <!-- JAL-2611 -->Click-drag in visible area allows fine
314 adjustment of visible position
318 <em>Data import/export</em>
321 <!-- JAL-2535 -->Posterior probability annotation from
322 Stockholm files imported as sequence associated annotation
325 <!-- JAL-2507 -->More robust per-sequence positional
326 annotation input/output via stockholm flatfile
329 <!-- JAL-2533 -->Sequence names don't include file
330 extension when importing structure files without embedded
331 names or PDB accessions
334 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
335 format sequence substitution matrices
338 <em>User Interface</em>
341 <!-- JAL-2447 --> Experimental Features Checkbox in
342 Desktop's Tools menu to hide or show untested features in
346 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
347 via Overview or sequence motif search operations
350 <!-- JAL-2547 -->Amend sequence features dialog box can be
351 opened by double clicking gaps within sequence feature
355 <!-- JAL-1476 -->Status bar message shown when not enough
356 aligned positions were available to create a 3D structure
360 <em>3D Structure</em>
363 <!-- JAL-2430 -->Hidden regions in alignment views are not
364 coloured in linked structure views
367 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
368 file-based command exchange
371 <!-- JAL-2375 -->Structure chooser automatically shows
372 Cached Structures rather than querying the PDBe if
373 structures are already available for sequences
376 <!-- JAL-2520 -->Structures imported via URL are cached in
377 the Jalview project rather than downloaded again when the
381 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
382 to transfer Chimera's structure attributes as Jalview
383 features, and vice-versa (<strong>Experimental
387 <em>Web Services</em>
390 <!-- JAL-2549 -->Updated JABAWS client to v2.2
393 <!-- JAL-2335 -->Filter non-standard amino acids and
394 nucleotides when submitting to AACon and other MSA
398 <!-- JAL-2316, -->URLs for viewing database
399 cross-references provided by identifiers.org and the
407 <!-- JAL-2344 -->FileFormatI interface for describing and
408 identifying file formats (instead of String constants)
411 <!-- JAL-2228 -->FeatureCounter script refactored for
412 efficiency when counting all displayed features (not
413 backwards compatible with 2.10.1)
416 <em>Example files</em>
419 <!-- JAL-2631 -->Graduated feature colour style example
420 included in the example feature file
423 <em>Documentation</em>
426 <!-- JAL-2339 -->Release notes reformatted for readability
427 with the built-in Java help viewer
430 <!-- JAL-1644 -->Find documentation updated with 'search
431 sequence description' option
437 <!-- JAL-2485, -->External service integration tests for
438 Uniprot REST Free Text Search Client
441 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
444 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
449 <td><div align="left">
450 <em>Calculations</em>
453 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
454 matrix - C->R should be '-3'<br />Old matrix restored
455 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
457 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
458 Jalview's treatment of gaps in PCA and substitution matrix
459 based Tree calculations.<br /> <br />In earlier versions
460 of Jalview, gaps matching gaps were penalised, and gaps
461 matching non-gaps penalised even more. In the PCA
462 calculation, gaps were actually treated as non-gaps - so
463 different costs were applied, which meant Jalview's PCAs
464 were different to those produced by SeqSpace.<br />Jalview
465 now treats gaps in the same way as SeqSpace (ie it scores
466 them as 0). <br /> <br />Enter the following in the
467 Groovy console to restore pre-2.10.2 behaviour:<br />
468 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
469 // for 2.10.1 mode <br />
470 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
471 // to restore 2.10.2 mode <br /> <br /> <em>Note:
472 these settings will affect all subsequent tree and PCA
473 calculations (not recommended)</em></li>
475 <!-- JAL-2424 -->Fixed off-by-one bug that affected
476 scaling of branch lengths for trees computed using
477 Sequence Feature Similarity.
480 <!-- JAL-2377 -->PCA calculation could hang when
481 generating output report when working with highly
485 <!-- JAL-2544 --> Sort by features includes features to
486 right of selected region when gaps present on right-hand
490 <em>User Interface</em>
493 <!-- JAL-2346 -->Reopening Colour by annotation dialog
494 doesn't reselect a specific sequence's associated
495 annotation after it was used for colouring a view
498 <!-- JAL-2419 -->Current selection lost if popup menu
499 opened on a region of alignment without groups
502 <!-- JAL-2374 -->Popup menu not always shown for regions
503 of an alignment with overlapping groups
506 <!-- JAL-2310 -->Finder double counts if both a sequence's
507 name and description match
510 <!-- JAL-2370 -->Hiding column selection containing two
511 hidden regions results in incorrect hidden regions
514 <!-- JAL-2386 -->'Apply to all groups' setting when
515 changing colour does not apply Conservation slider value
519 <!-- JAL-2373 -->Percentage identity and conservation menu
520 items do not show a tick or allow shading to be disabled
523 <!-- JAL-2385 -->Conservation shading or PID threshold
524 lost when base colourscheme changed if slider not visible
527 <!-- JAL-2547 -->Sequence features shown in tooltip for
528 gaps before start of features
531 <!-- JAL-2623 -->Graduated feature colour threshold not
532 restored to UI when feature colour is edited
535 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
536 a time when scrolling vertically in wrapped mode.
539 <!-- JAL-2630 -->Structure and alignment overview update
540 as graduate feature colour settings are modified via the
544 <!-- JAL-2034 -->Overview window doesn't always update
545 when a group defined on the alignment is resized
548 <!-- JAL-2605 -->Mouseovers on left/right scale region in
549 wrapped view result in positional status updates
553 <!-- JAL-2563 -->Status bar doesn't show position for
554 ambiguous amino acid and nucleotide symbols
557 <!-- JAL-2602 -->Copy consensus sequence failed if
558 alignment included gapped columns
561 <!-- JAL-2473 -->Minimum size set for Jalview windows so
562 widgets don't permanently disappear
565 <!-- JAL-2503 -->Cannot select or filter quantitative
566 annotation that are shown only as column labels (e.g.
567 T-Coffee column reliability scores)
570 <!-- JAL-2594 -->Exception thrown if trying to create a
571 sequence feature on gaps only
574 <!-- JAL-2504 -->Features created with 'New feature'
575 button from a Find inherit previously defined feature type
576 rather than the Find query string
579 <!-- JAL-2423 -->incorrect title in output window when
580 exporting tree calculated in Jalview
583 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
584 and then revealing them reorders sequences on the
588 <!-- JAL-964 -->Group panel in sequence feature settings
589 doesn't update to reflect available set of groups after
590 interactively adding or modifying features
593 <!-- JAL-2225 -->Sequence Database chooser unusable on
597 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
598 only excluded gaps in current sequence and ignored
605 <!-- JAL-2421 -->Overview window visible region moves
606 erratically when hidden rows or columns are present
609 <!-- JAL-2362 -->Per-residue colourschemes applied via the
610 Structure Viewer's colour menu don't correspond to
614 <!-- JAL-2405 -->Protein specific colours only offered in
615 colour and group colour menu for protein alignments
618 <!-- JAL-2385 -->Colour threshold slider doesn't update to
619 reflect currently selected view or group's shading
623 <!-- JAL-2624 -->Feature colour thresholds not respected
624 when rendered on overview and structures when opacity at
628 <!-- JAL-2589 -->User defined gap colour not shown in
629 overview when features overlaid on alignment
632 <em>Data import/export</em>
635 <!-- JAL-2576 -->Very large alignments take a long time to
639 <!-- JAL-2507 -->Per-sequence RNA secondary structures
640 added after a sequence was imported are not written to
644 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
645 when importing RNA secondary structure via Stockholm
648 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
649 not shown in correct direction for simple pseudoknots
652 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
653 with lightGray or darkGray via features file (but can
657 <!-- JAL-2383 -->Above PID colour threshold not recovered
658 when alignment view imported from project
661 <!-- JAL-2520,JAL-2465 -->No mappings generated between
662 structure and sequences extracted from structure files
663 imported via URL and viewed in Jmol
666 <!-- JAL-2520 -->Structures loaded via URL are saved in
667 Jalview Projects rather than fetched via URL again when
668 the project is loaded and the structure viewed
671 <em>Web Services</em>
674 <!-- JAL-2519 -->EnsemblGenomes example failing after
675 release of Ensembl v.88
678 <!-- JAL-2366 -->Proxy server address and port always
679 appear enabled in Preferences->Connections
682 <!-- JAL-2461 -->DAS registry not found exceptions
683 removed from console output
686 <!-- JAL-2582 -->Cannot retrieve protein products from
687 Ensembl by Peptide ID
690 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
691 created from SIFTs, and spurious 'Couldn't open structure
692 in Chimera' errors raised after April 2017 update (problem
693 due to 'null' string rather than empty string used for
694 residues with no corresponding PDB mapping).
697 <em>Application UI</em>
700 <!-- JAL-2361 -->User Defined Colours not added to Colour
704 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
705 case' residues (button in colourscheme editor debugged and
706 new documentation and tooltips added)
709 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
710 doesn't restore group-specific text colour thresholds
713 <!-- JAL-2243 -->Feature settings panel does not update as
714 new features are added to alignment
717 <!-- JAL-2532 -->Cancel in feature settings reverts
718 changes to feature colours via the Amend features dialog
721 <!-- JAL-2506 -->Null pointer exception when attempting to
722 edit graduated feature colour via amend features dialog
726 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
727 selection menu changes colours of alignment views
730 <!-- JAL-2426 -->Spurious exceptions in console raised
731 from alignment calculation workers after alignment has
735 <!-- JAL-1608 -->Typo in selection popup menu - Create
736 groups now 'Create Group'
739 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
740 Create/Undefine group doesn't always work
743 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
744 shown again after pressing 'Cancel'
747 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
748 adjusts start position in wrap mode
751 <!-- JAL-2563 -->Status bar doesn't show positions for
752 ambiguous amino acids
755 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
756 CDS/Protein view after CDS sequences added for aligned
760 <!-- JAL-2592 -->User defined colourschemes called 'User
761 Defined' don't appear in Colours menu
767 <!-- JAL-2468 -->Switching between Nucleotide and Protein
768 score models doesn't always result in an updated PCA plot
771 <!-- JAL-2442 -->Features not rendered as transparent on
772 overview or linked structure view
775 <!-- JAL-2372 -->Colour group by conservation doesn't
779 <!-- JAL-2517 -->Hitting Cancel after applying
780 user-defined colourscheme doesn't restore original
787 <!-- JAL-2314 -->Unit test failure:
788 jalview.ws.jabaws.RNAStructExportImport setup fails
791 <!-- JAL-2307 -->Unit test failure:
792 jalview.ws.sifts.SiftsClientTest due to compatibility
793 problems with deep array comparison equality asserts in
794 successive versions of TestNG
797 <!-- JAL-2479 -->Relocated StructureChooserTest and
798 ParameterUtilsTest Unit tests to Network suite
801 <em>New Known Issues</em>
804 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
805 phase after a sequence motif find operation
808 <!-- JAL-2550 -->Importing annotation file with rows
809 containing just upper and lower case letters are
810 interpreted as WUSS RNA secondary structure symbols
813 <!-- JAL-2590 -->Cannot load and display Newick trees
814 reliably from eggnog Ortholog database
817 <!-- JAL-2468 -->Status bar shows 'Marked x columns
818 containing features of type Highlight' when 'B' is pressed
819 to mark columns containing highlighted regions.
822 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
823 doesn't always add secondary structure annotation.
828 <td width="60" nowrap>
830 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
833 <td><div align="left">
837 <!-- JAL-98 -->Improved memory usage: sparse arrays used
838 for all consensus calculations
841 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
844 <li>Updated Jalview's Certum code signing certificate
850 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
851 set of database cross-references, sorted alphabetically
854 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
855 from database cross references. Users with custom links
856 will receive a <a href="webServices/urllinks.html#warning">warning
857 dialog</a> asking them to update their preferences.
860 <!-- JAL-2287-->Cancel button and escape listener on
861 dialog warning user about disconnecting Jalview from a
865 <!-- JAL-2320-->Jalview's Chimera control window closes if
866 the Chimera it is connected to is shut down
869 <!-- JAL-1738-->New keystroke (B) and Select highlighted
870 columns menu item to mark columns containing highlighted
871 regions (e.g. from structure selections or results of a
875 <!-- JAL-2284-->Command line option for batch-generation
876 of HTML pages rendering alignment data with the BioJS
886 <!-- JAL-2286 -->Columns with more than one modal residue
887 are not coloured or thresholded according to percent
888 identity (first observed in Jalview 2.8.2)
891 <!-- JAL-2301 -->Threonine incorrectly reported as not
895 <!-- JAL-2318 -->Updates to documentation pages (above PID
896 threshold, amino acid properties)
899 <!-- JAL-2292 -->Lower case residues in sequences are not
900 reported as mapped to residues in a structure file in the
904 <!--JAL-2324 -->Identical features with non-numeric scores
905 could be added multiple times to a sequence
908 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
909 bond features shown as two highlighted residues rather
910 than a range in linked structure views, and treated
911 correctly when selecting and computing trees from features
914 <!-- JAL-2281-->Custom URL links for database
915 cross-references are matched to database name regardless
923 <!-- JAL-2282-->Custom URL links for specific database
924 names without regular expressions also offer links from
928 <!-- JAL-2315-->Removing a single configured link in the
929 URL links pane in Connections preferences doesn't actually
930 update Jalview configuration
933 <!-- JAL-2272-->CTRL-Click on a selected region to open
934 the alignment area popup menu doesn't work on El-Capitan
937 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
938 files with similarly named sequences if dropped onto the
942 <!-- JAL-2312 -->Additional mappings are shown for PDB
943 entries where more chains exist in the PDB accession than
944 are reported in the SIFTS file
947 <!-- JAL-2317-->Certain structures do not get mapped to
948 the structure view when displayed with Chimera
951 <!-- JAL-2317-->No chains shown in the Chimera view
952 panel's View->Show Chains submenu
955 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
956 work for wrapped alignment views
959 <!--JAL-2197 -->Rename UI components for running JPred
960 predictions from 'JNet' to 'JPred'
963 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
964 corrupted when annotation panel vertical scroll is not at
968 <!--JAL-2332 -->Attempting to view structure for Hen
969 lysozyme results in a PDB Client error dialog box
972 <!-- JAL-2319 -->Structure View's mapping report switched
973 ranges for PDB and sequence for SIFTS
976 SIFTS 'Not_Observed' residues mapped to non-existant
980 <!-- <em>New Known Issues</em>
987 <td width="60" nowrap>
989 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
990 <em>25/10/2016</em></strong>
993 <td><em>Application</em>
995 <li>3D Structure chooser opens with 'Cached structures'
996 view if structures already loaded</li>
997 <li>Progress bar reports models as they are loaded to
1004 <li>Colour by conservation always enabled and no tick
1005 shown in menu when BLOSUM or PID shading applied</li>
1006 <li>FER1_ARATH and FER2_ARATH labels were switched in
1007 example sequences/projects/trees</li>
1009 <em>Application</em>
1011 <li>Jalview projects with views of local PDB structure
1012 files saved on Windows cannot be opened on OSX</li>
1013 <li>Multiple structure views can be opened and superposed
1014 without timeout for structures with multiple models or
1015 multiple sequences in alignment</li>
1016 <li>Cannot import or associated local PDB files without a
1017 PDB ID HEADER line</li>
1018 <li>RMSD is not output in Jmol console when superposition
1020 <li>Drag and drop of URL from Browser fails for Linux and
1021 OSX versions earlier than El Capitan</li>
1022 <li>ENA client ignores invalid content from ENA server</li>
1023 <li>Exceptions are not raised in console when ENA client
1024 attempts to fetch non-existent IDs via Fetch DB Refs UI
1026 <li>Exceptions are not raised in console when a new view
1027 is created on the alignment</li>
1028 <li>OSX right-click fixed for group selections: CMD-click
1029 to insert/remove gaps in groups and CTRL-click to open group
1032 <em>Build and deployment</em>
1034 <li>URL link checker now copes with multi-line anchor
1037 <em>New Known Issues</em>
1039 <li>Drag and drop from URL links in browsers do not work
1046 <td width="60" nowrap>
1047 <div align="center">
1048 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1051 <td><em>General</em>
1054 <!-- JAL-2124 -->Updated Spanish translations.
1057 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1058 for importing structure data to Jalview. Enables mmCIF and
1062 <!-- JAL-192 --->Alignment ruler shows positions relative to
1066 <!-- JAL-2202 -->Position/residue shown in status bar when
1067 mousing over sequence associated annotation
1070 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1074 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1075 '()', canonical '[]' and invalid '{}' base pair populations
1079 <!-- JAL-2092 -->Feature settings popup menu options for
1080 showing or hiding columns containing a feature
1083 <!-- JAL-1557 -->Edit selected group by double clicking on
1084 group and sequence associated annotation labels
1087 <!-- JAL-2236 -->Sequence name added to annotation label in
1088 select/hide columns by annotation and colour by annotation
1092 </ul> <em>Application</em>
1095 <!-- JAL-2050-->Automatically hide introns when opening a
1096 gene/transcript view
1099 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1103 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1104 structure mappings with the EMBL-EBI PDBe SIFTS database
1107 <!-- JAL-2079 -->Updated download sites used for Rfam and
1108 Pfam sources to xfam.org
1111 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1114 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1115 over sequences in Jalview
1118 <!-- JAL-2027-->Support for reverse-complement coding
1119 regions in ENA and EMBL
1122 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1123 for record retrieval via ENA rest API
1126 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1130 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1131 groovy script execution
1134 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1135 alignment window's Calculate menu
1138 <!-- JAL-1812 -->Allow groovy scripts that call
1139 Jalview.getAlignFrames() to run in headless mode
1142 <!-- JAL-2068 -->Support for creating new alignment
1143 calculation workers from groovy scripts
1146 <!-- JAL-1369 --->Store/restore reference sequence in
1150 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1151 associations are now saved/restored from project
1154 <!-- JAL-1993 -->Database selection dialog always shown
1155 before sequence fetcher is opened
1158 <!-- JAL-2183 -->Double click on an entry in Jalview's
1159 database chooser opens a sequence fetcher
1162 <!-- JAL-1563 -->Free-text search client for UniProt using
1163 the UniProt REST API
1166 <!-- JAL-2168 -->-nonews command line parameter to prevent
1167 the news reader opening
1170 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1171 querying stored in preferences
1174 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1178 <!-- JAL-1977-->Tooltips shown on database chooser
1181 <!-- JAL-391 -->Reverse complement function in calculate
1182 menu for nucleotide sequences
1185 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1186 and feature counts preserves alignment ordering (and
1187 debugged for complex feature sets).
1190 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1191 viewing structures with Jalview 2.10
1194 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1195 genome, transcript CCDS and gene ids via the Ensembl and
1196 Ensembl Genomes REST API
1199 <!-- JAL-2049 -->Protein sequence variant annotation
1200 computed for 'sequence_variant' annotation on CDS regions
1204 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1208 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1209 Ref Fetcher fails to match, or otherwise updates sequence
1210 data from external database records.
1213 <!-- JAL-2154 -->Revised Jalview Project format for
1214 efficient recovery of sequence coding and alignment
1215 annotation relationships.
1217 </ul> <!-- <em>Applet</em>
1228 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1232 <!-- JAL-2018-->Export features in Jalview format (again)
1233 includes graduated colourschemes
1236 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1237 working with big alignments and lots of hidden columns
1240 <!-- JAL-2053-->Hidden column markers not always rendered
1241 at right of alignment window
1244 <!-- JAL-2067 -->Tidied up links in help file table of
1248 <!-- JAL-2072 -->Feature based tree calculation not shown
1252 <!-- JAL-2075 -->Hidden columns ignored during feature
1253 based tree calculation
1256 <!-- JAL-2065 -->Alignment view stops updating when show
1257 unconserved enabled for group on alignment
1260 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1264 <!-- JAL-2146 -->Alignment column in status incorrectly
1265 shown as "Sequence position" when mousing over
1269 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1270 hidden columns present
1273 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1274 user created annotation added to alignment
1277 <!-- JAL-1841 -->RNA Structure consensus only computed for
1278 '()' base pair annotation
1281 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1282 in zero scores for all base pairs in RNA Structure
1286 <!-- JAL-2174-->Extend selection with columns containing
1290 <!-- JAL-2275 -->Pfam format writer puts extra space at
1291 beginning of sequence
1294 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1298 <!-- JAL-2238 -->Cannot create groups on an alignment from
1299 from a tree when t-coffee scores are shown
1302 <!-- JAL-1836,1967 -->Cannot import and view PDB
1303 structures with chains containing negative resnums (4q4h)
1306 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1310 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1311 to Clustal, PIR and PileUp output
1314 <!-- JAL-2008 -->Reordering sequence features that are
1315 not visible causes alignment window to repaint
1318 <!-- JAL-2006 -->Threshold sliders don't work in
1319 graduated colour and colour by annotation row for e-value
1320 scores associated with features and annotation rows
1323 <!-- JAL-1797 -->amino acid physicochemical conservation
1324 calculation should be case independent
1327 <!-- JAL-2173 -->Remove annotation also updates hidden
1331 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1332 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1333 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1336 <!-- JAL-2065 -->Null pointer exceptions and redraw
1337 problems when reference sequence defined and 'show
1338 non-conserved' enabled
1341 <!-- JAL-1306 -->Quality and Conservation are now shown on
1342 load even when Consensus calculation is disabled
1345 <!-- JAL-1932 -->Remove right on penultimate column of
1346 alignment does nothing
1349 <em>Application</em>
1352 <!-- JAL-1552-->URLs and links can't be imported by
1353 drag'n'drop on OSX when launched via webstart (note - not
1354 yet fixed for El Capitan)
1357 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1358 output when running on non-gb/us i18n platforms
1361 <!-- JAL-1944 -->Error thrown when exporting a view with
1362 hidden sequences as flat-file alignment
1365 <!-- JAL-2030-->InstallAnywhere distribution fails when
1369 <!-- JAL-2080-->Jalview very slow to launch via webstart
1370 (also hotfix for 2.9.0b2)
1373 <!-- JAL-2085 -->Cannot save project when view has a
1374 reference sequence defined
1377 <!-- JAL-1011 -->Columns are suddenly selected in other
1378 alignments and views when revealing hidden columns
1381 <!-- JAL-1989 -->Hide columns not mirrored in complement
1382 view in a cDNA/Protein splitframe
1385 <!-- JAL-1369 -->Cannot save/restore representative
1386 sequence from project when only one sequence is
1390 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1391 in Structure Chooser
1394 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1395 structure consensus didn't refresh annotation panel
1398 <!-- JAL-1962 -->View mapping in structure view shows
1399 mappings between sequence and all chains in a PDB file
1402 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1403 dialogs format columns correctly, don't display array
1404 data, sort columns according to type
1407 <!-- JAL-1975 -->Export complete shown after destination
1408 file chooser is cancelled during an image export
1411 <!-- JAL-2025 -->Error when querying PDB Service with
1412 sequence name containing special characters
1415 <!-- JAL-2024 -->Manual PDB structure querying should be
1419 <!-- JAL-2104 -->Large tooltips with broken HTML
1420 formatting don't wrap
1423 <!-- JAL-1128 -->Figures exported from wrapped view are
1424 truncated so L looks like I in consensus annotation
1427 <!-- JAL-2003 -->Export features should only export the
1428 currently displayed features for the current selection or
1432 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1433 after fetching cross-references, and restoring from
1437 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1438 followed in the structure viewer
1441 <!-- JAL-2163 -->Titles for individual alignments in
1442 splitframe not restored from project
1445 <!-- JAL-2145 -->missing autocalculated annotation at
1446 trailing end of protein alignment in transcript/product
1447 splitview when pad-gaps not enabled by default
1450 <!-- JAL-1797 -->amino acid physicochemical conservation
1454 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1455 article has been read (reopened issue due to
1456 internationalisation problems)
1459 <!-- JAL-1960 -->Only offer PDB structures in structure
1460 viewer based on sequence name, PDB and UniProt
1465 <!-- JAL-1976 -->No progress bar shown during export of
1469 <!-- JAL-2213 -->Structures not always superimposed after
1470 multiple structures are shown for one or more sequences.
1473 <!-- JAL-1370 -->Reference sequence characters should not
1474 be replaced with '.' when 'Show unconserved' format option
1478 <!-- JAL-1823 -->Cannot specify chain code when entering
1479 specific PDB id for sequence
1482 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1483 'Export hidden sequences' is enabled, but 'export hidden
1484 columns' is disabled.
1487 <!--JAL-2026-->Best Quality option in structure chooser
1488 selects lowest rather than highest resolution structures
1492 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1493 to sequence mapping in 'View Mappings' report
1496 <!-- JAL-2284 -->Unable to read old Jalview projects that
1497 contain non-XML data added after Jalvew wrote project.
1500 <!-- JAL-2118 -->Newly created annotation row reorders
1501 after clicking on it to create new annotation for a
1505 <!-- JAL-1980 -->Null Pointer Exception raised when
1506 pressing Add on an orphaned cut'n'paste window.
1508 <!-- may exclude, this is an external service stability issue JAL-1941
1509 -- > RNA 3D structure not added via DSSR service</li> -->
1514 <!-- JAL-2151 -->Incorrect columns are selected when
1515 hidden columns present before start of sequence
1518 <!-- JAL-1986 -->Missing dependencies on applet pages
1522 <!-- JAL-1947 -->Overview pixel size changes when
1523 sequences are hidden in applet
1526 <!-- JAL-1996 -->Updated instructions for applet
1527 deployment on examples pages.
1534 <td width="60" nowrap>
1535 <div align="center">
1536 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1537 <em>16/10/2015</em></strong>
1540 <td><em>General</em>
1542 <li>Time stamps for signed Jalview application and applet
1547 <em>Application</em>
1549 <li>Duplicate group consensus and conservation rows
1550 shown when tree is partitioned</li>
1551 <li>Erratic behaviour when tree partitions made with
1552 multiple cDNA/Protein split views</li>
1558 <td width="60" nowrap>
1559 <div align="center">
1560 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1561 <em>8/10/2015</em></strong>
1564 <td><em>General</em>
1566 <li>Updated Spanish translations of localized text for
1568 </ul> <em>Application</em>
1570 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1571 <li>Signed OSX InstallAnywhere installer<br></li>
1572 <li>Support for per-sequence based annotations in BioJSON</li>
1573 </ul> <em>Applet</em>
1575 <li>Split frame example added to applet examples page</li>
1576 </ul> <em>Build and Deployment</em>
1579 <!-- JAL-1888 -->New ant target for running Jalview's test
1587 <li>Mapping of cDNA to protein in split frames
1588 incorrect when sequence start > 1</li>
1589 <li>Broken images in filter column by annotation dialog
1591 <li>Feature colours not parsed from features file</li>
1592 <li>Exceptions and incomplete link URLs recovered when
1593 loading a features file containing HTML tags in feature
1597 <em>Application</em>
1599 <li>Annotations corrupted after BioJS export and
1601 <li>Incorrect sequence limits after Fetch DB References
1602 with 'trim retrieved sequences'</li>
1603 <li>Incorrect warning about deleting all data when
1604 deleting selected columns</li>
1605 <li>Patch to build system for shipping properly signed
1606 JNLP templates for webstart launch</li>
1607 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1608 unreleased structures for download or viewing</li>
1609 <li>Tab/space/return keystroke operation of EMBL-PDBe
1610 fetcher/viewer dialogs works correctly</li>
1611 <li>Disabled 'minimise' button on Jalview windows
1612 running on OSX to workaround redraw hang bug</li>
1613 <li>Split cDNA/Protein view position and geometry not
1614 recovered from jalview project</li>
1615 <li>Initial enabled/disabled state of annotation menu
1616 sorter 'show autocalculated first/last' corresponds to
1618 <li>Restoring of Clustal, RNA Helices and T-Coffee
1619 color schemes from BioJSON</li>
1623 <li>Reorder sequences mirrored in cDNA/Protein split
1625 <li>Applet with Jmol examples not loading correctly</li>
1631 <td><div align="center">
1632 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1634 <td><em>General</em>
1636 <li>Linked visualisation and analysis of DNA and Protein
1639 <li>Translated cDNA alignments shown as split protein
1640 and DNA alignment views</li>
1641 <li>Codon consensus annotation for linked protein and
1642 cDNA alignment views</li>
1643 <li>Link cDNA or Protein product sequences by loading
1644 them onto Protein or cDNA alignments</li>
1645 <li>Reconstruct linked cDNA alignment from aligned
1646 protein sequences</li>
1649 <li>Jmol integration updated to Jmol v14.2.14</li>
1650 <li>Import and export of Jalview alignment views as <a
1651 href="features/bioJsonFormat.html">BioJSON</a></li>
1652 <li>New alignment annotation file statements for
1653 reference sequences and marking hidden columns</li>
1654 <li>Reference sequence based alignment shading to
1655 highlight variation</li>
1656 <li>Select or hide columns according to alignment
1658 <li>Find option for locating sequences by description</li>
1659 <li>Conserved physicochemical properties shown in amino
1660 acid conservation row</li>
1661 <li>Alignments can be sorted by number of RNA helices</li>
1662 </ul> <em>Application</em>
1664 <li>New cDNA/Protein analysis capabilities
1666 <li>Get Cross-References should open a Split Frame
1667 view with cDNA/Protein</li>
1668 <li>Detect when nucleotide sequences and protein
1669 sequences are placed in the same alignment</li>
1670 <li>Split cDNA/Protein views are saved in Jalview
1675 <li>Use REST API to talk to Chimera</li>
1676 <li>Selected regions in Chimera are highlighted in linked
1677 Jalview windows</li>
1679 <li>VARNA RNA viewer updated to v3.93</li>
1680 <li>VARNA views are saved in Jalview Projects</li>
1681 <li>Pseudoknots displayed as Jalview RNA annotation can
1682 be shown in VARNA</li>
1684 <li>Make groups for selection uses marked columns as well
1685 as the active selected region</li>
1687 <li>Calculate UPGMA and NJ trees using sequence feature
1689 <li>New Export options
1691 <li>New Export Settings dialog to control hidden
1692 region export in flat file generation</li>
1694 <li>Export alignment views for display with the <a
1695 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1697 <li>Export scrollable SVG in HTML page</li>
1698 <li>Optional embedding of BioJSON data when exporting
1699 alignment figures to HTML</li>
1701 <li>3D structure retrieval and display
1703 <li>Free text and structured queries with the PDBe
1705 <li>PDBe Search API based discovery and selection of
1706 PDB structures for a sequence set</li>
1710 <li>JPred4 employed for protein secondary structure
1712 <li>Hide Insertions menu option to hide unaligned columns
1713 for one or a group of sequences</li>
1714 <li>Automatically hide insertions in alignments imported
1715 from the JPred4 web server</li>
1716 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1717 system on OSX<br />LGPL libraries courtesy of <a
1718 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1720 <li>changed 'View nucleotide structure' submenu to 'View
1721 VARNA 2D Structure'</li>
1722 <li>change "View protein structure" menu option to "3D
1725 </ul> <em>Applet</em>
1727 <li>New layout for applet example pages</li>
1728 <li>New parameters to enable SplitFrame view
1729 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1730 <li>New example demonstrating linked viewing of cDNA and
1731 Protein alignments</li>
1732 </ul> <em>Development and deployment</em>
1734 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1735 <li>Include installation type and git revision in build
1736 properties and console log output</li>
1737 <li>Jalview Github organisation, and new github site for
1738 storing BioJsMSA Templates</li>
1739 <li>Jalview's unit tests now managed with TestNG</li>
1742 <!-- <em>General</em>
1744 </ul> --> <!-- issues resolved --> <em>Application</em>
1746 <li>Escape should close any open find dialogs</li>
1747 <li>Typo in select-by-features status report</li>
1748 <li>Consensus RNA secondary secondary structure
1749 predictions are not highlighted in amber</li>
1750 <li>Missing gap character in v2.7 example file means
1751 alignment appears unaligned when pad-gaps is not enabled</li>
1752 <li>First switch to RNA Helices colouring doesn't colour
1753 associated structure views</li>
1754 <li>ID width preference option is greyed out when auto
1755 width checkbox not enabled</li>
1756 <li>Stopped a warning dialog from being shown when
1757 creating user defined colours</li>
1758 <li>'View Mapping' in structure viewer shows sequence
1759 mappings for just that viewer's sequences</li>
1760 <li>Workaround for superposing PDB files containing
1761 multiple models in Chimera</li>
1762 <li>Report sequence position in status bar when hovering
1763 over Jmol structure</li>
1764 <li>Cannot output gaps as '.' symbols with Selection ->
1765 output to text box</li>
1766 <li>Flat file exports of alignments with hidden columns
1767 have incorrect sequence start/end</li>
1768 <li>'Aligning' a second chain to a Chimera structure from
1770 <li>Colour schemes applied to structure viewers don't
1771 work for nucleotide</li>
1772 <li>Loading/cut'n'pasting an empty or invalid file leads
1773 to a grey/invisible alignment window</li>
1774 <li>Exported Jpred annotation from a sequence region
1775 imports to different position</li>
1776 <li>Space at beginning of sequence feature tooltips shown
1777 on some platforms</li>
1778 <li>Chimera viewer 'View | Show Chain' menu is not
1780 <li>'New View' fails with a Null Pointer Exception in
1781 console if Chimera has been opened</li>
1782 <li>Mouseover to Chimera not working</li>
1783 <li>Miscellaneous ENA XML feature qualifiers not
1785 <li>NPE in annotation renderer after 'Extract Scores'</li>
1786 <li>If two structures in one Chimera window, mouseover of
1787 either sequence shows on first structure</li>
1788 <li>'Show annotations' options should not make
1789 non-positional annotations visible</li>
1790 <li>Subsequence secondary structure annotation not shown
1791 in right place after 'view flanking regions'</li>
1792 <li>File Save As type unset when current file format is
1794 <li>Save as '.jar' option removed for saving Jalview
1796 <li>Colour by Sequence colouring in Chimera more
1798 <li>Cannot 'add reference annotation' for a sequence in
1799 several views on same alignment</li>
1800 <li>Cannot show linked products for EMBL / ENA records</li>
1801 <li>Jalview's tooltip wraps long texts containing no
1803 </ul> <em>Applet</em>
1805 <li>Jmol to JalviewLite mouseover/link not working</li>
1806 <li>JalviewLite can't import sequences with ID
1807 descriptions containing angle brackets</li>
1808 </ul> <em>General</em>
1810 <li>Cannot export and reimport RNA secondary structure
1811 via jalview annotation file</li>
1812 <li>Random helix colour palette for colour by annotation
1813 with RNA secondary structure</li>
1814 <li>Mouseover to cDNA from STOP residue in protein
1815 translation doesn't work.</li>
1816 <li>hints when using the select by annotation dialog box</li>
1817 <li>Jmol alignment incorrect if PDB file has alternate CA
1819 <li>FontChooser message dialog appears to hang after
1820 choosing 1pt font</li>
1821 <li>Peptide secondary structure incorrectly imported from
1822 annotation file when annotation display text includes 'e' or
1824 <li>Cannot set colour of new feature type whilst creating
1826 <li>cDNA translation alignment should not be sequence
1827 order dependent</li>
1828 <li>'Show unconserved' doesn't work for lower case
1830 <li>Nucleotide ambiguity codes involving R not recognised</li>
1831 </ul> <em>Deployment and Documentation</em>
1833 <li>Applet example pages appear different to the rest of
1834 www.jalview.org</li>
1835 </ul> <em>Application Known issues</em>
1837 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1838 <li>Misleading message appears after trying to delete
1840 <li>Jalview icon not shown in dock after InstallAnywhere
1841 version launches</li>
1842 <li>Fetching EMBL reference for an RNA sequence results
1843 fails with a sequence mismatch</li>
1844 <li>Corrupted or unreadable alignment display when
1845 scrolling alignment to right</li>
1846 <li>ArrayIndexOutOfBoundsException thrown when remove
1847 empty columns called on alignment with ragged gapped ends</li>
1848 <li>auto calculated alignment annotation rows do not get
1849 placed above or below non-autocalculated rows</li>
1850 <li>Jalview dekstop becomes sluggish at full screen in
1851 ultra-high resolution</li>
1852 <li>Cannot disable consensus calculation independently of
1853 quality and conservation</li>
1854 <li>Mouseover highlighting between cDNA and protein can
1855 become sluggish with more than one splitframe shown</li>
1856 </ul> <em>Applet Known Issues</em>
1858 <li>Core PDB parsing code requires Jmol</li>
1859 <li>Sequence canvas panel goes white when alignment
1860 window is being resized</li>
1866 <td><div align="center">
1867 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1869 <td><em>General</em>
1871 <li>Updated Java code signing certificate donated by
1873 <li>Features and annotation preserved when performing
1874 pairwise alignment</li>
1875 <li>RNA pseudoknot annotation can be
1876 imported/exported/displayed</li>
1877 <li>'colour by annotation' can colour by RNA and
1878 protein secondary structure</li>
1879 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1880 post-hoc with 2.9 release</em>)
1883 </ul> <em>Application</em>
1885 <li>Extract and display secondary structure for sequences
1886 with 3D structures</li>
1887 <li>Support for parsing RNAML</li>
1888 <li>Annotations menu for layout
1890 <li>sort sequence annotation rows by alignment</li>
1891 <li>place sequence annotation above/below alignment
1894 <li>Output in Stockholm format</li>
1895 <li>Internationalisation: improved Spanish (es)
1897 <li>Structure viewer preferences tab</li>
1898 <li>Disorder and Secondary Structure annotation tracks
1899 shared between alignments</li>
1900 <li>UCSF Chimera launch and linked highlighting from
1902 <li>Show/hide all sequence associated annotation rows for
1903 all or current selection</li>
1904 <li>disorder and secondary structure predictions
1905 available as dataset annotation</li>
1906 <li>Per-sequence rna helices colouring</li>
1909 <li>Sequence database accessions imported when fetching
1910 alignments from Rfam</li>
1911 <li>update VARNA version to 3.91</li>
1913 <li>New groovy scripts for exporting aligned positions,
1914 conservation values, and calculating sum of pairs scores.</li>
1915 <li>Command line argument to set default JABAWS server</li>
1916 <li>include installation type in build properties and
1917 console log output</li>
1918 <li>Updated Jalview project format to preserve dataset
1922 <!-- issues resolved --> <em>Application</em>
1924 <li>Distinguish alignment and sequence associated RNA
1925 structure in structure->view->VARNA</li>
1926 <li>Raise dialog box if user deletes all sequences in an
1928 <li>Pressing F1 results in documentation opening twice</li>
1929 <li>Sequence feature tooltip is wrapped</li>
1930 <li>Double click on sequence associated annotation
1931 selects only first column</li>
1932 <li>Redundancy removal doesn't result in unlinked
1933 leaves shown in tree</li>
1934 <li>Undos after several redundancy removals don't undo
1936 <li>Hide sequence doesn't hide associated annotation</li>
1937 <li>User defined colours dialog box too big to fit on
1938 screen and buttons not visible</li>
1939 <li>author list isn't updated if already written to
1940 Jalview properties</li>
1941 <li>Popup menu won't open after retrieving sequence
1943 <li>File open window for associate PDB doesn't open</li>
1944 <li>Left-then-right click on a sequence id opens a
1945 browser search window</li>
1946 <li>Cannot open sequence feature shading/sort popup menu
1947 in feature settings dialog</li>
1948 <li>better tooltip placement for some areas of Jalview
1950 <li>Allow addition of JABAWS Server which doesn't
1951 pass validation</li>
1952 <li>Web services parameters dialog box is too large to
1954 <li>Muscle nucleotide alignment preset obscured by
1956 <li>JABAWS preset submenus don't contain newly
1957 defined user preset</li>
1958 <li>MSA web services warns user if they were launched
1959 with invalid input</li>
1960 <li>Jalview cannot contact DAS Registy when running on
1963 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1964 'Superpose with' submenu not shown when new view
1968 </ul> <!-- <em>Applet</em>
1970 </ul> <em>General</em>
1972 </ul>--> <em>Deployment and Documentation</em>
1974 <li>2G and 1G options in launchApp have no effect on
1975 memory allocation</li>
1976 <li>launchApp service doesn't automatically open
1977 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1979 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1980 InstallAnywhere reports cannot find valid JVM when Java
1981 1.7_055 is available
1983 </ul> <em>Application Known issues</em>
1986 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1987 corrupted or unreadable alignment display when scrolling
1991 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1992 retrieval fails but progress bar continues for DAS retrieval
1993 with large number of ID
1996 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1997 flatfile output of visible region has incorrect sequence
2001 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2002 rna structure consensus doesn't update when secondary
2003 structure tracks are rearranged
2006 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2007 invalid rna structure positional highlighting does not
2008 highlight position of invalid base pairs
2011 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2012 out of memory errors are not raised when saving Jalview
2013 project from alignment window file menu
2016 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2017 Switching to RNA Helices colouring doesn't propagate to
2021 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2022 colour by RNA Helices not enabled when user created
2023 annotation added to alignment
2026 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2027 Jalview icon not shown on dock in Mountain Lion/Webstart
2029 </ul> <em>Applet Known Issues</em>
2032 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2033 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2036 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2037 Jalview and Jmol example not compatible with IE9
2040 <li>Sort by annotation score doesn't reverse order
2046 <td><div align="center">
2047 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2050 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2053 <li>Internationalisation of user interface (usually
2054 called i18n support) and translation for Spanish locale</li>
2055 <li>Define/Undefine group on current selection with
2056 Ctrl-G/Shift Ctrl-G</li>
2057 <li>Improved group creation/removal options in
2058 alignment/sequence Popup menu</li>
2059 <li>Sensible precision for symbol distribution
2060 percentages shown in logo tooltip.</li>
2061 <li>Annotation panel height set according to amount of
2062 annotation when alignment first opened</li>
2063 </ul> <em>Application</em>
2065 <li>Interactive consensus RNA secondary structure
2066 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2067 <li>Select columns containing particular features from
2068 Feature Settings dialog</li>
2069 <li>View all 'representative' PDB structures for selected
2071 <li>Update Jalview project format:
2073 <li>New file extension for Jalview projects '.jvp'</li>
2074 <li>Preserve sequence and annotation dataset (to
2075 store secondary structure annotation,etc)</li>
2076 <li>Per group and alignment annotation and RNA helix
2080 <li>New similarity measures for PCA and Tree calculation
2082 <li>Experimental support for retrieval and viewing of
2083 flanking regions for an alignment</li>
2087 <!-- issues resolved --> <em>Application</em>
2089 <li>logo keeps spinning and status remains at queued or
2090 running after job is cancelled</li>
2091 <li>cannot export features from alignments imported from
2092 Jalview/VAMSAS projects</li>
2093 <li>Buggy slider for web service parameters that take
2095 <li>Newly created RNA secondary structure line doesn't
2096 have 'display all symbols' flag set</li>
2097 <li>T-COFFEE alignment score shading scheme and other
2098 annotation shading not saved in Jalview project</li>
2099 <li>Local file cannot be loaded in freshly downloaded
2101 <li>Jalview icon not shown on dock in Mountain
2103 <li>Load file from desktop file browser fails</li>
2104 <li>Occasional NPE thrown when calculating large trees</li>
2105 <li>Cannot reorder or slide sequences after dragging an
2106 alignment onto desktop</li>
2107 <li>Colour by annotation dialog throws NPE after using
2108 'extract scores' function</li>
2109 <li>Loading/cut'n'pasting an empty file leads to a grey
2110 alignment window</li>
2111 <li>Disorder thresholds rendered incorrectly after
2112 performing IUPred disorder prediction</li>
2113 <li>Multiple group annotated consensus rows shown when
2114 changing 'normalise logo' display setting</li>
2115 <li>Find shows blank dialog after 'finished searching' if
2116 nothing matches query</li>
2117 <li>Null Pointer Exceptions raised when sorting by
2118 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2120 <li>Errors in Jmol console when structures in alignment
2121 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2123 <li>Not all working JABAWS services are shown in
2125 <li>JAVAWS version of Jalview fails to launch with
2126 'invalid literal/length code'</li>
2127 <li>Annotation/RNA Helix colourschemes cannot be applied
2128 to alignment with groups (actually fixed in 2.8.0b1)</li>
2129 <li>RNA Helices and T-Coffee Scores available as default
2132 </ul> <em>Applet</em>
2134 <li>Remove group option is shown even when selection is
2136 <li>Apply to all groups ticked but colourscheme changes
2137 don't affect groups</li>
2138 <li>Documented RNA Helices and T-Coffee Scores as valid
2139 colourscheme name</li>
2140 <li>Annotation labels drawn on sequence IDs when
2141 Annotation panel is not displayed</li>
2142 <li>Increased font size for dropdown menus on OSX and
2143 embedded windows</li>
2144 </ul> <em>Other</em>
2146 <li>Consensus sequence for alignments/groups with a
2147 single sequence were not calculated</li>
2148 <li>annotation files that contain only groups imported as
2149 annotation and junk sequences</li>
2150 <li>Fasta files with sequences containing '*' incorrectly
2151 recognised as PFAM or BLC</li>
2152 <li>conservation/PID slider apply all groups option
2153 doesn't affect background (2.8.0b1)
2155 <li>redundancy highlighting is erratic at 0% and 100%</li>
2156 <li>Remove gapped columns fails for sequences with ragged
2158 <li>AMSA annotation row with leading spaces is not
2159 registered correctly on import</li>
2160 <li>Jalview crashes when selecting PCA analysis for
2161 certain alignments</li>
2162 <li>Opening the colour by annotation dialog for an
2163 existing annotation based 'use original colours'
2164 colourscheme loses original colours setting</li>
2169 <td><div align="center">
2170 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2171 <em>30/1/2014</em></strong>
2175 <li>Trusted certificates for JalviewLite applet and
2176 Jalview Desktop application<br />Certificate was donated by
2177 <a href="https://www.certum.eu">Certum</a> to the Jalview
2178 open source project).
2180 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2181 <li>Output in Stockholm format</li>
2182 <li>Allow import of data from gzipped files</li>
2183 <li>Export/import group and sequence associated line
2184 graph thresholds</li>
2185 <li>Nucleotide substitution matrix that supports RNA and
2186 ambiguity codes</li>
2187 <li>Allow disorder predictions to be made on the current
2188 selection (or visible selection) in the same way that JPred
2190 <li>Groovy scripting for headless Jalview operation</li>
2191 </ul> <em>Other improvements</em>
2193 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2194 <li>COMBINE statement uses current SEQUENCE_REF and
2195 GROUP_REF scope to group annotation rows</li>
2196 <li>Support '' style escaping of quotes in Newick
2198 <li>Group options for JABAWS service by command line name</li>
2199 <li>Empty tooltip shown for JABA service options with a
2200 link but no description</li>
2201 <li>Select primary source when selecting authority in
2202 database fetcher GUI</li>
2203 <li>Add .mfa to FASTA file extensions recognised by
2205 <li>Annotation label tooltip text wrap</li>
2210 <li>Slow scrolling when lots of annotation rows are
2212 <li>Lots of NPE (and slowness) after creating RNA
2213 secondary structure annotation line</li>
2214 <li>Sequence database accessions not imported when
2215 fetching alignments from Rfam</li>
2216 <li>Incorrect SHMR submission for sequences with
2218 <li>View all structures does not always superpose
2220 <li>Option widgets in service parameters not updated to
2221 reflect user or preset settings</li>
2222 <li>Null pointer exceptions for some services without
2223 presets or adjustable parameters</li>
2224 <li>Discover PDB IDs entry in structure menu doesn't
2225 discover PDB xRefs</li>
2226 <li>Exception encountered while trying to retrieve
2227 features with DAS</li>
2228 <li>Lowest value in annotation row isn't coloured
2229 when colour by annotation (per sequence) is coloured</li>
2230 <li>Keyboard mode P jumps to start of gapped region when
2231 residue follows a gap</li>
2232 <li>Jalview appears to hang importing an alignment with
2233 Wrap as default or after enabling Wrap</li>
2234 <li>'Right click to add annotations' message
2235 shown in wrap mode when no annotations present</li>
2236 <li>Disorder predictions fail with NPE if no automatic
2237 annotation already exists on alignment</li>
2238 <li>oninit javascript function should be called after
2239 initialisation completes</li>
2240 <li>Remove redundancy after disorder prediction corrupts
2241 alignment window display</li>
2242 <li>Example annotation file in documentation is invalid</li>
2243 <li>Grouped line graph annotation rows are not exported
2244 to annotation file</li>
2245 <li>Multi-harmony analysis cannot be run when only two
2247 <li>Cannot create multiple groups of line graphs with
2248 several 'combine' statements in annotation file</li>
2249 <li>Pressing return several times causes Number Format
2250 exceptions in keyboard mode</li>
2251 <li>Multi-harmony (SHMMR) method doesn't submit
2252 correct partitions for input data</li>
2253 <li>Translation from DNA to Amino Acids fails</li>
2254 <li>Jalview fail to load newick tree with quoted label</li>
2255 <li>--headless flag isn't understood</li>
2256 <li>ClassCastException when generating EPS in headless
2258 <li>Adjusting sequence-associated shading threshold only
2259 changes one row's threshold</li>
2260 <li>Preferences and Feature settings panel panel
2261 doesn't open</li>
2262 <li>hide consensus histogram also hides conservation and
2263 quality histograms</li>
2268 <td><div align="center">
2269 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2271 <td><em>Application</em>
2273 <li>Support for JABAWS 2.0 Services (AACon alignment
2274 conservation, protein disorder and Clustal Omega)</li>
2275 <li>JABAWS server status indicator in Web Services
2277 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2278 in Jalview alignment window</li>
2279 <li>Updated Jalview build and deploy framework for OSX
2280 mountain lion, windows 7, and 8</li>
2281 <li>Nucleotide substitution matrix for PCA that supports
2282 RNA and ambiguity codes</li>
2284 <li>Improved sequence database retrieval GUI</li>
2285 <li>Support fetching and database reference look up
2286 against multiple DAS sources (Fetch all from in 'fetch db
2288 <li>Jalview project improvements
2290 <li>Store and retrieve the 'belowAlignment'
2291 flag for annotation</li>
2292 <li>calcId attribute to group annotation rows on the
2294 <li>Store AACon calculation settings for a view in
2295 Jalview project</li>
2299 <li>horizontal scrolling gesture support</li>
2300 <li>Visual progress indicator when PCA calculation is
2302 <li>Simpler JABA web services menus</li>
2303 <li>visual indication that web service results are still
2304 being retrieved from server</li>
2305 <li>Serialise the dialogs that are shown when Jalview
2306 starts up for first time</li>
2307 <li>Jalview user agent string for interacting with HTTP
2309 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2311 <li>Examples directory and Groovy library included in
2312 InstallAnywhere distribution</li>
2313 </ul> <em>Applet</em>
2315 <li>RNA alignment and secondary structure annotation
2316 visualization applet example</li>
2317 </ul> <em>General</em>
2319 <li>Normalise option for consensus sequence logo</li>
2320 <li>Reset button in PCA window to return dimensions to
2322 <li>Allow seqspace or Jalview variant of alignment PCA
2324 <li>PCA with either nucleic acid and protein substitution
2326 <li>Allow windows containing HTML reports to be exported
2328 <li>Interactive display and editing of RNA secondary
2329 structure contacts</li>
2330 <li>RNA Helix Alignment Colouring</li>
2331 <li>RNA base pair logo consensus</li>
2332 <li>Parse sequence associated secondary structure
2333 information in Stockholm files</li>
2334 <li>HTML Export database accessions and annotation
2335 information presented in tooltip for sequences</li>
2336 <li>Import secondary structure from LOCARNA clustalw
2337 style RNA alignment files</li>
2338 <li>import and visualise T-COFFEE quality scores for an
2340 <li>'colour by annotation' per sequence option to
2341 shade each sequence according to its associated alignment
2343 <li>New Jalview Logo</li>
2344 </ul> <em>Documentation and Development</em>
2346 <li>documentation for score matrices used in Jalview</li>
2347 <li>New Website!</li>
2349 <td><em>Application</em>
2351 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2352 wsdbfetch REST service</li>
2353 <li>Stop windows being moved outside desktop on OSX</li>
2354 <li>Filetype associations not installed for webstart
2356 <li>Jalview does not always retrieve progress of a JABAWS
2357 job execution in full once it is complete</li>
2358 <li>revise SHMR RSBS definition to ensure alignment is
2359 uploaded via ali_file parameter</li>
2360 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2361 <li>View all structures superposed fails with exception</li>
2362 <li>Jnet job queues forever if a very short sequence is
2363 submitted for prediction</li>
2364 <li>Cut and paste menu not opened when mouse clicked on
2366 <li>Putting fractional value into integer text box in
2367 alignment parameter dialog causes Jalview to hang</li>
2368 <li>Structure view highlighting doesn't work on
2370 <li>View all structures fails with exception shown in
2372 <li>Characters in filename associated with PDBEntry not
2373 escaped in a platform independent way</li>
2374 <li>Jalview desktop fails to launch with exception when
2376 <li>Tree calculation reports 'you must have 2 or more
2377 sequences selected' when selection is empty</li>
2378 <li>Jalview desktop fails to launch with jar signature
2379 failure when java web start temporary file caching is
2381 <li>DAS Sequence retrieval with range qualification
2382 results in sequence xref which includes range qualification</li>
2383 <li>Errors during processing of command line arguments
2384 cause progress bar (JAL-898) to be removed</li>
2385 <li>Replace comma for semi-colon option not disabled for
2386 DAS sources in sequence fetcher</li>
2387 <li>Cannot close news reader when JABAWS server warning
2388 dialog is shown</li>
2389 <li>Option widgets not updated to reflect user settings</li>
2390 <li>Edited sequence not submitted to web service</li>
2391 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2392 <li>InstallAnywhere installer doesn't unpack and run
2393 on OSX Mountain Lion</li>
2394 <li>Annotation panel not given a scroll bar when
2395 sequences with alignment annotation are pasted into the
2397 <li>Sequence associated annotation rows not associated
2398 when loaded from Jalview project</li>
2399 <li>Browser launch fails with NPE on java 1.7</li>
2400 <li>JABAWS alignment marked as finished when job was
2401 cancelled or job failed due to invalid input</li>
2402 <li>NPE with v2.7 example when clicking on Tree
2403 associated with all views</li>
2404 <li>Exceptions when copy/paste sequences with grouped
2405 annotation rows to new window</li>
2406 </ul> <em>Applet</em>
2408 <li>Sequence features are momentarily displayed before
2409 they are hidden using hidefeaturegroups applet parameter</li>
2410 <li>loading features via javascript API automatically
2411 enables feature display</li>
2412 <li>scrollToColumnIn javascript API method doesn't
2414 </ul> <em>General</em>
2416 <li>Redundancy removal fails for rna alignment</li>
2417 <li>PCA calculation fails when sequence has been selected
2418 and then deselected</li>
2419 <li>PCA window shows grey box when first opened on OSX</li>
2420 <li>Letters coloured pink in sequence logo when alignment
2421 coloured with clustalx</li>
2422 <li>Choosing fonts without letter symbols defined causes
2423 exceptions and redraw errors</li>
2424 <li>Initial PCA plot view is not same as manually
2425 reconfigured view</li>
2426 <li>Grouped annotation graph label has incorrect line
2428 <li>Grouped annotation graph label display is corrupted
2429 for lots of labels</li>
2434 <div align="center">
2435 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2438 <td><em>Application</em>
2440 <li>Jalview Desktop News Reader</li>
2441 <li>Tweaked default layout of web services menu</li>
2442 <li>View/alignment association menu to enable user to
2443 easily specify which alignment a multi-structure view takes
2444 its colours/correspondences from</li>
2445 <li>Allow properties file location to be specified as URL</li>
2446 <li>Extend Jalview project to preserve associations
2447 between many alignment views and a single Jmol display</li>
2448 <li>Store annotation row height in Jalview project file</li>
2449 <li>Annotation row column label formatting attributes
2450 stored in project file</li>
2451 <li>Annotation row order for auto-calculated annotation
2452 rows preserved in Jalview project file</li>
2453 <li>Visual progress indication when Jalview state is
2454 saved using Desktop window menu</li>
2455 <li>Visual indication that command line arguments are
2456 still being processed</li>
2457 <li>Groovy script execution from URL</li>
2458 <li>Colour by annotation default min and max colours in
2460 <li>Automatically associate PDB files dragged onto an
2461 alignment with sequences that have high similarity and
2463 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2464 <li>'view structures' option to open many
2465 structures in same window</li>
2466 <li>Sort associated views menu option for tree panel</li>
2467 <li>Group all JABA and non-JABA services for a particular
2468 analysis function in its own submenu</li>
2469 </ul> <em>Applet</em>
2471 <li>Userdefined and autogenerated annotation rows for
2473 <li>Adjustment of alignment annotation pane height</li>
2474 <li>Annotation scrollbar for annotation panel</li>
2475 <li>Drag to reorder annotation rows in annotation panel</li>
2476 <li>'automaticScrolling' parameter</li>
2477 <li>Allow sequences with partial ID string matches to be
2478 annotated from GFF/Jalview features files</li>
2479 <li>Sequence logo annotation row in applet</li>
2480 <li>Absolute paths relative to host server in applet
2481 parameters are treated as such</li>
2482 <li>New in the JalviewLite javascript API:
2484 <li>JalviewLite.js javascript library</li>
2485 <li>Javascript callbacks for
2487 <li>Applet initialisation</li>
2488 <li>Sequence/alignment mouse-overs and selections</li>
2491 <li>scrollTo row and column alignment scrolling
2493 <li>Select sequence/alignment regions from javascript</li>
2494 <li>javascript structure viewer harness to pass
2495 messages between Jmol and Jalview when running as
2496 distinct applets</li>
2497 <li>sortBy method</li>
2498 <li>Set of applet and application examples shipped
2499 with documentation</li>
2500 <li>New example to demonstrate JalviewLite and Jmol
2501 javascript message exchange</li>
2503 </ul> <em>General</em>
2505 <li>Enable Jmol displays to be associated with multiple
2506 multiple alignments</li>
2507 <li>Option to automatically sort alignment with new tree</li>
2508 <li>User configurable link to enable redirects to a
2509 www.Jalview.org mirror</li>
2510 <li>Jmol colours option for Jmol displays</li>
2511 <li>Configurable newline string when writing alignment
2512 and other flat files</li>
2513 <li>Allow alignment annotation description lines to
2514 contain html tags</li>
2515 </ul> <em>Documentation and Development</em>
2517 <li>Add groovy test harness for bulk load testing to
2519 <li>Groovy script to load and align a set of sequences
2520 using a web service before displaying the result in the
2521 Jalview desktop</li>
2522 <li>Restructured javascript and applet api documentation</li>
2523 <li>Ant target to publish example html files with applet
2525 <li>Netbeans project for building Jalview from source</li>
2526 <li>ant task to create online javadoc for Jalview source</li>
2528 <td><em>Application</em>
2530 <li>User defined colourscheme throws exception when
2531 current built in colourscheme is saved as new scheme</li>
2532 <li>AlignFrame->Save in application pops up save
2533 dialog for valid filename/format</li>
2534 <li>Cannot view associated structure for UniProt sequence</li>
2535 <li>PDB file association breaks for UniProt sequence
2537 <li>Associate PDB from file dialog does not tell you
2538 which sequence is to be associated with the file</li>
2539 <li>Find All raises null pointer exception when query
2540 only matches sequence IDs</li>
2541 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2542 <li>Jalview project with Jmol views created with Jalview
2543 2.4 cannot be loaded</li>
2544 <li>Filetype associations not installed for webstart
2546 <li>Two or more chains in a single PDB file associated
2547 with sequences in different alignments do not get coloured
2548 by their associated sequence</li>
2549 <li>Visibility status of autocalculated annotation row
2550 not preserved when project is loaded</li>
2551 <li>Annotation row height and visibility attributes not
2552 stored in Jalview project</li>
2553 <li>Tree bootstraps are not preserved when saved as a
2554 Jalview project</li>
2555 <li>Envision2 workflow tooltips are corrupted</li>
2556 <li>Enabling show group conservation also enables colour
2557 by conservation</li>
2558 <li>Duplicate group associated conservation or consensus
2559 created on new view</li>
2560 <li>Annotation scrollbar not displayed after 'show
2561 all hidden annotation rows' option selected</li>
2562 <li>Alignment quality not updated after alignment
2563 annotation row is hidden then shown</li>
2564 <li>Preserve colouring of structures coloured by
2565 sequences in pre Jalview 2.7 projects</li>
2566 <li>Web service job parameter dialog is not laid out
2568 <li>Web services menu not refreshed after 'reset
2569 services' button is pressed in preferences</li>
2570 <li>Annotation off by one in Jalview v2_3 example project</li>
2571 <li>Structures imported from file and saved in project
2572 get name like jalview_pdb1234.txt when reloaded</li>
2573 <li>Jalview does not always retrieve progress of a JABAWS
2574 job execution in full once it is complete</li>
2575 </ul> <em>Applet</em>
2577 <li>Alignment height set incorrectly when lots of
2578 annotation rows are displayed</li>
2579 <li>Relative URLs in feature HTML text not resolved to
2581 <li>View follows highlighting does not work for positions
2583 <li><= shown as = in tooltip</li>
2584 <li>Export features raises exception when no features
2586 <li>Separator string used for serialising lists of IDs
2587 for javascript api is modified when separator string
2588 provided as parameter</li>
2589 <li>Null pointer exception when selecting tree leaves for
2590 alignment with no existing selection</li>
2591 <li>Relative URLs for datasources assumed to be relative
2592 to applet's codebase</li>
2593 <li>Status bar not updated after finished searching and
2594 search wraps around to first result</li>
2595 <li>StructureSelectionManager instance shared between
2596 several Jalview applets causes race conditions and memory
2598 <li>Hover tooltip and mouseover of position on structure
2599 not sent from Jmol in applet</li>
2600 <li>Certain sequences of javascript method calls to
2601 applet API fatally hang browser</li>
2602 </ul> <em>General</em>
2604 <li>View follows structure mouseover scrolls beyond
2605 position with wrapped view and hidden regions</li>
2606 <li>Find sequence position moves to wrong residue
2607 with/without hidden columns</li>
2608 <li>Sequence length given in alignment properties window
2610 <li>InvalidNumberFormat exceptions thrown when trying to
2611 import PDB like structure files</li>
2612 <li>Positional search results are only highlighted
2613 between user-supplied sequence start/end bounds</li>
2614 <li>End attribute of sequence is not validated</li>
2615 <li>Find dialog only finds first sequence containing a
2616 given sequence position</li>
2617 <li>Sequence numbering not preserved in MSF alignment
2619 <li>Jalview PDB file reader does not extract sequence
2620 from nucleotide chains correctly</li>
2621 <li>Structure colours not updated when tree partition
2622 changed in alignment</li>
2623 <li>Sequence associated secondary structure not correctly
2624 parsed in interleaved stockholm</li>
2625 <li>Colour by annotation dialog does not restore current
2627 <li>Hiding (nearly) all sequences doesn't work
2629 <li>Sequences containing lowercase letters are not
2630 properly associated with their pdb files</li>
2631 </ul> <em>Documentation and Development</em>
2633 <li>schemas/JalviewWsParamSet.xsd corrupted by
2634 ApplyCopyright tool</li>
2639 <div align="center">
2640 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2643 <td><em>Application</em>
2645 <li>New warning dialog when the Jalview Desktop cannot
2646 contact web services</li>
2647 <li>JABA service parameters for a preset are shown in
2648 service job window</li>
2649 <li>JABA Service menu entries reworded</li>
2653 <li>Modeller PIR IO broken - cannot correctly import a
2654 pir file emitted by Jalview</li>
2655 <li>Existing feature settings transferred to new
2656 alignment view created from cut'n'paste</li>
2657 <li>Improved test for mixed amino/nucleotide chains when
2658 parsing PDB files</li>
2659 <li>Consensus and conservation annotation rows
2660 occasionally become blank for all new windows</li>
2661 <li>Exception raised when right clicking above sequences
2662 in wrapped view mode</li>
2663 </ul> <em>Application</em>
2665 <li>multiple multiply aligned structure views cause cpu
2666 usage to hit 100% and computer to hang</li>
2667 <li>Web Service parameter layout breaks for long user
2668 parameter names</li>
2669 <li>Jaba service discovery hangs desktop if Jaba server
2676 <div align="center">
2677 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2680 <td><em>Application</em>
2682 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2683 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2686 <li>Web Services preference tab</li>
2687 <li>Analysis parameters dialog box and user defined
2689 <li>Improved speed and layout of Envision2 service menu</li>
2690 <li>Superpose structures using associated sequence
2692 <li>Export coordinates and projection as CSV from PCA
2694 </ul> <em>Applet</em>
2696 <li>enable javascript: execution by the applet via the
2697 link out mechanism</li>
2698 </ul> <em>Other</em>
2700 <li>Updated the Jmol Jalview interface to work with Jmol
2702 <li>The Jalview Desktop and JalviewLite applet now
2703 require Java 1.5</li>
2704 <li>Allow Jalview feature colour specification for GFF
2705 sequence annotation files</li>
2706 <li>New 'colour by label' keword in Jalview feature file
2707 type colour specification</li>
2708 <li>New Jalview Desktop Groovy API method that allows a
2709 script to check if it being run in an interactive session or
2710 in a batch operation from the Jalview command line</li>
2714 <li>clustalx colourscheme colours Ds preferentially when
2715 both D+E are present in over 50% of the column</li>
2716 </ul> <em>Application</em>
2718 <li>typo in AlignmentFrame->View->Hide->all but
2719 selected Regions menu item</li>
2720 <li>sequence fetcher replaces ',' for ';' when the ',' is
2721 part of a valid accession ID</li>
2722 <li>fatal OOM if object retrieved by sequence fetcher
2723 runs out of memory</li>
2724 <li>unhandled Out of Memory Error when viewing pca
2725 analysis results</li>
2726 <li>InstallAnywhere builds fail to launch on OS X java
2727 10.5 update 4 (due to apple Java 1.6 update)</li>
2728 <li>Installanywhere Jalview silently fails to launch</li>
2729 </ul> <em>Applet</em>
2731 <li>Jalview.getFeatureGroups() raises an
2732 ArrayIndexOutOfBoundsException if no feature groups are
2739 <div align="center">
2740 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2746 <li>Alignment prettyprinter doesn't cope with long
2748 <li>clustalx colourscheme colours Ds preferentially when
2749 both D+E are present in over 50% of the column</li>
2750 <li>nucleic acid structures retrieved from PDB do not
2751 import correctly</li>
2752 <li>More columns get selected than were clicked on when a
2753 number of columns are hidden</li>
2754 <li>annotation label popup menu not providing correct
2755 add/hide/show options when rows are hidden or none are
2757 <li>Stockholm format shown in list of readable formats,
2758 and parser copes better with alignments from RFAM.</li>
2759 <li>CSV output of consensus only includes the percentage
2760 of all symbols if sequence logo display is enabled</li>
2762 </ul> <em>Applet</em>
2764 <li>annotation panel disappears when annotation is
2766 </ul> <em>Application</em>
2768 <li>Alignment view not redrawn properly when new
2769 alignment opened where annotation panel is visible but no
2770 annotations are present on alignment</li>
2771 <li>pasted region containing hidden columns is
2772 incorrectly displayed in new alignment window</li>
2773 <li>Jalview slow to complete operations when stdout is
2774 flooded (fix is to close the Jalview console)</li>
2775 <li>typo in AlignmentFrame->View->Hide->all but
2776 selected Rregions menu item.</li>
2777 <li>inconsistent group submenu and Format submenu entry
2778 'Un' or 'Non'conserved</li>
2779 <li>Sequence feature settings are being shared by
2780 multiple distinct alignments</li>
2781 <li>group annotation not recreated when tree partition is
2783 <li>double click on group annotation to select sequences
2784 does not propagate to associated trees</li>
2785 <li>Mac OSX specific issues:
2787 <li>exception raised when mouse clicked on desktop
2788 window background</li>
2789 <li>Desktop menu placed on menu bar and application
2790 name set correctly</li>
2791 <li>sequence feature settings not wide enough for the
2792 save feature colourscheme button</li>
2801 <div align="center">
2802 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2805 <td><em>New Capabilities</em>
2807 <li>URL links generated from description line for
2808 regular-expression based URL links (applet and application)
2810 <li>Non-positional feature URL links are shown in link
2812 <li>Linked viewing of nucleic acid sequences and
2814 <li>Automatic Scrolling option in View menu to display
2815 the currently highlighted region of an alignment.</li>
2816 <li>Order an alignment by sequence length, or using the
2817 average score or total feature count for each sequence.</li>
2818 <li>Shading features by score or associated description</li>
2819 <li>Subdivide alignment and groups based on identity of
2820 selected subsequence (Make Groups from Selection).</li>
2821 <li>New hide/show options including Shift+Control+H to
2822 hide everything but the currently selected region.</li>
2823 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2824 </ul> <em>Application</em>
2826 <li>Fetch DB References capabilities and UI expanded to
2827 support retrieval from DAS sequence sources</li>
2828 <li>Local DAS Sequence sources can be added via the
2829 command line or via the Add local source dialog box.</li>
2830 <li>DAS Dbref and DbxRef feature types are parsed as
2831 database references and protein_name is parsed as
2832 description line (BioSapiens terms).</li>
2833 <li>Enable or disable non-positional feature and database
2834 references in sequence ID tooltip from View menu in
2836 <!-- <li>New hidden columns and rows and representatives capabilities
2837 in annotations file (in progress - not yet fully implemented)</li> -->
2838 <li>Group-associated consensus, sequence logos and
2839 conservation plots</li>
2840 <li>Symbol distributions for each column can be exported
2841 and visualized as sequence logos</li>
2842 <li>Optionally scale multi-character column labels to fit
2843 within each column of annotation row<!-- todo for applet -->
2845 <li>Optional automatic sort of associated alignment view
2846 when a new tree is opened.</li>
2847 <li>Jalview Java Console</li>
2848 <li>Better placement of desktop window when moving
2849 between different screens.</li>
2850 <li>New preference items for sequence ID tooltip and
2851 consensus annotation</li>
2852 <li>Client to submit sequences and IDs to Envision2
2854 <li><em>Vamsas Capabilities</em>
2856 <li>Improved VAMSAS synchronization (Jalview archive
2857 used to preserve views, structures, and tree display
2859 <li>Import of vamsas documents from disk or URL via
2861 <li>Sharing of selected regions between views and
2862 with other VAMSAS applications (Experimental feature!)</li>
2863 <li>Updated API to VAMSAS version 0.2</li>
2865 </ul> <em>Applet</em>
2867 <li>Middle button resizes annotation row height</li>
2870 <li>sortByTree (true/false) - automatically sort the
2871 associated alignment view by the tree when a new tree is
2873 <li>showTreeBootstraps (true/false) - show or hide
2874 branch bootstraps (default is to show them if available)</li>
2875 <li>showTreeDistances (true/false) - show or hide
2876 branch lengths (default is to show them if available)</li>
2877 <li>showUnlinkedTreeNodes (true/false) - indicate if
2878 unassociated nodes should be highlighted in the tree
2880 <li>heightScale and widthScale (1.0 or more) -
2881 increase the height or width of a cell in the alignment
2882 grid relative to the current font size.</li>
2885 <li>Non-positional features displayed in sequence ID
2887 </ul> <em>Other</em>
2889 <li>Features format: graduated colour definitions and
2890 specification of feature scores</li>
2891 <li>Alignment Annotations format: new keywords for group
2892 associated annotation (GROUP_REF) and annotation row display
2893 properties (ROW_PROPERTIES)</li>
2894 <li>XML formats extended to support graduated feature
2895 colourschemes, group associated annotation, and profile
2896 visualization settings.</li></td>
2899 <li>Source field in GFF files parsed as feature source
2900 rather than description</li>
2901 <li>Non-positional features are now included in sequence
2902 feature and gff files (controlled via non-positional feature
2903 visibility in tooltip).</li>
2904 <li>URL links generated for all feature links (bugfix)</li>
2905 <li>Added URL embedding instructions to features file
2907 <li>Codons containing ambiguous nucleotides translated as
2908 'X' in peptide product</li>
2909 <li>Match case switch in find dialog box works for both
2910 sequence ID and sequence string and query strings do not
2911 have to be in upper case to match case-insensitively.</li>
2912 <li>AMSA files only contain first column of
2913 multi-character column annotation labels</li>
2914 <li>Jalview Annotation File generation/parsing consistent
2915 with documentation (e.g. Stockholm annotation can be
2916 exported and re-imported)</li>
2917 <li>PDB files without embedded PDB IDs given a friendly
2919 <li>Find incrementally searches ID string matches as well
2920 as subsequence matches, and correctly reports total number
2924 <li>Better handling of exceptions during sequence
2926 <li>Dasobert generated non-positional feature URL
2927 link text excludes the start_end suffix</li>
2928 <li>DAS feature and source retrieval buttons disabled
2929 when fetch or registry operations in progress.</li>
2930 <li>PDB files retrieved from URLs are cached properly</li>
2931 <li>Sequence description lines properly shared via
2933 <li>Sequence fetcher fetches multiple records for all
2935 <li>Ensured that command line das feature retrieval
2936 completes before alignment figures are generated.</li>
2937 <li>Reduced time taken when opening file browser for
2939 <li>isAligned check prior to calculating tree, PCA or
2940 submitting an MSA to JNet now excludes hidden sequences.</li>
2941 <li>User defined group colours properly recovered
2942 from Jalview projects.</li>
2951 <div align="center">
2952 <strong>2.4.0.b2</strong><br> 28/10/2009
2957 <li>Experimental support for google analytics usage
2959 <li>Jalview privacy settings (user preferences and docs).</li>
2964 <li>Race condition in applet preventing startup in
2966 <li>Exception when feature created from selection beyond
2967 length of sequence.</li>
2968 <li>Allow synthetic PDB files to be imported gracefully</li>
2969 <li>Sequence associated annotation rows associate with
2970 all sequences with a given id</li>
2971 <li>Find function matches case-insensitively for sequence
2972 ID string searches</li>
2973 <li>Non-standard characters do not cause pairwise
2974 alignment to fail with exception</li>
2975 </ul> <em>Application Issues</em>
2977 <li>Sequences are now validated against EMBL database</li>
2978 <li>Sequence fetcher fetches multiple records for all
2980 </ul> <em>InstallAnywhere Issues</em>
2982 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2983 issue with installAnywhere mechanism)</li>
2984 <li>Command line launching of JARs from InstallAnywhere
2985 version (java class versioning error fixed)</li>
2992 <div align="center">
2993 <strong>2.4</strong><br> 27/8/2008
2996 <td><em>User Interface</em>
2998 <li>Linked highlighting of codon and amino acid from
2999 translation and protein products</li>
3000 <li>Linked highlighting of structure associated with
3001 residue mapping to codon position</li>
3002 <li>Sequence Fetcher provides example accession numbers
3003 and 'clear' button</li>
3004 <li>MemoryMonitor added as an option under Desktop's
3006 <li>Extract score function to parse whitespace separated
3007 numeric data in description line</li>
3008 <li>Column labels in alignment annotation can be centred.</li>
3009 <li>Tooltip for sequence associated annotation give name
3011 </ul> <em>Web Services and URL fetching</em>
3013 <li>JPred3 web service</li>
3014 <li>Prototype sequence search client (no public services
3016 <li>Fetch either seed alignment or full alignment from
3018 <li>URL Links created for matching database cross
3019 references as well as sequence ID</li>
3020 <li>URL Links can be created using regular-expressions</li>
3021 </ul> <em>Sequence Database Connectivity</em>
3023 <li>Retrieval of cross-referenced sequences from other
3025 <li>Generalised database reference retrieval and
3026 validation to all fetchable databases</li>
3027 <li>Fetch sequences from DAS sources supporting the
3028 sequence command</li>
3029 </ul> <em>Import and Export</em>
3030 <li>export annotation rows as CSV for spreadsheet import</li>
3031 <li>Jalview projects record alignment dataset associations,
3032 EMBL products, and cDNA sequence mappings</li>
3033 <li>Sequence Group colour can be specified in Annotation
3035 <li>Ad-hoc colouring of group in Annotation File using RGB
3036 triplet as name of colourscheme</li>
3037 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3039 <li>treenode binding for VAMSAS tree exchange</li>
3040 <li>local editing and update of sequences in VAMSAS
3041 alignments (experimental)</li>
3042 <li>Create new or select existing session to join</li>
3043 <li>load and save of vamsas documents</li>
3044 </ul> <em>Application command line</em>
3046 <li>-tree parameter to open trees (introduced for passing
3048 <li>-fetchfrom command line argument to specify nicknames
3049 of DAS servers to query for alignment features</li>
3050 <li>-dasserver command line argument to add new servers
3051 that are also automatically queried for features</li>
3052 <li>-groovy command line argument executes a given groovy
3053 script after all input data has been loaded and parsed</li>
3054 </ul> <em>Applet-Application data exchange</em>
3056 <li>Trees passed as applet parameters can be passed to
3057 application (when using "View in full
3058 application")</li>
3059 </ul> <em>Applet Parameters</em>
3061 <li>feature group display control parameter</li>
3062 <li>debug parameter</li>
3063 <li>showbutton parameter</li>
3064 </ul> <em>Applet API methods</em>
3066 <li>newView public method</li>
3067 <li>Window (current view) specific get/set public methods</li>
3068 <li>Feature display control methods</li>
3069 <li>get list of currently selected sequences</li>
3070 </ul> <em>New Jalview distribution features</em>
3072 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3073 <li>RELEASE file gives build properties for the latest
3074 Jalview release.</li>
3075 <li>Java 1.1 Applet build made easier and donotobfuscate
3076 property controls execution of obfuscator</li>
3077 <li>Build target for generating source distribution</li>
3078 <li>Debug flag for javacc</li>
3079 <li>.jalview_properties file is documented (slightly) in
3080 jalview.bin.Cache</li>
3081 <li>Continuous Build Integration for stable and
3082 development version of Application, Applet and source
3087 <li>selected region output includes visible annotations
3088 (for certain formats)</li>
3089 <li>edit label/displaychar contains existing label/char
3091 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3092 <li>shorter peptide product names from EMBL records</li>
3093 <li>Newick string generator makes compact representations</li>
3094 <li>bootstrap values parsed correctly for tree files with
3096 <li>pathological filechooser bug avoided by not allowing
3097 filenames containing a ':'</li>
3098 <li>Fixed exception when parsing GFF files containing
3099 global sequence features</li>
3100 <li>Alignment datasets are finalized only when number of
3101 references from alignment sequences goes to zero</li>
3102 <li>Close of tree branch colour box without colour
3103 selection causes cascading exceptions</li>
3104 <li>occasional negative imgwidth exceptions</li>
3105 <li>better reporting of non-fatal warnings to user when
3106 file parsing fails.</li>
3107 <li>Save works when Jalview project is default format</li>
3108 <li>Save as dialog opened if current alignment format is
3109 not a valid output format</li>
3110 <li>UniProt canonical names introduced for both das and
3112 <li>Histidine should be midblue (not pink!) in Zappo</li>
3113 <li>error messages passed up and output when data read
3115 <li>edit undo recovers previous dataset sequence when
3116 sequence is edited</li>
3117 <li>allow PDB files without pdb ID HEADER lines (like
3118 those generated by MODELLER) to be read in properly</li>
3119 <li>allow reading of JPred concise files as a normal
3121 <li>Stockholm annotation parsing and alignment properties
3122 import fixed for PFAM records</li>
3123 <li>Structure view windows have correct name in Desktop
3125 <li>annotation consisting of sequence associated scores
3126 can be read and written correctly to annotation file</li>
3127 <li>Aligned cDNA translation to aligned peptide works
3129 <li>Fixed display of hidden sequence markers and
3130 non-italic font for representatives in Applet</li>
3131 <li>Applet Menus are always embedded in applet window on
3133 <li>Newly shown features appear at top of stack (in
3135 <li>Annotations added via parameter not drawn properly
3136 due to null pointer exceptions</li>
3137 <li>Secondary structure lines are drawn starting from
3138 first column of alignment</li>
3139 <li>UniProt XML import updated for new schema release in
3141 <li>Sequence feature to sequence ID match for Features
3142 file is case-insensitive</li>
3143 <li>Sequence features read from Features file appended to
3144 all sequences with matching IDs</li>
3145 <li>PDB structure coloured correctly for associated views
3146 containing a sub-sequence</li>
3147 <li>PDB files can be retrieved by applet from Jar files</li>
3148 <li>feature and annotation file applet parameters
3149 referring to different directories are retrieved correctly</li>
3150 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3151 <li>Fixed application hang whilst waiting for
3152 splash-screen version check to complete</li>
3153 <li>Applet properly URLencodes input parameter values
3154 when passing them to the launchApp service</li>
3155 <li>display name and local features preserved in results
3156 retrieved from web service</li>
3157 <li>Visual delay indication for sequence retrieval and
3158 sequence fetcher initialisation</li>
3159 <li>updated Application to use DAS 1.53e version of
3160 dasobert DAS client</li>
3161 <li>Re-instated Full AMSA support and .amsa file
3163 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3171 <div align="center">
3172 <strong>2.3</strong><br> 9/5/07
3177 <li>Jmol 11.0.2 integration</li>
3178 <li>PDB views stored in Jalview XML files</li>
3179 <li>Slide sequences</li>
3180 <li>Edit sequence in place</li>
3181 <li>EMBL CDS features</li>
3182 <li>DAS Feature mapping</li>
3183 <li>Feature ordering</li>
3184 <li>Alignment Properties</li>
3185 <li>Annotation Scores</li>
3186 <li>Sort by scores</li>
3187 <li>Feature/annotation editing in applet</li>
3192 <li>Headless state operation in 2.2.1</li>
3193 <li>Incorrect and unstable DNA pairwise alignment</li>
3194 <li>Cut and paste of sequences with annotation</li>
3195 <li>Feature group display state in XML</li>
3196 <li>Feature ordering in XML</li>
3197 <li>blc file iteration selection using filename # suffix</li>
3198 <li>Stockholm alignment properties</li>
3199 <li>Stockhom alignment secondary structure annotation</li>
3200 <li>2.2.1 applet had no feature transparency</li>
3201 <li>Number pad keys can be used in cursor mode</li>
3202 <li>Structure Viewer mirror image resolved</li>
3209 <div align="center">
3210 <strong>2.2.1</strong><br> 12/2/07
3215 <li>Non standard characters can be read and displayed
3216 <li>Annotations/Features can be imported/exported to the
3218 <li>Applet allows editing of sequence/annotation/group
3219 name & description
3220 <li>Preference setting to display sequence name in
3222 <li>Annotation file format extended to allow
3223 Sequence_groups to be defined
3224 <li>Default opening of alignment overview panel can be
3225 specified in preferences
3226 <li>PDB residue numbering annotation added to associated
3232 <li>Applet crash under certain Linux OS with Java 1.6
3234 <li>Annotation file export / import bugs fixed
3235 <li>PNG / EPS image output bugs fixed
3241 <div align="center">
3242 <strong>2.2</strong><br> 27/11/06
3247 <li>Multiple views on alignment
3248 <li>Sequence feature editing
3249 <li>"Reload" alignment
3250 <li>"Save" to current filename
3251 <li>Background dependent text colour
3252 <li>Right align sequence ids
3253 <li>User-defined lower case residue colours
3256 <li>Menu item accelerator keys
3257 <li>Control-V pastes to current alignment
3258 <li>Cancel button for DAS Feature Fetching
3259 <li>PCA and PDB Viewers zoom via mouse roller
3260 <li>User-defined sub-tree colours and sub-tree selection
3262 <li>'New Window' button on the 'Output to Text box'
3267 <li>New memory efficient Undo/Redo System
3268 <li>Optimised symbol lookups and conservation/consensus
3270 <li>Region Conservation/Consensus recalculated after
3272 <li>Fixed Remove Empty Columns Bug (empty columns at end
3274 <li>Slowed DAS Feature Fetching for increased robustness.
3276 <li>Made angle brackets in ASCII feature descriptions
3278 <li>Re-instated Zoom function for PCA
3279 <li>Sequence descriptions conserved in web service
3281 <li>UniProt ID discoverer uses any word separated by
3283 <li>WsDbFetch query/result association resolved
3284 <li>Tree leaf to sequence mapping improved
3285 <li>Smooth fonts switch moved to FontChooser dialog box.
3292 <div align="center">
3293 <strong>2.1.1</strong><br> 12/9/06
3298 <li>Copy consensus sequence to clipboard</li>
3303 <li>Image output - rightmost residues are rendered if
3304 sequence id panel has been resized</li>
3305 <li>Image output - all offscreen group boundaries are
3307 <li>Annotation files with sequence references - all
3308 elements in file are relative to sequence position</li>
3309 <li>Mac Applet users can use Alt key for group editing</li>
3315 <div align="center">
3316 <strong>2.1</strong><br> 22/8/06
3321 <li>MAFFT Multiple Alignment in default Web Service list</li>
3322 <li>DAS Feature fetching</li>
3323 <li>Hide sequences and columns</li>
3324 <li>Export Annotations and Features</li>
3325 <li>GFF file reading / writing</li>
3326 <li>Associate structures with sequences from local PDB
3328 <li>Add sequences to exisiting alignment</li>
3329 <li>Recently opened files / URL lists</li>
3330 <li>Applet can launch the full application</li>
3331 <li>Applet has transparency for features (Java 1.2
3333 <li>Applet has user defined colours parameter</li>
3334 <li>Applet can load sequences from parameter
3335 "sequence<em>x</em>"
3341 <li>Redundancy Panel reinstalled in the Applet</li>
3342 <li>Monospaced font - EPS / rescaling bug fixed</li>
3343 <li>Annotation files with sequence references bug fixed</li>
3349 <div align="center">
3350 <strong>2.08.1</strong><br> 2/5/06
3355 <li>Change case of selected region from Popup menu</li>
3356 <li>Choose to match case when searching</li>
3357 <li>Middle mouse button and mouse movement can compress /
3358 expand the visible width and height of the alignment</li>
3363 <li>Annotation Panel displays complete JNet results</li>
3369 <div align="center">
3370 <strong>2.08b</strong><br> 18/4/06
3376 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3377 <li>Righthand label on wrapped alignments shows correct
3384 <div align="center">
3385 <strong>2.08</strong><br> 10/4/06
3390 <li>Editing can be locked to the selection area</li>
3391 <li>Keyboard editing</li>
3392 <li>Create sequence features from searches</li>
3393 <li>Precalculated annotations can be loaded onto
3395 <li>Features file allows grouping of features</li>
3396 <li>Annotation Colouring scheme added</li>
3397 <li>Smooth fonts off by default - Faster rendering</li>
3398 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3403 <li>Drag & Drop fixed on Linux</li>
3404 <li>Jalview Archive file faster to load/save, sequence
3405 descriptions saved.</li>
3411 <div align="center">
3412 <strong>2.07</strong><br> 12/12/05
3417 <li>PDB Structure Viewer enhanced</li>
3418 <li>Sequence Feature retrieval and display enhanced</li>
3419 <li>Choose to output sequence start-end after sequence
3420 name for file output</li>
3421 <li>Sequence Fetcher WSDBFetch@EBI</li>
3422 <li>Applet can read feature files, PDB files and can be
3423 used for HTML form input</li>
3428 <li>HTML output writes groups and features</li>
3429 <li>Group editing is Control and mouse click</li>
3430 <li>File IO bugs</li>
3436 <div align="center">
3437 <strong>2.06</strong><br> 28/9/05
3442 <li>View annotations in wrapped mode</li>
3443 <li>More options for PCA viewer</li>
3448 <li>GUI bugs resolved</li>
3449 <li>Runs with -nodisplay from command line</li>
3455 <div align="center">
3456 <strong>2.05b</strong><br> 15/9/05
3461 <li>Choose EPS export as lineart or text</li>
3462 <li>Jar files are executable</li>
3463 <li>Can read in Uracil - maps to unknown residue</li>
3468 <li>Known OutOfMemory errors give warning message</li>
3469 <li>Overview window calculated more efficiently</li>
3470 <li>Several GUI bugs resolved</li>
3476 <div align="center">
3477 <strong>2.05</strong><br> 30/8/05
3482 <li>Edit and annotate in "Wrapped" view</li>
3487 <li>Several GUI bugs resolved</li>
3493 <div align="center">
3494 <strong>2.04</strong><br> 24/8/05
3499 <li>Hold down mouse wheel & scroll to change font
3505 <li>Improved JPred client reliability</li>
3506 <li>Improved loading of Jalview files</li>
3512 <div align="center">
3513 <strong>2.03</strong><br> 18/8/05
3518 <li>Set Proxy server name and port in preferences</li>
3519 <li>Multiple URL links from sequence ids</li>
3520 <li>User Defined Colours can have a scheme name and added
3522 <li>Choose to ignore gaps in consensus calculation</li>
3523 <li>Unix users can set default web browser</li>
3524 <li>Runs without GUI for batch processing</li>
3525 <li>Dynamically generated Web Service Menus</li>
3530 <li>InstallAnywhere download for Sparc Solaris</li>
3536 <div align="center">
3537 <strong>2.02</strong><br> 18/7/05
3543 <li>Copy & Paste order of sequences maintains
3544 alignment order.</li>
3550 <div align="center">
3551 <strong>2.01</strong><br> 12/7/05
3556 <li>Use delete key for deleting selection.</li>
3557 <li>Use Mouse wheel to scroll sequences.</li>
3558 <li>Help file updated to describe how to add alignment
3560 <li>Version and build date written to build properties
3562 <li>InstallAnywhere installation will check for updates
3563 at launch of Jalview.</li>
3568 <li>Delete gaps bug fixed.</li>
3569 <li>FileChooser sorts columns.</li>
3570 <li>Can remove groups one by one.</li>
3571 <li>Filechooser icons installed.</li>
3572 <li>Finder ignores return character when searching.
3573 Return key will initiate a search.<br>
3580 <div align="center">
3581 <strong>2.0</strong><br> 20/6/05
3586 <li>New codebase</li>