3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li>
84 <td><div align="left">
87 <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
90 <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views
97 <td width="60" nowrap>
99 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
102 <td><div align="left">
103 <ul><li>Updated Certum Codesigning Certificate
104 (Valid till 30th November 2018)</li></ul></div></td>
105 <td><div align="left">
108 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
109 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
110 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
111 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
112 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
113 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
114 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
120 <td width="60" nowrap>
122 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
125 <td><div align="left">
129 <!-- JAL-2446 -->Faster and more efficient management and
130 rendering of sequence features
133 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
134 429 rate limit request hander
137 <!-- JAL-2773 -->Structure views don't get updated unless
138 their colours have changed
141 <!-- JAL-2495 -->All linked sequences are highlighted for
142 a structure mousover (Jmol) or selection (Chimera)
145 <!-- JAL-2790 -->'Cancel' button in progress bar for
146 JABAWS AACon, RNAAliFold and Disorder prediction jobs
149 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
150 view from Ensembl locus cross-references
153 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
157 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
158 feature can be disabled
161 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
162 PDB easier retrieval of sequences for lists of IDs
165 <!-- JAL-2758 -->Short names for sequences retrieved from
171 <li>Groovy interpreter updated to 2.4.12</li>
172 <li>Example groovy script for generating a matrix of
173 percent identity scores for current alignment.</li>
175 <em>Testing and Deployment</em>
178 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
182 <td><div align="left">
186 <!-- JAL-2643 -->Pressing tab after updating the colour
187 threshold text field doesn't trigger an update to the
191 <!-- JAL-2682 -->Race condition when parsing sequence ID
195 <!-- JAL-2608 -->Overview windows are also closed when
196 alignment window is closed
199 <!-- JAL-2548 -->Export of features doesn't always respect
203 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
204 takes a long time in Cursor mode
210 <!-- JAL-2777 -->Structures with whitespace chainCode
211 cannot be viewed in Chimera
214 <!-- JAL-2728 -->Protein annotation panel too high in
218 <!-- JAL-2757 -->Can't edit the query after the server
219 error warning icon is shown in Uniprot and PDB Free Text
223 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
226 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
229 <!-- JAL-2739 -->Hidden column marker in last column not
230 rendered when switching back from Wrapped to normal view
233 <!-- JAL-2768 -->Annotation display corrupted when
234 scrolling right in unwapped alignment view
237 <!-- JAL-2542 -->Existing features on subsequence
238 incorrectly relocated when full sequence retrieved from
242 <!-- JAL-2733 -->Last reported memory still shown when
243 Desktop->Show Memory is unticked (OSX only)
246 <!-- JAL-2658 -->Amend Features dialog doesn't allow
247 features of same type and group to be selected for
251 <!-- JAL-2524 -->Jalview becomes sluggish in wide
252 alignments when hidden columns are present
255 <!-- JAL-2392 -->Jalview freezes when loading and
256 displaying several structures
259 <!-- JAL-2732 -->Black outlines left after resizing or
263 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
264 within the Jalview desktop on OSX
267 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
268 when in wrapped alignment mode
271 <!-- JAL-2636 -->Scale mark not shown when close to right
272 hand end of alignment
275 <!-- JAL-2684 -->Pairwise alignment of selected regions of
276 each selected sequence do not have correct start/end
280 <!-- JAL-2793 -->Alignment ruler height set incorrectly
281 after canceling the Alignment Window's Font dialog
284 <!-- JAL-2036 -->Show cross-references not enabled after
285 restoring project until a new view is created
288 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
289 URL links appears when only default EMBL-EBI link is
290 configured (since 2.10.2b2)
293 <!-- JAL-2775 -->Overview redraws whole window when box
297 <!-- JAL-2225 -->Structure viewer doesn't map all chains
298 in a multi-chain structure when viewing alignment
299 involving more than one chain (since 2.10)
302 <!-- JAL-2811 -->Double residue highlights in cursor mode
303 if new selection moves alignment window
306 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
307 arrow key in cursor mode to pass hidden column marker
310 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
311 that produces correctly annotated transcripts and products
314 <!-- JAL-2776 -->Toggling a feature group after first time
315 doesn't update associated structure view
318 <em>Applet</em><br />
321 <!-- JAL-2687 -->Concurrent modification exception when
322 closing alignment panel
325 <em>BioJSON</em><br />
328 <!-- JAL-2546 -->BioJSON export does not preserve
329 non-positional features
332 <em>New Known Issues</em>
335 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
336 sequence features correctly (for many previous versions of
340 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
341 using cursor in wrapped panel other than top
344 <!-- JAL-2791 -->Select columns containing feature ignores
345 graduated colour threshold
348 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
349 always preserve numbering and sequence features
352 <em>Known Java 9 Issues</em>
355 <!-- JAL-2902 -->Groovy Console very slow to open and is
356 not responsive when entering characters (Webstart, Java
363 <td width="60" nowrap>
365 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
366 <em>2/10/2017</em></strong>
369 <td><div align="left">
370 <em>New features in Jalview Desktop</em>
373 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
375 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
379 <td><div align="left">
383 <td width="60" nowrap>
385 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
386 <em>7/9/2017</em></strong>
389 <td><div align="left">
393 <!-- JAL-2588 -->Show gaps in overview window by colouring
394 in grey (sequences used to be coloured grey, and gaps were
398 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
402 <!-- JAL-2587 -->Overview updates immediately on increase
403 in size and progress bar shown as higher resolution
404 overview is recalculated
409 <td><div align="left">
413 <!-- JAL-2664 -->Overview window redraws every hidden
414 column region row by row
417 <!-- JAL-2681 -->duplicate protein sequences shown after
418 retrieving Ensembl crossrefs for sequences from Uniprot
421 <!-- JAL-2603 -->Overview window throws NPE if show boxes
422 format setting is unticked
425 <!-- JAL-2610 -->Groups are coloured wrongly in overview
426 if group has show boxes format setting unticked
429 <!-- JAL-2672,JAL-2665 -->Redraw problems when
430 autoscrolling whilst dragging current selection group to
431 include sequences and columns not currently displayed
434 <!-- JAL-2691 -->Not all chains are mapped when multimeric
435 assemblies are imported via CIF file
438 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
439 displayed when threshold or conservation colouring is also
443 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
447 <!-- JAL-2673 -->Jalview continues to scroll after
448 dragging a selected region off the visible region of the
452 <!-- JAL-2724 -->Cannot apply annotation based
453 colourscheme to all groups in a view
456 <!-- JAL-2511 -->IDs don't line up with sequences
457 initially after font size change using the Font chooser or
464 <td width="60" nowrap>
466 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
469 <td><div align="left">
470 <em>Calculations</em>
474 <!-- JAL-1933 -->Occupancy annotation row shows number of
475 ungapped positions in each column of the alignment.
478 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
479 a calculation dialog box
482 <!-- JAL-2379 -->Revised implementation of PCA for speed
483 and memory efficiency (~30x faster)
486 <!-- JAL-2403 -->Revised implementation of sequence
487 similarity scores as used by Tree, PCA, Shading Consensus
488 and other calculations
491 <!-- JAL-2416 -->Score matrices are stored as resource
492 files within the Jalview codebase
495 <!-- JAL-2500 -->Trees computed on Sequence Feature
496 Similarity may have different topology due to increased
503 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
504 model for alignments and groups
507 <!-- JAL-384 -->Custom shading schemes created via groovy
514 <!-- JAL-2526 -->Efficiency improvements for interacting
515 with alignment and overview windows
518 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
522 <!-- JAL-2388 -->Hidden columns and sequences can be
526 <!-- JAL-2611 -->Click-drag in visible area allows fine
527 adjustment of visible position
531 <em>Data import/export</em>
534 <!-- JAL-2535 -->Posterior probability annotation from
535 Stockholm files imported as sequence associated annotation
538 <!-- JAL-2507 -->More robust per-sequence positional
539 annotation input/output via stockholm flatfile
542 <!-- JAL-2533 -->Sequence names don't include file
543 extension when importing structure files without embedded
544 names or PDB accessions
547 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
548 format sequence substitution matrices
551 <em>User Interface</em>
554 <!-- JAL-2447 --> Experimental Features Checkbox in
555 Desktop's Tools menu to hide or show untested features in
559 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
560 via Overview or sequence motif search operations
563 <!-- JAL-2547 -->Amend sequence features dialog box can be
564 opened by double clicking gaps within sequence feature
568 <!-- JAL-1476 -->Status bar message shown when not enough
569 aligned positions were available to create a 3D structure
573 <em>3D Structure</em>
576 <!-- JAL-2430 -->Hidden regions in alignment views are not
577 coloured in linked structure views
580 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
581 file-based command exchange
584 <!-- JAL-2375 -->Structure chooser automatically shows
585 Cached Structures rather than querying the PDBe if
586 structures are already available for sequences
589 <!-- JAL-2520 -->Structures imported via URL are cached in
590 the Jalview project rather than downloaded again when the
594 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
595 to transfer Chimera's structure attributes as Jalview
596 features, and vice-versa (<strong>Experimental
600 <em>Web Services</em>
603 <!-- JAL-2549 -->Updated JABAWS client to v2.2
606 <!-- JAL-2335 -->Filter non-standard amino acids and
607 nucleotides when submitting to AACon and other MSA
611 <!-- JAL-2316, -->URLs for viewing database
612 cross-references provided by identifiers.org and the
620 <!-- JAL-2344 -->FileFormatI interface for describing and
621 identifying file formats (instead of String constants)
624 <!-- JAL-2228 -->FeatureCounter script refactored for
625 efficiency when counting all displayed features (not
626 backwards compatible with 2.10.1)
629 <em>Example files</em>
632 <!-- JAL-2631 -->Graduated feature colour style example
633 included in the example feature file
636 <em>Documentation</em>
639 <!-- JAL-2339 -->Release notes reformatted for readability
640 with the built-in Java help viewer
643 <!-- JAL-1644 -->Find documentation updated with 'search
644 sequence description' option
650 <!-- JAL-2485, -->External service integration tests for
651 Uniprot REST Free Text Search Client
654 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
657 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
662 <td><div align="left">
663 <em>Calculations</em>
666 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
667 matrix - C->R should be '-3'<br />Old matrix restored
668 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
670 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
671 Jalview's treatment of gaps in PCA and substitution matrix
672 based Tree calculations.<br /> <br />In earlier versions
673 of Jalview, gaps matching gaps were penalised, and gaps
674 matching non-gaps penalised even more. In the PCA
675 calculation, gaps were actually treated as non-gaps - so
676 different costs were applied, which meant Jalview's PCAs
677 were different to those produced by SeqSpace.<br />Jalview
678 now treats gaps in the same way as SeqSpace (ie it scores
679 them as 0). <br /> <br />Enter the following in the
680 Groovy console to restore pre-2.10.2 behaviour:<br />
681 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
682 // for 2.10.1 mode <br />
683 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
684 // to restore 2.10.2 mode <br /> <br /> <em>Note:
685 these settings will affect all subsequent tree and PCA
686 calculations (not recommended)</em></li>
688 <!-- JAL-2424 -->Fixed off-by-one bug that affected
689 scaling of branch lengths for trees computed using
690 Sequence Feature Similarity.
693 <!-- JAL-2377 -->PCA calculation could hang when
694 generating output report when working with highly
698 <!-- JAL-2544 --> Sort by features includes features to
699 right of selected region when gaps present on right-hand
703 <em>User Interface</em>
706 <!-- JAL-2346 -->Reopening Colour by annotation dialog
707 doesn't reselect a specific sequence's associated
708 annotation after it was used for colouring a view
711 <!-- JAL-2419 -->Current selection lost if popup menu
712 opened on a region of alignment without groups
715 <!-- JAL-2374 -->Popup menu not always shown for regions
716 of an alignment with overlapping groups
719 <!-- JAL-2310 -->Finder double counts if both a sequence's
720 name and description match
723 <!-- JAL-2370 -->Hiding column selection containing two
724 hidden regions results in incorrect hidden regions
727 <!-- JAL-2386 -->'Apply to all groups' setting when
728 changing colour does not apply Conservation slider value
732 <!-- JAL-2373 -->Percentage identity and conservation menu
733 items do not show a tick or allow shading to be disabled
736 <!-- JAL-2385 -->Conservation shading or PID threshold
737 lost when base colourscheme changed if slider not visible
740 <!-- JAL-2547 -->Sequence features shown in tooltip for
741 gaps before start of features
744 <!-- JAL-2623 -->Graduated feature colour threshold not
745 restored to UI when feature colour is edited
748 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
749 a time when scrolling vertically in wrapped mode.
752 <!-- JAL-2630 -->Structure and alignment overview update
753 as graduate feature colour settings are modified via the
757 <!-- JAL-2034 -->Overview window doesn't always update
758 when a group defined on the alignment is resized
761 <!-- JAL-2605 -->Mouseovers on left/right scale region in
762 wrapped view result in positional status updates
766 <!-- JAL-2563 -->Status bar doesn't show position for
767 ambiguous amino acid and nucleotide symbols
770 <!-- JAL-2602 -->Copy consensus sequence failed if
771 alignment included gapped columns
774 <!-- JAL-2473 -->Minimum size set for Jalview windows so
775 widgets don't permanently disappear
778 <!-- JAL-2503 -->Cannot select or filter quantitative
779 annotation that are shown only as column labels (e.g.
780 T-Coffee column reliability scores)
783 <!-- JAL-2594 -->Exception thrown if trying to create a
784 sequence feature on gaps only
787 <!-- JAL-2504 -->Features created with 'New feature'
788 button from a Find inherit previously defined feature type
789 rather than the Find query string
792 <!-- JAL-2423 -->incorrect title in output window when
793 exporting tree calculated in Jalview
796 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
797 and then revealing them reorders sequences on the
801 <!-- JAL-964 -->Group panel in sequence feature settings
802 doesn't update to reflect available set of groups after
803 interactively adding or modifying features
806 <!-- JAL-2225 -->Sequence Database chooser unusable on
810 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
811 only excluded gaps in current sequence and ignored
818 <!-- JAL-2421 -->Overview window visible region moves
819 erratically when hidden rows or columns are present
822 <!-- JAL-2362 -->Per-residue colourschemes applied via the
823 Structure Viewer's colour menu don't correspond to
827 <!-- JAL-2405 -->Protein specific colours only offered in
828 colour and group colour menu for protein alignments
831 <!-- JAL-2385 -->Colour threshold slider doesn't update to
832 reflect currently selected view or group's shading
836 <!-- JAL-2624 -->Feature colour thresholds not respected
837 when rendered on overview and structures when opacity at
841 <!-- JAL-2589 -->User defined gap colour not shown in
842 overview when features overlaid on alignment
845 <em>Data import/export</em>
848 <!-- JAL-2576 -->Very large alignments take a long time to
852 <!-- JAL-2507 -->Per-sequence RNA secondary structures
853 added after a sequence was imported are not written to
857 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
858 when importing RNA secondary structure via Stockholm
861 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
862 not shown in correct direction for simple pseudoknots
865 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
866 with lightGray or darkGray via features file (but can
870 <!-- JAL-2383 -->Above PID colour threshold not recovered
871 when alignment view imported from project
874 <!-- JAL-2520,JAL-2465 -->No mappings generated between
875 structure and sequences extracted from structure files
876 imported via URL and viewed in Jmol
879 <!-- JAL-2520 -->Structures loaded via URL are saved in
880 Jalview Projects rather than fetched via URL again when
881 the project is loaded and the structure viewed
884 <em>Web Services</em>
887 <!-- JAL-2519 -->EnsemblGenomes example failing after
888 release of Ensembl v.88
891 <!-- JAL-2366 -->Proxy server address and port always
892 appear enabled in Preferences->Connections
895 <!-- JAL-2461 -->DAS registry not found exceptions
896 removed from console output
899 <!-- JAL-2582 -->Cannot retrieve protein products from
900 Ensembl by Peptide ID
903 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
904 created from SIFTs, and spurious 'Couldn't open structure
905 in Chimera' errors raised after April 2017 update (problem
906 due to 'null' string rather than empty string used for
907 residues with no corresponding PDB mapping).
910 <em>Application UI</em>
913 <!-- JAL-2361 -->User Defined Colours not added to Colour
917 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
918 case' residues (button in colourscheme editor debugged and
919 new documentation and tooltips added)
922 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
923 doesn't restore group-specific text colour thresholds
926 <!-- JAL-2243 -->Feature settings panel does not update as
927 new features are added to alignment
930 <!-- JAL-2532 -->Cancel in feature settings reverts
931 changes to feature colours via the Amend features dialog
934 <!-- JAL-2506 -->Null pointer exception when attempting to
935 edit graduated feature colour via amend features dialog
939 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
940 selection menu changes colours of alignment views
943 <!-- JAL-2426 -->Spurious exceptions in console raised
944 from alignment calculation workers after alignment has
948 <!-- JAL-1608 -->Typo in selection popup menu - Create
949 groups now 'Create Group'
952 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
953 Create/Undefine group doesn't always work
956 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
957 shown again after pressing 'Cancel'
960 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
961 adjusts start position in wrap mode
964 <!-- JAL-2563 -->Status bar doesn't show positions for
965 ambiguous amino acids
968 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
969 CDS/Protein view after CDS sequences added for aligned
973 <!-- JAL-2592 -->User defined colourschemes called 'User
974 Defined' don't appear in Colours menu
980 <!-- JAL-2468 -->Switching between Nucleotide and Protein
981 score models doesn't always result in an updated PCA plot
984 <!-- JAL-2442 -->Features not rendered as transparent on
985 overview or linked structure view
988 <!-- JAL-2372 -->Colour group by conservation doesn't
992 <!-- JAL-2517 -->Hitting Cancel after applying
993 user-defined colourscheme doesn't restore original
1000 <!-- JAL-2314 -->Unit test failure:
1001 jalview.ws.jabaws.RNAStructExportImport setup fails
1004 <!-- JAL-2307 -->Unit test failure:
1005 jalview.ws.sifts.SiftsClientTest due to compatibility
1006 problems with deep array comparison equality asserts in
1007 successive versions of TestNG
1010 <!-- JAL-2479 -->Relocated StructureChooserTest and
1011 ParameterUtilsTest Unit tests to Network suite
1014 <em>New Known Issues</em>
1017 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1018 phase after a sequence motif find operation
1021 <!-- JAL-2550 -->Importing annotation file with rows
1022 containing just upper and lower case letters are
1023 interpreted as WUSS RNA secondary structure symbols
1026 <!-- JAL-2590 -->Cannot load and display Newick trees
1027 reliably from eggnog Ortholog database
1030 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1031 containing features of type Highlight' when 'B' is pressed
1032 to mark columns containing highlighted regions.
1035 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1036 doesn't always add secondary structure annotation.
1041 <td width="60" nowrap>
1042 <div align="center">
1043 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1046 <td><div align="left">
1050 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1051 for all consensus calculations
1054 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1057 <li>Updated Jalview's Certum code signing certificate
1060 <em>Application</em>
1063 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1064 set of database cross-references, sorted alphabetically
1067 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1068 from database cross references. Users with custom links
1069 will receive a <a href="webServices/urllinks.html#warning">warning
1070 dialog</a> asking them to update their preferences.
1073 <!-- JAL-2287-->Cancel button and escape listener on
1074 dialog warning user about disconnecting Jalview from a
1078 <!-- JAL-2320-->Jalview's Chimera control window closes if
1079 the Chimera it is connected to is shut down
1082 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1083 columns menu item to mark columns containing highlighted
1084 regions (e.g. from structure selections or results of a
1088 <!-- JAL-2284-->Command line option for batch-generation
1089 of HTML pages rendering alignment data with the BioJS
1099 <!-- JAL-2286 -->Columns with more than one modal residue
1100 are not coloured or thresholded according to percent
1101 identity (first observed in Jalview 2.8.2)
1104 <!-- JAL-2301 -->Threonine incorrectly reported as not
1108 <!-- JAL-2318 -->Updates to documentation pages (above PID
1109 threshold, amino acid properties)
1112 <!-- JAL-2292 -->Lower case residues in sequences are not
1113 reported as mapped to residues in a structure file in the
1117 <!--JAL-2324 -->Identical features with non-numeric scores
1118 could be added multiple times to a sequence
1121 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1122 bond features shown as two highlighted residues rather
1123 than a range in linked structure views, and treated
1124 correctly when selecting and computing trees from features
1127 <!-- JAL-2281-->Custom URL links for database
1128 cross-references are matched to database name regardless
1133 <em>Application</em>
1136 <!-- JAL-2282-->Custom URL links for specific database
1137 names without regular expressions also offer links from
1141 <!-- JAL-2315-->Removing a single configured link in the
1142 URL links pane in Connections preferences doesn't actually
1143 update Jalview configuration
1146 <!-- JAL-2272-->CTRL-Click on a selected region to open
1147 the alignment area popup menu doesn't work on El-Capitan
1150 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1151 files with similarly named sequences if dropped onto the
1155 <!-- JAL-2312 -->Additional mappings are shown for PDB
1156 entries where more chains exist in the PDB accession than
1157 are reported in the SIFTS file
1160 <!-- JAL-2317-->Certain structures do not get mapped to
1161 the structure view when displayed with Chimera
1164 <!-- JAL-2317-->No chains shown in the Chimera view
1165 panel's View->Show Chains submenu
1168 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1169 work for wrapped alignment views
1172 <!--JAL-2197 -->Rename UI components for running JPred
1173 predictions from 'JNet' to 'JPred'
1176 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1177 corrupted when annotation panel vertical scroll is not at
1178 first annotation row
1181 <!--JAL-2332 -->Attempting to view structure for Hen
1182 lysozyme results in a PDB Client error dialog box
1185 <!-- JAL-2319 -->Structure View's mapping report switched
1186 ranges for PDB and sequence for SIFTS
1189 SIFTS 'Not_Observed' residues mapped to non-existant
1193 <!-- <em>New Known Issues</em>
1200 <td width="60" nowrap>
1201 <div align="center">
1202 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1203 <em>25/10/2016</em></strong>
1206 <td><em>Application</em>
1208 <li>3D Structure chooser opens with 'Cached structures'
1209 view if structures already loaded</li>
1210 <li>Progress bar reports models as they are loaded to
1211 structure views</li>
1217 <li>Colour by conservation always enabled and no tick
1218 shown in menu when BLOSUM or PID shading applied</li>
1219 <li>FER1_ARATH and FER2_ARATH labels were switched in
1220 example sequences/projects/trees</li>
1222 <em>Application</em>
1224 <li>Jalview projects with views of local PDB structure
1225 files saved on Windows cannot be opened on OSX</li>
1226 <li>Multiple structure views can be opened and superposed
1227 without timeout for structures with multiple models or
1228 multiple sequences in alignment</li>
1229 <li>Cannot import or associated local PDB files without a
1230 PDB ID HEADER line</li>
1231 <li>RMSD is not output in Jmol console when superposition
1233 <li>Drag and drop of URL from Browser fails for Linux and
1234 OSX versions earlier than El Capitan</li>
1235 <li>ENA client ignores invalid content from ENA server</li>
1236 <li>Exceptions are not raised in console when ENA client
1237 attempts to fetch non-existent IDs via Fetch DB Refs UI
1239 <li>Exceptions are not raised in console when a new view
1240 is created on the alignment</li>
1241 <li>OSX right-click fixed for group selections: CMD-click
1242 to insert/remove gaps in groups and CTRL-click to open group
1245 <em>Build and deployment</em>
1247 <li>URL link checker now copes with multi-line anchor
1250 <em>New Known Issues</em>
1252 <li>Drag and drop from URL links in browsers do not work
1259 <td width="60" nowrap>
1260 <div align="center">
1261 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1264 <td><em>General</em>
1267 <!-- JAL-2124 -->Updated Spanish translations.
1270 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1271 for importing structure data to Jalview. Enables mmCIF and
1275 <!-- JAL-192 --->Alignment ruler shows positions relative to
1279 <!-- JAL-2202 -->Position/residue shown in status bar when
1280 mousing over sequence associated annotation
1283 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1287 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1288 '()', canonical '[]' and invalid '{}' base pair populations
1292 <!-- JAL-2092 -->Feature settings popup menu options for
1293 showing or hiding columns containing a feature
1296 <!-- JAL-1557 -->Edit selected group by double clicking on
1297 group and sequence associated annotation labels
1300 <!-- JAL-2236 -->Sequence name added to annotation label in
1301 select/hide columns by annotation and colour by annotation
1305 </ul> <em>Application</em>
1308 <!-- JAL-2050-->Automatically hide introns when opening a
1309 gene/transcript view
1312 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1316 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1317 structure mappings with the EMBL-EBI PDBe SIFTS database
1320 <!-- JAL-2079 -->Updated download sites used for Rfam and
1321 Pfam sources to xfam.org
1324 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1327 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1328 over sequences in Jalview
1331 <!-- JAL-2027-->Support for reverse-complement coding
1332 regions in ENA and EMBL
1335 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1336 for record retrieval via ENA rest API
1339 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1343 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1344 groovy script execution
1347 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1348 alignment window's Calculate menu
1351 <!-- JAL-1812 -->Allow groovy scripts that call
1352 Jalview.getAlignFrames() to run in headless mode
1355 <!-- JAL-2068 -->Support for creating new alignment
1356 calculation workers from groovy scripts
1359 <!-- JAL-1369 --->Store/restore reference sequence in
1363 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1364 associations are now saved/restored from project
1367 <!-- JAL-1993 -->Database selection dialog always shown
1368 before sequence fetcher is opened
1371 <!-- JAL-2183 -->Double click on an entry in Jalview's
1372 database chooser opens a sequence fetcher
1375 <!-- JAL-1563 -->Free-text search client for UniProt using
1376 the UniProt REST API
1379 <!-- JAL-2168 -->-nonews command line parameter to prevent
1380 the news reader opening
1383 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1384 querying stored in preferences
1387 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1391 <!-- JAL-1977-->Tooltips shown on database chooser
1394 <!-- JAL-391 -->Reverse complement function in calculate
1395 menu for nucleotide sequences
1398 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1399 and feature counts preserves alignment ordering (and
1400 debugged for complex feature sets).
1403 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1404 viewing structures with Jalview 2.10
1407 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1408 genome, transcript CCDS and gene ids via the Ensembl and
1409 Ensembl Genomes REST API
1412 <!-- JAL-2049 -->Protein sequence variant annotation
1413 computed for 'sequence_variant' annotation on CDS regions
1417 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1421 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1422 Ref Fetcher fails to match, or otherwise updates sequence
1423 data from external database records.
1426 <!-- JAL-2154 -->Revised Jalview Project format for
1427 efficient recovery of sequence coding and alignment
1428 annotation relationships.
1430 </ul> <!-- <em>Applet</em>
1441 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1445 <!-- JAL-2018-->Export features in Jalview format (again)
1446 includes graduated colourschemes
1449 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1450 working with big alignments and lots of hidden columns
1453 <!-- JAL-2053-->Hidden column markers not always rendered
1454 at right of alignment window
1457 <!-- JAL-2067 -->Tidied up links in help file table of
1461 <!-- JAL-2072 -->Feature based tree calculation not shown
1465 <!-- JAL-2075 -->Hidden columns ignored during feature
1466 based tree calculation
1469 <!-- JAL-2065 -->Alignment view stops updating when show
1470 unconserved enabled for group on alignment
1473 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1477 <!-- JAL-2146 -->Alignment column in status incorrectly
1478 shown as "Sequence position" when mousing over
1482 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1483 hidden columns present
1486 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1487 user created annotation added to alignment
1490 <!-- JAL-1841 -->RNA Structure consensus only computed for
1491 '()' base pair annotation
1494 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1495 in zero scores for all base pairs in RNA Structure
1499 <!-- JAL-2174-->Extend selection with columns containing
1503 <!-- JAL-2275 -->Pfam format writer puts extra space at
1504 beginning of sequence
1507 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1511 <!-- JAL-2238 -->Cannot create groups on an alignment from
1512 from a tree when t-coffee scores are shown
1515 <!-- JAL-1836,1967 -->Cannot import and view PDB
1516 structures with chains containing negative resnums (4q4h)
1519 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1523 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1524 to Clustal, PIR and PileUp output
1527 <!-- JAL-2008 -->Reordering sequence features that are
1528 not visible causes alignment window to repaint
1531 <!-- JAL-2006 -->Threshold sliders don't work in
1532 graduated colour and colour by annotation row for e-value
1533 scores associated with features and annotation rows
1536 <!-- JAL-1797 -->amino acid physicochemical conservation
1537 calculation should be case independent
1540 <!-- JAL-2173 -->Remove annotation also updates hidden
1544 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1545 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1546 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1549 <!-- JAL-2065 -->Null pointer exceptions and redraw
1550 problems when reference sequence defined and 'show
1551 non-conserved' enabled
1554 <!-- JAL-1306 -->Quality and Conservation are now shown on
1555 load even when Consensus calculation is disabled
1558 <!-- JAL-1932 -->Remove right on penultimate column of
1559 alignment does nothing
1562 <em>Application</em>
1565 <!-- JAL-1552-->URLs and links can't be imported by
1566 drag'n'drop on OSX when launched via webstart (note - not
1567 yet fixed for El Capitan)
1570 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1571 output when running on non-gb/us i18n platforms
1574 <!-- JAL-1944 -->Error thrown when exporting a view with
1575 hidden sequences as flat-file alignment
1578 <!-- JAL-2030-->InstallAnywhere distribution fails when
1582 <!-- JAL-2080-->Jalview very slow to launch via webstart
1583 (also hotfix for 2.9.0b2)
1586 <!-- JAL-2085 -->Cannot save project when view has a
1587 reference sequence defined
1590 <!-- JAL-1011 -->Columns are suddenly selected in other
1591 alignments and views when revealing hidden columns
1594 <!-- JAL-1989 -->Hide columns not mirrored in complement
1595 view in a cDNA/Protein splitframe
1598 <!-- JAL-1369 -->Cannot save/restore representative
1599 sequence from project when only one sequence is
1603 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1604 in Structure Chooser
1607 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1608 structure consensus didn't refresh annotation panel
1611 <!-- JAL-1962 -->View mapping in structure view shows
1612 mappings between sequence and all chains in a PDB file
1615 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1616 dialogs format columns correctly, don't display array
1617 data, sort columns according to type
1620 <!-- JAL-1975 -->Export complete shown after destination
1621 file chooser is cancelled during an image export
1624 <!-- JAL-2025 -->Error when querying PDB Service with
1625 sequence name containing special characters
1628 <!-- JAL-2024 -->Manual PDB structure querying should be
1632 <!-- JAL-2104 -->Large tooltips with broken HTML
1633 formatting don't wrap
1636 <!-- JAL-1128 -->Figures exported from wrapped view are
1637 truncated so L looks like I in consensus annotation
1640 <!-- JAL-2003 -->Export features should only export the
1641 currently displayed features for the current selection or
1645 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1646 after fetching cross-references, and restoring from
1650 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1651 followed in the structure viewer
1654 <!-- JAL-2163 -->Titles for individual alignments in
1655 splitframe not restored from project
1658 <!-- JAL-2145 -->missing autocalculated annotation at
1659 trailing end of protein alignment in transcript/product
1660 splitview when pad-gaps not enabled by default
1663 <!-- JAL-1797 -->amino acid physicochemical conservation
1667 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1668 article has been read (reopened issue due to
1669 internationalisation problems)
1672 <!-- JAL-1960 -->Only offer PDB structures in structure
1673 viewer based on sequence name, PDB and UniProt
1678 <!-- JAL-1976 -->No progress bar shown during export of
1682 <!-- JAL-2213 -->Structures not always superimposed after
1683 multiple structures are shown for one or more sequences.
1686 <!-- JAL-1370 -->Reference sequence characters should not
1687 be replaced with '.' when 'Show unconserved' format option
1691 <!-- JAL-1823 -->Cannot specify chain code when entering
1692 specific PDB id for sequence
1695 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1696 'Export hidden sequences' is enabled, but 'export hidden
1697 columns' is disabled.
1700 <!--JAL-2026-->Best Quality option in structure chooser
1701 selects lowest rather than highest resolution structures
1705 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1706 to sequence mapping in 'View Mappings' report
1709 <!-- JAL-2284 -->Unable to read old Jalview projects that
1710 contain non-XML data added after Jalvew wrote project.
1713 <!-- JAL-2118 -->Newly created annotation row reorders
1714 after clicking on it to create new annotation for a
1718 <!-- JAL-1980 -->Null Pointer Exception raised when
1719 pressing Add on an orphaned cut'n'paste window.
1721 <!-- may exclude, this is an external service stability issue JAL-1941
1722 -- > RNA 3D structure not added via DSSR service</li> -->
1727 <!-- JAL-2151 -->Incorrect columns are selected when
1728 hidden columns present before start of sequence
1731 <!-- JAL-1986 -->Missing dependencies on applet pages
1735 <!-- JAL-1947 -->Overview pixel size changes when
1736 sequences are hidden in applet
1739 <!-- JAL-1996 -->Updated instructions for applet
1740 deployment on examples pages.
1747 <td width="60" nowrap>
1748 <div align="center">
1749 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1750 <em>16/10/2015</em></strong>
1753 <td><em>General</em>
1755 <li>Time stamps for signed Jalview application and applet
1760 <em>Application</em>
1762 <li>Duplicate group consensus and conservation rows
1763 shown when tree is partitioned</li>
1764 <li>Erratic behaviour when tree partitions made with
1765 multiple cDNA/Protein split views</li>
1771 <td width="60" nowrap>
1772 <div align="center">
1773 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1774 <em>8/10/2015</em></strong>
1777 <td><em>General</em>
1779 <li>Updated Spanish translations of localized text for
1781 </ul> <em>Application</em>
1783 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1784 <li>Signed OSX InstallAnywhere installer<br></li>
1785 <li>Support for per-sequence based annotations in BioJSON</li>
1786 </ul> <em>Applet</em>
1788 <li>Split frame example added to applet examples page</li>
1789 </ul> <em>Build and Deployment</em>
1792 <!-- JAL-1888 -->New ant target for running Jalview's test
1800 <li>Mapping of cDNA to protein in split frames
1801 incorrect when sequence start > 1</li>
1802 <li>Broken images in filter column by annotation dialog
1804 <li>Feature colours not parsed from features file</li>
1805 <li>Exceptions and incomplete link URLs recovered when
1806 loading a features file containing HTML tags in feature
1810 <em>Application</em>
1812 <li>Annotations corrupted after BioJS export and
1814 <li>Incorrect sequence limits after Fetch DB References
1815 with 'trim retrieved sequences'</li>
1816 <li>Incorrect warning about deleting all data when
1817 deleting selected columns</li>
1818 <li>Patch to build system for shipping properly signed
1819 JNLP templates for webstart launch</li>
1820 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1821 unreleased structures for download or viewing</li>
1822 <li>Tab/space/return keystroke operation of EMBL-PDBe
1823 fetcher/viewer dialogs works correctly</li>
1824 <li>Disabled 'minimise' button on Jalview windows
1825 running on OSX to workaround redraw hang bug</li>
1826 <li>Split cDNA/Protein view position and geometry not
1827 recovered from jalview project</li>
1828 <li>Initial enabled/disabled state of annotation menu
1829 sorter 'show autocalculated first/last' corresponds to
1831 <li>Restoring of Clustal, RNA Helices and T-Coffee
1832 color schemes from BioJSON</li>
1836 <li>Reorder sequences mirrored in cDNA/Protein split
1838 <li>Applet with Jmol examples not loading correctly</li>
1844 <td><div align="center">
1845 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1847 <td><em>General</em>
1849 <li>Linked visualisation and analysis of DNA and Protein
1852 <li>Translated cDNA alignments shown as split protein
1853 and DNA alignment views</li>
1854 <li>Codon consensus annotation for linked protein and
1855 cDNA alignment views</li>
1856 <li>Link cDNA or Protein product sequences by loading
1857 them onto Protein or cDNA alignments</li>
1858 <li>Reconstruct linked cDNA alignment from aligned
1859 protein sequences</li>
1862 <li>Jmol integration updated to Jmol v14.2.14</li>
1863 <li>Import and export of Jalview alignment views as <a
1864 href="features/bioJsonFormat.html">BioJSON</a></li>
1865 <li>New alignment annotation file statements for
1866 reference sequences and marking hidden columns</li>
1867 <li>Reference sequence based alignment shading to
1868 highlight variation</li>
1869 <li>Select or hide columns according to alignment
1871 <li>Find option for locating sequences by description</li>
1872 <li>Conserved physicochemical properties shown in amino
1873 acid conservation row</li>
1874 <li>Alignments can be sorted by number of RNA helices</li>
1875 </ul> <em>Application</em>
1877 <li>New cDNA/Protein analysis capabilities
1879 <li>Get Cross-References should open a Split Frame
1880 view with cDNA/Protein</li>
1881 <li>Detect when nucleotide sequences and protein
1882 sequences are placed in the same alignment</li>
1883 <li>Split cDNA/Protein views are saved in Jalview
1888 <li>Use REST API to talk to Chimera</li>
1889 <li>Selected regions in Chimera are highlighted in linked
1890 Jalview windows</li>
1892 <li>VARNA RNA viewer updated to v3.93</li>
1893 <li>VARNA views are saved in Jalview Projects</li>
1894 <li>Pseudoknots displayed as Jalview RNA annotation can
1895 be shown in VARNA</li>
1897 <li>Make groups for selection uses marked columns as well
1898 as the active selected region</li>
1900 <li>Calculate UPGMA and NJ trees using sequence feature
1902 <li>New Export options
1904 <li>New Export Settings dialog to control hidden
1905 region export in flat file generation</li>
1907 <li>Export alignment views for display with the <a
1908 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1910 <li>Export scrollable SVG in HTML page</li>
1911 <li>Optional embedding of BioJSON data when exporting
1912 alignment figures to HTML</li>
1914 <li>3D structure retrieval and display
1916 <li>Free text and structured queries with the PDBe
1918 <li>PDBe Search API based discovery and selection of
1919 PDB structures for a sequence set</li>
1923 <li>JPred4 employed for protein secondary structure
1925 <li>Hide Insertions menu option to hide unaligned columns
1926 for one or a group of sequences</li>
1927 <li>Automatically hide insertions in alignments imported
1928 from the JPred4 web server</li>
1929 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1930 system on OSX<br />LGPL libraries courtesy of <a
1931 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1933 <li>changed 'View nucleotide structure' submenu to 'View
1934 VARNA 2D Structure'</li>
1935 <li>change "View protein structure" menu option to "3D
1938 </ul> <em>Applet</em>
1940 <li>New layout for applet example pages</li>
1941 <li>New parameters to enable SplitFrame view
1942 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1943 <li>New example demonstrating linked viewing of cDNA and
1944 Protein alignments</li>
1945 </ul> <em>Development and deployment</em>
1947 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1948 <li>Include installation type and git revision in build
1949 properties and console log output</li>
1950 <li>Jalview Github organisation, and new github site for
1951 storing BioJsMSA Templates</li>
1952 <li>Jalview's unit tests now managed with TestNG</li>
1955 <!-- <em>General</em>
1957 </ul> --> <!-- issues resolved --> <em>Application</em>
1959 <li>Escape should close any open find dialogs</li>
1960 <li>Typo in select-by-features status report</li>
1961 <li>Consensus RNA secondary secondary structure
1962 predictions are not highlighted in amber</li>
1963 <li>Missing gap character in v2.7 example file means
1964 alignment appears unaligned when pad-gaps is not enabled</li>
1965 <li>First switch to RNA Helices colouring doesn't colour
1966 associated structure views</li>
1967 <li>ID width preference option is greyed out when auto
1968 width checkbox not enabled</li>
1969 <li>Stopped a warning dialog from being shown when
1970 creating user defined colours</li>
1971 <li>'View Mapping' in structure viewer shows sequence
1972 mappings for just that viewer's sequences</li>
1973 <li>Workaround for superposing PDB files containing
1974 multiple models in Chimera</li>
1975 <li>Report sequence position in status bar when hovering
1976 over Jmol structure</li>
1977 <li>Cannot output gaps as '.' symbols with Selection ->
1978 output to text box</li>
1979 <li>Flat file exports of alignments with hidden columns
1980 have incorrect sequence start/end</li>
1981 <li>'Aligning' a second chain to a Chimera structure from
1983 <li>Colour schemes applied to structure viewers don't
1984 work for nucleotide</li>
1985 <li>Loading/cut'n'pasting an empty or invalid file leads
1986 to a grey/invisible alignment window</li>
1987 <li>Exported Jpred annotation from a sequence region
1988 imports to different position</li>
1989 <li>Space at beginning of sequence feature tooltips shown
1990 on some platforms</li>
1991 <li>Chimera viewer 'View | Show Chain' menu is not
1993 <li>'New View' fails with a Null Pointer Exception in
1994 console if Chimera has been opened</li>
1995 <li>Mouseover to Chimera not working</li>
1996 <li>Miscellaneous ENA XML feature qualifiers not
1998 <li>NPE in annotation renderer after 'Extract Scores'</li>
1999 <li>If two structures in one Chimera window, mouseover of
2000 either sequence shows on first structure</li>
2001 <li>'Show annotations' options should not make
2002 non-positional annotations visible</li>
2003 <li>Subsequence secondary structure annotation not shown
2004 in right place after 'view flanking regions'</li>
2005 <li>File Save As type unset when current file format is
2007 <li>Save as '.jar' option removed for saving Jalview
2009 <li>Colour by Sequence colouring in Chimera more
2011 <li>Cannot 'add reference annotation' for a sequence in
2012 several views on same alignment</li>
2013 <li>Cannot show linked products for EMBL / ENA records</li>
2014 <li>Jalview's tooltip wraps long texts containing no
2016 </ul> <em>Applet</em>
2018 <li>Jmol to JalviewLite mouseover/link not working</li>
2019 <li>JalviewLite can't import sequences with ID
2020 descriptions containing angle brackets</li>
2021 </ul> <em>General</em>
2023 <li>Cannot export and reimport RNA secondary structure
2024 via jalview annotation file</li>
2025 <li>Random helix colour palette for colour by annotation
2026 with RNA secondary structure</li>
2027 <li>Mouseover to cDNA from STOP residue in protein
2028 translation doesn't work.</li>
2029 <li>hints when using the select by annotation dialog box</li>
2030 <li>Jmol alignment incorrect if PDB file has alternate CA
2032 <li>FontChooser message dialog appears to hang after
2033 choosing 1pt font</li>
2034 <li>Peptide secondary structure incorrectly imported from
2035 annotation file when annotation display text includes 'e' or
2037 <li>Cannot set colour of new feature type whilst creating
2039 <li>cDNA translation alignment should not be sequence
2040 order dependent</li>
2041 <li>'Show unconserved' doesn't work for lower case
2043 <li>Nucleotide ambiguity codes involving R not recognised</li>
2044 </ul> <em>Deployment and Documentation</em>
2046 <li>Applet example pages appear different to the rest of
2047 www.jalview.org</li>
2048 </ul> <em>Application Known issues</em>
2050 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2051 <li>Misleading message appears after trying to delete
2053 <li>Jalview icon not shown in dock after InstallAnywhere
2054 version launches</li>
2055 <li>Fetching EMBL reference for an RNA sequence results
2056 fails with a sequence mismatch</li>
2057 <li>Corrupted or unreadable alignment display when
2058 scrolling alignment to right</li>
2059 <li>ArrayIndexOutOfBoundsException thrown when remove
2060 empty columns called on alignment with ragged gapped ends</li>
2061 <li>auto calculated alignment annotation rows do not get
2062 placed above or below non-autocalculated rows</li>
2063 <li>Jalview dekstop becomes sluggish at full screen in
2064 ultra-high resolution</li>
2065 <li>Cannot disable consensus calculation independently of
2066 quality and conservation</li>
2067 <li>Mouseover highlighting between cDNA and protein can
2068 become sluggish with more than one splitframe shown</li>
2069 </ul> <em>Applet Known Issues</em>
2071 <li>Core PDB parsing code requires Jmol</li>
2072 <li>Sequence canvas panel goes white when alignment
2073 window is being resized</li>
2079 <td><div align="center">
2080 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2082 <td><em>General</em>
2084 <li>Updated Java code signing certificate donated by
2086 <li>Features and annotation preserved when performing
2087 pairwise alignment</li>
2088 <li>RNA pseudoknot annotation can be
2089 imported/exported/displayed</li>
2090 <li>'colour by annotation' can colour by RNA and
2091 protein secondary structure</li>
2092 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2093 post-hoc with 2.9 release</em>)
2096 </ul> <em>Application</em>
2098 <li>Extract and display secondary structure for sequences
2099 with 3D structures</li>
2100 <li>Support for parsing RNAML</li>
2101 <li>Annotations menu for layout
2103 <li>sort sequence annotation rows by alignment</li>
2104 <li>place sequence annotation above/below alignment
2107 <li>Output in Stockholm format</li>
2108 <li>Internationalisation: improved Spanish (es)
2110 <li>Structure viewer preferences tab</li>
2111 <li>Disorder and Secondary Structure annotation tracks
2112 shared between alignments</li>
2113 <li>UCSF Chimera launch and linked highlighting from
2115 <li>Show/hide all sequence associated annotation rows for
2116 all or current selection</li>
2117 <li>disorder and secondary structure predictions
2118 available as dataset annotation</li>
2119 <li>Per-sequence rna helices colouring</li>
2122 <li>Sequence database accessions imported when fetching
2123 alignments from Rfam</li>
2124 <li>update VARNA version to 3.91</li>
2126 <li>New groovy scripts for exporting aligned positions,
2127 conservation values, and calculating sum of pairs scores.</li>
2128 <li>Command line argument to set default JABAWS server</li>
2129 <li>include installation type in build properties and
2130 console log output</li>
2131 <li>Updated Jalview project format to preserve dataset
2135 <!-- issues resolved --> <em>Application</em>
2137 <li>Distinguish alignment and sequence associated RNA
2138 structure in structure->view->VARNA</li>
2139 <li>Raise dialog box if user deletes all sequences in an
2141 <li>Pressing F1 results in documentation opening twice</li>
2142 <li>Sequence feature tooltip is wrapped</li>
2143 <li>Double click on sequence associated annotation
2144 selects only first column</li>
2145 <li>Redundancy removal doesn't result in unlinked
2146 leaves shown in tree</li>
2147 <li>Undos after several redundancy removals don't undo
2149 <li>Hide sequence doesn't hide associated annotation</li>
2150 <li>User defined colours dialog box too big to fit on
2151 screen and buttons not visible</li>
2152 <li>author list isn't updated if already written to
2153 Jalview properties</li>
2154 <li>Popup menu won't open after retrieving sequence
2156 <li>File open window for associate PDB doesn't open</li>
2157 <li>Left-then-right click on a sequence id opens a
2158 browser search window</li>
2159 <li>Cannot open sequence feature shading/sort popup menu
2160 in feature settings dialog</li>
2161 <li>better tooltip placement for some areas of Jalview
2163 <li>Allow addition of JABAWS Server which doesn't
2164 pass validation</li>
2165 <li>Web services parameters dialog box is too large to
2167 <li>Muscle nucleotide alignment preset obscured by
2169 <li>JABAWS preset submenus don't contain newly
2170 defined user preset</li>
2171 <li>MSA web services warns user if they were launched
2172 with invalid input</li>
2173 <li>Jalview cannot contact DAS Registy when running on
2176 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2177 'Superpose with' submenu not shown when new view
2181 </ul> <!-- <em>Applet</em>
2183 </ul> <em>General</em>
2185 </ul>--> <em>Deployment and Documentation</em>
2187 <li>2G and 1G options in launchApp have no effect on
2188 memory allocation</li>
2189 <li>launchApp service doesn't automatically open
2190 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2192 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2193 InstallAnywhere reports cannot find valid JVM when Java
2194 1.7_055 is available
2196 </ul> <em>Application Known issues</em>
2199 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2200 corrupted or unreadable alignment display when scrolling
2204 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2205 retrieval fails but progress bar continues for DAS retrieval
2206 with large number of ID
2209 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2210 flatfile output of visible region has incorrect sequence
2214 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2215 rna structure consensus doesn't update when secondary
2216 structure tracks are rearranged
2219 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2220 invalid rna structure positional highlighting does not
2221 highlight position of invalid base pairs
2224 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2225 out of memory errors are not raised when saving Jalview
2226 project from alignment window file menu
2229 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2230 Switching to RNA Helices colouring doesn't propagate to
2234 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2235 colour by RNA Helices not enabled when user created
2236 annotation added to alignment
2239 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2240 Jalview icon not shown on dock in Mountain Lion/Webstart
2242 </ul> <em>Applet Known Issues</em>
2245 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2246 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2249 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2250 Jalview and Jmol example not compatible with IE9
2253 <li>Sort by annotation score doesn't reverse order
2259 <td><div align="center">
2260 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2263 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2266 <li>Internationalisation of user interface (usually
2267 called i18n support) and translation for Spanish locale</li>
2268 <li>Define/Undefine group on current selection with
2269 Ctrl-G/Shift Ctrl-G</li>
2270 <li>Improved group creation/removal options in
2271 alignment/sequence Popup menu</li>
2272 <li>Sensible precision for symbol distribution
2273 percentages shown in logo tooltip.</li>
2274 <li>Annotation panel height set according to amount of
2275 annotation when alignment first opened</li>
2276 </ul> <em>Application</em>
2278 <li>Interactive consensus RNA secondary structure
2279 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2280 <li>Select columns containing particular features from
2281 Feature Settings dialog</li>
2282 <li>View all 'representative' PDB structures for selected
2284 <li>Update Jalview project format:
2286 <li>New file extension for Jalview projects '.jvp'</li>
2287 <li>Preserve sequence and annotation dataset (to
2288 store secondary structure annotation,etc)</li>
2289 <li>Per group and alignment annotation and RNA helix
2293 <li>New similarity measures for PCA and Tree calculation
2295 <li>Experimental support for retrieval and viewing of
2296 flanking regions for an alignment</li>
2300 <!-- issues resolved --> <em>Application</em>
2302 <li>logo keeps spinning and status remains at queued or
2303 running after job is cancelled</li>
2304 <li>cannot export features from alignments imported from
2305 Jalview/VAMSAS projects</li>
2306 <li>Buggy slider for web service parameters that take
2308 <li>Newly created RNA secondary structure line doesn't
2309 have 'display all symbols' flag set</li>
2310 <li>T-COFFEE alignment score shading scheme and other
2311 annotation shading not saved in Jalview project</li>
2312 <li>Local file cannot be loaded in freshly downloaded
2314 <li>Jalview icon not shown on dock in Mountain
2316 <li>Load file from desktop file browser fails</li>
2317 <li>Occasional NPE thrown when calculating large trees</li>
2318 <li>Cannot reorder or slide sequences after dragging an
2319 alignment onto desktop</li>
2320 <li>Colour by annotation dialog throws NPE after using
2321 'extract scores' function</li>
2322 <li>Loading/cut'n'pasting an empty file leads to a grey
2323 alignment window</li>
2324 <li>Disorder thresholds rendered incorrectly after
2325 performing IUPred disorder prediction</li>
2326 <li>Multiple group annotated consensus rows shown when
2327 changing 'normalise logo' display setting</li>
2328 <li>Find shows blank dialog after 'finished searching' if
2329 nothing matches query</li>
2330 <li>Null Pointer Exceptions raised when sorting by
2331 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2333 <li>Errors in Jmol console when structures in alignment
2334 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2336 <li>Not all working JABAWS services are shown in
2338 <li>JAVAWS version of Jalview fails to launch with
2339 'invalid literal/length code'</li>
2340 <li>Annotation/RNA Helix colourschemes cannot be applied
2341 to alignment with groups (actually fixed in 2.8.0b1)</li>
2342 <li>RNA Helices and T-Coffee Scores available as default
2345 </ul> <em>Applet</em>
2347 <li>Remove group option is shown even when selection is
2349 <li>Apply to all groups ticked but colourscheme changes
2350 don't affect groups</li>
2351 <li>Documented RNA Helices and T-Coffee Scores as valid
2352 colourscheme name</li>
2353 <li>Annotation labels drawn on sequence IDs when
2354 Annotation panel is not displayed</li>
2355 <li>Increased font size for dropdown menus on OSX and
2356 embedded windows</li>
2357 </ul> <em>Other</em>
2359 <li>Consensus sequence for alignments/groups with a
2360 single sequence were not calculated</li>
2361 <li>annotation files that contain only groups imported as
2362 annotation and junk sequences</li>
2363 <li>Fasta files with sequences containing '*' incorrectly
2364 recognised as PFAM or BLC</li>
2365 <li>conservation/PID slider apply all groups option
2366 doesn't affect background (2.8.0b1)
2368 <li>redundancy highlighting is erratic at 0% and 100%</li>
2369 <li>Remove gapped columns fails for sequences with ragged
2371 <li>AMSA annotation row with leading spaces is not
2372 registered correctly on import</li>
2373 <li>Jalview crashes when selecting PCA analysis for
2374 certain alignments</li>
2375 <li>Opening the colour by annotation dialog for an
2376 existing annotation based 'use original colours'
2377 colourscheme loses original colours setting</li>
2382 <td><div align="center">
2383 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2384 <em>30/1/2014</em></strong>
2388 <li>Trusted certificates for JalviewLite applet and
2389 Jalview Desktop application<br />Certificate was donated by
2390 <a href="https://www.certum.eu">Certum</a> to the Jalview
2391 open source project).
2393 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2394 <li>Output in Stockholm format</li>
2395 <li>Allow import of data from gzipped files</li>
2396 <li>Export/import group and sequence associated line
2397 graph thresholds</li>
2398 <li>Nucleotide substitution matrix that supports RNA and
2399 ambiguity codes</li>
2400 <li>Allow disorder predictions to be made on the current
2401 selection (or visible selection) in the same way that JPred
2403 <li>Groovy scripting for headless Jalview operation</li>
2404 </ul> <em>Other improvements</em>
2406 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2407 <li>COMBINE statement uses current SEQUENCE_REF and
2408 GROUP_REF scope to group annotation rows</li>
2409 <li>Support '' style escaping of quotes in Newick
2411 <li>Group options for JABAWS service by command line name</li>
2412 <li>Empty tooltip shown for JABA service options with a
2413 link but no description</li>
2414 <li>Select primary source when selecting authority in
2415 database fetcher GUI</li>
2416 <li>Add .mfa to FASTA file extensions recognised by
2418 <li>Annotation label tooltip text wrap</li>
2423 <li>Slow scrolling when lots of annotation rows are
2425 <li>Lots of NPE (and slowness) after creating RNA
2426 secondary structure annotation line</li>
2427 <li>Sequence database accessions not imported when
2428 fetching alignments from Rfam</li>
2429 <li>Incorrect SHMR submission for sequences with
2431 <li>View all structures does not always superpose
2433 <li>Option widgets in service parameters not updated to
2434 reflect user or preset settings</li>
2435 <li>Null pointer exceptions for some services without
2436 presets or adjustable parameters</li>
2437 <li>Discover PDB IDs entry in structure menu doesn't
2438 discover PDB xRefs</li>
2439 <li>Exception encountered while trying to retrieve
2440 features with DAS</li>
2441 <li>Lowest value in annotation row isn't coloured
2442 when colour by annotation (per sequence) is coloured</li>
2443 <li>Keyboard mode P jumps to start of gapped region when
2444 residue follows a gap</li>
2445 <li>Jalview appears to hang importing an alignment with
2446 Wrap as default or after enabling Wrap</li>
2447 <li>'Right click to add annotations' message
2448 shown in wrap mode when no annotations present</li>
2449 <li>Disorder predictions fail with NPE if no automatic
2450 annotation already exists on alignment</li>
2451 <li>oninit javascript function should be called after
2452 initialisation completes</li>
2453 <li>Remove redundancy after disorder prediction corrupts
2454 alignment window display</li>
2455 <li>Example annotation file in documentation is invalid</li>
2456 <li>Grouped line graph annotation rows are not exported
2457 to annotation file</li>
2458 <li>Multi-harmony analysis cannot be run when only two
2460 <li>Cannot create multiple groups of line graphs with
2461 several 'combine' statements in annotation file</li>
2462 <li>Pressing return several times causes Number Format
2463 exceptions in keyboard mode</li>
2464 <li>Multi-harmony (SHMMR) method doesn't submit
2465 correct partitions for input data</li>
2466 <li>Translation from DNA to Amino Acids fails</li>
2467 <li>Jalview fail to load newick tree with quoted label</li>
2468 <li>--headless flag isn't understood</li>
2469 <li>ClassCastException when generating EPS in headless
2471 <li>Adjusting sequence-associated shading threshold only
2472 changes one row's threshold</li>
2473 <li>Preferences and Feature settings panel panel
2474 doesn't open</li>
2475 <li>hide consensus histogram also hides conservation and
2476 quality histograms</li>
2481 <td><div align="center">
2482 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2484 <td><em>Application</em>
2486 <li>Support for JABAWS 2.0 Services (AACon alignment
2487 conservation, protein disorder and Clustal Omega)</li>
2488 <li>JABAWS server status indicator in Web Services
2490 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2491 in Jalview alignment window</li>
2492 <li>Updated Jalview build and deploy framework for OSX
2493 mountain lion, windows 7, and 8</li>
2494 <li>Nucleotide substitution matrix for PCA that supports
2495 RNA and ambiguity codes</li>
2497 <li>Improved sequence database retrieval GUI</li>
2498 <li>Support fetching and database reference look up
2499 against multiple DAS sources (Fetch all from in 'fetch db
2501 <li>Jalview project improvements
2503 <li>Store and retrieve the 'belowAlignment'
2504 flag for annotation</li>
2505 <li>calcId attribute to group annotation rows on the
2507 <li>Store AACon calculation settings for a view in
2508 Jalview project</li>
2512 <li>horizontal scrolling gesture support</li>
2513 <li>Visual progress indicator when PCA calculation is
2515 <li>Simpler JABA web services menus</li>
2516 <li>visual indication that web service results are still
2517 being retrieved from server</li>
2518 <li>Serialise the dialogs that are shown when Jalview
2519 starts up for first time</li>
2520 <li>Jalview user agent string for interacting with HTTP
2522 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2524 <li>Examples directory and Groovy library included in
2525 InstallAnywhere distribution</li>
2526 </ul> <em>Applet</em>
2528 <li>RNA alignment and secondary structure annotation
2529 visualization applet example</li>
2530 </ul> <em>General</em>
2532 <li>Normalise option for consensus sequence logo</li>
2533 <li>Reset button in PCA window to return dimensions to
2535 <li>Allow seqspace or Jalview variant of alignment PCA
2537 <li>PCA with either nucleic acid and protein substitution
2539 <li>Allow windows containing HTML reports to be exported
2541 <li>Interactive display and editing of RNA secondary
2542 structure contacts</li>
2543 <li>RNA Helix Alignment Colouring</li>
2544 <li>RNA base pair logo consensus</li>
2545 <li>Parse sequence associated secondary structure
2546 information in Stockholm files</li>
2547 <li>HTML Export database accessions and annotation
2548 information presented in tooltip for sequences</li>
2549 <li>Import secondary structure from LOCARNA clustalw
2550 style RNA alignment files</li>
2551 <li>import and visualise T-COFFEE quality scores for an
2553 <li>'colour by annotation' per sequence option to
2554 shade each sequence according to its associated alignment
2556 <li>New Jalview Logo</li>
2557 </ul> <em>Documentation and Development</em>
2559 <li>documentation for score matrices used in Jalview</li>
2560 <li>New Website!</li>
2562 <td><em>Application</em>
2564 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2565 wsdbfetch REST service</li>
2566 <li>Stop windows being moved outside desktop on OSX</li>
2567 <li>Filetype associations not installed for webstart
2569 <li>Jalview does not always retrieve progress of a JABAWS
2570 job execution in full once it is complete</li>
2571 <li>revise SHMR RSBS definition to ensure alignment is
2572 uploaded via ali_file parameter</li>
2573 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2574 <li>View all structures superposed fails with exception</li>
2575 <li>Jnet job queues forever if a very short sequence is
2576 submitted for prediction</li>
2577 <li>Cut and paste menu not opened when mouse clicked on
2579 <li>Putting fractional value into integer text box in
2580 alignment parameter dialog causes Jalview to hang</li>
2581 <li>Structure view highlighting doesn't work on
2583 <li>View all structures fails with exception shown in
2585 <li>Characters in filename associated with PDBEntry not
2586 escaped in a platform independent way</li>
2587 <li>Jalview desktop fails to launch with exception when
2589 <li>Tree calculation reports 'you must have 2 or more
2590 sequences selected' when selection is empty</li>
2591 <li>Jalview desktop fails to launch with jar signature
2592 failure when java web start temporary file caching is
2594 <li>DAS Sequence retrieval with range qualification
2595 results in sequence xref which includes range qualification</li>
2596 <li>Errors during processing of command line arguments
2597 cause progress bar (JAL-898) to be removed</li>
2598 <li>Replace comma for semi-colon option not disabled for
2599 DAS sources in sequence fetcher</li>
2600 <li>Cannot close news reader when JABAWS server warning
2601 dialog is shown</li>
2602 <li>Option widgets not updated to reflect user settings</li>
2603 <li>Edited sequence not submitted to web service</li>
2604 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2605 <li>InstallAnywhere installer doesn't unpack and run
2606 on OSX Mountain Lion</li>
2607 <li>Annotation panel not given a scroll bar when
2608 sequences with alignment annotation are pasted into the
2610 <li>Sequence associated annotation rows not associated
2611 when loaded from Jalview project</li>
2612 <li>Browser launch fails with NPE on java 1.7</li>
2613 <li>JABAWS alignment marked as finished when job was
2614 cancelled or job failed due to invalid input</li>
2615 <li>NPE with v2.7 example when clicking on Tree
2616 associated with all views</li>
2617 <li>Exceptions when copy/paste sequences with grouped
2618 annotation rows to new window</li>
2619 </ul> <em>Applet</em>
2621 <li>Sequence features are momentarily displayed before
2622 they are hidden using hidefeaturegroups applet parameter</li>
2623 <li>loading features via javascript API automatically
2624 enables feature display</li>
2625 <li>scrollToColumnIn javascript API method doesn't
2627 </ul> <em>General</em>
2629 <li>Redundancy removal fails for rna alignment</li>
2630 <li>PCA calculation fails when sequence has been selected
2631 and then deselected</li>
2632 <li>PCA window shows grey box when first opened on OSX</li>
2633 <li>Letters coloured pink in sequence logo when alignment
2634 coloured with clustalx</li>
2635 <li>Choosing fonts without letter symbols defined causes
2636 exceptions and redraw errors</li>
2637 <li>Initial PCA plot view is not same as manually
2638 reconfigured view</li>
2639 <li>Grouped annotation graph label has incorrect line
2641 <li>Grouped annotation graph label display is corrupted
2642 for lots of labels</li>
2647 <div align="center">
2648 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2651 <td><em>Application</em>
2653 <li>Jalview Desktop News Reader</li>
2654 <li>Tweaked default layout of web services menu</li>
2655 <li>View/alignment association menu to enable user to
2656 easily specify which alignment a multi-structure view takes
2657 its colours/correspondences from</li>
2658 <li>Allow properties file location to be specified as URL</li>
2659 <li>Extend Jalview project to preserve associations
2660 between many alignment views and a single Jmol display</li>
2661 <li>Store annotation row height in Jalview project file</li>
2662 <li>Annotation row column label formatting attributes
2663 stored in project file</li>
2664 <li>Annotation row order for auto-calculated annotation
2665 rows preserved in Jalview project file</li>
2666 <li>Visual progress indication when Jalview state is
2667 saved using Desktop window menu</li>
2668 <li>Visual indication that command line arguments are
2669 still being processed</li>
2670 <li>Groovy script execution from URL</li>
2671 <li>Colour by annotation default min and max colours in
2673 <li>Automatically associate PDB files dragged onto an
2674 alignment with sequences that have high similarity and
2676 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2677 <li>'view structures' option to open many
2678 structures in same window</li>
2679 <li>Sort associated views menu option for tree panel</li>
2680 <li>Group all JABA and non-JABA services for a particular
2681 analysis function in its own submenu</li>
2682 </ul> <em>Applet</em>
2684 <li>Userdefined and autogenerated annotation rows for
2686 <li>Adjustment of alignment annotation pane height</li>
2687 <li>Annotation scrollbar for annotation panel</li>
2688 <li>Drag to reorder annotation rows in annotation panel</li>
2689 <li>'automaticScrolling' parameter</li>
2690 <li>Allow sequences with partial ID string matches to be
2691 annotated from GFF/Jalview features files</li>
2692 <li>Sequence logo annotation row in applet</li>
2693 <li>Absolute paths relative to host server in applet
2694 parameters are treated as such</li>
2695 <li>New in the JalviewLite javascript API:
2697 <li>JalviewLite.js javascript library</li>
2698 <li>Javascript callbacks for
2700 <li>Applet initialisation</li>
2701 <li>Sequence/alignment mouse-overs and selections</li>
2704 <li>scrollTo row and column alignment scrolling
2706 <li>Select sequence/alignment regions from javascript</li>
2707 <li>javascript structure viewer harness to pass
2708 messages between Jmol and Jalview when running as
2709 distinct applets</li>
2710 <li>sortBy method</li>
2711 <li>Set of applet and application examples shipped
2712 with documentation</li>
2713 <li>New example to demonstrate JalviewLite and Jmol
2714 javascript message exchange</li>
2716 </ul> <em>General</em>
2718 <li>Enable Jmol displays to be associated with multiple
2719 multiple alignments</li>
2720 <li>Option to automatically sort alignment with new tree</li>
2721 <li>User configurable link to enable redirects to a
2722 www.Jalview.org mirror</li>
2723 <li>Jmol colours option for Jmol displays</li>
2724 <li>Configurable newline string when writing alignment
2725 and other flat files</li>
2726 <li>Allow alignment annotation description lines to
2727 contain html tags</li>
2728 </ul> <em>Documentation and Development</em>
2730 <li>Add groovy test harness for bulk load testing to
2732 <li>Groovy script to load and align a set of sequences
2733 using a web service before displaying the result in the
2734 Jalview desktop</li>
2735 <li>Restructured javascript and applet api documentation</li>
2736 <li>Ant target to publish example html files with applet
2738 <li>Netbeans project for building Jalview from source</li>
2739 <li>ant task to create online javadoc for Jalview source</li>
2741 <td><em>Application</em>
2743 <li>User defined colourscheme throws exception when
2744 current built in colourscheme is saved as new scheme</li>
2745 <li>AlignFrame->Save in application pops up save
2746 dialog for valid filename/format</li>
2747 <li>Cannot view associated structure for UniProt sequence</li>
2748 <li>PDB file association breaks for UniProt sequence
2750 <li>Associate PDB from file dialog does not tell you
2751 which sequence is to be associated with the file</li>
2752 <li>Find All raises null pointer exception when query
2753 only matches sequence IDs</li>
2754 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2755 <li>Jalview project with Jmol views created with Jalview
2756 2.4 cannot be loaded</li>
2757 <li>Filetype associations not installed for webstart
2759 <li>Two or more chains in a single PDB file associated
2760 with sequences in different alignments do not get coloured
2761 by their associated sequence</li>
2762 <li>Visibility status of autocalculated annotation row
2763 not preserved when project is loaded</li>
2764 <li>Annotation row height and visibility attributes not
2765 stored in Jalview project</li>
2766 <li>Tree bootstraps are not preserved when saved as a
2767 Jalview project</li>
2768 <li>Envision2 workflow tooltips are corrupted</li>
2769 <li>Enabling show group conservation also enables colour
2770 by conservation</li>
2771 <li>Duplicate group associated conservation or consensus
2772 created on new view</li>
2773 <li>Annotation scrollbar not displayed after 'show
2774 all hidden annotation rows' option selected</li>
2775 <li>Alignment quality not updated after alignment
2776 annotation row is hidden then shown</li>
2777 <li>Preserve colouring of structures coloured by
2778 sequences in pre Jalview 2.7 projects</li>
2779 <li>Web service job parameter dialog is not laid out
2781 <li>Web services menu not refreshed after 'reset
2782 services' button is pressed in preferences</li>
2783 <li>Annotation off by one in Jalview v2_3 example project</li>
2784 <li>Structures imported from file and saved in project
2785 get name like jalview_pdb1234.txt when reloaded</li>
2786 <li>Jalview does not always retrieve progress of a JABAWS
2787 job execution in full once it is complete</li>
2788 </ul> <em>Applet</em>
2790 <li>Alignment height set incorrectly when lots of
2791 annotation rows are displayed</li>
2792 <li>Relative URLs in feature HTML text not resolved to
2794 <li>View follows highlighting does not work for positions
2796 <li><= shown as = in tooltip</li>
2797 <li>Export features raises exception when no features
2799 <li>Separator string used for serialising lists of IDs
2800 for javascript api is modified when separator string
2801 provided as parameter</li>
2802 <li>Null pointer exception when selecting tree leaves for
2803 alignment with no existing selection</li>
2804 <li>Relative URLs for datasources assumed to be relative
2805 to applet's codebase</li>
2806 <li>Status bar not updated after finished searching and
2807 search wraps around to first result</li>
2808 <li>StructureSelectionManager instance shared between
2809 several Jalview applets causes race conditions and memory
2811 <li>Hover tooltip and mouseover of position on structure
2812 not sent from Jmol in applet</li>
2813 <li>Certain sequences of javascript method calls to
2814 applet API fatally hang browser</li>
2815 </ul> <em>General</em>
2817 <li>View follows structure mouseover scrolls beyond
2818 position with wrapped view and hidden regions</li>
2819 <li>Find sequence position moves to wrong residue
2820 with/without hidden columns</li>
2821 <li>Sequence length given in alignment properties window
2823 <li>InvalidNumberFormat exceptions thrown when trying to
2824 import PDB like structure files</li>
2825 <li>Positional search results are only highlighted
2826 between user-supplied sequence start/end bounds</li>
2827 <li>End attribute of sequence is not validated</li>
2828 <li>Find dialog only finds first sequence containing a
2829 given sequence position</li>
2830 <li>Sequence numbering not preserved in MSF alignment
2832 <li>Jalview PDB file reader does not extract sequence
2833 from nucleotide chains correctly</li>
2834 <li>Structure colours not updated when tree partition
2835 changed in alignment</li>
2836 <li>Sequence associated secondary structure not correctly
2837 parsed in interleaved stockholm</li>
2838 <li>Colour by annotation dialog does not restore current
2840 <li>Hiding (nearly) all sequences doesn't work
2842 <li>Sequences containing lowercase letters are not
2843 properly associated with their pdb files</li>
2844 </ul> <em>Documentation and Development</em>
2846 <li>schemas/JalviewWsParamSet.xsd corrupted by
2847 ApplyCopyright tool</li>
2852 <div align="center">
2853 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2856 <td><em>Application</em>
2858 <li>New warning dialog when the Jalview Desktop cannot
2859 contact web services</li>
2860 <li>JABA service parameters for a preset are shown in
2861 service job window</li>
2862 <li>JABA Service menu entries reworded</li>
2866 <li>Modeller PIR IO broken - cannot correctly import a
2867 pir file emitted by Jalview</li>
2868 <li>Existing feature settings transferred to new
2869 alignment view created from cut'n'paste</li>
2870 <li>Improved test for mixed amino/nucleotide chains when
2871 parsing PDB files</li>
2872 <li>Consensus and conservation annotation rows
2873 occasionally become blank for all new windows</li>
2874 <li>Exception raised when right clicking above sequences
2875 in wrapped view mode</li>
2876 </ul> <em>Application</em>
2878 <li>multiple multiply aligned structure views cause cpu
2879 usage to hit 100% and computer to hang</li>
2880 <li>Web Service parameter layout breaks for long user
2881 parameter names</li>
2882 <li>Jaba service discovery hangs desktop if Jaba server
2889 <div align="center">
2890 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2893 <td><em>Application</em>
2895 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2896 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2899 <li>Web Services preference tab</li>
2900 <li>Analysis parameters dialog box and user defined
2902 <li>Improved speed and layout of Envision2 service menu</li>
2903 <li>Superpose structures using associated sequence
2905 <li>Export coordinates and projection as CSV from PCA
2907 </ul> <em>Applet</em>
2909 <li>enable javascript: execution by the applet via the
2910 link out mechanism</li>
2911 </ul> <em>Other</em>
2913 <li>Updated the Jmol Jalview interface to work with Jmol
2915 <li>The Jalview Desktop and JalviewLite applet now
2916 require Java 1.5</li>
2917 <li>Allow Jalview feature colour specification for GFF
2918 sequence annotation files</li>
2919 <li>New 'colour by label' keword in Jalview feature file
2920 type colour specification</li>
2921 <li>New Jalview Desktop Groovy API method that allows a
2922 script to check if it being run in an interactive session or
2923 in a batch operation from the Jalview command line</li>
2927 <li>clustalx colourscheme colours Ds preferentially when
2928 both D+E are present in over 50% of the column</li>
2929 </ul> <em>Application</em>
2931 <li>typo in AlignmentFrame->View->Hide->all but
2932 selected Regions menu item</li>
2933 <li>sequence fetcher replaces ',' for ';' when the ',' is
2934 part of a valid accession ID</li>
2935 <li>fatal OOM if object retrieved by sequence fetcher
2936 runs out of memory</li>
2937 <li>unhandled Out of Memory Error when viewing pca
2938 analysis results</li>
2939 <li>InstallAnywhere builds fail to launch on OS X java
2940 10.5 update 4 (due to apple Java 1.6 update)</li>
2941 <li>Installanywhere Jalview silently fails to launch</li>
2942 </ul> <em>Applet</em>
2944 <li>Jalview.getFeatureGroups() raises an
2945 ArrayIndexOutOfBoundsException if no feature groups are
2952 <div align="center">
2953 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2959 <li>Alignment prettyprinter doesn't cope with long
2961 <li>clustalx colourscheme colours Ds preferentially when
2962 both D+E are present in over 50% of the column</li>
2963 <li>nucleic acid structures retrieved from PDB do not
2964 import correctly</li>
2965 <li>More columns get selected than were clicked on when a
2966 number of columns are hidden</li>
2967 <li>annotation label popup menu not providing correct
2968 add/hide/show options when rows are hidden or none are
2970 <li>Stockholm format shown in list of readable formats,
2971 and parser copes better with alignments from RFAM.</li>
2972 <li>CSV output of consensus only includes the percentage
2973 of all symbols if sequence logo display is enabled</li>
2975 </ul> <em>Applet</em>
2977 <li>annotation panel disappears when annotation is
2979 </ul> <em>Application</em>
2981 <li>Alignment view not redrawn properly when new
2982 alignment opened where annotation panel is visible but no
2983 annotations are present on alignment</li>
2984 <li>pasted region containing hidden columns is
2985 incorrectly displayed in new alignment window</li>
2986 <li>Jalview slow to complete operations when stdout is
2987 flooded (fix is to close the Jalview console)</li>
2988 <li>typo in AlignmentFrame->View->Hide->all but
2989 selected Rregions menu item.</li>
2990 <li>inconsistent group submenu and Format submenu entry
2991 'Un' or 'Non'conserved</li>
2992 <li>Sequence feature settings are being shared by
2993 multiple distinct alignments</li>
2994 <li>group annotation not recreated when tree partition is
2996 <li>double click on group annotation to select sequences
2997 does not propagate to associated trees</li>
2998 <li>Mac OSX specific issues:
3000 <li>exception raised when mouse clicked on desktop
3001 window background</li>
3002 <li>Desktop menu placed on menu bar and application
3003 name set correctly</li>
3004 <li>sequence feature settings not wide enough for the
3005 save feature colourscheme button</li>
3014 <div align="center">
3015 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3018 <td><em>New Capabilities</em>
3020 <li>URL links generated from description line for
3021 regular-expression based URL links (applet and application)
3023 <li>Non-positional feature URL links are shown in link
3025 <li>Linked viewing of nucleic acid sequences and
3027 <li>Automatic Scrolling option in View menu to display
3028 the currently highlighted region of an alignment.</li>
3029 <li>Order an alignment by sequence length, or using the
3030 average score or total feature count for each sequence.</li>
3031 <li>Shading features by score or associated description</li>
3032 <li>Subdivide alignment and groups based on identity of
3033 selected subsequence (Make Groups from Selection).</li>
3034 <li>New hide/show options including Shift+Control+H to
3035 hide everything but the currently selected region.</li>
3036 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3037 </ul> <em>Application</em>
3039 <li>Fetch DB References capabilities and UI expanded to
3040 support retrieval from DAS sequence sources</li>
3041 <li>Local DAS Sequence sources can be added via the
3042 command line or via the Add local source dialog box.</li>
3043 <li>DAS Dbref and DbxRef feature types are parsed as
3044 database references and protein_name is parsed as
3045 description line (BioSapiens terms).</li>
3046 <li>Enable or disable non-positional feature and database
3047 references in sequence ID tooltip from View menu in
3049 <!-- <li>New hidden columns and rows and representatives capabilities
3050 in annotations file (in progress - not yet fully implemented)</li> -->
3051 <li>Group-associated consensus, sequence logos and
3052 conservation plots</li>
3053 <li>Symbol distributions for each column can be exported
3054 and visualized as sequence logos</li>
3055 <li>Optionally scale multi-character column labels to fit
3056 within each column of annotation row<!-- todo for applet -->
3058 <li>Optional automatic sort of associated alignment view
3059 when a new tree is opened.</li>
3060 <li>Jalview Java Console</li>
3061 <li>Better placement of desktop window when moving
3062 between different screens.</li>
3063 <li>New preference items for sequence ID tooltip and
3064 consensus annotation</li>
3065 <li>Client to submit sequences and IDs to Envision2
3067 <li><em>Vamsas Capabilities</em>
3069 <li>Improved VAMSAS synchronization (Jalview archive
3070 used to preserve views, structures, and tree display
3072 <li>Import of vamsas documents from disk or URL via
3074 <li>Sharing of selected regions between views and
3075 with other VAMSAS applications (Experimental feature!)</li>
3076 <li>Updated API to VAMSAS version 0.2</li>
3078 </ul> <em>Applet</em>
3080 <li>Middle button resizes annotation row height</li>
3083 <li>sortByTree (true/false) - automatically sort the
3084 associated alignment view by the tree when a new tree is
3086 <li>showTreeBootstraps (true/false) - show or hide
3087 branch bootstraps (default is to show them if available)</li>
3088 <li>showTreeDistances (true/false) - show or hide
3089 branch lengths (default is to show them if available)</li>
3090 <li>showUnlinkedTreeNodes (true/false) - indicate if
3091 unassociated nodes should be highlighted in the tree
3093 <li>heightScale and widthScale (1.0 or more) -
3094 increase the height or width of a cell in the alignment
3095 grid relative to the current font size.</li>
3098 <li>Non-positional features displayed in sequence ID
3100 </ul> <em>Other</em>
3102 <li>Features format: graduated colour definitions and
3103 specification of feature scores</li>
3104 <li>Alignment Annotations format: new keywords for group
3105 associated annotation (GROUP_REF) and annotation row display
3106 properties (ROW_PROPERTIES)</li>
3107 <li>XML formats extended to support graduated feature
3108 colourschemes, group associated annotation, and profile
3109 visualization settings.</li></td>
3112 <li>Source field in GFF files parsed as feature source
3113 rather than description</li>
3114 <li>Non-positional features are now included in sequence
3115 feature and gff files (controlled via non-positional feature
3116 visibility in tooltip).</li>
3117 <li>URL links generated for all feature links (bugfix)</li>
3118 <li>Added URL embedding instructions to features file
3120 <li>Codons containing ambiguous nucleotides translated as
3121 'X' in peptide product</li>
3122 <li>Match case switch in find dialog box works for both
3123 sequence ID and sequence string and query strings do not
3124 have to be in upper case to match case-insensitively.</li>
3125 <li>AMSA files only contain first column of
3126 multi-character column annotation labels</li>
3127 <li>Jalview Annotation File generation/parsing consistent
3128 with documentation (e.g. Stockholm annotation can be
3129 exported and re-imported)</li>
3130 <li>PDB files without embedded PDB IDs given a friendly
3132 <li>Find incrementally searches ID string matches as well
3133 as subsequence matches, and correctly reports total number
3137 <li>Better handling of exceptions during sequence
3139 <li>Dasobert generated non-positional feature URL
3140 link text excludes the start_end suffix</li>
3141 <li>DAS feature and source retrieval buttons disabled
3142 when fetch or registry operations in progress.</li>
3143 <li>PDB files retrieved from URLs are cached properly</li>
3144 <li>Sequence description lines properly shared via
3146 <li>Sequence fetcher fetches multiple records for all
3148 <li>Ensured that command line das feature retrieval
3149 completes before alignment figures are generated.</li>
3150 <li>Reduced time taken when opening file browser for
3152 <li>isAligned check prior to calculating tree, PCA or
3153 submitting an MSA to JNet now excludes hidden sequences.</li>
3154 <li>User defined group colours properly recovered
3155 from Jalview projects.</li>
3164 <div align="center">
3165 <strong>2.4.0.b2</strong><br> 28/10/2009
3170 <li>Experimental support for google analytics usage
3172 <li>Jalview privacy settings (user preferences and docs).</li>
3177 <li>Race condition in applet preventing startup in
3179 <li>Exception when feature created from selection beyond
3180 length of sequence.</li>
3181 <li>Allow synthetic PDB files to be imported gracefully</li>
3182 <li>Sequence associated annotation rows associate with
3183 all sequences with a given id</li>
3184 <li>Find function matches case-insensitively for sequence
3185 ID string searches</li>
3186 <li>Non-standard characters do not cause pairwise
3187 alignment to fail with exception</li>
3188 </ul> <em>Application Issues</em>
3190 <li>Sequences are now validated against EMBL database</li>
3191 <li>Sequence fetcher fetches multiple records for all
3193 </ul> <em>InstallAnywhere Issues</em>
3195 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3196 issue with installAnywhere mechanism)</li>
3197 <li>Command line launching of JARs from InstallAnywhere
3198 version (java class versioning error fixed)</li>
3205 <div align="center">
3206 <strong>2.4</strong><br> 27/8/2008
3209 <td><em>User Interface</em>
3211 <li>Linked highlighting of codon and amino acid from
3212 translation and protein products</li>
3213 <li>Linked highlighting of structure associated with
3214 residue mapping to codon position</li>
3215 <li>Sequence Fetcher provides example accession numbers
3216 and 'clear' button</li>
3217 <li>MemoryMonitor added as an option under Desktop's
3219 <li>Extract score function to parse whitespace separated
3220 numeric data in description line</li>
3221 <li>Column labels in alignment annotation can be centred.</li>
3222 <li>Tooltip for sequence associated annotation give name
3224 </ul> <em>Web Services and URL fetching</em>
3226 <li>JPred3 web service</li>
3227 <li>Prototype sequence search client (no public services
3229 <li>Fetch either seed alignment or full alignment from
3231 <li>URL Links created for matching database cross
3232 references as well as sequence ID</li>
3233 <li>URL Links can be created using regular-expressions</li>
3234 </ul> <em>Sequence Database Connectivity</em>
3236 <li>Retrieval of cross-referenced sequences from other
3238 <li>Generalised database reference retrieval and
3239 validation to all fetchable databases</li>
3240 <li>Fetch sequences from DAS sources supporting the
3241 sequence command</li>
3242 </ul> <em>Import and Export</em>
3243 <li>export annotation rows as CSV for spreadsheet import</li>
3244 <li>Jalview projects record alignment dataset associations,
3245 EMBL products, and cDNA sequence mappings</li>
3246 <li>Sequence Group colour can be specified in Annotation
3248 <li>Ad-hoc colouring of group in Annotation File using RGB
3249 triplet as name of colourscheme</li>
3250 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3252 <li>treenode binding for VAMSAS tree exchange</li>
3253 <li>local editing and update of sequences in VAMSAS
3254 alignments (experimental)</li>
3255 <li>Create new or select existing session to join</li>
3256 <li>load and save of vamsas documents</li>
3257 </ul> <em>Application command line</em>
3259 <li>-tree parameter to open trees (introduced for passing
3261 <li>-fetchfrom command line argument to specify nicknames
3262 of DAS servers to query for alignment features</li>
3263 <li>-dasserver command line argument to add new servers
3264 that are also automatically queried for features</li>
3265 <li>-groovy command line argument executes a given groovy
3266 script after all input data has been loaded and parsed</li>
3267 </ul> <em>Applet-Application data exchange</em>
3269 <li>Trees passed as applet parameters can be passed to
3270 application (when using "View in full
3271 application")</li>
3272 </ul> <em>Applet Parameters</em>
3274 <li>feature group display control parameter</li>
3275 <li>debug parameter</li>
3276 <li>showbutton parameter</li>
3277 </ul> <em>Applet API methods</em>
3279 <li>newView public method</li>
3280 <li>Window (current view) specific get/set public methods</li>
3281 <li>Feature display control methods</li>
3282 <li>get list of currently selected sequences</li>
3283 </ul> <em>New Jalview distribution features</em>
3285 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3286 <li>RELEASE file gives build properties for the latest
3287 Jalview release.</li>
3288 <li>Java 1.1 Applet build made easier and donotobfuscate
3289 property controls execution of obfuscator</li>
3290 <li>Build target for generating source distribution</li>
3291 <li>Debug flag for javacc</li>
3292 <li>.jalview_properties file is documented (slightly) in
3293 jalview.bin.Cache</li>
3294 <li>Continuous Build Integration for stable and
3295 development version of Application, Applet and source
3300 <li>selected region output includes visible annotations
3301 (for certain formats)</li>
3302 <li>edit label/displaychar contains existing label/char
3304 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3305 <li>shorter peptide product names from EMBL records</li>
3306 <li>Newick string generator makes compact representations</li>
3307 <li>bootstrap values parsed correctly for tree files with
3309 <li>pathological filechooser bug avoided by not allowing
3310 filenames containing a ':'</li>
3311 <li>Fixed exception when parsing GFF files containing
3312 global sequence features</li>
3313 <li>Alignment datasets are finalized only when number of
3314 references from alignment sequences goes to zero</li>
3315 <li>Close of tree branch colour box without colour
3316 selection causes cascading exceptions</li>
3317 <li>occasional negative imgwidth exceptions</li>
3318 <li>better reporting of non-fatal warnings to user when
3319 file parsing fails.</li>
3320 <li>Save works when Jalview project is default format</li>
3321 <li>Save as dialog opened if current alignment format is
3322 not a valid output format</li>
3323 <li>UniProt canonical names introduced for both das and
3325 <li>Histidine should be midblue (not pink!) in Zappo</li>
3326 <li>error messages passed up and output when data read
3328 <li>edit undo recovers previous dataset sequence when
3329 sequence is edited</li>
3330 <li>allow PDB files without pdb ID HEADER lines (like
3331 those generated by MODELLER) to be read in properly</li>
3332 <li>allow reading of JPred concise files as a normal
3334 <li>Stockholm annotation parsing and alignment properties
3335 import fixed for PFAM records</li>
3336 <li>Structure view windows have correct name in Desktop
3338 <li>annotation consisting of sequence associated scores
3339 can be read and written correctly to annotation file</li>
3340 <li>Aligned cDNA translation to aligned peptide works
3342 <li>Fixed display of hidden sequence markers and
3343 non-italic font for representatives in Applet</li>
3344 <li>Applet Menus are always embedded in applet window on
3346 <li>Newly shown features appear at top of stack (in
3348 <li>Annotations added via parameter not drawn properly
3349 due to null pointer exceptions</li>
3350 <li>Secondary structure lines are drawn starting from
3351 first column of alignment</li>
3352 <li>UniProt XML import updated for new schema release in
3354 <li>Sequence feature to sequence ID match for Features
3355 file is case-insensitive</li>
3356 <li>Sequence features read from Features file appended to
3357 all sequences with matching IDs</li>
3358 <li>PDB structure coloured correctly for associated views
3359 containing a sub-sequence</li>
3360 <li>PDB files can be retrieved by applet from Jar files</li>
3361 <li>feature and annotation file applet parameters
3362 referring to different directories are retrieved correctly</li>
3363 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3364 <li>Fixed application hang whilst waiting for
3365 splash-screen version check to complete</li>
3366 <li>Applet properly URLencodes input parameter values
3367 when passing them to the launchApp service</li>
3368 <li>display name and local features preserved in results
3369 retrieved from web service</li>
3370 <li>Visual delay indication for sequence retrieval and
3371 sequence fetcher initialisation</li>
3372 <li>updated Application to use DAS 1.53e version of
3373 dasobert DAS client</li>
3374 <li>Re-instated Full AMSA support and .amsa file
3376 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3384 <div align="center">
3385 <strong>2.3</strong><br> 9/5/07
3390 <li>Jmol 11.0.2 integration</li>
3391 <li>PDB views stored in Jalview XML files</li>
3392 <li>Slide sequences</li>
3393 <li>Edit sequence in place</li>
3394 <li>EMBL CDS features</li>
3395 <li>DAS Feature mapping</li>
3396 <li>Feature ordering</li>
3397 <li>Alignment Properties</li>
3398 <li>Annotation Scores</li>
3399 <li>Sort by scores</li>
3400 <li>Feature/annotation editing in applet</li>
3405 <li>Headless state operation in 2.2.1</li>
3406 <li>Incorrect and unstable DNA pairwise alignment</li>
3407 <li>Cut and paste of sequences with annotation</li>
3408 <li>Feature group display state in XML</li>
3409 <li>Feature ordering in XML</li>
3410 <li>blc file iteration selection using filename # suffix</li>
3411 <li>Stockholm alignment properties</li>
3412 <li>Stockhom alignment secondary structure annotation</li>
3413 <li>2.2.1 applet had no feature transparency</li>
3414 <li>Number pad keys can be used in cursor mode</li>
3415 <li>Structure Viewer mirror image resolved</li>
3422 <div align="center">
3423 <strong>2.2.1</strong><br> 12/2/07
3428 <li>Non standard characters can be read and displayed
3429 <li>Annotations/Features can be imported/exported to the
3431 <li>Applet allows editing of sequence/annotation/group
3432 name & description
3433 <li>Preference setting to display sequence name in
3435 <li>Annotation file format extended to allow
3436 Sequence_groups to be defined
3437 <li>Default opening of alignment overview panel can be
3438 specified in preferences
3439 <li>PDB residue numbering annotation added to associated
3445 <li>Applet crash under certain Linux OS with Java 1.6
3447 <li>Annotation file export / import bugs fixed
3448 <li>PNG / EPS image output bugs fixed
3454 <div align="center">
3455 <strong>2.2</strong><br> 27/11/06
3460 <li>Multiple views on alignment
3461 <li>Sequence feature editing
3462 <li>"Reload" alignment
3463 <li>"Save" to current filename
3464 <li>Background dependent text colour
3465 <li>Right align sequence ids
3466 <li>User-defined lower case residue colours
3469 <li>Menu item accelerator keys
3470 <li>Control-V pastes to current alignment
3471 <li>Cancel button for DAS Feature Fetching
3472 <li>PCA and PDB Viewers zoom via mouse roller
3473 <li>User-defined sub-tree colours and sub-tree selection
3475 <li>'New Window' button on the 'Output to Text box'
3480 <li>New memory efficient Undo/Redo System
3481 <li>Optimised symbol lookups and conservation/consensus
3483 <li>Region Conservation/Consensus recalculated after
3485 <li>Fixed Remove Empty Columns Bug (empty columns at end
3487 <li>Slowed DAS Feature Fetching for increased robustness.
3489 <li>Made angle brackets in ASCII feature descriptions
3491 <li>Re-instated Zoom function for PCA
3492 <li>Sequence descriptions conserved in web service
3494 <li>UniProt ID discoverer uses any word separated by
3496 <li>WsDbFetch query/result association resolved
3497 <li>Tree leaf to sequence mapping improved
3498 <li>Smooth fonts switch moved to FontChooser dialog box.
3505 <div align="center">
3506 <strong>2.1.1</strong><br> 12/9/06
3511 <li>Copy consensus sequence to clipboard</li>
3516 <li>Image output - rightmost residues are rendered if
3517 sequence id panel has been resized</li>
3518 <li>Image output - all offscreen group boundaries are
3520 <li>Annotation files with sequence references - all
3521 elements in file are relative to sequence position</li>
3522 <li>Mac Applet users can use Alt key for group editing</li>
3528 <div align="center">
3529 <strong>2.1</strong><br> 22/8/06
3534 <li>MAFFT Multiple Alignment in default Web Service list</li>
3535 <li>DAS Feature fetching</li>
3536 <li>Hide sequences and columns</li>
3537 <li>Export Annotations and Features</li>
3538 <li>GFF file reading / writing</li>
3539 <li>Associate structures with sequences from local PDB
3541 <li>Add sequences to exisiting alignment</li>
3542 <li>Recently opened files / URL lists</li>
3543 <li>Applet can launch the full application</li>
3544 <li>Applet has transparency for features (Java 1.2
3546 <li>Applet has user defined colours parameter</li>
3547 <li>Applet can load sequences from parameter
3548 "sequence<em>x</em>"
3554 <li>Redundancy Panel reinstalled in the Applet</li>
3555 <li>Monospaced font - EPS / rescaling bug fixed</li>
3556 <li>Annotation files with sequence references bug fixed</li>
3562 <div align="center">
3563 <strong>2.08.1</strong><br> 2/5/06
3568 <li>Change case of selected region from Popup menu</li>
3569 <li>Choose to match case when searching</li>
3570 <li>Middle mouse button and mouse movement can compress /
3571 expand the visible width and height of the alignment</li>
3576 <li>Annotation Panel displays complete JNet results</li>
3582 <div align="center">
3583 <strong>2.08b</strong><br> 18/4/06
3589 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3590 <li>Righthand label on wrapped alignments shows correct
3597 <div align="center">
3598 <strong>2.08</strong><br> 10/4/06
3603 <li>Editing can be locked to the selection area</li>
3604 <li>Keyboard editing</li>
3605 <li>Create sequence features from searches</li>
3606 <li>Precalculated annotations can be loaded onto
3608 <li>Features file allows grouping of features</li>
3609 <li>Annotation Colouring scheme added</li>
3610 <li>Smooth fonts off by default - Faster rendering</li>
3611 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3616 <li>Drag & Drop fixed on Linux</li>
3617 <li>Jalview Archive file faster to load/save, sequence
3618 descriptions saved.</li>
3624 <div align="center">
3625 <strong>2.07</strong><br> 12/12/05
3630 <li>PDB Structure Viewer enhanced</li>
3631 <li>Sequence Feature retrieval and display enhanced</li>
3632 <li>Choose to output sequence start-end after sequence
3633 name for file output</li>
3634 <li>Sequence Fetcher WSDBFetch@EBI</li>
3635 <li>Applet can read feature files, PDB files and can be
3636 used for HTML form input</li>
3641 <li>HTML output writes groups and features</li>
3642 <li>Group editing is Control and mouse click</li>
3643 <li>File IO bugs</li>
3649 <div align="center">
3650 <strong>2.06</strong><br> 28/9/05
3655 <li>View annotations in wrapped mode</li>
3656 <li>More options for PCA viewer</li>
3661 <li>GUI bugs resolved</li>
3662 <li>Runs with -nodisplay from command line</li>
3668 <div align="center">
3669 <strong>2.05b</strong><br> 15/9/05
3674 <li>Choose EPS export as lineart or text</li>
3675 <li>Jar files are executable</li>
3676 <li>Can read in Uracil - maps to unknown residue</li>
3681 <li>Known OutOfMemory errors give warning message</li>
3682 <li>Overview window calculated more efficiently</li>
3683 <li>Several GUI bugs resolved</li>
3689 <div align="center">
3690 <strong>2.05</strong><br> 30/8/05
3695 <li>Edit and annotate in "Wrapped" view</li>
3700 <li>Several GUI bugs resolved</li>
3706 <div align="center">
3707 <strong>2.04</strong><br> 24/8/05
3712 <li>Hold down mouse wheel & scroll to change font
3718 <li>Improved JPred client reliability</li>
3719 <li>Improved loading of Jalview files</li>
3725 <div align="center">
3726 <strong>2.03</strong><br> 18/8/05
3731 <li>Set Proxy server name and port in preferences</li>
3732 <li>Multiple URL links from sequence ids</li>
3733 <li>User Defined Colours can have a scheme name and added
3735 <li>Choose to ignore gaps in consensus calculation</li>
3736 <li>Unix users can set default web browser</li>
3737 <li>Runs without GUI for batch processing</li>
3738 <li>Dynamically generated Web Service Menus</li>
3743 <li>InstallAnywhere download for Sparc Solaris</li>
3749 <div align="center">
3750 <strong>2.02</strong><br> 18/7/05
3756 <li>Copy & Paste order of sequences maintains
3757 alignment order.</li>
3763 <div align="center">
3764 <strong>2.01</strong><br> 12/7/05
3769 <li>Use delete key for deleting selection.</li>
3770 <li>Use Mouse wheel to scroll sequences.</li>
3771 <li>Help file updated to describe how to add alignment
3773 <li>Version and build date written to build properties
3775 <li>InstallAnywhere installation will check for updates
3776 at launch of Jalview.</li>
3781 <li>Delete gaps bug fixed.</li>
3782 <li>FileChooser sorts columns.</li>
3783 <li>Can remove groups one by one.</li>
3784 <li>Filechooser icons installed.</li>
3785 <li>Finder ignores return character when searching.
3786 Return key will initiate a search.<br>
3793 <div align="center">
3794 <strong>2.0</strong><br> 20/6/05
3799 <li>New codebase</li>