3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
81 for disabling automatic superposition of multiple
82 structures and open structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
98 <!-- JAL-2593 -->Improved performance when rendering lots
99 of features (particularly when transparency is disabled)
104 <td><div align="left">
107 <!-- JAL-2899 -->Structure and Overview aren't updated
108 when Colour By Annotation threshold slider is adjusted
111 <!-- JAL-2778 -->Slow redraw when Overview panel shown
112 overlapping alignment panel
115 <!-- JAL-2929 -->Overview doesn't show end of unpadded
119 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
120 improved: CDS not handled correctly if transcript has no
124 <!-- JAL-2321 -->Secondary structure and temperature
125 factor annotation not added to sequence when local PDB
126 file associated with it by drag'n'drop or structure
130 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
131 dialog doesn't import PDB files dropped on an alignment
134 <!-- JAL-2666 -->Linked scrolling via protein horizontal
135 scroll bar doesn't work for some CDS/Protein views
138 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
139 Java 1.8u153 onwards and Java 1.9u4+.
142 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
143 columns in annotation row
146 <!-- JAL-2913 -->Preferences panel's ID Width control is not
147 honored in batch mode
150 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
151 for structures added to existing Jmol view
154 <!-- JAL-2223 -->'View Mappings' includes duplicate
155 entries after importing project with multiple views
158 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
159 protein sequences via SIFTS from associated PDB entries
160 with negative residue numbers or missing residues fails
163 <!-- JAL-2952 -->Exception when shading sequence with negative
164 Temperature Factor values from annotated PDB files (e.g.
165 as generated by CONSURF)
168 <!-- JAL-2922 -->Invert displayed features very slow when
169 structure and/or overview windows are also shown
172 <!-- JAL-2954 -->Selecting columns from highlighted regions
173 very slow for alignments with large numbers of sequences
176 <!-- JAL-2925 -->Copy Consensus fails for group consensus
177 with 'StringIndexOutOfBounds'
180 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
181 platforms running Java 10
184 <!-- JAL-2960 -->Adding a structure to existing structure
185 view appears to do nothing because the view is hidden behind the alignment view
191 <!-- JAL-2926 -->Copy consensus sequence option in applet
192 should copy the group consensus when popup is opened on it
198 <!-- JAL-2913 -->Fixed ID width preference is not respected
201 <em>New Known Defects</em>
204 <!-- JAL-2973 --> Exceptions occasionally raised when
205 editing a large alignment and overview is displayed
208 <!-- JAL-2974 -->'Overview updating' progress bar is shown
209 repeatedly after a series of edits even when the overview
210 is no longer reflecting updates
213 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
214 structures for protein subsequence (if 'Trim Retrieved
215 Sequences' enabled) or Ensembl isoforms (Workaround in
216 2.10.4 is to fail back to N&W mapping)
223 <td width="60" nowrap>
225 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
228 <td><div align="left">
229 <ul><li>Updated Certum Codesigning Certificate
230 (Valid till 30th November 2018)</li></ul></div></td>
231 <td><div align="left">
234 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
235 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
236 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
237 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
238 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
239 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
240 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
246 <td width="60" nowrap>
248 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
251 <td><div align="left">
255 <!-- JAL-2446 -->Faster and more efficient management and
256 rendering of sequence features
259 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
260 429 rate limit request hander
263 <!-- JAL-2773 -->Structure views don't get updated unless
264 their colours have changed
267 <!-- JAL-2495 -->All linked sequences are highlighted for
268 a structure mousover (Jmol) or selection (Chimera)
271 <!-- JAL-2790 -->'Cancel' button in progress bar for
272 JABAWS AACon, RNAAliFold and Disorder prediction jobs
275 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
276 view from Ensembl locus cross-references
279 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
283 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
284 feature can be disabled
287 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
288 PDB easier retrieval of sequences for lists of IDs
291 <!-- JAL-2758 -->Short names for sequences retrieved from
297 <li>Groovy interpreter updated to 2.4.12</li>
298 <li>Example groovy script for generating a matrix of
299 percent identity scores for current alignment.</li>
301 <em>Testing and Deployment</em>
304 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
308 <td><div align="left">
312 <!-- JAL-2643 -->Pressing tab after updating the colour
313 threshold text field doesn't trigger an update to the
317 <!-- JAL-2682 -->Race condition when parsing sequence ID
321 <!-- JAL-2608 -->Overview windows are also closed when
322 alignment window is closed
325 <!-- JAL-2548 -->Export of features doesn't always respect
329 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
330 takes a long time in Cursor mode
336 <!-- JAL-2777 -->Structures with whitespace chainCode
337 cannot be viewed in Chimera
340 <!-- JAL-2728 -->Protein annotation panel too high in
344 <!-- JAL-2757 -->Can't edit the query after the server
345 error warning icon is shown in Uniprot and PDB Free Text
349 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
352 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
355 <!-- JAL-2739 -->Hidden column marker in last column not
356 rendered when switching back from Wrapped to normal view
359 <!-- JAL-2768 -->Annotation display corrupted when
360 scrolling right in unwapped alignment view
363 <!-- JAL-2542 -->Existing features on subsequence
364 incorrectly relocated when full sequence retrieved from
368 <!-- JAL-2733 -->Last reported memory still shown when
369 Desktop->Show Memory is unticked (OSX only)
372 <!-- JAL-2658 -->Amend Features dialog doesn't allow
373 features of same type and group to be selected for
377 <!-- JAL-2524 -->Jalview becomes sluggish in wide
378 alignments when hidden columns are present
381 <!-- JAL-2392 -->Jalview freezes when loading and
382 displaying several structures
385 <!-- JAL-2732 -->Black outlines left after resizing or
389 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
390 within the Jalview desktop on OSX
393 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
394 when in wrapped alignment mode
397 <!-- JAL-2636 -->Scale mark not shown when close to right
398 hand end of alignment
401 <!-- JAL-2684 -->Pairwise alignment of selected regions of
402 each selected sequence do not have correct start/end
406 <!-- JAL-2793 -->Alignment ruler height set incorrectly
407 after canceling the Alignment Window's Font dialog
410 <!-- JAL-2036 -->Show cross-references not enabled after
411 restoring project until a new view is created
414 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
415 URL links appears when only default EMBL-EBI link is
416 configured (since 2.10.2b2)
419 <!-- JAL-2775 -->Overview redraws whole window when box
423 <!-- JAL-2225 -->Structure viewer doesn't map all chains
424 in a multi-chain structure when viewing alignment
425 involving more than one chain (since 2.10)
428 <!-- JAL-2811 -->Double residue highlights in cursor mode
429 if new selection moves alignment window
432 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
433 arrow key in cursor mode to pass hidden column marker
436 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
437 that produces correctly annotated transcripts and products
440 <!-- JAL-2776 -->Toggling a feature group after first time
441 doesn't update associated structure view
444 <em>Applet</em><br />
447 <!-- JAL-2687 -->Concurrent modification exception when
448 closing alignment panel
451 <em>BioJSON</em><br />
454 <!-- JAL-2546 -->BioJSON export does not preserve
455 non-positional features
458 <em>New Known Issues</em>
461 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
462 sequence features correctly (for many previous versions of
466 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
467 using cursor in wrapped panel other than top
470 <!-- JAL-2791 -->Select columns containing feature ignores
471 graduated colour threshold
474 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
475 always preserve numbering and sequence features
478 <em>Known Java 9 Issues</em>
481 <!-- JAL-2902 -->Groovy Console very slow to open and is
482 not responsive when entering characters (Webstart, Java
489 <td width="60" nowrap>
491 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
492 <em>2/10/2017</em></strong>
495 <td><div align="left">
496 <em>New features in Jalview Desktop</em>
499 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
501 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
505 <td><div align="left">
509 <td width="60" nowrap>
511 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
512 <em>7/9/2017</em></strong>
515 <td><div align="left">
519 <!-- JAL-2588 -->Show gaps in overview window by colouring
520 in grey (sequences used to be coloured grey, and gaps were
524 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
528 <!-- JAL-2587 -->Overview updates immediately on increase
529 in size and progress bar shown as higher resolution
530 overview is recalculated
535 <td><div align="left">
539 <!-- JAL-2664 -->Overview window redraws every hidden
540 column region row by row
543 <!-- JAL-2681 -->duplicate protein sequences shown after
544 retrieving Ensembl crossrefs for sequences from Uniprot
547 <!-- JAL-2603 -->Overview window throws NPE if show boxes
548 format setting is unticked
551 <!-- JAL-2610 -->Groups are coloured wrongly in overview
552 if group has show boxes format setting unticked
555 <!-- JAL-2672,JAL-2665 -->Redraw problems when
556 autoscrolling whilst dragging current selection group to
557 include sequences and columns not currently displayed
560 <!-- JAL-2691 -->Not all chains are mapped when multimeric
561 assemblies are imported via CIF file
564 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
565 displayed when threshold or conservation colouring is also
569 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
573 <!-- JAL-2673 -->Jalview continues to scroll after
574 dragging a selected region off the visible region of the
578 <!-- JAL-2724 -->Cannot apply annotation based
579 colourscheme to all groups in a view
582 <!-- JAL-2511 -->IDs don't line up with sequences
583 initially after font size change using the Font chooser or
590 <td width="60" nowrap>
592 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
595 <td><div align="left">
596 <em>Calculations</em>
600 <!-- JAL-1933 -->Occupancy annotation row shows number of
601 ungapped positions in each column of the alignment.
604 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
605 a calculation dialog box
608 <!-- JAL-2379 -->Revised implementation of PCA for speed
609 and memory efficiency (~30x faster)
612 <!-- JAL-2403 -->Revised implementation of sequence
613 similarity scores as used by Tree, PCA, Shading Consensus
614 and other calculations
617 <!-- JAL-2416 -->Score matrices are stored as resource
618 files within the Jalview codebase
621 <!-- JAL-2500 -->Trees computed on Sequence Feature
622 Similarity may have different topology due to increased
629 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
630 model for alignments and groups
633 <!-- JAL-384 -->Custom shading schemes created via groovy
640 <!-- JAL-2526 -->Efficiency improvements for interacting
641 with alignment and overview windows
644 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
648 <!-- JAL-2388 -->Hidden columns and sequences can be
652 <!-- JAL-2611 -->Click-drag in visible area allows fine
653 adjustment of visible position
657 <em>Data import/export</em>
660 <!-- JAL-2535 -->Posterior probability annotation from
661 Stockholm files imported as sequence associated annotation
664 <!-- JAL-2507 -->More robust per-sequence positional
665 annotation input/output via stockholm flatfile
668 <!-- JAL-2533 -->Sequence names don't include file
669 extension when importing structure files without embedded
670 names or PDB accessions
673 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
674 format sequence substitution matrices
677 <em>User Interface</em>
680 <!-- JAL-2447 --> Experimental Features Checkbox in
681 Desktop's Tools menu to hide or show untested features in
685 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
686 via Overview or sequence motif search operations
689 <!-- JAL-2547 -->Amend sequence features dialog box can be
690 opened by double clicking gaps within sequence feature
694 <!-- JAL-1476 -->Status bar message shown when not enough
695 aligned positions were available to create a 3D structure
699 <em>3D Structure</em>
702 <!-- JAL-2430 -->Hidden regions in alignment views are not
703 coloured in linked structure views
706 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
707 file-based command exchange
710 <!-- JAL-2375 -->Structure chooser automatically shows
711 Cached Structures rather than querying the PDBe if
712 structures are already available for sequences
715 <!-- JAL-2520 -->Structures imported via URL are cached in
716 the Jalview project rather than downloaded again when the
720 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
721 to transfer Chimera's structure attributes as Jalview
722 features, and vice-versa (<strong>Experimental
726 <em>Web Services</em>
729 <!-- JAL-2549 -->Updated JABAWS client to v2.2
732 <!-- JAL-2335 -->Filter non-standard amino acids and
733 nucleotides when submitting to AACon and other MSA
737 <!-- JAL-2316, -->URLs for viewing database
738 cross-references provided by identifiers.org and the
746 <!-- JAL-2344 -->FileFormatI interface for describing and
747 identifying file formats (instead of String constants)
750 <!-- JAL-2228 -->FeatureCounter script refactored for
751 efficiency when counting all displayed features (not
752 backwards compatible with 2.10.1)
755 <em>Example files</em>
758 <!-- JAL-2631 -->Graduated feature colour style example
759 included in the example feature file
762 <em>Documentation</em>
765 <!-- JAL-2339 -->Release notes reformatted for readability
766 with the built-in Java help viewer
769 <!-- JAL-1644 -->Find documentation updated with 'search
770 sequence description' option
776 <!-- JAL-2485, -->External service integration tests for
777 Uniprot REST Free Text Search Client
780 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
783 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
788 <td><div align="left">
789 <em>Calculations</em>
792 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
793 matrix - C->R should be '-3'<br />Old matrix restored
794 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
796 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
797 Jalview's treatment of gaps in PCA and substitution matrix
798 based Tree calculations.<br /> <br />In earlier versions
799 of Jalview, gaps matching gaps were penalised, and gaps
800 matching non-gaps penalised even more. In the PCA
801 calculation, gaps were actually treated as non-gaps - so
802 different costs were applied, which meant Jalview's PCAs
803 were different to those produced by SeqSpace.<br />Jalview
804 now treats gaps in the same way as SeqSpace (ie it scores
805 them as 0). <br /> <br />Enter the following in the
806 Groovy console to restore pre-2.10.2 behaviour:<br />
807 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
808 // for 2.10.1 mode <br />
809 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
810 // to restore 2.10.2 mode <br /> <br /> <em>Note:
811 these settings will affect all subsequent tree and PCA
812 calculations (not recommended)</em></li>
814 <!-- JAL-2424 -->Fixed off-by-one bug that affected
815 scaling of branch lengths for trees computed using
816 Sequence Feature Similarity.
819 <!-- JAL-2377 -->PCA calculation could hang when
820 generating output report when working with highly
824 <!-- JAL-2544 --> Sort by features includes features to
825 right of selected region when gaps present on right-hand
829 <em>User Interface</em>
832 <!-- JAL-2346 -->Reopening Colour by annotation dialog
833 doesn't reselect a specific sequence's associated
834 annotation after it was used for colouring a view
837 <!-- JAL-2419 -->Current selection lost if popup menu
838 opened on a region of alignment without groups
841 <!-- JAL-2374 -->Popup menu not always shown for regions
842 of an alignment with overlapping groups
845 <!-- JAL-2310 -->Finder double counts if both a sequence's
846 name and description match
849 <!-- JAL-2370 -->Hiding column selection containing two
850 hidden regions results in incorrect hidden regions
853 <!-- JAL-2386 -->'Apply to all groups' setting when
854 changing colour does not apply Conservation slider value
858 <!-- JAL-2373 -->Percentage identity and conservation menu
859 items do not show a tick or allow shading to be disabled
862 <!-- JAL-2385 -->Conservation shading or PID threshold
863 lost when base colourscheme changed if slider not visible
866 <!-- JAL-2547 -->Sequence features shown in tooltip for
867 gaps before start of features
870 <!-- JAL-2623 -->Graduated feature colour threshold not
871 restored to UI when feature colour is edited
874 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
875 a time when scrolling vertically in wrapped mode.
878 <!-- JAL-2630 -->Structure and alignment overview update
879 as graduate feature colour settings are modified via the
883 <!-- JAL-2034 -->Overview window doesn't always update
884 when a group defined on the alignment is resized
887 <!-- JAL-2605 -->Mouseovers on left/right scale region in
888 wrapped view result in positional status updates
892 <!-- JAL-2563 -->Status bar doesn't show position for
893 ambiguous amino acid and nucleotide symbols
896 <!-- JAL-2602 -->Copy consensus sequence failed if
897 alignment included gapped columns
900 <!-- JAL-2473 -->Minimum size set for Jalview windows so
901 widgets don't permanently disappear
904 <!-- JAL-2503 -->Cannot select or filter quantitative
905 annotation that are shown only as column labels (e.g.
906 T-Coffee column reliability scores)
909 <!-- JAL-2594 -->Exception thrown if trying to create a
910 sequence feature on gaps only
913 <!-- JAL-2504 -->Features created with 'New feature'
914 button from a Find inherit previously defined feature type
915 rather than the Find query string
918 <!-- JAL-2423 -->incorrect title in output window when
919 exporting tree calculated in Jalview
922 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
923 and then revealing them reorders sequences on the
927 <!-- JAL-964 -->Group panel in sequence feature settings
928 doesn't update to reflect available set of groups after
929 interactively adding or modifying features
932 <!-- JAL-2225 -->Sequence Database chooser unusable on
936 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
937 only excluded gaps in current sequence and ignored
944 <!-- JAL-2421 -->Overview window visible region moves
945 erratically when hidden rows or columns are present
948 <!-- JAL-2362 -->Per-residue colourschemes applied via the
949 Structure Viewer's colour menu don't correspond to
953 <!-- JAL-2405 -->Protein specific colours only offered in
954 colour and group colour menu for protein alignments
957 <!-- JAL-2385 -->Colour threshold slider doesn't update to
958 reflect currently selected view or group's shading
962 <!-- JAL-2624 -->Feature colour thresholds not respected
963 when rendered on overview and structures when opacity at
967 <!-- JAL-2589 -->User defined gap colour not shown in
968 overview when features overlaid on alignment
971 <em>Data import/export</em>
974 <!-- JAL-2576 -->Very large alignments take a long time to
978 <!-- JAL-2507 -->Per-sequence RNA secondary structures
979 added after a sequence was imported are not written to
983 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
984 when importing RNA secondary structure via Stockholm
987 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
988 not shown in correct direction for simple pseudoknots
991 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
992 with lightGray or darkGray via features file (but can
996 <!-- JAL-2383 -->Above PID colour threshold not recovered
997 when alignment view imported from project
1000 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1001 structure and sequences extracted from structure files
1002 imported via URL and viewed in Jmol
1005 <!-- JAL-2520 -->Structures loaded via URL are saved in
1006 Jalview Projects rather than fetched via URL again when
1007 the project is loaded and the structure viewed
1010 <em>Web Services</em>
1013 <!-- JAL-2519 -->EnsemblGenomes example failing after
1014 release of Ensembl v.88
1017 <!-- JAL-2366 -->Proxy server address and port always
1018 appear enabled in Preferences->Connections
1021 <!-- JAL-2461 -->DAS registry not found exceptions
1022 removed from console output
1025 <!-- JAL-2582 -->Cannot retrieve protein products from
1026 Ensembl by Peptide ID
1029 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1030 created from SIFTs, and spurious 'Couldn't open structure
1031 in Chimera' errors raised after April 2017 update (problem
1032 due to 'null' string rather than empty string used for
1033 residues with no corresponding PDB mapping).
1036 <em>Application UI</em>
1039 <!-- JAL-2361 -->User Defined Colours not added to Colour
1043 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1044 case' residues (button in colourscheme editor debugged and
1045 new documentation and tooltips added)
1048 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1049 doesn't restore group-specific text colour thresholds
1052 <!-- JAL-2243 -->Feature settings panel does not update as
1053 new features are added to alignment
1056 <!-- JAL-2532 -->Cancel in feature settings reverts
1057 changes to feature colours via the Amend features dialog
1060 <!-- JAL-2506 -->Null pointer exception when attempting to
1061 edit graduated feature colour via amend features dialog
1065 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1066 selection menu changes colours of alignment views
1069 <!-- JAL-2426 -->Spurious exceptions in console raised
1070 from alignment calculation workers after alignment has
1074 <!-- JAL-1608 -->Typo in selection popup menu - Create
1075 groups now 'Create Group'
1078 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1079 Create/Undefine group doesn't always work
1082 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1083 shown again after pressing 'Cancel'
1086 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1087 adjusts start position in wrap mode
1090 <!-- JAL-2563 -->Status bar doesn't show positions for
1091 ambiguous amino acids
1094 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1095 CDS/Protein view after CDS sequences added for aligned
1099 <!-- JAL-2592 -->User defined colourschemes called 'User
1100 Defined' don't appear in Colours menu
1106 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1107 score models doesn't always result in an updated PCA plot
1110 <!-- JAL-2442 -->Features not rendered as transparent on
1111 overview or linked structure view
1114 <!-- JAL-2372 -->Colour group by conservation doesn't
1118 <!-- JAL-2517 -->Hitting Cancel after applying
1119 user-defined colourscheme doesn't restore original
1126 <!-- JAL-2314 -->Unit test failure:
1127 jalview.ws.jabaws.RNAStructExportImport setup fails
1130 <!-- JAL-2307 -->Unit test failure:
1131 jalview.ws.sifts.SiftsClientTest due to compatibility
1132 problems with deep array comparison equality asserts in
1133 successive versions of TestNG
1136 <!-- JAL-2479 -->Relocated StructureChooserTest and
1137 ParameterUtilsTest Unit tests to Network suite
1140 <em>New Known Issues</em>
1143 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1144 phase after a sequence motif find operation
1147 <!-- JAL-2550 -->Importing annotation file with rows
1148 containing just upper and lower case letters are
1149 interpreted as WUSS RNA secondary structure symbols
1152 <!-- JAL-2590 -->Cannot load and display Newick trees
1153 reliably from eggnog Ortholog database
1156 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1157 containing features of type Highlight' when 'B' is pressed
1158 to mark columns containing highlighted regions.
1161 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1162 doesn't always add secondary structure annotation.
1167 <td width="60" nowrap>
1168 <div align="center">
1169 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1172 <td><div align="left">
1176 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1177 for all consensus calculations
1180 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1183 <li>Updated Jalview's Certum code signing certificate
1186 <em>Application</em>
1189 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1190 set of database cross-references, sorted alphabetically
1193 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1194 from database cross references. Users with custom links
1195 will receive a <a href="webServices/urllinks.html#warning">warning
1196 dialog</a> asking them to update their preferences.
1199 <!-- JAL-2287-->Cancel button and escape listener on
1200 dialog warning user about disconnecting Jalview from a
1204 <!-- JAL-2320-->Jalview's Chimera control window closes if
1205 the Chimera it is connected to is shut down
1208 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1209 columns menu item to mark columns containing highlighted
1210 regions (e.g. from structure selections or results of a
1214 <!-- JAL-2284-->Command line option for batch-generation
1215 of HTML pages rendering alignment data with the BioJS
1225 <!-- JAL-2286 -->Columns with more than one modal residue
1226 are not coloured or thresholded according to percent
1227 identity (first observed in Jalview 2.8.2)
1230 <!-- JAL-2301 -->Threonine incorrectly reported as not
1234 <!-- JAL-2318 -->Updates to documentation pages (above PID
1235 threshold, amino acid properties)
1238 <!-- JAL-2292 -->Lower case residues in sequences are not
1239 reported as mapped to residues in a structure file in the
1243 <!--JAL-2324 -->Identical features with non-numeric scores
1244 could be added multiple times to a sequence
1247 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1248 bond features shown as two highlighted residues rather
1249 than a range in linked structure views, and treated
1250 correctly when selecting and computing trees from features
1253 <!-- JAL-2281-->Custom URL links for database
1254 cross-references are matched to database name regardless
1259 <em>Application</em>
1262 <!-- JAL-2282-->Custom URL links for specific database
1263 names without regular expressions also offer links from
1267 <!-- JAL-2315-->Removing a single configured link in the
1268 URL links pane in Connections preferences doesn't actually
1269 update Jalview configuration
1272 <!-- JAL-2272-->CTRL-Click on a selected region to open
1273 the alignment area popup menu doesn't work on El-Capitan
1276 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1277 files with similarly named sequences if dropped onto the
1281 <!-- JAL-2312 -->Additional mappings are shown for PDB
1282 entries where more chains exist in the PDB accession than
1283 are reported in the SIFTS file
1286 <!-- JAL-2317-->Certain structures do not get mapped to
1287 the structure view when displayed with Chimera
1290 <!-- JAL-2317-->No chains shown in the Chimera view
1291 panel's View->Show Chains submenu
1294 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1295 work for wrapped alignment views
1298 <!--JAL-2197 -->Rename UI components for running JPred
1299 predictions from 'JNet' to 'JPred'
1302 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1303 corrupted when annotation panel vertical scroll is not at
1304 first annotation row
1307 <!--JAL-2332 -->Attempting to view structure for Hen
1308 lysozyme results in a PDB Client error dialog box
1311 <!-- JAL-2319 -->Structure View's mapping report switched
1312 ranges for PDB and sequence for SIFTS
1315 SIFTS 'Not_Observed' residues mapped to non-existant
1319 <!-- <em>New Known Issues</em>
1326 <td width="60" nowrap>
1327 <div align="center">
1328 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1329 <em>25/10/2016</em></strong>
1332 <td><em>Application</em>
1334 <li>3D Structure chooser opens with 'Cached structures'
1335 view if structures already loaded</li>
1336 <li>Progress bar reports models as they are loaded to
1337 structure views</li>
1343 <li>Colour by conservation always enabled and no tick
1344 shown in menu when BLOSUM or PID shading applied</li>
1345 <li>FER1_ARATH and FER2_ARATH labels were switched in
1346 example sequences/projects/trees</li>
1348 <em>Application</em>
1350 <li>Jalview projects with views of local PDB structure
1351 files saved on Windows cannot be opened on OSX</li>
1352 <li>Multiple structure views can be opened and superposed
1353 without timeout for structures with multiple models or
1354 multiple sequences in alignment</li>
1355 <li>Cannot import or associated local PDB files without a
1356 PDB ID HEADER line</li>
1357 <li>RMSD is not output in Jmol console when superposition
1359 <li>Drag and drop of URL from Browser fails for Linux and
1360 OSX versions earlier than El Capitan</li>
1361 <li>ENA client ignores invalid content from ENA server</li>
1362 <li>Exceptions are not raised in console when ENA client
1363 attempts to fetch non-existent IDs via Fetch DB Refs UI
1365 <li>Exceptions are not raised in console when a new view
1366 is created on the alignment</li>
1367 <li>OSX right-click fixed for group selections: CMD-click
1368 to insert/remove gaps in groups and CTRL-click to open group
1371 <em>Build and deployment</em>
1373 <li>URL link checker now copes with multi-line anchor
1376 <em>New Known Issues</em>
1378 <li>Drag and drop from URL links in browsers do not work
1385 <td width="60" nowrap>
1386 <div align="center">
1387 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1390 <td><em>General</em>
1393 <!-- JAL-2124 -->Updated Spanish translations.
1396 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1397 for importing structure data to Jalview. Enables mmCIF and
1401 <!-- JAL-192 --->Alignment ruler shows positions relative to
1405 <!-- JAL-2202 -->Position/residue shown in status bar when
1406 mousing over sequence associated annotation
1409 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1413 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1414 '()', canonical '[]' and invalid '{}' base pair populations
1418 <!-- JAL-2092 -->Feature settings popup menu options for
1419 showing or hiding columns containing a feature
1422 <!-- JAL-1557 -->Edit selected group by double clicking on
1423 group and sequence associated annotation labels
1426 <!-- JAL-2236 -->Sequence name added to annotation label in
1427 select/hide columns by annotation and colour by annotation
1431 </ul> <em>Application</em>
1434 <!-- JAL-2050-->Automatically hide introns when opening a
1435 gene/transcript view
1438 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1442 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1443 structure mappings with the EMBL-EBI PDBe SIFTS database
1446 <!-- JAL-2079 -->Updated download sites used for Rfam and
1447 Pfam sources to xfam.org
1450 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1453 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1454 over sequences in Jalview
1457 <!-- JAL-2027-->Support for reverse-complement coding
1458 regions in ENA and EMBL
1461 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1462 for record retrieval via ENA rest API
1465 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1469 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1470 groovy script execution
1473 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1474 alignment window's Calculate menu
1477 <!-- JAL-1812 -->Allow groovy scripts that call
1478 Jalview.getAlignFrames() to run in headless mode
1481 <!-- JAL-2068 -->Support for creating new alignment
1482 calculation workers from groovy scripts
1485 <!-- JAL-1369 --->Store/restore reference sequence in
1489 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1490 associations are now saved/restored from project
1493 <!-- JAL-1993 -->Database selection dialog always shown
1494 before sequence fetcher is opened
1497 <!-- JAL-2183 -->Double click on an entry in Jalview's
1498 database chooser opens a sequence fetcher
1501 <!-- JAL-1563 -->Free-text search client for UniProt using
1502 the UniProt REST API
1505 <!-- JAL-2168 -->-nonews command line parameter to prevent
1506 the news reader opening
1509 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1510 querying stored in preferences
1513 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1517 <!-- JAL-1977-->Tooltips shown on database chooser
1520 <!-- JAL-391 -->Reverse complement function in calculate
1521 menu for nucleotide sequences
1524 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1525 and feature counts preserves alignment ordering (and
1526 debugged for complex feature sets).
1529 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1530 viewing structures with Jalview 2.10
1533 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1534 genome, transcript CCDS and gene ids via the Ensembl and
1535 Ensembl Genomes REST API
1538 <!-- JAL-2049 -->Protein sequence variant annotation
1539 computed for 'sequence_variant' annotation on CDS regions
1543 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1547 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1548 Ref Fetcher fails to match, or otherwise updates sequence
1549 data from external database records.
1552 <!-- JAL-2154 -->Revised Jalview Project format for
1553 efficient recovery of sequence coding and alignment
1554 annotation relationships.
1556 </ul> <!-- <em>Applet</em>
1567 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1571 <!-- JAL-2018-->Export features in Jalview format (again)
1572 includes graduated colourschemes
1575 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1576 working with big alignments and lots of hidden columns
1579 <!-- JAL-2053-->Hidden column markers not always rendered
1580 at right of alignment window
1583 <!-- JAL-2067 -->Tidied up links in help file table of
1587 <!-- JAL-2072 -->Feature based tree calculation not shown
1591 <!-- JAL-2075 -->Hidden columns ignored during feature
1592 based tree calculation
1595 <!-- JAL-2065 -->Alignment view stops updating when show
1596 unconserved enabled for group on alignment
1599 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1603 <!-- JAL-2146 -->Alignment column in status incorrectly
1604 shown as "Sequence position" when mousing over
1608 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1609 hidden columns present
1612 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1613 user created annotation added to alignment
1616 <!-- JAL-1841 -->RNA Structure consensus only computed for
1617 '()' base pair annotation
1620 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1621 in zero scores for all base pairs in RNA Structure
1625 <!-- JAL-2174-->Extend selection with columns containing
1629 <!-- JAL-2275 -->Pfam format writer puts extra space at
1630 beginning of sequence
1633 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1637 <!-- JAL-2238 -->Cannot create groups on an alignment from
1638 from a tree when t-coffee scores are shown
1641 <!-- JAL-1836,1967 -->Cannot import and view PDB
1642 structures with chains containing negative resnums (4q4h)
1645 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1649 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1650 to Clustal, PIR and PileUp output
1653 <!-- JAL-2008 -->Reordering sequence features that are
1654 not visible causes alignment window to repaint
1657 <!-- JAL-2006 -->Threshold sliders don't work in
1658 graduated colour and colour by annotation row for e-value
1659 scores associated with features and annotation rows
1662 <!-- JAL-1797 -->amino acid physicochemical conservation
1663 calculation should be case independent
1666 <!-- JAL-2173 -->Remove annotation also updates hidden
1670 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1671 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1672 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1675 <!-- JAL-2065 -->Null pointer exceptions and redraw
1676 problems when reference sequence defined and 'show
1677 non-conserved' enabled
1680 <!-- JAL-1306 -->Quality and Conservation are now shown on
1681 load even when Consensus calculation is disabled
1684 <!-- JAL-1932 -->Remove right on penultimate column of
1685 alignment does nothing
1688 <em>Application</em>
1691 <!-- JAL-1552-->URLs and links can't be imported by
1692 drag'n'drop on OSX when launched via webstart (note - not
1693 yet fixed for El Capitan)
1696 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1697 output when running on non-gb/us i18n platforms
1700 <!-- JAL-1944 -->Error thrown when exporting a view with
1701 hidden sequences as flat-file alignment
1704 <!-- JAL-2030-->InstallAnywhere distribution fails when
1708 <!-- JAL-2080-->Jalview very slow to launch via webstart
1709 (also hotfix for 2.9.0b2)
1712 <!-- JAL-2085 -->Cannot save project when view has a
1713 reference sequence defined
1716 <!-- JAL-1011 -->Columns are suddenly selected in other
1717 alignments and views when revealing hidden columns
1720 <!-- JAL-1989 -->Hide columns not mirrored in complement
1721 view in a cDNA/Protein splitframe
1724 <!-- JAL-1369 -->Cannot save/restore representative
1725 sequence from project when only one sequence is
1729 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1730 in Structure Chooser
1733 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1734 structure consensus didn't refresh annotation panel
1737 <!-- JAL-1962 -->View mapping in structure view shows
1738 mappings between sequence and all chains in a PDB file
1741 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1742 dialogs format columns correctly, don't display array
1743 data, sort columns according to type
1746 <!-- JAL-1975 -->Export complete shown after destination
1747 file chooser is cancelled during an image export
1750 <!-- JAL-2025 -->Error when querying PDB Service with
1751 sequence name containing special characters
1754 <!-- JAL-2024 -->Manual PDB structure querying should be
1758 <!-- JAL-2104 -->Large tooltips with broken HTML
1759 formatting don't wrap
1762 <!-- JAL-1128 -->Figures exported from wrapped view are
1763 truncated so L looks like I in consensus annotation
1766 <!-- JAL-2003 -->Export features should only export the
1767 currently displayed features for the current selection or
1771 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1772 after fetching cross-references, and restoring from
1776 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1777 followed in the structure viewer
1780 <!-- JAL-2163 -->Titles for individual alignments in
1781 splitframe not restored from project
1784 <!-- JAL-2145 -->missing autocalculated annotation at
1785 trailing end of protein alignment in transcript/product
1786 splitview when pad-gaps not enabled by default
1789 <!-- JAL-1797 -->amino acid physicochemical conservation
1793 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1794 article has been read (reopened issue due to
1795 internationalisation problems)
1798 <!-- JAL-1960 -->Only offer PDB structures in structure
1799 viewer based on sequence name, PDB and UniProt
1804 <!-- JAL-1976 -->No progress bar shown during export of
1808 <!-- JAL-2213 -->Structures not always superimposed after
1809 multiple structures are shown for one or more sequences.
1812 <!-- JAL-1370 -->Reference sequence characters should not
1813 be replaced with '.' when 'Show unconserved' format option
1817 <!-- JAL-1823 -->Cannot specify chain code when entering
1818 specific PDB id for sequence
1821 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1822 'Export hidden sequences' is enabled, but 'export hidden
1823 columns' is disabled.
1826 <!--JAL-2026-->Best Quality option in structure chooser
1827 selects lowest rather than highest resolution structures
1831 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1832 to sequence mapping in 'View Mappings' report
1835 <!-- JAL-2284 -->Unable to read old Jalview projects that
1836 contain non-XML data added after Jalvew wrote project.
1839 <!-- JAL-2118 -->Newly created annotation row reorders
1840 after clicking on it to create new annotation for a
1844 <!-- JAL-1980 -->Null Pointer Exception raised when
1845 pressing Add on an orphaned cut'n'paste window.
1847 <!-- may exclude, this is an external service stability issue JAL-1941
1848 -- > RNA 3D structure not added via DSSR service</li> -->
1853 <!-- JAL-2151 -->Incorrect columns are selected when
1854 hidden columns present before start of sequence
1857 <!-- JAL-1986 -->Missing dependencies on applet pages
1861 <!-- JAL-1947 -->Overview pixel size changes when
1862 sequences are hidden in applet
1865 <!-- JAL-1996 -->Updated instructions for applet
1866 deployment on examples pages.
1873 <td width="60" nowrap>
1874 <div align="center">
1875 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1876 <em>16/10/2015</em></strong>
1879 <td><em>General</em>
1881 <li>Time stamps for signed Jalview application and applet
1886 <em>Application</em>
1888 <li>Duplicate group consensus and conservation rows
1889 shown when tree is partitioned</li>
1890 <li>Erratic behaviour when tree partitions made with
1891 multiple cDNA/Protein split views</li>
1897 <td width="60" nowrap>
1898 <div align="center">
1899 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1900 <em>8/10/2015</em></strong>
1903 <td><em>General</em>
1905 <li>Updated Spanish translations of localized text for
1907 </ul> <em>Application</em>
1909 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1910 <li>Signed OSX InstallAnywhere installer<br></li>
1911 <li>Support for per-sequence based annotations in BioJSON</li>
1912 </ul> <em>Applet</em>
1914 <li>Split frame example added to applet examples page</li>
1915 </ul> <em>Build and Deployment</em>
1918 <!-- JAL-1888 -->New ant target for running Jalview's test
1926 <li>Mapping of cDNA to protein in split frames
1927 incorrect when sequence start > 1</li>
1928 <li>Broken images in filter column by annotation dialog
1930 <li>Feature colours not parsed from features file</li>
1931 <li>Exceptions and incomplete link URLs recovered when
1932 loading a features file containing HTML tags in feature
1936 <em>Application</em>
1938 <li>Annotations corrupted after BioJS export and
1940 <li>Incorrect sequence limits after Fetch DB References
1941 with 'trim retrieved sequences'</li>
1942 <li>Incorrect warning about deleting all data when
1943 deleting selected columns</li>
1944 <li>Patch to build system for shipping properly signed
1945 JNLP templates for webstart launch</li>
1946 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1947 unreleased structures for download or viewing</li>
1948 <li>Tab/space/return keystroke operation of EMBL-PDBe
1949 fetcher/viewer dialogs works correctly</li>
1950 <li>Disabled 'minimise' button on Jalview windows
1951 running on OSX to workaround redraw hang bug</li>
1952 <li>Split cDNA/Protein view position and geometry not
1953 recovered from jalview project</li>
1954 <li>Initial enabled/disabled state of annotation menu
1955 sorter 'show autocalculated first/last' corresponds to
1957 <li>Restoring of Clustal, RNA Helices and T-Coffee
1958 color schemes from BioJSON</li>
1962 <li>Reorder sequences mirrored in cDNA/Protein split
1964 <li>Applet with Jmol examples not loading correctly</li>
1970 <td><div align="center">
1971 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1973 <td><em>General</em>
1975 <li>Linked visualisation and analysis of DNA and Protein
1978 <li>Translated cDNA alignments shown as split protein
1979 and DNA alignment views</li>
1980 <li>Codon consensus annotation for linked protein and
1981 cDNA alignment views</li>
1982 <li>Link cDNA or Protein product sequences by loading
1983 them onto Protein or cDNA alignments</li>
1984 <li>Reconstruct linked cDNA alignment from aligned
1985 protein sequences</li>
1988 <li>Jmol integration updated to Jmol v14.2.14</li>
1989 <li>Import and export of Jalview alignment views as <a
1990 href="features/bioJsonFormat.html">BioJSON</a></li>
1991 <li>New alignment annotation file statements for
1992 reference sequences and marking hidden columns</li>
1993 <li>Reference sequence based alignment shading to
1994 highlight variation</li>
1995 <li>Select or hide columns according to alignment
1997 <li>Find option for locating sequences by description</li>
1998 <li>Conserved physicochemical properties shown in amino
1999 acid conservation row</li>
2000 <li>Alignments can be sorted by number of RNA helices</li>
2001 </ul> <em>Application</em>
2003 <li>New cDNA/Protein analysis capabilities
2005 <li>Get Cross-References should open a Split Frame
2006 view with cDNA/Protein</li>
2007 <li>Detect when nucleotide sequences and protein
2008 sequences are placed in the same alignment</li>
2009 <li>Split cDNA/Protein views are saved in Jalview
2014 <li>Use REST API to talk to Chimera</li>
2015 <li>Selected regions in Chimera are highlighted in linked
2016 Jalview windows</li>
2018 <li>VARNA RNA viewer updated to v3.93</li>
2019 <li>VARNA views are saved in Jalview Projects</li>
2020 <li>Pseudoknots displayed as Jalview RNA annotation can
2021 be shown in VARNA</li>
2023 <li>Make groups for selection uses marked columns as well
2024 as the active selected region</li>
2026 <li>Calculate UPGMA and NJ trees using sequence feature
2028 <li>New Export options
2030 <li>New Export Settings dialog to control hidden
2031 region export in flat file generation</li>
2033 <li>Export alignment views for display with the <a
2034 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2036 <li>Export scrollable SVG in HTML page</li>
2037 <li>Optional embedding of BioJSON data when exporting
2038 alignment figures to HTML</li>
2040 <li>3D structure retrieval and display
2042 <li>Free text and structured queries with the PDBe
2044 <li>PDBe Search API based discovery and selection of
2045 PDB structures for a sequence set</li>
2049 <li>JPred4 employed for protein secondary structure
2051 <li>Hide Insertions menu option to hide unaligned columns
2052 for one or a group of sequences</li>
2053 <li>Automatically hide insertions in alignments imported
2054 from the JPred4 web server</li>
2055 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2056 system on OSX<br />LGPL libraries courtesy of <a
2057 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2059 <li>changed 'View nucleotide structure' submenu to 'View
2060 VARNA 2D Structure'</li>
2061 <li>change "View protein structure" menu option to "3D
2064 </ul> <em>Applet</em>
2066 <li>New layout for applet example pages</li>
2067 <li>New parameters to enable SplitFrame view
2068 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2069 <li>New example demonstrating linked viewing of cDNA and
2070 Protein alignments</li>
2071 </ul> <em>Development and deployment</em>
2073 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2074 <li>Include installation type and git revision in build
2075 properties and console log output</li>
2076 <li>Jalview Github organisation, and new github site for
2077 storing BioJsMSA Templates</li>
2078 <li>Jalview's unit tests now managed with TestNG</li>
2081 <!-- <em>General</em>
2083 </ul> --> <!-- issues resolved --> <em>Application</em>
2085 <li>Escape should close any open find dialogs</li>
2086 <li>Typo in select-by-features status report</li>
2087 <li>Consensus RNA secondary secondary structure
2088 predictions are not highlighted in amber</li>
2089 <li>Missing gap character in v2.7 example file means
2090 alignment appears unaligned when pad-gaps is not enabled</li>
2091 <li>First switch to RNA Helices colouring doesn't colour
2092 associated structure views</li>
2093 <li>ID width preference option is greyed out when auto
2094 width checkbox not enabled</li>
2095 <li>Stopped a warning dialog from being shown when
2096 creating user defined colours</li>
2097 <li>'View Mapping' in structure viewer shows sequence
2098 mappings for just that viewer's sequences</li>
2099 <li>Workaround for superposing PDB files containing
2100 multiple models in Chimera</li>
2101 <li>Report sequence position in status bar when hovering
2102 over Jmol structure</li>
2103 <li>Cannot output gaps as '.' symbols with Selection ->
2104 output to text box</li>
2105 <li>Flat file exports of alignments with hidden columns
2106 have incorrect sequence start/end</li>
2107 <li>'Aligning' a second chain to a Chimera structure from
2109 <li>Colour schemes applied to structure viewers don't
2110 work for nucleotide</li>
2111 <li>Loading/cut'n'pasting an empty or invalid file leads
2112 to a grey/invisible alignment window</li>
2113 <li>Exported Jpred annotation from a sequence region
2114 imports to different position</li>
2115 <li>Space at beginning of sequence feature tooltips shown
2116 on some platforms</li>
2117 <li>Chimera viewer 'View | Show Chain' menu is not
2119 <li>'New View' fails with a Null Pointer Exception in
2120 console if Chimera has been opened</li>
2121 <li>Mouseover to Chimera not working</li>
2122 <li>Miscellaneous ENA XML feature qualifiers not
2124 <li>NPE in annotation renderer after 'Extract Scores'</li>
2125 <li>If two structures in one Chimera window, mouseover of
2126 either sequence shows on first structure</li>
2127 <li>'Show annotations' options should not make
2128 non-positional annotations visible</li>
2129 <li>Subsequence secondary structure annotation not shown
2130 in right place after 'view flanking regions'</li>
2131 <li>File Save As type unset when current file format is
2133 <li>Save as '.jar' option removed for saving Jalview
2135 <li>Colour by Sequence colouring in Chimera more
2137 <li>Cannot 'add reference annotation' for a sequence in
2138 several views on same alignment</li>
2139 <li>Cannot show linked products for EMBL / ENA records</li>
2140 <li>Jalview's tooltip wraps long texts containing no
2142 </ul> <em>Applet</em>
2144 <li>Jmol to JalviewLite mouseover/link not working</li>
2145 <li>JalviewLite can't import sequences with ID
2146 descriptions containing angle brackets</li>
2147 </ul> <em>General</em>
2149 <li>Cannot export and reimport RNA secondary structure
2150 via jalview annotation file</li>
2151 <li>Random helix colour palette for colour by annotation
2152 with RNA secondary structure</li>
2153 <li>Mouseover to cDNA from STOP residue in protein
2154 translation doesn't work.</li>
2155 <li>hints when using the select by annotation dialog box</li>
2156 <li>Jmol alignment incorrect if PDB file has alternate CA
2158 <li>FontChooser message dialog appears to hang after
2159 choosing 1pt font</li>
2160 <li>Peptide secondary structure incorrectly imported from
2161 annotation file when annotation display text includes 'e' or
2163 <li>Cannot set colour of new feature type whilst creating
2165 <li>cDNA translation alignment should not be sequence
2166 order dependent</li>
2167 <li>'Show unconserved' doesn't work for lower case
2169 <li>Nucleotide ambiguity codes involving R not recognised</li>
2170 </ul> <em>Deployment and Documentation</em>
2172 <li>Applet example pages appear different to the rest of
2173 www.jalview.org</li>
2174 </ul> <em>Application Known issues</em>
2176 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2177 <li>Misleading message appears after trying to delete
2179 <li>Jalview icon not shown in dock after InstallAnywhere
2180 version launches</li>
2181 <li>Fetching EMBL reference for an RNA sequence results
2182 fails with a sequence mismatch</li>
2183 <li>Corrupted or unreadable alignment display when
2184 scrolling alignment to right</li>
2185 <li>ArrayIndexOutOfBoundsException thrown when remove
2186 empty columns called on alignment with ragged gapped ends</li>
2187 <li>auto calculated alignment annotation rows do not get
2188 placed above or below non-autocalculated rows</li>
2189 <li>Jalview dekstop becomes sluggish at full screen in
2190 ultra-high resolution</li>
2191 <li>Cannot disable consensus calculation independently of
2192 quality and conservation</li>
2193 <li>Mouseover highlighting between cDNA and protein can
2194 become sluggish with more than one splitframe shown</li>
2195 </ul> <em>Applet Known Issues</em>
2197 <li>Core PDB parsing code requires Jmol</li>
2198 <li>Sequence canvas panel goes white when alignment
2199 window is being resized</li>
2205 <td><div align="center">
2206 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2208 <td><em>General</em>
2210 <li>Updated Java code signing certificate donated by
2212 <li>Features and annotation preserved when performing
2213 pairwise alignment</li>
2214 <li>RNA pseudoknot annotation can be
2215 imported/exported/displayed</li>
2216 <li>'colour by annotation' can colour by RNA and
2217 protein secondary structure</li>
2218 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2219 post-hoc with 2.9 release</em>)
2222 </ul> <em>Application</em>
2224 <li>Extract and display secondary structure for sequences
2225 with 3D structures</li>
2226 <li>Support for parsing RNAML</li>
2227 <li>Annotations menu for layout
2229 <li>sort sequence annotation rows by alignment</li>
2230 <li>place sequence annotation above/below alignment
2233 <li>Output in Stockholm format</li>
2234 <li>Internationalisation: improved Spanish (es)
2236 <li>Structure viewer preferences tab</li>
2237 <li>Disorder and Secondary Structure annotation tracks
2238 shared between alignments</li>
2239 <li>UCSF Chimera launch and linked highlighting from
2241 <li>Show/hide all sequence associated annotation rows for
2242 all or current selection</li>
2243 <li>disorder and secondary structure predictions
2244 available as dataset annotation</li>
2245 <li>Per-sequence rna helices colouring</li>
2248 <li>Sequence database accessions imported when fetching
2249 alignments from Rfam</li>
2250 <li>update VARNA version to 3.91</li>
2252 <li>New groovy scripts for exporting aligned positions,
2253 conservation values, and calculating sum of pairs scores.</li>
2254 <li>Command line argument to set default JABAWS server</li>
2255 <li>include installation type in build properties and
2256 console log output</li>
2257 <li>Updated Jalview project format to preserve dataset
2261 <!-- issues resolved --> <em>Application</em>
2263 <li>Distinguish alignment and sequence associated RNA
2264 structure in structure->view->VARNA</li>
2265 <li>Raise dialog box if user deletes all sequences in an
2267 <li>Pressing F1 results in documentation opening twice</li>
2268 <li>Sequence feature tooltip is wrapped</li>
2269 <li>Double click on sequence associated annotation
2270 selects only first column</li>
2271 <li>Redundancy removal doesn't result in unlinked
2272 leaves shown in tree</li>
2273 <li>Undos after several redundancy removals don't undo
2275 <li>Hide sequence doesn't hide associated annotation</li>
2276 <li>User defined colours dialog box too big to fit on
2277 screen and buttons not visible</li>
2278 <li>author list isn't updated if already written to
2279 Jalview properties</li>
2280 <li>Popup menu won't open after retrieving sequence
2282 <li>File open window for associate PDB doesn't open</li>
2283 <li>Left-then-right click on a sequence id opens a
2284 browser search window</li>
2285 <li>Cannot open sequence feature shading/sort popup menu
2286 in feature settings dialog</li>
2287 <li>better tooltip placement for some areas of Jalview
2289 <li>Allow addition of JABAWS Server which doesn't
2290 pass validation</li>
2291 <li>Web services parameters dialog box is too large to
2293 <li>Muscle nucleotide alignment preset obscured by
2295 <li>JABAWS preset submenus don't contain newly
2296 defined user preset</li>
2297 <li>MSA web services warns user if they were launched
2298 with invalid input</li>
2299 <li>Jalview cannot contact DAS Registy when running on
2302 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2303 'Superpose with' submenu not shown when new view
2307 </ul> <!-- <em>Applet</em>
2309 </ul> <em>General</em>
2311 </ul>--> <em>Deployment and Documentation</em>
2313 <li>2G and 1G options in launchApp have no effect on
2314 memory allocation</li>
2315 <li>launchApp service doesn't automatically open
2316 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2318 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2319 InstallAnywhere reports cannot find valid JVM when Java
2320 1.7_055 is available
2322 </ul> <em>Application Known issues</em>
2325 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2326 corrupted or unreadable alignment display when scrolling
2330 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2331 retrieval fails but progress bar continues for DAS retrieval
2332 with large number of ID
2335 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2336 flatfile output of visible region has incorrect sequence
2340 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2341 rna structure consensus doesn't update when secondary
2342 structure tracks are rearranged
2345 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2346 invalid rna structure positional highlighting does not
2347 highlight position of invalid base pairs
2350 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2351 out of memory errors are not raised when saving Jalview
2352 project from alignment window file menu
2355 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2356 Switching to RNA Helices colouring doesn't propagate to
2360 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2361 colour by RNA Helices not enabled when user created
2362 annotation added to alignment
2365 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2366 Jalview icon not shown on dock in Mountain Lion/Webstart
2368 </ul> <em>Applet Known Issues</em>
2371 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2372 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2375 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2376 Jalview and Jmol example not compatible with IE9
2379 <li>Sort by annotation score doesn't reverse order
2385 <td><div align="center">
2386 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2389 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2392 <li>Internationalisation of user interface (usually
2393 called i18n support) and translation for Spanish locale</li>
2394 <li>Define/Undefine group on current selection with
2395 Ctrl-G/Shift Ctrl-G</li>
2396 <li>Improved group creation/removal options in
2397 alignment/sequence Popup menu</li>
2398 <li>Sensible precision for symbol distribution
2399 percentages shown in logo tooltip.</li>
2400 <li>Annotation panel height set according to amount of
2401 annotation when alignment first opened</li>
2402 </ul> <em>Application</em>
2404 <li>Interactive consensus RNA secondary structure
2405 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2406 <li>Select columns containing particular features from
2407 Feature Settings dialog</li>
2408 <li>View all 'representative' PDB structures for selected
2410 <li>Update Jalview project format:
2412 <li>New file extension for Jalview projects '.jvp'</li>
2413 <li>Preserve sequence and annotation dataset (to
2414 store secondary structure annotation,etc)</li>
2415 <li>Per group and alignment annotation and RNA helix
2419 <li>New similarity measures for PCA and Tree calculation
2421 <li>Experimental support for retrieval and viewing of
2422 flanking regions for an alignment</li>
2426 <!-- issues resolved --> <em>Application</em>
2428 <li>logo keeps spinning and status remains at queued or
2429 running after job is cancelled</li>
2430 <li>cannot export features from alignments imported from
2431 Jalview/VAMSAS projects</li>
2432 <li>Buggy slider for web service parameters that take
2434 <li>Newly created RNA secondary structure line doesn't
2435 have 'display all symbols' flag set</li>
2436 <li>T-COFFEE alignment score shading scheme and other
2437 annotation shading not saved in Jalview project</li>
2438 <li>Local file cannot be loaded in freshly downloaded
2440 <li>Jalview icon not shown on dock in Mountain
2442 <li>Load file from desktop file browser fails</li>
2443 <li>Occasional NPE thrown when calculating large trees</li>
2444 <li>Cannot reorder or slide sequences after dragging an
2445 alignment onto desktop</li>
2446 <li>Colour by annotation dialog throws NPE after using
2447 'extract scores' function</li>
2448 <li>Loading/cut'n'pasting an empty file leads to a grey
2449 alignment window</li>
2450 <li>Disorder thresholds rendered incorrectly after
2451 performing IUPred disorder prediction</li>
2452 <li>Multiple group annotated consensus rows shown when
2453 changing 'normalise logo' display setting</li>
2454 <li>Find shows blank dialog after 'finished searching' if
2455 nothing matches query</li>
2456 <li>Null Pointer Exceptions raised when sorting by
2457 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2459 <li>Errors in Jmol console when structures in alignment
2460 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2462 <li>Not all working JABAWS services are shown in
2464 <li>JAVAWS version of Jalview fails to launch with
2465 'invalid literal/length code'</li>
2466 <li>Annotation/RNA Helix colourschemes cannot be applied
2467 to alignment with groups (actually fixed in 2.8.0b1)</li>
2468 <li>RNA Helices and T-Coffee Scores available as default
2471 </ul> <em>Applet</em>
2473 <li>Remove group option is shown even when selection is
2475 <li>Apply to all groups ticked but colourscheme changes
2476 don't affect groups</li>
2477 <li>Documented RNA Helices and T-Coffee Scores as valid
2478 colourscheme name</li>
2479 <li>Annotation labels drawn on sequence IDs when
2480 Annotation panel is not displayed</li>
2481 <li>Increased font size for dropdown menus on OSX and
2482 embedded windows</li>
2483 </ul> <em>Other</em>
2485 <li>Consensus sequence for alignments/groups with a
2486 single sequence were not calculated</li>
2487 <li>annotation files that contain only groups imported as
2488 annotation and junk sequences</li>
2489 <li>Fasta files with sequences containing '*' incorrectly
2490 recognised as PFAM or BLC</li>
2491 <li>conservation/PID slider apply all groups option
2492 doesn't affect background (2.8.0b1)
2494 <li>redundancy highlighting is erratic at 0% and 100%</li>
2495 <li>Remove gapped columns fails for sequences with ragged
2497 <li>AMSA annotation row with leading spaces is not
2498 registered correctly on import</li>
2499 <li>Jalview crashes when selecting PCA analysis for
2500 certain alignments</li>
2501 <li>Opening the colour by annotation dialog for an
2502 existing annotation based 'use original colours'
2503 colourscheme loses original colours setting</li>
2508 <td><div align="center">
2509 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2510 <em>30/1/2014</em></strong>
2514 <li>Trusted certificates for JalviewLite applet and
2515 Jalview Desktop application<br />Certificate was donated by
2516 <a href="https://www.certum.eu">Certum</a> to the Jalview
2517 open source project).
2519 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2520 <li>Output in Stockholm format</li>
2521 <li>Allow import of data from gzipped files</li>
2522 <li>Export/import group and sequence associated line
2523 graph thresholds</li>
2524 <li>Nucleotide substitution matrix that supports RNA and
2525 ambiguity codes</li>
2526 <li>Allow disorder predictions to be made on the current
2527 selection (or visible selection) in the same way that JPred
2529 <li>Groovy scripting for headless Jalview operation</li>
2530 </ul> <em>Other improvements</em>
2532 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2533 <li>COMBINE statement uses current SEQUENCE_REF and
2534 GROUP_REF scope to group annotation rows</li>
2535 <li>Support '' style escaping of quotes in Newick
2537 <li>Group options for JABAWS service by command line name</li>
2538 <li>Empty tooltip shown for JABA service options with a
2539 link but no description</li>
2540 <li>Select primary source when selecting authority in
2541 database fetcher GUI</li>
2542 <li>Add .mfa to FASTA file extensions recognised by
2544 <li>Annotation label tooltip text wrap</li>
2549 <li>Slow scrolling when lots of annotation rows are
2551 <li>Lots of NPE (and slowness) after creating RNA
2552 secondary structure annotation line</li>
2553 <li>Sequence database accessions not imported when
2554 fetching alignments from Rfam</li>
2555 <li>Incorrect SHMR submission for sequences with
2557 <li>View all structures does not always superpose
2559 <li>Option widgets in service parameters not updated to
2560 reflect user or preset settings</li>
2561 <li>Null pointer exceptions for some services without
2562 presets or adjustable parameters</li>
2563 <li>Discover PDB IDs entry in structure menu doesn't
2564 discover PDB xRefs</li>
2565 <li>Exception encountered while trying to retrieve
2566 features with DAS</li>
2567 <li>Lowest value in annotation row isn't coloured
2568 when colour by annotation (per sequence) is coloured</li>
2569 <li>Keyboard mode P jumps to start of gapped region when
2570 residue follows a gap</li>
2571 <li>Jalview appears to hang importing an alignment with
2572 Wrap as default or after enabling Wrap</li>
2573 <li>'Right click to add annotations' message
2574 shown in wrap mode when no annotations present</li>
2575 <li>Disorder predictions fail with NPE if no automatic
2576 annotation already exists on alignment</li>
2577 <li>oninit javascript function should be called after
2578 initialisation completes</li>
2579 <li>Remove redundancy after disorder prediction corrupts
2580 alignment window display</li>
2581 <li>Example annotation file in documentation is invalid</li>
2582 <li>Grouped line graph annotation rows are not exported
2583 to annotation file</li>
2584 <li>Multi-harmony analysis cannot be run when only two
2586 <li>Cannot create multiple groups of line graphs with
2587 several 'combine' statements in annotation file</li>
2588 <li>Pressing return several times causes Number Format
2589 exceptions in keyboard mode</li>
2590 <li>Multi-harmony (SHMMR) method doesn't submit
2591 correct partitions for input data</li>
2592 <li>Translation from DNA to Amino Acids fails</li>
2593 <li>Jalview fail to load newick tree with quoted label</li>
2594 <li>--headless flag isn't understood</li>
2595 <li>ClassCastException when generating EPS in headless
2597 <li>Adjusting sequence-associated shading threshold only
2598 changes one row's threshold</li>
2599 <li>Preferences and Feature settings panel panel
2600 doesn't open</li>
2601 <li>hide consensus histogram also hides conservation and
2602 quality histograms</li>
2607 <td><div align="center">
2608 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2610 <td><em>Application</em>
2612 <li>Support for JABAWS 2.0 Services (AACon alignment
2613 conservation, protein disorder and Clustal Omega)</li>
2614 <li>JABAWS server status indicator in Web Services
2616 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2617 in Jalview alignment window</li>
2618 <li>Updated Jalview build and deploy framework for OSX
2619 mountain lion, windows 7, and 8</li>
2620 <li>Nucleotide substitution matrix for PCA that supports
2621 RNA and ambiguity codes</li>
2623 <li>Improved sequence database retrieval GUI</li>
2624 <li>Support fetching and database reference look up
2625 against multiple DAS sources (Fetch all from in 'fetch db
2627 <li>Jalview project improvements
2629 <li>Store and retrieve the 'belowAlignment'
2630 flag for annotation</li>
2631 <li>calcId attribute to group annotation rows on the
2633 <li>Store AACon calculation settings for a view in
2634 Jalview project</li>
2638 <li>horizontal scrolling gesture support</li>
2639 <li>Visual progress indicator when PCA calculation is
2641 <li>Simpler JABA web services menus</li>
2642 <li>visual indication that web service results are still
2643 being retrieved from server</li>
2644 <li>Serialise the dialogs that are shown when Jalview
2645 starts up for first time</li>
2646 <li>Jalview user agent string for interacting with HTTP
2648 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2650 <li>Examples directory and Groovy library included in
2651 InstallAnywhere distribution</li>
2652 </ul> <em>Applet</em>
2654 <li>RNA alignment and secondary structure annotation
2655 visualization applet example</li>
2656 </ul> <em>General</em>
2658 <li>Normalise option for consensus sequence logo</li>
2659 <li>Reset button in PCA window to return dimensions to
2661 <li>Allow seqspace or Jalview variant of alignment PCA
2663 <li>PCA with either nucleic acid and protein substitution
2665 <li>Allow windows containing HTML reports to be exported
2667 <li>Interactive display and editing of RNA secondary
2668 structure contacts</li>
2669 <li>RNA Helix Alignment Colouring</li>
2670 <li>RNA base pair logo consensus</li>
2671 <li>Parse sequence associated secondary structure
2672 information in Stockholm files</li>
2673 <li>HTML Export database accessions and annotation
2674 information presented in tooltip for sequences</li>
2675 <li>Import secondary structure from LOCARNA clustalw
2676 style RNA alignment files</li>
2677 <li>import and visualise T-COFFEE quality scores for an
2679 <li>'colour by annotation' per sequence option to
2680 shade each sequence according to its associated alignment
2682 <li>New Jalview Logo</li>
2683 </ul> <em>Documentation and Development</em>
2685 <li>documentation for score matrices used in Jalview</li>
2686 <li>New Website!</li>
2688 <td><em>Application</em>
2690 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2691 wsdbfetch REST service</li>
2692 <li>Stop windows being moved outside desktop on OSX</li>
2693 <li>Filetype associations not installed for webstart
2695 <li>Jalview does not always retrieve progress of a JABAWS
2696 job execution in full once it is complete</li>
2697 <li>revise SHMR RSBS definition to ensure alignment is
2698 uploaded via ali_file parameter</li>
2699 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2700 <li>View all structures superposed fails with exception</li>
2701 <li>Jnet job queues forever if a very short sequence is
2702 submitted for prediction</li>
2703 <li>Cut and paste menu not opened when mouse clicked on
2705 <li>Putting fractional value into integer text box in
2706 alignment parameter dialog causes Jalview to hang</li>
2707 <li>Structure view highlighting doesn't work on
2709 <li>View all structures fails with exception shown in
2711 <li>Characters in filename associated with PDBEntry not
2712 escaped in a platform independent way</li>
2713 <li>Jalview desktop fails to launch with exception when
2715 <li>Tree calculation reports 'you must have 2 or more
2716 sequences selected' when selection is empty</li>
2717 <li>Jalview desktop fails to launch with jar signature
2718 failure when java web start temporary file caching is
2720 <li>DAS Sequence retrieval with range qualification
2721 results in sequence xref which includes range qualification</li>
2722 <li>Errors during processing of command line arguments
2723 cause progress bar (JAL-898) to be removed</li>
2724 <li>Replace comma for semi-colon option not disabled for
2725 DAS sources in sequence fetcher</li>
2726 <li>Cannot close news reader when JABAWS server warning
2727 dialog is shown</li>
2728 <li>Option widgets not updated to reflect user settings</li>
2729 <li>Edited sequence not submitted to web service</li>
2730 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2731 <li>InstallAnywhere installer doesn't unpack and run
2732 on OSX Mountain Lion</li>
2733 <li>Annotation panel not given a scroll bar when
2734 sequences with alignment annotation are pasted into the
2736 <li>Sequence associated annotation rows not associated
2737 when loaded from Jalview project</li>
2738 <li>Browser launch fails with NPE on java 1.7</li>
2739 <li>JABAWS alignment marked as finished when job was
2740 cancelled or job failed due to invalid input</li>
2741 <li>NPE with v2.7 example when clicking on Tree
2742 associated with all views</li>
2743 <li>Exceptions when copy/paste sequences with grouped
2744 annotation rows to new window</li>
2745 </ul> <em>Applet</em>
2747 <li>Sequence features are momentarily displayed before
2748 they are hidden using hidefeaturegroups applet parameter</li>
2749 <li>loading features via javascript API automatically
2750 enables feature display</li>
2751 <li>scrollToColumnIn javascript API method doesn't
2753 </ul> <em>General</em>
2755 <li>Redundancy removal fails for rna alignment</li>
2756 <li>PCA calculation fails when sequence has been selected
2757 and then deselected</li>
2758 <li>PCA window shows grey box when first opened on OSX</li>
2759 <li>Letters coloured pink in sequence logo when alignment
2760 coloured with clustalx</li>
2761 <li>Choosing fonts without letter symbols defined causes
2762 exceptions and redraw errors</li>
2763 <li>Initial PCA plot view is not same as manually
2764 reconfigured view</li>
2765 <li>Grouped annotation graph label has incorrect line
2767 <li>Grouped annotation graph label display is corrupted
2768 for lots of labels</li>
2773 <div align="center">
2774 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2777 <td><em>Application</em>
2779 <li>Jalview Desktop News Reader</li>
2780 <li>Tweaked default layout of web services menu</li>
2781 <li>View/alignment association menu to enable user to
2782 easily specify which alignment a multi-structure view takes
2783 its colours/correspondences from</li>
2784 <li>Allow properties file location to be specified as URL</li>
2785 <li>Extend Jalview project to preserve associations
2786 between many alignment views and a single Jmol display</li>
2787 <li>Store annotation row height in Jalview project file</li>
2788 <li>Annotation row column label formatting attributes
2789 stored in project file</li>
2790 <li>Annotation row order for auto-calculated annotation
2791 rows preserved in Jalview project file</li>
2792 <li>Visual progress indication when Jalview state is
2793 saved using Desktop window menu</li>
2794 <li>Visual indication that command line arguments are
2795 still being processed</li>
2796 <li>Groovy script execution from URL</li>
2797 <li>Colour by annotation default min and max colours in
2799 <li>Automatically associate PDB files dragged onto an
2800 alignment with sequences that have high similarity and
2802 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2803 <li>'view structures' option to open many
2804 structures in same window</li>
2805 <li>Sort associated views menu option for tree panel</li>
2806 <li>Group all JABA and non-JABA services for a particular
2807 analysis function in its own submenu</li>
2808 </ul> <em>Applet</em>
2810 <li>Userdefined and autogenerated annotation rows for
2812 <li>Adjustment of alignment annotation pane height</li>
2813 <li>Annotation scrollbar for annotation panel</li>
2814 <li>Drag to reorder annotation rows in annotation panel</li>
2815 <li>'automaticScrolling' parameter</li>
2816 <li>Allow sequences with partial ID string matches to be
2817 annotated from GFF/Jalview features files</li>
2818 <li>Sequence logo annotation row in applet</li>
2819 <li>Absolute paths relative to host server in applet
2820 parameters are treated as such</li>
2821 <li>New in the JalviewLite javascript API:
2823 <li>JalviewLite.js javascript library</li>
2824 <li>Javascript callbacks for
2826 <li>Applet initialisation</li>
2827 <li>Sequence/alignment mouse-overs and selections</li>
2830 <li>scrollTo row and column alignment scrolling
2832 <li>Select sequence/alignment regions from javascript</li>
2833 <li>javascript structure viewer harness to pass
2834 messages between Jmol and Jalview when running as
2835 distinct applets</li>
2836 <li>sortBy method</li>
2837 <li>Set of applet and application examples shipped
2838 with documentation</li>
2839 <li>New example to demonstrate JalviewLite and Jmol
2840 javascript message exchange</li>
2842 </ul> <em>General</em>
2844 <li>Enable Jmol displays to be associated with multiple
2845 multiple alignments</li>
2846 <li>Option to automatically sort alignment with new tree</li>
2847 <li>User configurable link to enable redirects to a
2848 www.Jalview.org mirror</li>
2849 <li>Jmol colours option for Jmol displays</li>
2850 <li>Configurable newline string when writing alignment
2851 and other flat files</li>
2852 <li>Allow alignment annotation description lines to
2853 contain html tags</li>
2854 </ul> <em>Documentation and Development</em>
2856 <li>Add groovy test harness for bulk load testing to
2858 <li>Groovy script to load and align a set of sequences
2859 using a web service before displaying the result in the
2860 Jalview desktop</li>
2861 <li>Restructured javascript and applet api documentation</li>
2862 <li>Ant target to publish example html files with applet
2864 <li>Netbeans project for building Jalview from source</li>
2865 <li>ant task to create online javadoc for Jalview source</li>
2867 <td><em>Application</em>
2869 <li>User defined colourscheme throws exception when
2870 current built in colourscheme is saved as new scheme</li>
2871 <li>AlignFrame->Save in application pops up save
2872 dialog for valid filename/format</li>
2873 <li>Cannot view associated structure for UniProt sequence</li>
2874 <li>PDB file association breaks for UniProt sequence
2876 <li>Associate PDB from file dialog does not tell you
2877 which sequence is to be associated with the file</li>
2878 <li>Find All raises null pointer exception when query
2879 only matches sequence IDs</li>
2880 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2881 <li>Jalview project with Jmol views created with Jalview
2882 2.4 cannot be loaded</li>
2883 <li>Filetype associations not installed for webstart
2885 <li>Two or more chains in a single PDB file associated
2886 with sequences in different alignments do not get coloured
2887 by their associated sequence</li>
2888 <li>Visibility status of autocalculated annotation row
2889 not preserved when project is loaded</li>
2890 <li>Annotation row height and visibility attributes not
2891 stored in Jalview project</li>
2892 <li>Tree bootstraps are not preserved when saved as a
2893 Jalview project</li>
2894 <li>Envision2 workflow tooltips are corrupted</li>
2895 <li>Enabling show group conservation also enables colour
2896 by conservation</li>
2897 <li>Duplicate group associated conservation or consensus
2898 created on new view</li>
2899 <li>Annotation scrollbar not displayed after 'show
2900 all hidden annotation rows' option selected</li>
2901 <li>Alignment quality not updated after alignment
2902 annotation row is hidden then shown</li>
2903 <li>Preserve colouring of structures coloured by
2904 sequences in pre Jalview 2.7 projects</li>
2905 <li>Web service job parameter dialog is not laid out
2907 <li>Web services menu not refreshed after 'reset
2908 services' button is pressed in preferences</li>
2909 <li>Annotation off by one in Jalview v2_3 example project</li>
2910 <li>Structures imported from file and saved in project
2911 get name like jalview_pdb1234.txt when reloaded</li>
2912 <li>Jalview does not always retrieve progress of a JABAWS
2913 job execution in full once it is complete</li>
2914 </ul> <em>Applet</em>
2916 <li>Alignment height set incorrectly when lots of
2917 annotation rows are displayed</li>
2918 <li>Relative URLs in feature HTML text not resolved to
2920 <li>View follows highlighting does not work for positions
2922 <li><= shown as = in tooltip</li>
2923 <li>Export features raises exception when no features
2925 <li>Separator string used for serialising lists of IDs
2926 for javascript api is modified when separator string
2927 provided as parameter</li>
2928 <li>Null pointer exception when selecting tree leaves for
2929 alignment with no existing selection</li>
2930 <li>Relative URLs for datasources assumed to be relative
2931 to applet's codebase</li>
2932 <li>Status bar not updated after finished searching and
2933 search wraps around to first result</li>
2934 <li>StructureSelectionManager instance shared between
2935 several Jalview applets causes race conditions and memory
2937 <li>Hover tooltip and mouseover of position on structure
2938 not sent from Jmol in applet</li>
2939 <li>Certain sequences of javascript method calls to
2940 applet API fatally hang browser</li>
2941 </ul> <em>General</em>
2943 <li>View follows structure mouseover scrolls beyond
2944 position with wrapped view and hidden regions</li>
2945 <li>Find sequence position moves to wrong residue
2946 with/without hidden columns</li>
2947 <li>Sequence length given in alignment properties window
2949 <li>InvalidNumberFormat exceptions thrown when trying to
2950 import PDB like structure files</li>
2951 <li>Positional search results are only highlighted
2952 between user-supplied sequence start/end bounds</li>
2953 <li>End attribute of sequence is not validated</li>
2954 <li>Find dialog only finds first sequence containing a
2955 given sequence position</li>
2956 <li>Sequence numbering not preserved in MSF alignment
2958 <li>Jalview PDB file reader does not extract sequence
2959 from nucleotide chains correctly</li>
2960 <li>Structure colours not updated when tree partition
2961 changed in alignment</li>
2962 <li>Sequence associated secondary structure not correctly
2963 parsed in interleaved stockholm</li>
2964 <li>Colour by annotation dialog does not restore current
2966 <li>Hiding (nearly) all sequences doesn't work
2968 <li>Sequences containing lowercase letters are not
2969 properly associated with their pdb files</li>
2970 </ul> <em>Documentation and Development</em>
2972 <li>schemas/JalviewWsParamSet.xsd corrupted by
2973 ApplyCopyright tool</li>
2978 <div align="center">
2979 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2982 <td><em>Application</em>
2984 <li>New warning dialog when the Jalview Desktop cannot
2985 contact web services</li>
2986 <li>JABA service parameters for a preset are shown in
2987 service job window</li>
2988 <li>JABA Service menu entries reworded</li>
2992 <li>Modeller PIR IO broken - cannot correctly import a
2993 pir file emitted by Jalview</li>
2994 <li>Existing feature settings transferred to new
2995 alignment view created from cut'n'paste</li>
2996 <li>Improved test for mixed amino/nucleotide chains when
2997 parsing PDB files</li>
2998 <li>Consensus and conservation annotation rows
2999 occasionally become blank for all new windows</li>
3000 <li>Exception raised when right clicking above sequences
3001 in wrapped view mode</li>
3002 </ul> <em>Application</em>
3004 <li>multiple multiply aligned structure views cause cpu
3005 usage to hit 100% and computer to hang</li>
3006 <li>Web Service parameter layout breaks for long user
3007 parameter names</li>
3008 <li>Jaba service discovery hangs desktop if Jaba server
3015 <div align="center">
3016 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3019 <td><em>Application</em>
3021 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3022 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3025 <li>Web Services preference tab</li>
3026 <li>Analysis parameters dialog box and user defined
3028 <li>Improved speed and layout of Envision2 service menu</li>
3029 <li>Superpose structures using associated sequence
3031 <li>Export coordinates and projection as CSV from PCA
3033 </ul> <em>Applet</em>
3035 <li>enable javascript: execution by the applet via the
3036 link out mechanism</li>
3037 </ul> <em>Other</em>
3039 <li>Updated the Jmol Jalview interface to work with Jmol
3041 <li>The Jalview Desktop and JalviewLite applet now
3042 require Java 1.5</li>
3043 <li>Allow Jalview feature colour specification for GFF
3044 sequence annotation files</li>
3045 <li>New 'colour by label' keword in Jalview feature file
3046 type colour specification</li>
3047 <li>New Jalview Desktop Groovy API method that allows a
3048 script to check if it being run in an interactive session or
3049 in a batch operation from the Jalview command line</li>
3053 <li>clustalx colourscheme colours Ds preferentially when
3054 both D+E are present in over 50% of the column</li>
3055 </ul> <em>Application</em>
3057 <li>typo in AlignmentFrame->View->Hide->all but
3058 selected Regions menu item</li>
3059 <li>sequence fetcher replaces ',' for ';' when the ',' is
3060 part of a valid accession ID</li>
3061 <li>fatal OOM if object retrieved by sequence fetcher
3062 runs out of memory</li>
3063 <li>unhandled Out of Memory Error when viewing pca
3064 analysis results</li>
3065 <li>InstallAnywhere builds fail to launch on OS X java
3066 10.5 update 4 (due to apple Java 1.6 update)</li>
3067 <li>Installanywhere Jalview silently fails to launch</li>
3068 </ul> <em>Applet</em>
3070 <li>Jalview.getFeatureGroups() raises an
3071 ArrayIndexOutOfBoundsException if no feature groups are
3078 <div align="center">
3079 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3085 <li>Alignment prettyprinter doesn't cope with long
3087 <li>clustalx colourscheme colours Ds preferentially when
3088 both D+E are present in over 50% of the column</li>
3089 <li>nucleic acid structures retrieved from PDB do not
3090 import correctly</li>
3091 <li>More columns get selected than were clicked on when a
3092 number of columns are hidden</li>
3093 <li>annotation label popup menu not providing correct
3094 add/hide/show options when rows are hidden or none are
3096 <li>Stockholm format shown in list of readable formats,
3097 and parser copes better with alignments from RFAM.</li>
3098 <li>CSV output of consensus only includes the percentage
3099 of all symbols if sequence logo display is enabled</li>
3101 </ul> <em>Applet</em>
3103 <li>annotation panel disappears when annotation is
3105 </ul> <em>Application</em>
3107 <li>Alignment view not redrawn properly when new
3108 alignment opened where annotation panel is visible but no
3109 annotations are present on alignment</li>
3110 <li>pasted region containing hidden columns is
3111 incorrectly displayed in new alignment window</li>
3112 <li>Jalview slow to complete operations when stdout is
3113 flooded (fix is to close the Jalview console)</li>
3114 <li>typo in AlignmentFrame->View->Hide->all but
3115 selected Rregions menu item.</li>
3116 <li>inconsistent group submenu and Format submenu entry
3117 'Un' or 'Non'conserved</li>
3118 <li>Sequence feature settings are being shared by
3119 multiple distinct alignments</li>
3120 <li>group annotation not recreated when tree partition is
3122 <li>double click on group annotation to select sequences
3123 does not propagate to associated trees</li>
3124 <li>Mac OSX specific issues:
3126 <li>exception raised when mouse clicked on desktop
3127 window background</li>
3128 <li>Desktop menu placed on menu bar and application
3129 name set correctly</li>
3130 <li>sequence feature settings not wide enough for the
3131 save feature colourscheme button</li>
3140 <div align="center">
3141 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3144 <td><em>New Capabilities</em>
3146 <li>URL links generated from description line for
3147 regular-expression based URL links (applet and application)
3149 <li>Non-positional feature URL links are shown in link
3151 <li>Linked viewing of nucleic acid sequences and
3153 <li>Automatic Scrolling option in View menu to display
3154 the currently highlighted region of an alignment.</li>
3155 <li>Order an alignment by sequence length, or using the
3156 average score or total feature count for each sequence.</li>
3157 <li>Shading features by score or associated description</li>
3158 <li>Subdivide alignment and groups based on identity of
3159 selected subsequence (Make Groups from Selection).</li>
3160 <li>New hide/show options including Shift+Control+H to
3161 hide everything but the currently selected region.</li>
3162 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3163 </ul> <em>Application</em>
3165 <li>Fetch DB References capabilities and UI expanded to
3166 support retrieval from DAS sequence sources</li>
3167 <li>Local DAS Sequence sources can be added via the
3168 command line or via the Add local source dialog box.</li>
3169 <li>DAS Dbref and DbxRef feature types are parsed as
3170 database references and protein_name is parsed as
3171 description line (BioSapiens terms).</li>
3172 <li>Enable or disable non-positional feature and database
3173 references in sequence ID tooltip from View menu in
3175 <!-- <li>New hidden columns and rows and representatives capabilities
3176 in annotations file (in progress - not yet fully implemented)</li> -->
3177 <li>Group-associated consensus, sequence logos and
3178 conservation plots</li>
3179 <li>Symbol distributions for each column can be exported
3180 and visualized as sequence logos</li>
3181 <li>Optionally scale multi-character column labels to fit
3182 within each column of annotation row<!-- todo for applet -->
3184 <li>Optional automatic sort of associated alignment view
3185 when a new tree is opened.</li>
3186 <li>Jalview Java Console</li>
3187 <li>Better placement of desktop window when moving
3188 between different screens.</li>
3189 <li>New preference items for sequence ID tooltip and
3190 consensus annotation</li>
3191 <li>Client to submit sequences and IDs to Envision2
3193 <li><em>Vamsas Capabilities</em>
3195 <li>Improved VAMSAS synchronization (Jalview archive
3196 used to preserve views, structures, and tree display
3198 <li>Import of vamsas documents from disk or URL via
3200 <li>Sharing of selected regions between views and
3201 with other VAMSAS applications (Experimental feature!)</li>
3202 <li>Updated API to VAMSAS version 0.2</li>
3204 </ul> <em>Applet</em>
3206 <li>Middle button resizes annotation row height</li>
3209 <li>sortByTree (true/false) - automatically sort the
3210 associated alignment view by the tree when a new tree is
3212 <li>showTreeBootstraps (true/false) - show or hide
3213 branch bootstraps (default is to show them if available)</li>
3214 <li>showTreeDistances (true/false) - show or hide
3215 branch lengths (default is to show them if available)</li>
3216 <li>showUnlinkedTreeNodes (true/false) - indicate if
3217 unassociated nodes should be highlighted in the tree
3219 <li>heightScale and widthScale (1.0 or more) -
3220 increase the height or width of a cell in the alignment
3221 grid relative to the current font size.</li>
3224 <li>Non-positional features displayed in sequence ID
3226 </ul> <em>Other</em>
3228 <li>Features format: graduated colour definitions and
3229 specification of feature scores</li>
3230 <li>Alignment Annotations format: new keywords for group
3231 associated annotation (GROUP_REF) and annotation row display
3232 properties (ROW_PROPERTIES)</li>
3233 <li>XML formats extended to support graduated feature
3234 colourschemes, group associated annotation, and profile
3235 visualization settings.</li></td>
3238 <li>Source field in GFF files parsed as feature source
3239 rather than description</li>
3240 <li>Non-positional features are now included in sequence
3241 feature and gff files (controlled via non-positional feature
3242 visibility in tooltip).</li>
3243 <li>URL links generated for all feature links (bugfix)</li>
3244 <li>Added URL embedding instructions to features file
3246 <li>Codons containing ambiguous nucleotides translated as
3247 'X' in peptide product</li>
3248 <li>Match case switch in find dialog box works for both
3249 sequence ID and sequence string and query strings do not
3250 have to be in upper case to match case-insensitively.</li>
3251 <li>AMSA files only contain first column of
3252 multi-character column annotation labels</li>
3253 <li>Jalview Annotation File generation/parsing consistent
3254 with documentation (e.g. Stockholm annotation can be
3255 exported and re-imported)</li>
3256 <li>PDB files without embedded PDB IDs given a friendly
3258 <li>Find incrementally searches ID string matches as well
3259 as subsequence matches, and correctly reports total number
3263 <li>Better handling of exceptions during sequence
3265 <li>Dasobert generated non-positional feature URL
3266 link text excludes the start_end suffix</li>
3267 <li>DAS feature and source retrieval buttons disabled
3268 when fetch or registry operations in progress.</li>
3269 <li>PDB files retrieved from URLs are cached properly</li>
3270 <li>Sequence description lines properly shared via
3272 <li>Sequence fetcher fetches multiple records for all
3274 <li>Ensured that command line das feature retrieval
3275 completes before alignment figures are generated.</li>
3276 <li>Reduced time taken when opening file browser for
3278 <li>isAligned check prior to calculating tree, PCA or
3279 submitting an MSA to JNet now excludes hidden sequences.</li>
3280 <li>User defined group colours properly recovered
3281 from Jalview projects.</li>
3290 <div align="center">
3291 <strong>2.4.0.b2</strong><br> 28/10/2009
3296 <li>Experimental support for google analytics usage
3298 <li>Jalview privacy settings (user preferences and docs).</li>
3303 <li>Race condition in applet preventing startup in
3305 <li>Exception when feature created from selection beyond
3306 length of sequence.</li>
3307 <li>Allow synthetic PDB files to be imported gracefully</li>
3308 <li>Sequence associated annotation rows associate with
3309 all sequences with a given id</li>
3310 <li>Find function matches case-insensitively for sequence
3311 ID string searches</li>
3312 <li>Non-standard characters do not cause pairwise
3313 alignment to fail with exception</li>
3314 </ul> <em>Application Issues</em>
3316 <li>Sequences are now validated against EMBL database</li>
3317 <li>Sequence fetcher fetches multiple records for all
3319 </ul> <em>InstallAnywhere Issues</em>
3321 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3322 issue with installAnywhere mechanism)</li>
3323 <li>Command line launching of JARs from InstallAnywhere
3324 version (java class versioning error fixed)</li>
3331 <div align="center">
3332 <strong>2.4</strong><br> 27/8/2008
3335 <td><em>User Interface</em>
3337 <li>Linked highlighting of codon and amino acid from
3338 translation and protein products</li>
3339 <li>Linked highlighting of structure associated with
3340 residue mapping to codon position</li>
3341 <li>Sequence Fetcher provides example accession numbers
3342 and 'clear' button</li>
3343 <li>MemoryMonitor added as an option under Desktop's
3345 <li>Extract score function to parse whitespace separated
3346 numeric data in description line</li>
3347 <li>Column labels in alignment annotation can be centred.</li>
3348 <li>Tooltip for sequence associated annotation give name
3350 </ul> <em>Web Services and URL fetching</em>
3352 <li>JPred3 web service</li>
3353 <li>Prototype sequence search client (no public services
3355 <li>Fetch either seed alignment or full alignment from
3357 <li>URL Links created for matching database cross
3358 references as well as sequence ID</li>
3359 <li>URL Links can be created using regular-expressions</li>
3360 </ul> <em>Sequence Database Connectivity</em>
3362 <li>Retrieval of cross-referenced sequences from other
3364 <li>Generalised database reference retrieval and
3365 validation to all fetchable databases</li>
3366 <li>Fetch sequences from DAS sources supporting the
3367 sequence command</li>
3368 </ul> <em>Import and Export</em>
3369 <li>export annotation rows as CSV for spreadsheet import</li>
3370 <li>Jalview projects record alignment dataset associations,
3371 EMBL products, and cDNA sequence mappings</li>
3372 <li>Sequence Group colour can be specified in Annotation
3374 <li>Ad-hoc colouring of group in Annotation File using RGB
3375 triplet as name of colourscheme</li>
3376 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3378 <li>treenode binding for VAMSAS tree exchange</li>
3379 <li>local editing and update of sequences in VAMSAS
3380 alignments (experimental)</li>
3381 <li>Create new or select existing session to join</li>
3382 <li>load and save of vamsas documents</li>
3383 </ul> <em>Application command line</em>
3385 <li>-tree parameter to open trees (introduced for passing
3387 <li>-fetchfrom command line argument to specify nicknames
3388 of DAS servers to query for alignment features</li>
3389 <li>-dasserver command line argument to add new servers
3390 that are also automatically queried for features</li>
3391 <li>-groovy command line argument executes a given groovy
3392 script after all input data has been loaded and parsed</li>
3393 </ul> <em>Applet-Application data exchange</em>
3395 <li>Trees passed as applet parameters can be passed to
3396 application (when using "View in full
3397 application")</li>
3398 </ul> <em>Applet Parameters</em>
3400 <li>feature group display control parameter</li>
3401 <li>debug parameter</li>
3402 <li>showbutton parameter</li>
3403 </ul> <em>Applet API methods</em>
3405 <li>newView public method</li>
3406 <li>Window (current view) specific get/set public methods</li>
3407 <li>Feature display control methods</li>
3408 <li>get list of currently selected sequences</li>
3409 </ul> <em>New Jalview distribution features</em>
3411 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3412 <li>RELEASE file gives build properties for the latest
3413 Jalview release.</li>
3414 <li>Java 1.1 Applet build made easier and donotobfuscate
3415 property controls execution of obfuscator</li>
3416 <li>Build target for generating source distribution</li>
3417 <li>Debug flag for javacc</li>
3418 <li>.jalview_properties file is documented (slightly) in
3419 jalview.bin.Cache</li>
3420 <li>Continuous Build Integration for stable and
3421 development version of Application, Applet and source
3426 <li>selected region output includes visible annotations
3427 (for certain formats)</li>
3428 <li>edit label/displaychar contains existing label/char
3430 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3431 <li>shorter peptide product names from EMBL records</li>
3432 <li>Newick string generator makes compact representations</li>
3433 <li>bootstrap values parsed correctly for tree files with
3435 <li>pathological filechooser bug avoided by not allowing
3436 filenames containing a ':'</li>
3437 <li>Fixed exception when parsing GFF files containing
3438 global sequence features</li>
3439 <li>Alignment datasets are finalized only when number of
3440 references from alignment sequences goes to zero</li>
3441 <li>Close of tree branch colour box without colour
3442 selection causes cascading exceptions</li>
3443 <li>occasional negative imgwidth exceptions</li>
3444 <li>better reporting of non-fatal warnings to user when
3445 file parsing fails.</li>
3446 <li>Save works when Jalview project is default format</li>
3447 <li>Save as dialog opened if current alignment format is
3448 not a valid output format</li>
3449 <li>UniProt canonical names introduced for both das and
3451 <li>Histidine should be midblue (not pink!) in Zappo</li>
3452 <li>error messages passed up and output when data read
3454 <li>edit undo recovers previous dataset sequence when
3455 sequence is edited</li>
3456 <li>allow PDB files without pdb ID HEADER lines (like
3457 those generated by MODELLER) to be read in properly</li>
3458 <li>allow reading of JPred concise files as a normal
3460 <li>Stockholm annotation parsing and alignment properties
3461 import fixed for PFAM records</li>
3462 <li>Structure view windows have correct name in Desktop
3464 <li>annotation consisting of sequence associated scores
3465 can be read and written correctly to annotation file</li>
3466 <li>Aligned cDNA translation to aligned peptide works
3468 <li>Fixed display of hidden sequence markers and
3469 non-italic font for representatives in Applet</li>
3470 <li>Applet Menus are always embedded in applet window on
3472 <li>Newly shown features appear at top of stack (in
3474 <li>Annotations added via parameter not drawn properly
3475 due to null pointer exceptions</li>
3476 <li>Secondary structure lines are drawn starting from
3477 first column of alignment</li>
3478 <li>UniProt XML import updated for new schema release in
3480 <li>Sequence feature to sequence ID match for Features
3481 file is case-insensitive</li>
3482 <li>Sequence features read from Features file appended to
3483 all sequences with matching IDs</li>
3484 <li>PDB structure coloured correctly for associated views
3485 containing a sub-sequence</li>
3486 <li>PDB files can be retrieved by applet from Jar files</li>
3487 <li>feature and annotation file applet parameters
3488 referring to different directories are retrieved correctly</li>
3489 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3490 <li>Fixed application hang whilst waiting for
3491 splash-screen version check to complete</li>
3492 <li>Applet properly URLencodes input parameter values
3493 when passing them to the launchApp service</li>
3494 <li>display name and local features preserved in results
3495 retrieved from web service</li>
3496 <li>Visual delay indication for sequence retrieval and
3497 sequence fetcher initialisation</li>
3498 <li>updated Application to use DAS 1.53e version of
3499 dasobert DAS client</li>
3500 <li>Re-instated Full AMSA support and .amsa file
3502 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3510 <div align="center">
3511 <strong>2.3</strong><br> 9/5/07
3516 <li>Jmol 11.0.2 integration</li>
3517 <li>PDB views stored in Jalview XML files</li>
3518 <li>Slide sequences</li>
3519 <li>Edit sequence in place</li>
3520 <li>EMBL CDS features</li>
3521 <li>DAS Feature mapping</li>
3522 <li>Feature ordering</li>
3523 <li>Alignment Properties</li>
3524 <li>Annotation Scores</li>
3525 <li>Sort by scores</li>
3526 <li>Feature/annotation editing in applet</li>
3531 <li>Headless state operation in 2.2.1</li>
3532 <li>Incorrect and unstable DNA pairwise alignment</li>
3533 <li>Cut and paste of sequences with annotation</li>
3534 <li>Feature group display state in XML</li>
3535 <li>Feature ordering in XML</li>
3536 <li>blc file iteration selection using filename # suffix</li>
3537 <li>Stockholm alignment properties</li>
3538 <li>Stockhom alignment secondary structure annotation</li>
3539 <li>2.2.1 applet had no feature transparency</li>
3540 <li>Number pad keys can be used in cursor mode</li>
3541 <li>Structure Viewer mirror image resolved</li>
3548 <div align="center">
3549 <strong>2.2.1</strong><br> 12/2/07
3554 <li>Non standard characters can be read and displayed
3555 <li>Annotations/Features can be imported/exported to the
3557 <li>Applet allows editing of sequence/annotation/group
3558 name & description
3559 <li>Preference setting to display sequence name in
3561 <li>Annotation file format extended to allow
3562 Sequence_groups to be defined
3563 <li>Default opening of alignment overview panel can be
3564 specified in preferences
3565 <li>PDB residue numbering annotation added to associated
3571 <li>Applet crash under certain Linux OS with Java 1.6
3573 <li>Annotation file export / import bugs fixed
3574 <li>PNG / EPS image output bugs fixed
3580 <div align="center">
3581 <strong>2.2</strong><br> 27/11/06
3586 <li>Multiple views on alignment
3587 <li>Sequence feature editing
3588 <li>"Reload" alignment
3589 <li>"Save" to current filename
3590 <li>Background dependent text colour
3591 <li>Right align sequence ids
3592 <li>User-defined lower case residue colours
3595 <li>Menu item accelerator keys
3596 <li>Control-V pastes to current alignment
3597 <li>Cancel button for DAS Feature Fetching
3598 <li>PCA and PDB Viewers zoom via mouse roller
3599 <li>User-defined sub-tree colours and sub-tree selection
3601 <li>'New Window' button on the 'Output to Text box'
3606 <li>New memory efficient Undo/Redo System
3607 <li>Optimised symbol lookups and conservation/consensus
3609 <li>Region Conservation/Consensus recalculated after
3611 <li>Fixed Remove Empty Columns Bug (empty columns at end
3613 <li>Slowed DAS Feature Fetching for increased robustness.
3615 <li>Made angle brackets in ASCII feature descriptions
3617 <li>Re-instated Zoom function for PCA
3618 <li>Sequence descriptions conserved in web service
3620 <li>UniProt ID discoverer uses any word separated by
3622 <li>WsDbFetch query/result association resolved
3623 <li>Tree leaf to sequence mapping improved
3624 <li>Smooth fonts switch moved to FontChooser dialog box.
3631 <div align="center">
3632 <strong>2.1.1</strong><br> 12/9/06
3637 <li>Copy consensus sequence to clipboard</li>
3642 <li>Image output - rightmost residues are rendered if
3643 sequence id panel has been resized</li>
3644 <li>Image output - all offscreen group boundaries are
3646 <li>Annotation files with sequence references - all
3647 elements in file are relative to sequence position</li>
3648 <li>Mac Applet users can use Alt key for group editing</li>
3654 <div align="center">
3655 <strong>2.1</strong><br> 22/8/06
3660 <li>MAFFT Multiple Alignment in default Web Service list</li>
3661 <li>DAS Feature fetching</li>
3662 <li>Hide sequences and columns</li>
3663 <li>Export Annotations and Features</li>
3664 <li>GFF file reading / writing</li>
3665 <li>Associate structures with sequences from local PDB
3667 <li>Add sequences to exisiting alignment</li>
3668 <li>Recently opened files / URL lists</li>
3669 <li>Applet can launch the full application</li>
3670 <li>Applet has transparency for features (Java 1.2
3672 <li>Applet has user defined colours parameter</li>
3673 <li>Applet can load sequences from parameter
3674 "sequence<em>x</em>"
3680 <li>Redundancy Panel reinstalled in the Applet</li>
3681 <li>Monospaced font - EPS / rescaling bug fixed</li>
3682 <li>Annotation files with sequence references bug fixed</li>
3688 <div align="center">
3689 <strong>2.08.1</strong><br> 2/5/06
3694 <li>Change case of selected region from Popup menu</li>
3695 <li>Choose to match case when searching</li>
3696 <li>Middle mouse button and mouse movement can compress /
3697 expand the visible width and height of the alignment</li>
3702 <li>Annotation Panel displays complete JNet results</li>
3708 <div align="center">
3709 <strong>2.08b</strong><br> 18/4/06
3715 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3716 <li>Righthand label on wrapped alignments shows correct
3723 <div align="center">
3724 <strong>2.08</strong><br> 10/4/06
3729 <li>Editing can be locked to the selection area</li>
3730 <li>Keyboard editing</li>
3731 <li>Create sequence features from searches</li>
3732 <li>Precalculated annotations can be loaded onto
3734 <li>Features file allows grouping of features</li>
3735 <li>Annotation Colouring scheme added</li>
3736 <li>Smooth fonts off by default - Faster rendering</li>
3737 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3742 <li>Drag & Drop fixed on Linux</li>
3743 <li>Jalview Archive file faster to load/save, sequence
3744 descriptions saved.</li>
3750 <div align="center">
3751 <strong>2.07</strong><br> 12/12/05
3756 <li>PDB Structure Viewer enhanced</li>
3757 <li>Sequence Feature retrieval and display enhanced</li>
3758 <li>Choose to output sequence start-end after sequence
3759 name for file output</li>
3760 <li>Sequence Fetcher WSDBFetch@EBI</li>
3761 <li>Applet can read feature files, PDB files and can be
3762 used for HTML form input</li>
3767 <li>HTML output writes groups and features</li>
3768 <li>Group editing is Control and mouse click</li>
3769 <li>File IO bugs</li>
3775 <div align="center">
3776 <strong>2.06</strong><br> 28/9/05
3781 <li>View annotations in wrapped mode</li>
3782 <li>More options for PCA viewer</li>
3787 <li>GUI bugs resolved</li>
3788 <li>Runs with -nodisplay from command line</li>
3794 <div align="center">
3795 <strong>2.05b</strong><br> 15/9/05
3800 <li>Choose EPS export as lineart or text</li>
3801 <li>Jar files are executable</li>
3802 <li>Can read in Uracil - maps to unknown residue</li>
3807 <li>Known OutOfMemory errors give warning message</li>
3808 <li>Overview window calculated more efficiently</li>
3809 <li>Several GUI bugs resolved</li>
3815 <div align="center">
3816 <strong>2.05</strong><br> 30/8/05
3821 <li>Edit and annotate in "Wrapped" view</li>
3826 <li>Several GUI bugs resolved</li>
3832 <div align="center">
3833 <strong>2.04</strong><br> 24/8/05
3838 <li>Hold down mouse wheel & scroll to change font
3844 <li>Improved JPred client reliability</li>
3845 <li>Improved loading of Jalview files</li>
3851 <div align="center">
3852 <strong>2.03</strong><br> 18/8/05
3857 <li>Set Proxy server name and port in preferences</li>
3858 <li>Multiple URL links from sequence ids</li>
3859 <li>User Defined Colours can have a scheme name and added
3861 <li>Choose to ignore gaps in consensus calculation</li>
3862 <li>Unix users can set default web browser</li>
3863 <li>Runs without GUI for batch processing</li>
3864 <li>Dynamically generated Web Service Menus</li>
3869 <li>InstallAnywhere download for Sparc Solaris</li>
3875 <div align="center">
3876 <strong>2.02</strong><br> 18/7/05
3882 <li>Copy & Paste order of sequences maintains
3883 alignment order.</li>
3889 <div align="center">
3890 <strong>2.01</strong><br> 12/7/05
3895 <li>Use delete key for deleting selection.</li>
3896 <li>Use Mouse wheel to scroll sequences.</li>
3897 <li>Help file updated to describe how to add alignment
3899 <li>Version and build date written to build properties
3901 <li>InstallAnywhere installation will check for updates
3902 at launch of Jalview.</li>
3907 <li>Delete gaps bug fixed.</li>
3908 <li>FileChooser sorts columns.</li>
3909 <li>Can remove groups one by one.</li>
3910 <li>Filechooser icons installed.</li>
3911 <li>Finder ignores return character when searching.
3912 Return key will initiate a search.<br>
3919 <div align="center">
3920 <strong>2.0</strong><br> 20/6/05
3925 <li>New codebase</li>