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.2.10.4b1">2.10.4b1</a><br />
74 <em>7/06/2018</em></strong>
77 <td><div align="left">
81 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
82 onto the Jalview Desktop
85 <!-- JAL-2920 -->Use HGVS nomenclature for variant
86 annotation retrieved from Uniprot
90 <td><div align="left">
94 <!-- JAL-3017 -->Cannot import features with multiple
98 <!-- JAL-2997 -->Clustal files with sequence positions in
99 right-hand column parsed correctly
102 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
103 not alignment area in exported graphic
106 <!-- JAL-2992 -->Annotation panel set too high when
107 annotation added to view
110 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
111 window has input focus
114 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
115 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
116 the currently open URL and links from a page viewed in
117 Firefox or Chrome on Windows is now fully supported. If
118 you are using Edge, only links in the page can be
119 dragged, and with Internet Explorer, only the currently
120 open URL in the browser can be dropped onto Jalview.</em>
126 <td width="60" nowrap>
128 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
131 <td><div align="left">
135 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
136 for disabling automatic superposition of multiple
137 structures and open structures in existing views
140 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
141 ID and annotation area margins can be click-dragged to
145 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
149 <!-- JAL-2759 -->Improved performance for large alignments
150 and lots of hidden columns
153 <!-- JAL-2593 -->Improved performance when rendering lots
154 of features (particularly when transparency is disabled)
159 <td><div align="left">
162 <!-- JAL-2899 -->Structure and Overview aren't updated
163 when Colour By Annotation threshold slider is adjusted
166 <!-- JAL-2778 -->Slow redraw when Overview panel shown
167 overlapping alignment panel
170 <!-- JAL-2929 -->Overview doesn't show end of unpadded
174 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
175 improved: CDS not handled correctly if transcript has no
179 <!-- JAL-2321 -->Secondary structure and temperature
180 factor annotation not added to sequence when local PDB
181 file associated with it by drag'n'drop or structure
185 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
186 dialog doesn't import PDB files dropped on an alignment
189 <!-- JAL-2666 -->Linked scrolling via protein horizontal
190 scroll bar doesn't work for some CDS/Protein views
193 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
194 Java 1.8u153 onwards and Java 1.9u4+.
197 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
198 columns in annotation row
201 <!-- JAL-2913 -->Preferences panel's ID Width control is not
202 honored in batch mode
205 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
206 for structures added to existing Jmol view
209 <!-- JAL-2223 -->'View Mappings' includes duplicate
210 entries after importing project with multiple views
213 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
214 protein sequences via SIFTS from associated PDB entries
215 with negative residue numbers or missing residues fails
218 <!-- JAL-2952 -->Exception when shading sequence with negative
219 Temperature Factor values from annotated PDB files (e.g.
220 as generated by CONSURF)
223 <!-- JAL-2920 -->Uniprot 'sequence variant' features
224 tooltip doesn't include a text description of mutation
227 <!-- JAL-2922 -->Invert displayed features very slow when
228 structure and/or overview windows are also shown
231 <!-- JAL-2954 -->Selecting columns from highlighted regions
232 very slow for alignments with large numbers of sequences
235 <!-- JAL-2925 -->Copy Consensus fails for group consensus
236 with 'StringIndexOutOfBounds'
239 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
240 platforms running Java 10
243 <!-- JAL-2960 -->Adding a structure to existing structure
244 view appears to do nothing because the view is hidden behind the alignment view
250 <!-- JAL-2926 -->Copy consensus sequence option in applet
251 should copy the group consensus when popup is opened on it
257 <!-- JAL-2913 -->Fixed ID width preference is not respected
260 <em>New Known Defects</em>
263 <!-- JAL-2973 --> Exceptions occasionally raised when
264 editing a large alignment and overview is displayed
267 <!-- JAL-2974 -->'Overview updating' progress bar is shown
268 repeatedly after a series of edits even when the overview
269 is no longer reflecting updates
272 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
273 structures for protein subsequence (if 'Trim Retrieved
274 Sequences' enabled) or Ensembl isoforms (Workaround in
275 2.10.4 is to fail back to N&W mapping)
282 <td width="60" nowrap>
284 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
287 <td><div align="left">
288 <ul><li>Updated Certum Codesigning Certificate
289 (Valid till 30th November 2018)</li></ul></div></td>
290 <td><div align="left">
293 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
294 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
295 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
296 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
297 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
298 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
299 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
305 <td width="60" nowrap>
307 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
310 <td><div align="left">
314 <!-- JAL-2446 -->Faster and more efficient management and
315 rendering of sequence features
318 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
319 429 rate limit request hander
322 <!-- JAL-2773 -->Structure views don't get updated unless
323 their colours have changed
326 <!-- JAL-2495 -->All linked sequences are highlighted for
327 a structure mousover (Jmol) or selection (Chimera)
330 <!-- JAL-2790 -->'Cancel' button in progress bar for
331 JABAWS AACon, RNAAliFold and Disorder prediction jobs
334 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
335 view from Ensembl locus cross-references
338 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
342 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
343 feature can be disabled
346 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
347 PDB easier retrieval of sequences for lists of IDs
350 <!-- JAL-2758 -->Short names for sequences retrieved from
356 <li>Groovy interpreter updated to 2.4.12</li>
357 <li>Example groovy script for generating a matrix of
358 percent identity scores for current alignment.</li>
360 <em>Testing and Deployment</em>
363 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
367 <td><div align="left">
371 <!-- JAL-2643 -->Pressing tab after updating the colour
372 threshold text field doesn't trigger an update to the
376 <!-- JAL-2682 -->Race condition when parsing sequence ID
380 <!-- JAL-2608 -->Overview windows are also closed when
381 alignment window is closed
384 <!-- JAL-2548 -->Export of features doesn't always respect
388 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
389 takes a long time in Cursor mode
395 <!-- JAL-2777 -->Structures with whitespace chainCode
396 cannot be viewed in Chimera
399 <!-- JAL-2728 -->Protein annotation panel too high in
403 <!-- JAL-2757 -->Can't edit the query after the server
404 error warning icon is shown in Uniprot and PDB Free Text
408 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
411 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
414 <!-- JAL-2739 -->Hidden column marker in last column not
415 rendered when switching back from Wrapped to normal view
418 <!-- JAL-2768 -->Annotation display corrupted when
419 scrolling right in unwapped alignment view
422 <!-- JAL-2542 -->Existing features on subsequence
423 incorrectly relocated when full sequence retrieved from
427 <!-- JAL-2733 -->Last reported memory still shown when
428 Desktop->Show Memory is unticked (OSX only)
431 <!-- JAL-2658 -->Amend Features dialog doesn't allow
432 features of same type and group to be selected for
436 <!-- JAL-2524 -->Jalview becomes sluggish in wide
437 alignments when hidden columns are present
440 <!-- JAL-2392 -->Jalview freezes when loading and
441 displaying several structures
444 <!-- JAL-2732 -->Black outlines left after resizing or
448 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
449 within the Jalview desktop on OSX
452 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
453 when in wrapped alignment mode
456 <!-- JAL-2636 -->Scale mark not shown when close to right
457 hand end of alignment
460 <!-- JAL-2684 -->Pairwise alignment of selected regions of
461 each selected sequence do not have correct start/end
465 <!-- JAL-2793 -->Alignment ruler height set incorrectly
466 after canceling the Alignment Window's Font dialog
469 <!-- JAL-2036 -->Show cross-references not enabled after
470 restoring project until a new view is created
473 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
474 URL links appears when only default EMBL-EBI link is
475 configured (since 2.10.2b2)
478 <!-- JAL-2775 -->Overview redraws whole window when box
482 <!-- JAL-2225 -->Structure viewer doesn't map all chains
483 in a multi-chain structure when viewing alignment
484 involving more than one chain (since 2.10)
487 <!-- JAL-2811 -->Double residue highlights in cursor mode
488 if new selection moves alignment window
491 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
492 arrow key in cursor mode to pass hidden column marker
495 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
496 that produces correctly annotated transcripts and products
499 <!-- JAL-2776 -->Toggling a feature group after first time
500 doesn't update associated structure view
503 <em>Applet</em><br />
506 <!-- JAL-2687 -->Concurrent modification exception when
507 closing alignment panel
510 <em>BioJSON</em><br />
513 <!-- JAL-2546 -->BioJSON export does not preserve
514 non-positional features
517 <em>New Known Issues</em>
520 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
521 sequence features correctly (for many previous versions of
525 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
526 using cursor in wrapped panel other than top
529 <!-- JAL-2791 -->Select columns containing feature ignores
530 graduated colour threshold
533 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
534 always preserve numbering and sequence features
537 <em>Known Java 9 Issues</em>
540 <!-- JAL-2902 -->Groovy Console very slow to open and is
541 not responsive when entering characters (Webstart, Java
548 <td width="60" nowrap>
550 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
551 <em>2/10/2017</em></strong>
554 <td><div align="left">
555 <em>New features in Jalview Desktop</em>
558 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
560 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
564 <td><div align="left">
568 <td width="60" nowrap>
570 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
571 <em>7/9/2017</em></strong>
574 <td><div align="left">
578 <!-- JAL-2588 -->Show gaps in overview window by colouring
579 in grey (sequences used to be coloured grey, and gaps were
583 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
587 <!-- JAL-2587 -->Overview updates immediately on increase
588 in size and progress bar shown as higher resolution
589 overview is recalculated
594 <td><div align="left">
598 <!-- JAL-2664 -->Overview window redraws every hidden
599 column region row by row
602 <!-- JAL-2681 -->duplicate protein sequences shown after
603 retrieving Ensembl crossrefs for sequences from Uniprot
606 <!-- JAL-2603 -->Overview window throws NPE if show boxes
607 format setting is unticked
610 <!-- JAL-2610 -->Groups are coloured wrongly in overview
611 if group has show boxes format setting unticked
614 <!-- JAL-2672,JAL-2665 -->Redraw problems when
615 autoscrolling whilst dragging current selection group to
616 include sequences and columns not currently displayed
619 <!-- JAL-2691 -->Not all chains are mapped when multimeric
620 assemblies are imported via CIF file
623 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
624 displayed when threshold or conservation colouring is also
628 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
632 <!-- JAL-2673 -->Jalview continues to scroll after
633 dragging a selected region off the visible region of the
637 <!-- JAL-2724 -->Cannot apply annotation based
638 colourscheme to all groups in a view
641 <!-- JAL-2511 -->IDs don't line up with sequences
642 initially after font size change using the Font chooser or
649 <td width="60" nowrap>
651 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
654 <td><div align="left">
655 <em>Calculations</em>
659 <!-- JAL-1933 -->Occupancy annotation row shows number of
660 ungapped positions in each column of the alignment.
663 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
664 a calculation dialog box
667 <!-- JAL-2379 -->Revised implementation of PCA for speed
668 and memory efficiency (~30x faster)
671 <!-- JAL-2403 -->Revised implementation of sequence
672 similarity scores as used by Tree, PCA, Shading Consensus
673 and other calculations
676 <!-- JAL-2416 -->Score matrices are stored as resource
677 files within the Jalview codebase
680 <!-- JAL-2500 -->Trees computed on Sequence Feature
681 Similarity may have different topology due to increased
688 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
689 model for alignments and groups
692 <!-- JAL-384 -->Custom shading schemes created via groovy
699 <!-- JAL-2526 -->Efficiency improvements for interacting
700 with alignment and overview windows
703 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
707 <!-- JAL-2388 -->Hidden columns and sequences can be
711 <!-- JAL-2611 -->Click-drag in visible area allows fine
712 adjustment of visible position
716 <em>Data import/export</em>
719 <!-- JAL-2535 -->Posterior probability annotation from
720 Stockholm files imported as sequence associated annotation
723 <!-- JAL-2507 -->More robust per-sequence positional
724 annotation input/output via stockholm flatfile
727 <!-- JAL-2533 -->Sequence names don't include file
728 extension when importing structure files without embedded
729 names or PDB accessions
732 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
733 format sequence substitution matrices
736 <em>User Interface</em>
739 <!-- JAL-2447 --> Experimental Features Checkbox in
740 Desktop's Tools menu to hide or show untested features in
744 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
745 via Overview or sequence motif search operations
748 <!-- JAL-2547 -->Amend sequence features dialog box can be
749 opened by double clicking gaps within sequence feature
753 <!-- JAL-1476 -->Status bar message shown when not enough
754 aligned positions were available to create a 3D structure
758 <em>3D Structure</em>
761 <!-- JAL-2430 -->Hidden regions in alignment views are not
762 coloured in linked structure views
765 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
766 file-based command exchange
769 <!-- JAL-2375 -->Structure chooser automatically shows
770 Cached Structures rather than querying the PDBe if
771 structures are already available for sequences
774 <!-- JAL-2520 -->Structures imported via URL are cached in
775 the Jalview project rather than downloaded again when the
779 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
780 to transfer Chimera's structure attributes as Jalview
781 features, and vice-versa (<strong>Experimental
785 <em>Web Services</em>
788 <!-- JAL-2549 -->Updated JABAWS client to v2.2
791 <!-- JAL-2335 -->Filter non-standard amino acids and
792 nucleotides when submitting to AACon and other MSA
796 <!-- JAL-2316, -->URLs for viewing database
797 cross-references provided by identifiers.org and the
805 <!-- JAL-2344 -->FileFormatI interface for describing and
806 identifying file formats (instead of String constants)
809 <!-- JAL-2228 -->FeatureCounter script refactored for
810 efficiency when counting all displayed features (not
811 backwards compatible with 2.10.1)
814 <em>Example files</em>
817 <!-- JAL-2631 -->Graduated feature colour style example
818 included in the example feature file
821 <em>Documentation</em>
824 <!-- JAL-2339 -->Release notes reformatted for readability
825 with the built-in Java help viewer
828 <!-- JAL-1644 -->Find documentation updated with 'search
829 sequence description' option
835 <!-- JAL-2485, -->External service integration tests for
836 Uniprot REST Free Text Search Client
839 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
842 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
847 <td><div align="left">
848 <em>Calculations</em>
851 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
852 matrix - C->R should be '-3'<br />Old matrix restored
853 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
855 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
856 Jalview's treatment of gaps in PCA and substitution matrix
857 based Tree calculations.<br /> <br />In earlier versions
858 of Jalview, gaps matching gaps were penalised, and gaps
859 matching non-gaps penalised even more. In the PCA
860 calculation, gaps were actually treated as non-gaps - so
861 different costs were applied, which meant Jalview's PCAs
862 were different to those produced by SeqSpace.<br />Jalview
863 now treats gaps in the same way as SeqSpace (ie it scores
864 them as 0). <br /> <br />Enter the following in the
865 Groovy console to restore pre-2.10.2 behaviour:<br />
866 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
867 // for 2.10.1 mode <br />
868 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
869 // to restore 2.10.2 mode <br /> <br /> <em>Note:
870 these settings will affect all subsequent tree and PCA
871 calculations (not recommended)</em></li>
873 <!-- JAL-2424 -->Fixed off-by-one bug that affected
874 scaling of branch lengths for trees computed using
875 Sequence Feature Similarity.
878 <!-- JAL-2377 -->PCA calculation could hang when
879 generating output report when working with highly
883 <!-- JAL-2544 --> Sort by features includes features to
884 right of selected region when gaps present on right-hand
888 <em>User Interface</em>
891 <!-- JAL-2346 -->Reopening Colour by annotation dialog
892 doesn't reselect a specific sequence's associated
893 annotation after it was used for colouring a view
896 <!-- JAL-2419 -->Current selection lost if popup menu
897 opened on a region of alignment without groups
900 <!-- JAL-2374 -->Popup menu not always shown for regions
901 of an alignment with overlapping groups
904 <!-- JAL-2310 -->Finder double counts if both a sequence's
905 name and description match
908 <!-- JAL-2370 -->Hiding column selection containing two
909 hidden regions results in incorrect hidden regions
912 <!-- JAL-2386 -->'Apply to all groups' setting when
913 changing colour does not apply Conservation slider value
917 <!-- JAL-2373 -->Percentage identity and conservation menu
918 items do not show a tick or allow shading to be disabled
921 <!-- JAL-2385 -->Conservation shading or PID threshold
922 lost when base colourscheme changed if slider not visible
925 <!-- JAL-2547 -->Sequence features shown in tooltip for
926 gaps before start of features
929 <!-- JAL-2623 -->Graduated feature colour threshold not
930 restored to UI when feature colour is edited
933 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
934 a time when scrolling vertically in wrapped mode.
937 <!-- JAL-2630 -->Structure and alignment overview update
938 as graduate feature colour settings are modified via the
942 <!-- JAL-2034 -->Overview window doesn't always update
943 when a group defined on the alignment is resized
946 <!-- JAL-2605 -->Mouseovers on left/right scale region in
947 wrapped view result in positional status updates
951 <!-- JAL-2563 -->Status bar doesn't show position for
952 ambiguous amino acid and nucleotide symbols
955 <!-- JAL-2602 -->Copy consensus sequence failed if
956 alignment included gapped columns
959 <!-- JAL-2473 -->Minimum size set for Jalview windows so
960 widgets don't permanently disappear
963 <!-- JAL-2503 -->Cannot select or filter quantitative
964 annotation that are shown only as column labels (e.g.
965 T-Coffee column reliability scores)
968 <!-- JAL-2594 -->Exception thrown if trying to create a
969 sequence feature on gaps only
972 <!-- JAL-2504 -->Features created with 'New feature'
973 button from a Find inherit previously defined feature type
974 rather than the Find query string
977 <!-- JAL-2423 -->incorrect title in output window when
978 exporting tree calculated in Jalview
981 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
982 and then revealing them reorders sequences on the
986 <!-- JAL-964 -->Group panel in sequence feature settings
987 doesn't update to reflect available set of groups after
988 interactively adding or modifying features
991 <!-- JAL-2225 -->Sequence Database chooser unusable on
995 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
996 only excluded gaps in current sequence and ignored
1003 <!-- JAL-2421 -->Overview window visible region moves
1004 erratically when hidden rows or columns are present
1007 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1008 Structure Viewer's colour menu don't correspond to
1012 <!-- JAL-2405 -->Protein specific colours only offered in
1013 colour and group colour menu for protein alignments
1016 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1017 reflect currently selected view or group's shading
1021 <!-- JAL-2624 -->Feature colour thresholds not respected
1022 when rendered on overview and structures when opacity at
1026 <!-- JAL-2589 -->User defined gap colour not shown in
1027 overview when features overlaid on alignment
1030 <em>Data import/export</em>
1033 <!-- JAL-2576 -->Very large alignments take a long time to
1037 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1038 added after a sequence was imported are not written to
1042 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1043 when importing RNA secondary structure via Stockholm
1046 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1047 not shown in correct direction for simple pseudoknots
1050 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1051 with lightGray or darkGray via features file (but can
1055 <!-- JAL-2383 -->Above PID colour threshold not recovered
1056 when alignment view imported from project
1059 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1060 structure and sequences extracted from structure files
1061 imported via URL and viewed in Jmol
1064 <!-- JAL-2520 -->Structures loaded via URL are saved in
1065 Jalview Projects rather than fetched via URL again when
1066 the project is loaded and the structure viewed
1069 <em>Web Services</em>
1072 <!-- JAL-2519 -->EnsemblGenomes example failing after
1073 release of Ensembl v.88
1076 <!-- JAL-2366 -->Proxy server address and port always
1077 appear enabled in Preferences->Connections
1080 <!-- JAL-2461 -->DAS registry not found exceptions
1081 removed from console output
1084 <!-- JAL-2582 -->Cannot retrieve protein products from
1085 Ensembl by Peptide ID
1088 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1089 created from SIFTs, and spurious 'Couldn't open structure
1090 in Chimera' errors raised after April 2017 update (problem
1091 due to 'null' string rather than empty string used for
1092 residues with no corresponding PDB mapping).
1095 <em>Application UI</em>
1098 <!-- JAL-2361 -->User Defined Colours not added to Colour
1102 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1103 case' residues (button in colourscheme editor debugged and
1104 new documentation and tooltips added)
1107 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1108 doesn't restore group-specific text colour thresholds
1111 <!-- JAL-2243 -->Feature settings panel does not update as
1112 new features are added to alignment
1115 <!-- JAL-2532 -->Cancel in feature settings reverts
1116 changes to feature colours via the Amend features dialog
1119 <!-- JAL-2506 -->Null pointer exception when attempting to
1120 edit graduated feature colour via amend features dialog
1124 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1125 selection menu changes colours of alignment views
1128 <!-- JAL-2426 -->Spurious exceptions in console raised
1129 from alignment calculation workers after alignment has
1133 <!-- JAL-1608 -->Typo in selection popup menu - Create
1134 groups now 'Create Group'
1137 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1138 Create/Undefine group doesn't always work
1141 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1142 shown again after pressing 'Cancel'
1145 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1146 adjusts start position in wrap mode
1149 <!-- JAL-2563 -->Status bar doesn't show positions for
1150 ambiguous amino acids
1153 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1154 CDS/Protein view after CDS sequences added for aligned
1158 <!-- JAL-2592 -->User defined colourschemes called 'User
1159 Defined' don't appear in Colours menu
1165 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1166 score models doesn't always result in an updated PCA plot
1169 <!-- JAL-2442 -->Features not rendered as transparent on
1170 overview or linked structure view
1173 <!-- JAL-2372 -->Colour group by conservation doesn't
1177 <!-- JAL-2517 -->Hitting Cancel after applying
1178 user-defined colourscheme doesn't restore original
1185 <!-- JAL-2314 -->Unit test failure:
1186 jalview.ws.jabaws.RNAStructExportImport setup fails
1189 <!-- JAL-2307 -->Unit test failure:
1190 jalview.ws.sifts.SiftsClientTest due to compatibility
1191 problems with deep array comparison equality asserts in
1192 successive versions of TestNG
1195 <!-- JAL-2479 -->Relocated StructureChooserTest and
1196 ParameterUtilsTest Unit tests to Network suite
1199 <em>New Known Issues</em>
1202 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1203 phase after a sequence motif find operation
1206 <!-- JAL-2550 -->Importing annotation file with rows
1207 containing just upper and lower case letters are
1208 interpreted as WUSS RNA secondary structure symbols
1211 <!-- JAL-2590 -->Cannot load and display Newick trees
1212 reliably from eggnog Ortholog database
1215 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1216 containing features of type Highlight' when 'B' is pressed
1217 to mark columns containing highlighted regions.
1220 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1221 doesn't always add secondary structure annotation.
1226 <td width="60" nowrap>
1227 <div align="center">
1228 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1231 <td><div align="left">
1235 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1236 for all consensus calculations
1239 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1242 <li>Updated Jalview's Certum code signing certificate
1245 <em>Application</em>
1248 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1249 set of database cross-references, sorted alphabetically
1252 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1253 from database cross references. Users with custom links
1254 will receive a <a href="webServices/urllinks.html#warning">warning
1255 dialog</a> asking them to update their preferences.
1258 <!-- JAL-2287-->Cancel button and escape listener on
1259 dialog warning user about disconnecting Jalview from a
1263 <!-- JAL-2320-->Jalview's Chimera control window closes if
1264 the Chimera it is connected to is shut down
1267 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1268 columns menu item to mark columns containing highlighted
1269 regions (e.g. from structure selections or results of a
1273 <!-- JAL-2284-->Command line option for batch-generation
1274 of HTML pages rendering alignment data with the BioJS
1284 <!-- JAL-2286 -->Columns with more than one modal residue
1285 are not coloured or thresholded according to percent
1286 identity (first observed in Jalview 2.8.2)
1289 <!-- JAL-2301 -->Threonine incorrectly reported as not
1293 <!-- JAL-2318 -->Updates to documentation pages (above PID
1294 threshold, amino acid properties)
1297 <!-- JAL-2292 -->Lower case residues in sequences are not
1298 reported as mapped to residues in a structure file in the
1302 <!--JAL-2324 -->Identical features with non-numeric scores
1303 could be added multiple times to a sequence
1306 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1307 bond features shown as two highlighted residues rather
1308 than a range in linked structure views, and treated
1309 correctly when selecting and computing trees from features
1312 <!-- JAL-2281-->Custom URL links for database
1313 cross-references are matched to database name regardless
1318 <em>Application</em>
1321 <!-- JAL-2282-->Custom URL links for specific database
1322 names without regular expressions also offer links from
1326 <!-- JAL-2315-->Removing a single configured link in the
1327 URL links pane in Connections preferences doesn't actually
1328 update Jalview configuration
1331 <!-- JAL-2272-->CTRL-Click on a selected region to open
1332 the alignment area popup menu doesn't work on El-Capitan
1335 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1336 files with similarly named sequences if dropped onto the
1340 <!-- JAL-2312 -->Additional mappings are shown for PDB
1341 entries where more chains exist in the PDB accession than
1342 are reported in the SIFTS file
1345 <!-- JAL-2317-->Certain structures do not get mapped to
1346 the structure view when displayed with Chimera
1349 <!-- JAL-2317-->No chains shown in the Chimera view
1350 panel's View->Show Chains submenu
1353 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1354 work for wrapped alignment views
1357 <!--JAL-2197 -->Rename UI components for running JPred
1358 predictions from 'JNet' to 'JPred'
1361 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1362 corrupted when annotation panel vertical scroll is not at
1363 first annotation row
1366 <!--JAL-2332 -->Attempting to view structure for Hen
1367 lysozyme results in a PDB Client error dialog box
1370 <!-- JAL-2319 -->Structure View's mapping report switched
1371 ranges for PDB and sequence for SIFTS
1374 SIFTS 'Not_Observed' residues mapped to non-existant
1378 <!-- <em>New Known Issues</em>
1385 <td width="60" nowrap>
1386 <div align="center">
1387 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1388 <em>25/10/2016</em></strong>
1391 <td><em>Application</em>
1393 <li>3D Structure chooser opens with 'Cached structures'
1394 view if structures already loaded</li>
1395 <li>Progress bar reports models as they are loaded to
1396 structure views</li>
1402 <li>Colour by conservation always enabled and no tick
1403 shown in menu when BLOSUM or PID shading applied</li>
1404 <li>FER1_ARATH and FER2_ARATH labels were switched in
1405 example sequences/projects/trees</li>
1407 <em>Application</em>
1409 <li>Jalview projects with views of local PDB structure
1410 files saved on Windows cannot be opened on OSX</li>
1411 <li>Multiple structure views can be opened and superposed
1412 without timeout for structures with multiple models or
1413 multiple sequences in alignment</li>
1414 <li>Cannot import or associated local PDB files without a
1415 PDB ID HEADER line</li>
1416 <li>RMSD is not output in Jmol console when superposition
1418 <li>Drag and drop of URL from Browser fails for Linux and
1419 OSX versions earlier than El Capitan</li>
1420 <li>ENA client ignores invalid content from ENA server</li>
1421 <li>Exceptions are not raised in console when ENA client
1422 attempts to fetch non-existent IDs via Fetch DB Refs UI
1424 <li>Exceptions are not raised in console when a new view
1425 is created on the alignment</li>
1426 <li>OSX right-click fixed for group selections: CMD-click
1427 to insert/remove gaps in groups and CTRL-click to open group
1430 <em>Build and deployment</em>
1432 <li>URL link checker now copes with multi-line anchor
1435 <em>New Known Issues</em>
1437 <li>Drag and drop from URL links in browsers do not work
1444 <td width="60" nowrap>
1445 <div align="center">
1446 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1449 <td><em>General</em>
1452 <!-- JAL-2124 -->Updated Spanish translations.
1455 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1456 for importing structure data to Jalview. Enables mmCIF and
1460 <!-- JAL-192 --->Alignment ruler shows positions relative to
1464 <!-- JAL-2202 -->Position/residue shown in status bar when
1465 mousing over sequence associated annotation
1468 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1472 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1473 '()', canonical '[]' and invalid '{}' base pair populations
1477 <!-- JAL-2092 -->Feature settings popup menu options for
1478 showing or hiding columns containing a feature
1481 <!-- JAL-1557 -->Edit selected group by double clicking on
1482 group and sequence associated annotation labels
1485 <!-- JAL-2236 -->Sequence name added to annotation label in
1486 select/hide columns by annotation and colour by annotation
1490 </ul> <em>Application</em>
1493 <!-- JAL-2050-->Automatically hide introns when opening a
1494 gene/transcript view
1497 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1501 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1502 structure mappings with the EMBL-EBI PDBe SIFTS database
1505 <!-- JAL-2079 -->Updated download sites used for Rfam and
1506 Pfam sources to xfam.org
1509 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1512 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1513 over sequences in Jalview
1516 <!-- JAL-2027-->Support for reverse-complement coding
1517 regions in ENA and EMBL
1520 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1521 for record retrieval via ENA rest API
1524 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1528 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1529 groovy script execution
1532 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1533 alignment window's Calculate menu
1536 <!-- JAL-1812 -->Allow groovy scripts that call
1537 Jalview.getAlignFrames() to run in headless mode
1540 <!-- JAL-2068 -->Support for creating new alignment
1541 calculation workers from groovy scripts
1544 <!-- JAL-1369 --->Store/restore reference sequence in
1548 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1549 associations are now saved/restored from project
1552 <!-- JAL-1993 -->Database selection dialog always shown
1553 before sequence fetcher is opened
1556 <!-- JAL-2183 -->Double click on an entry in Jalview's
1557 database chooser opens a sequence fetcher
1560 <!-- JAL-1563 -->Free-text search client for UniProt using
1561 the UniProt REST API
1564 <!-- JAL-2168 -->-nonews command line parameter to prevent
1565 the news reader opening
1568 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1569 querying stored in preferences
1572 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1576 <!-- JAL-1977-->Tooltips shown on database chooser
1579 <!-- JAL-391 -->Reverse complement function in calculate
1580 menu for nucleotide sequences
1583 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1584 and feature counts preserves alignment ordering (and
1585 debugged for complex feature sets).
1588 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1589 viewing structures with Jalview 2.10
1592 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1593 genome, transcript CCDS and gene ids via the Ensembl and
1594 Ensembl Genomes REST API
1597 <!-- JAL-2049 -->Protein sequence variant annotation
1598 computed for 'sequence_variant' annotation on CDS regions
1602 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1606 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1607 Ref Fetcher fails to match, or otherwise updates sequence
1608 data from external database records.
1611 <!-- JAL-2154 -->Revised Jalview Project format for
1612 efficient recovery of sequence coding and alignment
1613 annotation relationships.
1615 </ul> <!-- <em>Applet</em>
1626 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1630 <!-- JAL-2018-->Export features in Jalview format (again)
1631 includes graduated colourschemes
1634 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1635 working with big alignments and lots of hidden columns
1638 <!-- JAL-2053-->Hidden column markers not always rendered
1639 at right of alignment window
1642 <!-- JAL-2067 -->Tidied up links in help file table of
1646 <!-- JAL-2072 -->Feature based tree calculation not shown
1650 <!-- JAL-2075 -->Hidden columns ignored during feature
1651 based tree calculation
1654 <!-- JAL-2065 -->Alignment view stops updating when show
1655 unconserved enabled for group on alignment
1658 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1662 <!-- JAL-2146 -->Alignment column in status incorrectly
1663 shown as "Sequence position" when mousing over
1667 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1668 hidden columns present
1671 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1672 user created annotation added to alignment
1675 <!-- JAL-1841 -->RNA Structure consensus only computed for
1676 '()' base pair annotation
1679 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1680 in zero scores for all base pairs in RNA Structure
1684 <!-- JAL-2174-->Extend selection with columns containing
1688 <!-- JAL-2275 -->Pfam format writer puts extra space at
1689 beginning of sequence
1692 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1696 <!-- JAL-2238 -->Cannot create groups on an alignment from
1697 from a tree when t-coffee scores are shown
1700 <!-- JAL-1836,1967 -->Cannot import and view PDB
1701 structures with chains containing negative resnums (4q4h)
1704 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1708 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1709 to Clustal, PIR and PileUp output
1712 <!-- JAL-2008 -->Reordering sequence features that are
1713 not visible causes alignment window to repaint
1716 <!-- JAL-2006 -->Threshold sliders don't work in
1717 graduated colour and colour by annotation row for e-value
1718 scores associated with features and annotation rows
1721 <!-- JAL-1797 -->amino acid physicochemical conservation
1722 calculation should be case independent
1725 <!-- JAL-2173 -->Remove annotation also updates hidden
1729 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1730 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1731 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1734 <!-- JAL-2065 -->Null pointer exceptions and redraw
1735 problems when reference sequence defined and 'show
1736 non-conserved' enabled
1739 <!-- JAL-1306 -->Quality and Conservation are now shown on
1740 load even when Consensus calculation is disabled
1743 <!-- JAL-1932 -->Remove right on penultimate column of
1744 alignment does nothing
1747 <em>Application</em>
1750 <!-- JAL-1552-->URLs and links can't be imported by
1751 drag'n'drop on OSX when launched via webstart (note - not
1752 yet fixed for El Capitan)
1755 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1756 output when running on non-gb/us i18n platforms
1759 <!-- JAL-1944 -->Error thrown when exporting a view with
1760 hidden sequences as flat-file alignment
1763 <!-- JAL-2030-->InstallAnywhere distribution fails when
1767 <!-- JAL-2080-->Jalview very slow to launch via webstart
1768 (also hotfix for 2.9.0b2)
1771 <!-- JAL-2085 -->Cannot save project when view has a
1772 reference sequence defined
1775 <!-- JAL-1011 -->Columns are suddenly selected in other
1776 alignments and views when revealing hidden columns
1779 <!-- JAL-1989 -->Hide columns not mirrored in complement
1780 view in a cDNA/Protein splitframe
1783 <!-- JAL-1369 -->Cannot save/restore representative
1784 sequence from project when only one sequence is
1788 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1789 in Structure Chooser
1792 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1793 structure consensus didn't refresh annotation panel
1796 <!-- JAL-1962 -->View mapping in structure view shows
1797 mappings between sequence and all chains in a PDB file
1800 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1801 dialogs format columns correctly, don't display array
1802 data, sort columns according to type
1805 <!-- JAL-1975 -->Export complete shown after destination
1806 file chooser is cancelled during an image export
1809 <!-- JAL-2025 -->Error when querying PDB Service with
1810 sequence name containing special characters
1813 <!-- JAL-2024 -->Manual PDB structure querying should be
1817 <!-- JAL-2104 -->Large tooltips with broken HTML
1818 formatting don't wrap
1821 <!-- JAL-1128 -->Figures exported from wrapped view are
1822 truncated so L looks like I in consensus annotation
1825 <!-- JAL-2003 -->Export features should only export the
1826 currently displayed features for the current selection or
1830 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1831 after fetching cross-references, and restoring from
1835 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1836 followed in the structure viewer
1839 <!-- JAL-2163 -->Titles for individual alignments in
1840 splitframe not restored from project
1843 <!-- JAL-2145 -->missing autocalculated annotation at
1844 trailing end of protein alignment in transcript/product
1845 splitview when pad-gaps not enabled by default
1848 <!-- JAL-1797 -->amino acid physicochemical conservation
1852 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1853 article has been read (reopened issue due to
1854 internationalisation problems)
1857 <!-- JAL-1960 -->Only offer PDB structures in structure
1858 viewer based on sequence name, PDB and UniProt
1863 <!-- JAL-1976 -->No progress bar shown during export of
1867 <!-- JAL-2213 -->Structures not always superimposed after
1868 multiple structures are shown for one or more sequences.
1871 <!-- JAL-1370 -->Reference sequence characters should not
1872 be replaced with '.' when 'Show unconserved' format option
1876 <!-- JAL-1823 -->Cannot specify chain code when entering
1877 specific PDB id for sequence
1880 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1881 'Export hidden sequences' is enabled, but 'export hidden
1882 columns' is disabled.
1885 <!--JAL-2026-->Best Quality option in structure chooser
1886 selects lowest rather than highest resolution structures
1890 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1891 to sequence mapping in 'View Mappings' report
1894 <!-- JAL-2284 -->Unable to read old Jalview projects that
1895 contain non-XML data added after Jalvew wrote project.
1898 <!-- JAL-2118 -->Newly created annotation row reorders
1899 after clicking on it to create new annotation for a
1903 <!-- JAL-1980 -->Null Pointer Exception raised when
1904 pressing Add on an orphaned cut'n'paste window.
1906 <!-- may exclude, this is an external service stability issue JAL-1941
1907 -- > RNA 3D structure not added via DSSR service</li> -->
1912 <!-- JAL-2151 -->Incorrect columns are selected when
1913 hidden columns present before start of sequence
1916 <!-- JAL-1986 -->Missing dependencies on applet pages
1920 <!-- JAL-1947 -->Overview pixel size changes when
1921 sequences are hidden in applet
1924 <!-- JAL-1996 -->Updated instructions for applet
1925 deployment on examples pages.
1932 <td width="60" nowrap>
1933 <div align="center">
1934 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1935 <em>16/10/2015</em></strong>
1938 <td><em>General</em>
1940 <li>Time stamps for signed Jalview application and applet
1945 <em>Application</em>
1947 <li>Duplicate group consensus and conservation rows
1948 shown when tree is partitioned</li>
1949 <li>Erratic behaviour when tree partitions made with
1950 multiple cDNA/Protein split views</li>
1956 <td width="60" nowrap>
1957 <div align="center">
1958 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1959 <em>8/10/2015</em></strong>
1962 <td><em>General</em>
1964 <li>Updated Spanish translations of localized text for
1966 </ul> <em>Application</em>
1968 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1969 <li>Signed OSX InstallAnywhere installer<br></li>
1970 <li>Support for per-sequence based annotations in BioJSON</li>
1971 </ul> <em>Applet</em>
1973 <li>Split frame example added to applet examples page</li>
1974 </ul> <em>Build and Deployment</em>
1977 <!-- JAL-1888 -->New ant target for running Jalview's test
1985 <li>Mapping of cDNA to protein in split frames
1986 incorrect when sequence start > 1</li>
1987 <li>Broken images in filter column by annotation dialog
1989 <li>Feature colours not parsed from features file</li>
1990 <li>Exceptions and incomplete link URLs recovered when
1991 loading a features file containing HTML tags in feature
1995 <em>Application</em>
1997 <li>Annotations corrupted after BioJS export and
1999 <li>Incorrect sequence limits after Fetch DB References
2000 with 'trim retrieved sequences'</li>
2001 <li>Incorrect warning about deleting all data when
2002 deleting selected columns</li>
2003 <li>Patch to build system for shipping properly signed
2004 JNLP templates for webstart launch</li>
2005 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2006 unreleased structures for download or viewing</li>
2007 <li>Tab/space/return keystroke operation of EMBL-PDBe
2008 fetcher/viewer dialogs works correctly</li>
2009 <li>Disabled 'minimise' button on Jalview windows
2010 running on OSX to workaround redraw hang bug</li>
2011 <li>Split cDNA/Protein view position and geometry not
2012 recovered from jalview project</li>
2013 <li>Initial enabled/disabled state of annotation menu
2014 sorter 'show autocalculated first/last' corresponds to
2016 <li>Restoring of Clustal, RNA Helices and T-Coffee
2017 color schemes from BioJSON</li>
2021 <li>Reorder sequences mirrored in cDNA/Protein split
2023 <li>Applet with Jmol examples not loading correctly</li>
2029 <td><div align="center">
2030 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2032 <td><em>General</em>
2034 <li>Linked visualisation and analysis of DNA and Protein
2037 <li>Translated cDNA alignments shown as split protein
2038 and DNA alignment views</li>
2039 <li>Codon consensus annotation for linked protein and
2040 cDNA alignment views</li>
2041 <li>Link cDNA or Protein product sequences by loading
2042 them onto Protein or cDNA alignments</li>
2043 <li>Reconstruct linked cDNA alignment from aligned
2044 protein sequences</li>
2047 <li>Jmol integration updated to Jmol v14.2.14</li>
2048 <li>Import and export of Jalview alignment views as <a
2049 href="features/bioJsonFormat.html">BioJSON</a></li>
2050 <li>New alignment annotation file statements for
2051 reference sequences and marking hidden columns</li>
2052 <li>Reference sequence based alignment shading to
2053 highlight variation</li>
2054 <li>Select or hide columns according to alignment
2056 <li>Find option for locating sequences by description</li>
2057 <li>Conserved physicochemical properties shown in amino
2058 acid conservation row</li>
2059 <li>Alignments can be sorted by number of RNA helices</li>
2060 </ul> <em>Application</em>
2062 <li>New cDNA/Protein analysis capabilities
2064 <li>Get Cross-References should open a Split Frame
2065 view with cDNA/Protein</li>
2066 <li>Detect when nucleotide sequences and protein
2067 sequences are placed in the same alignment</li>
2068 <li>Split cDNA/Protein views are saved in Jalview
2073 <li>Use REST API to talk to Chimera</li>
2074 <li>Selected regions in Chimera are highlighted in linked
2075 Jalview windows</li>
2077 <li>VARNA RNA viewer updated to v3.93</li>
2078 <li>VARNA views are saved in Jalview Projects</li>
2079 <li>Pseudoknots displayed as Jalview RNA annotation can
2080 be shown in VARNA</li>
2082 <li>Make groups for selection uses marked columns as well
2083 as the active selected region</li>
2085 <li>Calculate UPGMA and NJ trees using sequence feature
2087 <li>New Export options
2089 <li>New Export Settings dialog to control hidden
2090 region export in flat file generation</li>
2092 <li>Export alignment views for display with the <a
2093 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2095 <li>Export scrollable SVG in HTML page</li>
2096 <li>Optional embedding of BioJSON data when exporting
2097 alignment figures to HTML</li>
2099 <li>3D structure retrieval and display
2101 <li>Free text and structured queries with the PDBe
2103 <li>PDBe Search API based discovery and selection of
2104 PDB structures for a sequence set</li>
2108 <li>JPred4 employed for protein secondary structure
2110 <li>Hide Insertions menu option to hide unaligned columns
2111 for one or a group of sequences</li>
2112 <li>Automatically hide insertions in alignments imported
2113 from the JPred4 web server</li>
2114 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2115 system on OSX<br />LGPL libraries courtesy of <a
2116 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2118 <li>changed 'View nucleotide structure' submenu to 'View
2119 VARNA 2D Structure'</li>
2120 <li>change "View protein structure" menu option to "3D
2123 </ul> <em>Applet</em>
2125 <li>New layout for applet example pages</li>
2126 <li>New parameters to enable SplitFrame view
2127 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2128 <li>New example demonstrating linked viewing of cDNA and
2129 Protein alignments</li>
2130 </ul> <em>Development and deployment</em>
2132 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2133 <li>Include installation type and git revision in build
2134 properties and console log output</li>
2135 <li>Jalview Github organisation, and new github site for
2136 storing BioJsMSA Templates</li>
2137 <li>Jalview's unit tests now managed with TestNG</li>
2140 <!-- <em>General</em>
2142 </ul> --> <!-- issues resolved --> <em>Application</em>
2144 <li>Escape should close any open find dialogs</li>
2145 <li>Typo in select-by-features status report</li>
2146 <li>Consensus RNA secondary secondary structure
2147 predictions are not highlighted in amber</li>
2148 <li>Missing gap character in v2.7 example file means
2149 alignment appears unaligned when pad-gaps is not enabled</li>
2150 <li>First switch to RNA Helices colouring doesn't colour
2151 associated structure views</li>
2152 <li>ID width preference option is greyed out when auto
2153 width checkbox not enabled</li>
2154 <li>Stopped a warning dialog from being shown when
2155 creating user defined colours</li>
2156 <li>'View Mapping' in structure viewer shows sequence
2157 mappings for just that viewer's sequences</li>
2158 <li>Workaround for superposing PDB files containing
2159 multiple models in Chimera</li>
2160 <li>Report sequence position in status bar when hovering
2161 over Jmol structure</li>
2162 <li>Cannot output gaps as '.' symbols with Selection ->
2163 output to text box</li>
2164 <li>Flat file exports of alignments with hidden columns
2165 have incorrect sequence start/end</li>
2166 <li>'Aligning' a second chain to a Chimera structure from
2168 <li>Colour schemes applied to structure viewers don't
2169 work for nucleotide</li>
2170 <li>Loading/cut'n'pasting an empty or invalid file leads
2171 to a grey/invisible alignment window</li>
2172 <li>Exported Jpred annotation from a sequence region
2173 imports to different position</li>
2174 <li>Space at beginning of sequence feature tooltips shown
2175 on some platforms</li>
2176 <li>Chimera viewer 'View | Show Chain' menu is not
2178 <li>'New View' fails with a Null Pointer Exception in
2179 console if Chimera has been opened</li>
2180 <li>Mouseover to Chimera not working</li>
2181 <li>Miscellaneous ENA XML feature qualifiers not
2183 <li>NPE in annotation renderer after 'Extract Scores'</li>
2184 <li>If two structures in one Chimera window, mouseover of
2185 either sequence shows on first structure</li>
2186 <li>'Show annotations' options should not make
2187 non-positional annotations visible</li>
2188 <li>Subsequence secondary structure annotation not shown
2189 in right place after 'view flanking regions'</li>
2190 <li>File Save As type unset when current file format is
2192 <li>Save as '.jar' option removed for saving Jalview
2194 <li>Colour by Sequence colouring in Chimera more
2196 <li>Cannot 'add reference annotation' for a sequence in
2197 several views on same alignment</li>
2198 <li>Cannot show linked products for EMBL / ENA records</li>
2199 <li>Jalview's tooltip wraps long texts containing no
2201 </ul> <em>Applet</em>
2203 <li>Jmol to JalviewLite mouseover/link not working</li>
2204 <li>JalviewLite can't import sequences with ID
2205 descriptions containing angle brackets</li>
2206 </ul> <em>General</em>
2208 <li>Cannot export and reimport RNA secondary structure
2209 via jalview annotation file</li>
2210 <li>Random helix colour palette for colour by annotation
2211 with RNA secondary structure</li>
2212 <li>Mouseover to cDNA from STOP residue in protein
2213 translation doesn't work.</li>
2214 <li>hints when using the select by annotation dialog box</li>
2215 <li>Jmol alignment incorrect if PDB file has alternate CA
2217 <li>FontChooser message dialog appears to hang after
2218 choosing 1pt font</li>
2219 <li>Peptide secondary structure incorrectly imported from
2220 annotation file when annotation display text includes 'e' or
2222 <li>Cannot set colour of new feature type whilst creating
2224 <li>cDNA translation alignment should not be sequence
2225 order dependent</li>
2226 <li>'Show unconserved' doesn't work for lower case
2228 <li>Nucleotide ambiguity codes involving R not recognised</li>
2229 </ul> <em>Deployment and Documentation</em>
2231 <li>Applet example pages appear different to the rest of
2232 www.jalview.org</li>
2233 </ul> <em>Application Known issues</em>
2235 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2236 <li>Misleading message appears after trying to delete
2238 <li>Jalview icon not shown in dock after InstallAnywhere
2239 version launches</li>
2240 <li>Fetching EMBL reference for an RNA sequence results
2241 fails with a sequence mismatch</li>
2242 <li>Corrupted or unreadable alignment display when
2243 scrolling alignment to right</li>
2244 <li>ArrayIndexOutOfBoundsException thrown when remove
2245 empty columns called on alignment with ragged gapped ends</li>
2246 <li>auto calculated alignment annotation rows do not get
2247 placed above or below non-autocalculated rows</li>
2248 <li>Jalview dekstop becomes sluggish at full screen in
2249 ultra-high resolution</li>
2250 <li>Cannot disable consensus calculation independently of
2251 quality and conservation</li>
2252 <li>Mouseover highlighting between cDNA and protein can
2253 become sluggish with more than one splitframe shown</li>
2254 </ul> <em>Applet Known Issues</em>
2256 <li>Core PDB parsing code requires Jmol</li>
2257 <li>Sequence canvas panel goes white when alignment
2258 window is being resized</li>
2264 <td><div align="center">
2265 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2267 <td><em>General</em>
2269 <li>Updated Java code signing certificate donated by
2271 <li>Features and annotation preserved when performing
2272 pairwise alignment</li>
2273 <li>RNA pseudoknot annotation can be
2274 imported/exported/displayed</li>
2275 <li>'colour by annotation' can colour by RNA and
2276 protein secondary structure</li>
2277 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2278 post-hoc with 2.9 release</em>)
2281 </ul> <em>Application</em>
2283 <li>Extract and display secondary structure for sequences
2284 with 3D structures</li>
2285 <li>Support for parsing RNAML</li>
2286 <li>Annotations menu for layout
2288 <li>sort sequence annotation rows by alignment</li>
2289 <li>place sequence annotation above/below alignment
2292 <li>Output in Stockholm format</li>
2293 <li>Internationalisation: improved Spanish (es)
2295 <li>Structure viewer preferences tab</li>
2296 <li>Disorder and Secondary Structure annotation tracks
2297 shared between alignments</li>
2298 <li>UCSF Chimera launch and linked highlighting from
2300 <li>Show/hide all sequence associated annotation rows for
2301 all or current selection</li>
2302 <li>disorder and secondary structure predictions
2303 available as dataset annotation</li>
2304 <li>Per-sequence rna helices colouring</li>
2307 <li>Sequence database accessions imported when fetching
2308 alignments from Rfam</li>
2309 <li>update VARNA version to 3.91</li>
2311 <li>New groovy scripts for exporting aligned positions,
2312 conservation values, and calculating sum of pairs scores.</li>
2313 <li>Command line argument to set default JABAWS server</li>
2314 <li>include installation type in build properties and
2315 console log output</li>
2316 <li>Updated Jalview project format to preserve dataset
2320 <!-- issues resolved --> <em>Application</em>
2322 <li>Distinguish alignment and sequence associated RNA
2323 structure in structure->view->VARNA</li>
2324 <li>Raise dialog box if user deletes all sequences in an
2326 <li>Pressing F1 results in documentation opening twice</li>
2327 <li>Sequence feature tooltip is wrapped</li>
2328 <li>Double click on sequence associated annotation
2329 selects only first column</li>
2330 <li>Redundancy removal doesn't result in unlinked
2331 leaves shown in tree</li>
2332 <li>Undos after several redundancy removals don't undo
2334 <li>Hide sequence doesn't hide associated annotation</li>
2335 <li>User defined colours dialog box too big to fit on
2336 screen and buttons not visible</li>
2337 <li>author list isn't updated if already written to
2338 Jalview properties</li>
2339 <li>Popup menu won't open after retrieving sequence
2341 <li>File open window for associate PDB doesn't open</li>
2342 <li>Left-then-right click on a sequence id opens a
2343 browser search window</li>
2344 <li>Cannot open sequence feature shading/sort popup menu
2345 in feature settings dialog</li>
2346 <li>better tooltip placement for some areas of Jalview
2348 <li>Allow addition of JABAWS Server which doesn't
2349 pass validation</li>
2350 <li>Web services parameters dialog box is too large to
2352 <li>Muscle nucleotide alignment preset obscured by
2354 <li>JABAWS preset submenus don't contain newly
2355 defined user preset</li>
2356 <li>MSA web services warns user if they were launched
2357 with invalid input</li>
2358 <li>Jalview cannot contact DAS Registy when running on
2361 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2362 'Superpose with' submenu not shown when new view
2366 </ul> <!-- <em>Applet</em>
2368 </ul> <em>General</em>
2370 </ul>--> <em>Deployment and Documentation</em>
2372 <li>2G and 1G options in launchApp have no effect on
2373 memory allocation</li>
2374 <li>launchApp service doesn't automatically open
2375 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2377 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2378 InstallAnywhere reports cannot find valid JVM when Java
2379 1.7_055 is available
2381 </ul> <em>Application Known issues</em>
2384 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2385 corrupted or unreadable alignment display when scrolling
2389 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2390 retrieval fails but progress bar continues for DAS retrieval
2391 with large number of ID
2394 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2395 flatfile output of visible region has incorrect sequence
2399 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2400 rna structure consensus doesn't update when secondary
2401 structure tracks are rearranged
2404 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2405 invalid rna structure positional highlighting does not
2406 highlight position of invalid base pairs
2409 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2410 out of memory errors are not raised when saving Jalview
2411 project from alignment window file menu
2414 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2415 Switching to RNA Helices colouring doesn't propagate to
2419 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2420 colour by RNA Helices not enabled when user created
2421 annotation added to alignment
2424 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2425 Jalview icon not shown on dock in Mountain Lion/Webstart
2427 </ul> <em>Applet Known Issues</em>
2430 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2431 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2434 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2435 Jalview and Jmol example not compatible with IE9
2438 <li>Sort by annotation score doesn't reverse order
2444 <td><div align="center">
2445 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2448 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2451 <li>Internationalisation of user interface (usually
2452 called i18n support) and translation for Spanish locale</li>
2453 <li>Define/Undefine group on current selection with
2454 Ctrl-G/Shift Ctrl-G</li>
2455 <li>Improved group creation/removal options in
2456 alignment/sequence Popup menu</li>
2457 <li>Sensible precision for symbol distribution
2458 percentages shown in logo tooltip.</li>
2459 <li>Annotation panel height set according to amount of
2460 annotation when alignment first opened</li>
2461 </ul> <em>Application</em>
2463 <li>Interactive consensus RNA secondary structure
2464 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2465 <li>Select columns containing particular features from
2466 Feature Settings dialog</li>
2467 <li>View all 'representative' PDB structures for selected
2469 <li>Update Jalview project format:
2471 <li>New file extension for Jalview projects '.jvp'</li>
2472 <li>Preserve sequence and annotation dataset (to
2473 store secondary structure annotation,etc)</li>
2474 <li>Per group and alignment annotation and RNA helix
2478 <li>New similarity measures for PCA and Tree calculation
2480 <li>Experimental support for retrieval and viewing of
2481 flanking regions for an alignment</li>
2485 <!-- issues resolved --> <em>Application</em>
2487 <li>logo keeps spinning and status remains at queued or
2488 running after job is cancelled</li>
2489 <li>cannot export features from alignments imported from
2490 Jalview/VAMSAS projects</li>
2491 <li>Buggy slider for web service parameters that take
2493 <li>Newly created RNA secondary structure line doesn't
2494 have 'display all symbols' flag set</li>
2495 <li>T-COFFEE alignment score shading scheme and other
2496 annotation shading not saved in Jalview project</li>
2497 <li>Local file cannot be loaded in freshly downloaded
2499 <li>Jalview icon not shown on dock in Mountain
2501 <li>Load file from desktop file browser fails</li>
2502 <li>Occasional NPE thrown when calculating large trees</li>
2503 <li>Cannot reorder or slide sequences after dragging an
2504 alignment onto desktop</li>
2505 <li>Colour by annotation dialog throws NPE after using
2506 'extract scores' function</li>
2507 <li>Loading/cut'n'pasting an empty file leads to a grey
2508 alignment window</li>
2509 <li>Disorder thresholds rendered incorrectly after
2510 performing IUPred disorder prediction</li>
2511 <li>Multiple group annotated consensus rows shown when
2512 changing 'normalise logo' display setting</li>
2513 <li>Find shows blank dialog after 'finished searching' if
2514 nothing matches query</li>
2515 <li>Null Pointer Exceptions raised when sorting by
2516 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2518 <li>Errors in Jmol console when structures in alignment
2519 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2521 <li>Not all working JABAWS services are shown in
2523 <li>JAVAWS version of Jalview fails to launch with
2524 'invalid literal/length code'</li>
2525 <li>Annotation/RNA Helix colourschemes cannot be applied
2526 to alignment with groups (actually fixed in 2.8.0b1)</li>
2527 <li>RNA Helices and T-Coffee Scores available as default
2530 </ul> <em>Applet</em>
2532 <li>Remove group option is shown even when selection is
2534 <li>Apply to all groups ticked but colourscheme changes
2535 don't affect groups</li>
2536 <li>Documented RNA Helices and T-Coffee Scores as valid
2537 colourscheme name</li>
2538 <li>Annotation labels drawn on sequence IDs when
2539 Annotation panel is not displayed</li>
2540 <li>Increased font size for dropdown menus on OSX and
2541 embedded windows</li>
2542 </ul> <em>Other</em>
2544 <li>Consensus sequence for alignments/groups with a
2545 single sequence were not calculated</li>
2546 <li>annotation files that contain only groups imported as
2547 annotation and junk sequences</li>
2548 <li>Fasta files with sequences containing '*' incorrectly
2549 recognised as PFAM or BLC</li>
2550 <li>conservation/PID slider apply all groups option
2551 doesn't affect background (2.8.0b1)
2553 <li>redundancy highlighting is erratic at 0% and 100%</li>
2554 <li>Remove gapped columns fails for sequences with ragged
2556 <li>AMSA annotation row with leading spaces is not
2557 registered correctly on import</li>
2558 <li>Jalview crashes when selecting PCA analysis for
2559 certain alignments</li>
2560 <li>Opening the colour by annotation dialog for an
2561 existing annotation based 'use original colours'
2562 colourscheme loses original colours setting</li>
2567 <td><div align="center">
2568 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2569 <em>30/1/2014</em></strong>
2573 <li>Trusted certificates for JalviewLite applet and
2574 Jalview Desktop application<br />Certificate was donated by
2575 <a href="https://www.certum.eu">Certum</a> to the Jalview
2576 open source project).
2578 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2579 <li>Output in Stockholm format</li>
2580 <li>Allow import of data from gzipped files</li>
2581 <li>Export/import group and sequence associated line
2582 graph thresholds</li>
2583 <li>Nucleotide substitution matrix that supports RNA and
2584 ambiguity codes</li>
2585 <li>Allow disorder predictions to be made on the current
2586 selection (or visible selection) in the same way that JPred
2588 <li>Groovy scripting for headless Jalview operation</li>
2589 </ul> <em>Other improvements</em>
2591 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2592 <li>COMBINE statement uses current SEQUENCE_REF and
2593 GROUP_REF scope to group annotation rows</li>
2594 <li>Support '' style escaping of quotes in Newick
2596 <li>Group options for JABAWS service by command line name</li>
2597 <li>Empty tooltip shown for JABA service options with a
2598 link but no description</li>
2599 <li>Select primary source when selecting authority in
2600 database fetcher GUI</li>
2601 <li>Add .mfa to FASTA file extensions recognised by
2603 <li>Annotation label tooltip text wrap</li>
2608 <li>Slow scrolling when lots of annotation rows are
2610 <li>Lots of NPE (and slowness) after creating RNA
2611 secondary structure annotation line</li>
2612 <li>Sequence database accessions not imported when
2613 fetching alignments from Rfam</li>
2614 <li>Incorrect SHMR submission for sequences with
2616 <li>View all structures does not always superpose
2618 <li>Option widgets in service parameters not updated to
2619 reflect user or preset settings</li>
2620 <li>Null pointer exceptions for some services without
2621 presets or adjustable parameters</li>
2622 <li>Discover PDB IDs entry in structure menu doesn't
2623 discover PDB xRefs</li>
2624 <li>Exception encountered while trying to retrieve
2625 features with DAS</li>
2626 <li>Lowest value in annotation row isn't coloured
2627 when colour by annotation (per sequence) is coloured</li>
2628 <li>Keyboard mode P jumps to start of gapped region when
2629 residue follows a gap</li>
2630 <li>Jalview appears to hang importing an alignment with
2631 Wrap as default or after enabling Wrap</li>
2632 <li>'Right click to add annotations' message
2633 shown in wrap mode when no annotations present</li>
2634 <li>Disorder predictions fail with NPE if no automatic
2635 annotation already exists on alignment</li>
2636 <li>oninit javascript function should be called after
2637 initialisation completes</li>
2638 <li>Remove redundancy after disorder prediction corrupts
2639 alignment window display</li>
2640 <li>Example annotation file in documentation is invalid</li>
2641 <li>Grouped line graph annotation rows are not exported
2642 to annotation file</li>
2643 <li>Multi-harmony analysis cannot be run when only two
2645 <li>Cannot create multiple groups of line graphs with
2646 several 'combine' statements in annotation file</li>
2647 <li>Pressing return several times causes Number Format
2648 exceptions in keyboard mode</li>
2649 <li>Multi-harmony (SHMMR) method doesn't submit
2650 correct partitions for input data</li>
2651 <li>Translation from DNA to Amino Acids fails</li>
2652 <li>Jalview fail to load newick tree with quoted label</li>
2653 <li>--headless flag isn't understood</li>
2654 <li>ClassCastException when generating EPS in headless
2656 <li>Adjusting sequence-associated shading threshold only
2657 changes one row's threshold</li>
2658 <li>Preferences and Feature settings panel panel
2659 doesn't open</li>
2660 <li>hide consensus histogram also hides conservation and
2661 quality histograms</li>
2666 <td><div align="center">
2667 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2669 <td><em>Application</em>
2671 <li>Support for JABAWS 2.0 Services (AACon alignment
2672 conservation, protein disorder and Clustal Omega)</li>
2673 <li>JABAWS server status indicator in Web Services
2675 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2676 in Jalview alignment window</li>
2677 <li>Updated Jalview build and deploy framework for OSX
2678 mountain lion, windows 7, and 8</li>
2679 <li>Nucleotide substitution matrix for PCA that supports
2680 RNA and ambiguity codes</li>
2682 <li>Improved sequence database retrieval GUI</li>
2683 <li>Support fetching and database reference look up
2684 against multiple DAS sources (Fetch all from in 'fetch db
2686 <li>Jalview project improvements
2688 <li>Store and retrieve the 'belowAlignment'
2689 flag for annotation</li>
2690 <li>calcId attribute to group annotation rows on the
2692 <li>Store AACon calculation settings for a view in
2693 Jalview project</li>
2697 <li>horizontal scrolling gesture support</li>
2698 <li>Visual progress indicator when PCA calculation is
2700 <li>Simpler JABA web services menus</li>
2701 <li>visual indication that web service results are still
2702 being retrieved from server</li>
2703 <li>Serialise the dialogs that are shown when Jalview
2704 starts up for first time</li>
2705 <li>Jalview user agent string for interacting with HTTP
2707 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2709 <li>Examples directory and Groovy library included in
2710 InstallAnywhere distribution</li>
2711 </ul> <em>Applet</em>
2713 <li>RNA alignment and secondary structure annotation
2714 visualization applet example</li>
2715 </ul> <em>General</em>
2717 <li>Normalise option for consensus sequence logo</li>
2718 <li>Reset button in PCA window to return dimensions to
2720 <li>Allow seqspace or Jalview variant of alignment PCA
2722 <li>PCA with either nucleic acid and protein substitution
2724 <li>Allow windows containing HTML reports to be exported
2726 <li>Interactive display and editing of RNA secondary
2727 structure contacts</li>
2728 <li>RNA Helix Alignment Colouring</li>
2729 <li>RNA base pair logo consensus</li>
2730 <li>Parse sequence associated secondary structure
2731 information in Stockholm files</li>
2732 <li>HTML Export database accessions and annotation
2733 information presented in tooltip for sequences</li>
2734 <li>Import secondary structure from LOCARNA clustalw
2735 style RNA alignment files</li>
2736 <li>import and visualise T-COFFEE quality scores for an
2738 <li>'colour by annotation' per sequence option to
2739 shade each sequence according to its associated alignment
2741 <li>New Jalview Logo</li>
2742 </ul> <em>Documentation and Development</em>
2744 <li>documentation for score matrices used in Jalview</li>
2745 <li>New Website!</li>
2747 <td><em>Application</em>
2749 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2750 wsdbfetch REST service</li>
2751 <li>Stop windows being moved outside desktop on OSX</li>
2752 <li>Filetype associations not installed for webstart
2754 <li>Jalview does not always retrieve progress of a JABAWS
2755 job execution in full once it is complete</li>
2756 <li>revise SHMR RSBS definition to ensure alignment is
2757 uploaded via ali_file parameter</li>
2758 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2759 <li>View all structures superposed fails with exception</li>
2760 <li>Jnet job queues forever if a very short sequence is
2761 submitted for prediction</li>
2762 <li>Cut and paste menu not opened when mouse clicked on
2764 <li>Putting fractional value into integer text box in
2765 alignment parameter dialog causes Jalview to hang</li>
2766 <li>Structure view highlighting doesn't work on
2768 <li>View all structures fails with exception shown in
2770 <li>Characters in filename associated with PDBEntry not
2771 escaped in a platform independent way</li>
2772 <li>Jalview desktop fails to launch with exception when
2774 <li>Tree calculation reports 'you must have 2 or more
2775 sequences selected' when selection is empty</li>
2776 <li>Jalview desktop fails to launch with jar signature
2777 failure when java web start temporary file caching is
2779 <li>DAS Sequence retrieval with range qualification
2780 results in sequence xref which includes range qualification</li>
2781 <li>Errors during processing of command line arguments
2782 cause progress bar (JAL-898) to be removed</li>
2783 <li>Replace comma for semi-colon option not disabled for
2784 DAS sources in sequence fetcher</li>
2785 <li>Cannot close news reader when JABAWS server warning
2786 dialog is shown</li>
2787 <li>Option widgets not updated to reflect user settings</li>
2788 <li>Edited sequence not submitted to web service</li>
2789 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2790 <li>InstallAnywhere installer doesn't unpack and run
2791 on OSX Mountain Lion</li>
2792 <li>Annotation panel not given a scroll bar when
2793 sequences with alignment annotation are pasted into the
2795 <li>Sequence associated annotation rows not associated
2796 when loaded from Jalview project</li>
2797 <li>Browser launch fails with NPE on java 1.7</li>
2798 <li>JABAWS alignment marked as finished when job was
2799 cancelled or job failed due to invalid input</li>
2800 <li>NPE with v2.7 example when clicking on Tree
2801 associated with all views</li>
2802 <li>Exceptions when copy/paste sequences with grouped
2803 annotation rows to new window</li>
2804 </ul> <em>Applet</em>
2806 <li>Sequence features are momentarily displayed before
2807 they are hidden using hidefeaturegroups applet parameter</li>
2808 <li>loading features via javascript API automatically
2809 enables feature display</li>
2810 <li>scrollToColumnIn javascript API method doesn't
2812 </ul> <em>General</em>
2814 <li>Redundancy removal fails for rna alignment</li>
2815 <li>PCA calculation fails when sequence has been selected
2816 and then deselected</li>
2817 <li>PCA window shows grey box when first opened on OSX</li>
2818 <li>Letters coloured pink in sequence logo when alignment
2819 coloured with clustalx</li>
2820 <li>Choosing fonts without letter symbols defined causes
2821 exceptions and redraw errors</li>
2822 <li>Initial PCA plot view is not same as manually
2823 reconfigured view</li>
2824 <li>Grouped annotation graph label has incorrect line
2826 <li>Grouped annotation graph label display is corrupted
2827 for lots of labels</li>
2832 <div align="center">
2833 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2836 <td><em>Application</em>
2838 <li>Jalview Desktop News Reader</li>
2839 <li>Tweaked default layout of web services menu</li>
2840 <li>View/alignment association menu to enable user to
2841 easily specify which alignment a multi-structure view takes
2842 its colours/correspondences from</li>
2843 <li>Allow properties file location to be specified as URL</li>
2844 <li>Extend Jalview project to preserve associations
2845 between many alignment views and a single Jmol display</li>
2846 <li>Store annotation row height in Jalview project file</li>
2847 <li>Annotation row column label formatting attributes
2848 stored in project file</li>
2849 <li>Annotation row order for auto-calculated annotation
2850 rows preserved in Jalview project file</li>
2851 <li>Visual progress indication when Jalview state is
2852 saved using Desktop window menu</li>
2853 <li>Visual indication that command line arguments are
2854 still being processed</li>
2855 <li>Groovy script execution from URL</li>
2856 <li>Colour by annotation default min and max colours in
2858 <li>Automatically associate PDB files dragged onto an
2859 alignment with sequences that have high similarity and
2861 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2862 <li>'view structures' option to open many
2863 structures in same window</li>
2864 <li>Sort associated views menu option for tree panel</li>
2865 <li>Group all JABA and non-JABA services for a particular
2866 analysis function in its own submenu</li>
2867 </ul> <em>Applet</em>
2869 <li>Userdefined and autogenerated annotation rows for
2871 <li>Adjustment of alignment annotation pane height</li>
2872 <li>Annotation scrollbar for annotation panel</li>
2873 <li>Drag to reorder annotation rows in annotation panel</li>
2874 <li>'automaticScrolling' parameter</li>
2875 <li>Allow sequences with partial ID string matches to be
2876 annotated from GFF/Jalview features files</li>
2877 <li>Sequence logo annotation row in applet</li>
2878 <li>Absolute paths relative to host server in applet
2879 parameters are treated as such</li>
2880 <li>New in the JalviewLite javascript API:
2882 <li>JalviewLite.js javascript library</li>
2883 <li>Javascript callbacks for
2885 <li>Applet initialisation</li>
2886 <li>Sequence/alignment mouse-overs and selections</li>
2889 <li>scrollTo row and column alignment scrolling
2891 <li>Select sequence/alignment regions from javascript</li>
2892 <li>javascript structure viewer harness to pass
2893 messages between Jmol and Jalview when running as
2894 distinct applets</li>
2895 <li>sortBy method</li>
2896 <li>Set of applet and application examples shipped
2897 with documentation</li>
2898 <li>New example to demonstrate JalviewLite and Jmol
2899 javascript message exchange</li>
2901 </ul> <em>General</em>
2903 <li>Enable Jmol displays to be associated with multiple
2904 multiple alignments</li>
2905 <li>Option to automatically sort alignment with new tree</li>
2906 <li>User configurable link to enable redirects to a
2907 www.Jalview.org mirror</li>
2908 <li>Jmol colours option for Jmol displays</li>
2909 <li>Configurable newline string when writing alignment
2910 and other flat files</li>
2911 <li>Allow alignment annotation description lines to
2912 contain html tags</li>
2913 </ul> <em>Documentation and Development</em>
2915 <li>Add groovy test harness for bulk load testing to
2917 <li>Groovy script to load and align a set of sequences
2918 using a web service before displaying the result in the
2919 Jalview desktop</li>
2920 <li>Restructured javascript and applet api documentation</li>
2921 <li>Ant target to publish example html files with applet
2923 <li>Netbeans project for building Jalview from source</li>
2924 <li>ant task to create online javadoc for Jalview source</li>
2926 <td><em>Application</em>
2928 <li>User defined colourscheme throws exception when
2929 current built in colourscheme is saved as new scheme</li>
2930 <li>AlignFrame->Save in application pops up save
2931 dialog for valid filename/format</li>
2932 <li>Cannot view associated structure for UniProt sequence</li>
2933 <li>PDB file association breaks for UniProt sequence
2935 <li>Associate PDB from file dialog does not tell you
2936 which sequence is to be associated with the file</li>
2937 <li>Find All raises null pointer exception when query
2938 only matches sequence IDs</li>
2939 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2940 <li>Jalview project with Jmol views created with Jalview
2941 2.4 cannot be loaded</li>
2942 <li>Filetype associations not installed for webstart
2944 <li>Two or more chains in a single PDB file associated
2945 with sequences in different alignments do not get coloured
2946 by their associated sequence</li>
2947 <li>Visibility status of autocalculated annotation row
2948 not preserved when project is loaded</li>
2949 <li>Annotation row height and visibility attributes not
2950 stored in Jalview project</li>
2951 <li>Tree bootstraps are not preserved when saved as a
2952 Jalview project</li>
2953 <li>Envision2 workflow tooltips are corrupted</li>
2954 <li>Enabling show group conservation also enables colour
2955 by conservation</li>
2956 <li>Duplicate group associated conservation or consensus
2957 created on new view</li>
2958 <li>Annotation scrollbar not displayed after 'show
2959 all hidden annotation rows' option selected</li>
2960 <li>Alignment quality not updated after alignment
2961 annotation row is hidden then shown</li>
2962 <li>Preserve colouring of structures coloured by
2963 sequences in pre Jalview 2.7 projects</li>
2964 <li>Web service job parameter dialog is not laid out
2966 <li>Web services menu not refreshed after 'reset
2967 services' button is pressed in preferences</li>
2968 <li>Annotation off by one in Jalview v2_3 example project</li>
2969 <li>Structures imported from file and saved in project
2970 get name like jalview_pdb1234.txt when reloaded</li>
2971 <li>Jalview does not always retrieve progress of a JABAWS
2972 job execution in full once it is complete</li>
2973 </ul> <em>Applet</em>
2975 <li>Alignment height set incorrectly when lots of
2976 annotation rows are displayed</li>
2977 <li>Relative URLs in feature HTML text not resolved to
2979 <li>View follows highlighting does not work for positions
2981 <li><= shown as = in tooltip</li>
2982 <li>Export features raises exception when no features
2984 <li>Separator string used for serialising lists of IDs
2985 for javascript api is modified when separator string
2986 provided as parameter</li>
2987 <li>Null pointer exception when selecting tree leaves for
2988 alignment with no existing selection</li>
2989 <li>Relative URLs for datasources assumed to be relative
2990 to applet's codebase</li>
2991 <li>Status bar not updated after finished searching and
2992 search wraps around to first result</li>
2993 <li>StructureSelectionManager instance shared between
2994 several Jalview applets causes race conditions and memory
2996 <li>Hover tooltip and mouseover of position on structure
2997 not sent from Jmol in applet</li>
2998 <li>Certain sequences of javascript method calls to
2999 applet API fatally hang browser</li>
3000 </ul> <em>General</em>
3002 <li>View follows structure mouseover scrolls beyond
3003 position with wrapped view and hidden regions</li>
3004 <li>Find sequence position moves to wrong residue
3005 with/without hidden columns</li>
3006 <li>Sequence length given in alignment properties window
3008 <li>InvalidNumberFormat exceptions thrown when trying to
3009 import PDB like structure files</li>
3010 <li>Positional search results are only highlighted
3011 between user-supplied sequence start/end bounds</li>
3012 <li>End attribute of sequence is not validated</li>
3013 <li>Find dialog only finds first sequence containing a
3014 given sequence position</li>
3015 <li>Sequence numbering not preserved in MSF alignment
3017 <li>Jalview PDB file reader does not extract sequence
3018 from nucleotide chains correctly</li>
3019 <li>Structure colours not updated when tree partition
3020 changed in alignment</li>
3021 <li>Sequence associated secondary structure not correctly
3022 parsed in interleaved stockholm</li>
3023 <li>Colour by annotation dialog does not restore current
3025 <li>Hiding (nearly) all sequences doesn't work
3027 <li>Sequences containing lowercase letters are not
3028 properly associated with their pdb files</li>
3029 </ul> <em>Documentation and Development</em>
3031 <li>schemas/JalviewWsParamSet.xsd corrupted by
3032 ApplyCopyright tool</li>
3037 <div align="center">
3038 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3041 <td><em>Application</em>
3043 <li>New warning dialog when the Jalview Desktop cannot
3044 contact web services</li>
3045 <li>JABA service parameters for a preset are shown in
3046 service job window</li>
3047 <li>JABA Service menu entries reworded</li>
3051 <li>Modeller PIR IO broken - cannot correctly import a
3052 pir file emitted by Jalview</li>
3053 <li>Existing feature settings transferred to new
3054 alignment view created from cut'n'paste</li>
3055 <li>Improved test for mixed amino/nucleotide chains when
3056 parsing PDB files</li>
3057 <li>Consensus and conservation annotation rows
3058 occasionally become blank for all new windows</li>
3059 <li>Exception raised when right clicking above sequences
3060 in wrapped view mode</li>
3061 </ul> <em>Application</em>
3063 <li>multiple multiply aligned structure views cause cpu
3064 usage to hit 100% and computer to hang</li>
3065 <li>Web Service parameter layout breaks for long user
3066 parameter names</li>
3067 <li>Jaba service discovery hangs desktop if Jaba server
3074 <div align="center">
3075 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3078 <td><em>Application</em>
3080 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3081 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3084 <li>Web Services preference tab</li>
3085 <li>Analysis parameters dialog box and user defined
3087 <li>Improved speed and layout of Envision2 service menu</li>
3088 <li>Superpose structures using associated sequence
3090 <li>Export coordinates and projection as CSV from PCA
3092 </ul> <em>Applet</em>
3094 <li>enable javascript: execution by the applet via the
3095 link out mechanism</li>
3096 </ul> <em>Other</em>
3098 <li>Updated the Jmol Jalview interface to work with Jmol
3100 <li>The Jalview Desktop and JalviewLite applet now
3101 require Java 1.5</li>
3102 <li>Allow Jalview feature colour specification for GFF
3103 sequence annotation files</li>
3104 <li>New 'colour by label' keword in Jalview feature file
3105 type colour specification</li>
3106 <li>New Jalview Desktop Groovy API method that allows a
3107 script to check if it being run in an interactive session or
3108 in a batch operation from the Jalview command line</li>
3112 <li>clustalx colourscheme colours Ds preferentially when
3113 both D+E are present in over 50% of the column</li>
3114 </ul> <em>Application</em>
3116 <li>typo in AlignmentFrame->View->Hide->all but
3117 selected Regions menu item</li>
3118 <li>sequence fetcher replaces ',' for ';' when the ',' is
3119 part of a valid accession ID</li>
3120 <li>fatal OOM if object retrieved by sequence fetcher
3121 runs out of memory</li>
3122 <li>unhandled Out of Memory Error when viewing pca
3123 analysis results</li>
3124 <li>InstallAnywhere builds fail to launch on OS X java
3125 10.5 update 4 (due to apple Java 1.6 update)</li>
3126 <li>Installanywhere Jalview silently fails to launch</li>
3127 </ul> <em>Applet</em>
3129 <li>Jalview.getFeatureGroups() raises an
3130 ArrayIndexOutOfBoundsException if no feature groups are
3137 <div align="center">
3138 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3144 <li>Alignment prettyprinter doesn't cope with long
3146 <li>clustalx colourscheme colours Ds preferentially when
3147 both D+E are present in over 50% of the column</li>
3148 <li>nucleic acid structures retrieved from PDB do not
3149 import correctly</li>
3150 <li>More columns get selected than were clicked on when a
3151 number of columns are hidden</li>
3152 <li>annotation label popup menu not providing correct
3153 add/hide/show options when rows are hidden or none are
3155 <li>Stockholm format shown in list of readable formats,
3156 and parser copes better with alignments from RFAM.</li>
3157 <li>CSV output of consensus only includes the percentage
3158 of all symbols if sequence logo display is enabled</li>
3160 </ul> <em>Applet</em>
3162 <li>annotation panel disappears when annotation is
3164 </ul> <em>Application</em>
3166 <li>Alignment view not redrawn properly when new
3167 alignment opened where annotation panel is visible but no
3168 annotations are present on alignment</li>
3169 <li>pasted region containing hidden columns is
3170 incorrectly displayed in new alignment window</li>
3171 <li>Jalview slow to complete operations when stdout is
3172 flooded (fix is to close the Jalview console)</li>
3173 <li>typo in AlignmentFrame->View->Hide->all but
3174 selected Rregions menu item.</li>
3175 <li>inconsistent group submenu and Format submenu entry
3176 'Un' or 'Non'conserved</li>
3177 <li>Sequence feature settings are being shared by
3178 multiple distinct alignments</li>
3179 <li>group annotation not recreated when tree partition is
3181 <li>double click on group annotation to select sequences
3182 does not propagate to associated trees</li>
3183 <li>Mac OSX specific issues:
3185 <li>exception raised when mouse clicked on desktop
3186 window background</li>
3187 <li>Desktop menu placed on menu bar and application
3188 name set correctly</li>
3189 <li>sequence feature settings not wide enough for the
3190 save feature colourscheme button</li>
3199 <div align="center">
3200 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3203 <td><em>New Capabilities</em>
3205 <li>URL links generated from description line for
3206 regular-expression based URL links (applet and application)
3208 <li>Non-positional feature URL links are shown in link
3210 <li>Linked viewing of nucleic acid sequences and
3212 <li>Automatic Scrolling option in View menu to display
3213 the currently highlighted region of an alignment.</li>
3214 <li>Order an alignment by sequence length, or using the
3215 average score or total feature count for each sequence.</li>
3216 <li>Shading features by score or associated description</li>
3217 <li>Subdivide alignment and groups based on identity of
3218 selected subsequence (Make Groups from Selection).</li>
3219 <li>New hide/show options including Shift+Control+H to
3220 hide everything but the currently selected region.</li>
3221 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3222 </ul> <em>Application</em>
3224 <li>Fetch DB References capabilities and UI expanded to
3225 support retrieval from DAS sequence sources</li>
3226 <li>Local DAS Sequence sources can be added via the
3227 command line or via the Add local source dialog box.</li>
3228 <li>DAS Dbref and DbxRef feature types are parsed as
3229 database references and protein_name is parsed as
3230 description line (BioSapiens terms).</li>
3231 <li>Enable or disable non-positional feature and database
3232 references in sequence ID tooltip from View menu in
3234 <!-- <li>New hidden columns and rows and representatives capabilities
3235 in annotations file (in progress - not yet fully implemented)</li> -->
3236 <li>Group-associated consensus, sequence logos and
3237 conservation plots</li>
3238 <li>Symbol distributions for each column can be exported
3239 and visualized as sequence logos</li>
3240 <li>Optionally scale multi-character column labels to fit
3241 within each column of annotation row<!-- todo for applet -->
3243 <li>Optional automatic sort of associated alignment view
3244 when a new tree is opened.</li>
3245 <li>Jalview Java Console</li>
3246 <li>Better placement of desktop window when moving
3247 between different screens.</li>
3248 <li>New preference items for sequence ID tooltip and
3249 consensus annotation</li>
3250 <li>Client to submit sequences and IDs to Envision2
3252 <li><em>Vamsas Capabilities</em>
3254 <li>Improved VAMSAS synchronization (Jalview archive
3255 used to preserve views, structures, and tree display
3257 <li>Import of vamsas documents from disk or URL via
3259 <li>Sharing of selected regions between views and
3260 with other VAMSAS applications (Experimental feature!)</li>
3261 <li>Updated API to VAMSAS version 0.2</li>
3263 </ul> <em>Applet</em>
3265 <li>Middle button resizes annotation row height</li>
3268 <li>sortByTree (true/false) - automatically sort the
3269 associated alignment view by the tree when a new tree is
3271 <li>showTreeBootstraps (true/false) - show or hide
3272 branch bootstraps (default is to show them if available)</li>
3273 <li>showTreeDistances (true/false) - show or hide
3274 branch lengths (default is to show them if available)</li>
3275 <li>showUnlinkedTreeNodes (true/false) - indicate if
3276 unassociated nodes should be highlighted in the tree
3278 <li>heightScale and widthScale (1.0 or more) -
3279 increase the height or width of a cell in the alignment
3280 grid relative to the current font size.</li>
3283 <li>Non-positional features displayed in sequence ID
3285 </ul> <em>Other</em>
3287 <li>Features format: graduated colour definitions and
3288 specification of feature scores</li>
3289 <li>Alignment Annotations format: new keywords for group
3290 associated annotation (GROUP_REF) and annotation row display
3291 properties (ROW_PROPERTIES)</li>
3292 <li>XML formats extended to support graduated feature
3293 colourschemes, group associated annotation, and profile
3294 visualization settings.</li></td>
3297 <li>Source field in GFF files parsed as feature source
3298 rather than description</li>
3299 <li>Non-positional features are now included in sequence
3300 feature and gff files (controlled via non-positional feature
3301 visibility in tooltip).</li>
3302 <li>URL links generated for all feature links (bugfix)</li>
3303 <li>Added URL embedding instructions to features file
3305 <li>Codons containing ambiguous nucleotides translated as
3306 'X' in peptide product</li>
3307 <li>Match case switch in find dialog box works for both
3308 sequence ID and sequence string and query strings do not
3309 have to be in upper case to match case-insensitively.</li>
3310 <li>AMSA files only contain first column of
3311 multi-character column annotation labels</li>
3312 <li>Jalview Annotation File generation/parsing consistent
3313 with documentation (e.g. Stockholm annotation can be
3314 exported and re-imported)</li>
3315 <li>PDB files without embedded PDB IDs given a friendly
3317 <li>Find incrementally searches ID string matches as well
3318 as subsequence matches, and correctly reports total number
3322 <li>Better handling of exceptions during sequence
3324 <li>Dasobert generated non-positional feature URL
3325 link text excludes the start_end suffix</li>
3326 <li>DAS feature and source retrieval buttons disabled
3327 when fetch or registry operations in progress.</li>
3328 <li>PDB files retrieved from URLs are cached properly</li>
3329 <li>Sequence description lines properly shared via
3331 <li>Sequence fetcher fetches multiple records for all
3333 <li>Ensured that command line das feature retrieval
3334 completes before alignment figures are generated.</li>
3335 <li>Reduced time taken when opening file browser for
3337 <li>isAligned check prior to calculating tree, PCA or
3338 submitting an MSA to JNet now excludes hidden sequences.</li>
3339 <li>User defined group colours properly recovered
3340 from Jalview projects.</li>
3349 <div align="center">
3350 <strong>2.4.0.b2</strong><br> 28/10/2009
3355 <li>Experimental support for google analytics usage
3357 <li>Jalview privacy settings (user preferences and docs).</li>
3362 <li>Race condition in applet preventing startup in
3364 <li>Exception when feature created from selection beyond
3365 length of sequence.</li>
3366 <li>Allow synthetic PDB files to be imported gracefully</li>
3367 <li>Sequence associated annotation rows associate with
3368 all sequences with a given id</li>
3369 <li>Find function matches case-insensitively for sequence
3370 ID string searches</li>
3371 <li>Non-standard characters do not cause pairwise
3372 alignment to fail with exception</li>
3373 </ul> <em>Application Issues</em>
3375 <li>Sequences are now validated against EMBL database</li>
3376 <li>Sequence fetcher fetches multiple records for all
3378 </ul> <em>InstallAnywhere Issues</em>
3380 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3381 issue with installAnywhere mechanism)</li>
3382 <li>Command line launching of JARs from InstallAnywhere
3383 version (java class versioning error fixed)</li>
3390 <div align="center">
3391 <strong>2.4</strong><br> 27/8/2008
3394 <td><em>User Interface</em>
3396 <li>Linked highlighting of codon and amino acid from
3397 translation and protein products</li>
3398 <li>Linked highlighting of structure associated with
3399 residue mapping to codon position</li>
3400 <li>Sequence Fetcher provides example accession numbers
3401 and 'clear' button</li>
3402 <li>MemoryMonitor added as an option under Desktop's
3404 <li>Extract score function to parse whitespace separated
3405 numeric data in description line</li>
3406 <li>Column labels in alignment annotation can be centred.</li>
3407 <li>Tooltip for sequence associated annotation give name
3409 </ul> <em>Web Services and URL fetching</em>
3411 <li>JPred3 web service</li>
3412 <li>Prototype sequence search client (no public services
3414 <li>Fetch either seed alignment or full alignment from
3416 <li>URL Links created for matching database cross
3417 references as well as sequence ID</li>
3418 <li>URL Links can be created using regular-expressions</li>
3419 </ul> <em>Sequence Database Connectivity</em>
3421 <li>Retrieval of cross-referenced sequences from other
3423 <li>Generalised database reference retrieval and
3424 validation to all fetchable databases</li>
3425 <li>Fetch sequences from DAS sources supporting the
3426 sequence command</li>
3427 </ul> <em>Import and Export</em>
3428 <li>export annotation rows as CSV for spreadsheet import</li>
3429 <li>Jalview projects record alignment dataset associations,
3430 EMBL products, and cDNA sequence mappings</li>
3431 <li>Sequence Group colour can be specified in Annotation
3433 <li>Ad-hoc colouring of group in Annotation File using RGB
3434 triplet as name of colourscheme</li>
3435 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3437 <li>treenode binding for VAMSAS tree exchange</li>
3438 <li>local editing and update of sequences in VAMSAS
3439 alignments (experimental)</li>
3440 <li>Create new or select existing session to join</li>
3441 <li>load and save of vamsas documents</li>
3442 </ul> <em>Application command line</em>
3444 <li>-tree parameter to open trees (introduced for passing
3446 <li>-fetchfrom command line argument to specify nicknames
3447 of DAS servers to query for alignment features</li>
3448 <li>-dasserver command line argument to add new servers
3449 that are also automatically queried for features</li>
3450 <li>-groovy command line argument executes a given groovy
3451 script after all input data has been loaded and parsed</li>
3452 </ul> <em>Applet-Application data exchange</em>
3454 <li>Trees passed as applet parameters can be passed to
3455 application (when using "View in full
3456 application")</li>
3457 </ul> <em>Applet Parameters</em>
3459 <li>feature group display control parameter</li>
3460 <li>debug parameter</li>
3461 <li>showbutton parameter</li>
3462 </ul> <em>Applet API methods</em>
3464 <li>newView public method</li>
3465 <li>Window (current view) specific get/set public methods</li>
3466 <li>Feature display control methods</li>
3467 <li>get list of currently selected sequences</li>
3468 </ul> <em>New Jalview distribution features</em>
3470 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3471 <li>RELEASE file gives build properties for the latest
3472 Jalview release.</li>
3473 <li>Java 1.1 Applet build made easier and donotobfuscate
3474 property controls execution of obfuscator</li>
3475 <li>Build target for generating source distribution</li>
3476 <li>Debug flag for javacc</li>
3477 <li>.jalview_properties file is documented (slightly) in
3478 jalview.bin.Cache</li>
3479 <li>Continuous Build Integration for stable and
3480 development version of Application, Applet and source
3485 <li>selected region output includes visible annotations
3486 (for certain formats)</li>
3487 <li>edit label/displaychar contains existing label/char
3489 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3490 <li>shorter peptide product names from EMBL records</li>
3491 <li>Newick string generator makes compact representations</li>
3492 <li>bootstrap values parsed correctly for tree files with
3494 <li>pathological filechooser bug avoided by not allowing
3495 filenames containing a ':'</li>
3496 <li>Fixed exception when parsing GFF files containing
3497 global sequence features</li>
3498 <li>Alignment datasets are finalized only when number of
3499 references from alignment sequences goes to zero</li>
3500 <li>Close of tree branch colour box without colour
3501 selection causes cascading exceptions</li>
3502 <li>occasional negative imgwidth exceptions</li>
3503 <li>better reporting of non-fatal warnings to user when
3504 file parsing fails.</li>
3505 <li>Save works when Jalview project is default format</li>
3506 <li>Save as dialog opened if current alignment format is
3507 not a valid output format</li>
3508 <li>UniProt canonical names introduced for both das and
3510 <li>Histidine should be midblue (not pink!) in Zappo</li>
3511 <li>error messages passed up and output when data read
3513 <li>edit undo recovers previous dataset sequence when
3514 sequence is edited</li>
3515 <li>allow PDB files without pdb ID HEADER lines (like
3516 those generated by MODELLER) to be read in properly</li>
3517 <li>allow reading of JPred concise files as a normal
3519 <li>Stockholm annotation parsing and alignment properties
3520 import fixed for PFAM records</li>
3521 <li>Structure view windows have correct name in Desktop
3523 <li>annotation consisting of sequence associated scores
3524 can be read and written correctly to annotation file</li>
3525 <li>Aligned cDNA translation to aligned peptide works
3527 <li>Fixed display of hidden sequence markers and
3528 non-italic font for representatives in Applet</li>
3529 <li>Applet Menus are always embedded in applet window on
3531 <li>Newly shown features appear at top of stack (in
3533 <li>Annotations added via parameter not drawn properly
3534 due to null pointer exceptions</li>
3535 <li>Secondary structure lines are drawn starting from
3536 first column of alignment</li>
3537 <li>UniProt XML import updated for new schema release in
3539 <li>Sequence feature to sequence ID match for Features
3540 file is case-insensitive</li>
3541 <li>Sequence features read from Features file appended to
3542 all sequences with matching IDs</li>
3543 <li>PDB structure coloured correctly for associated views
3544 containing a sub-sequence</li>
3545 <li>PDB files can be retrieved by applet from Jar files</li>
3546 <li>feature and annotation file applet parameters
3547 referring to different directories are retrieved correctly</li>
3548 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3549 <li>Fixed application hang whilst waiting for
3550 splash-screen version check to complete</li>
3551 <li>Applet properly URLencodes input parameter values
3552 when passing them to the launchApp service</li>
3553 <li>display name and local features preserved in results
3554 retrieved from web service</li>
3555 <li>Visual delay indication for sequence retrieval and
3556 sequence fetcher initialisation</li>
3557 <li>updated Application to use DAS 1.53e version of
3558 dasobert DAS client</li>
3559 <li>Re-instated Full AMSA support and .amsa file
3561 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3569 <div align="center">
3570 <strong>2.3</strong><br> 9/5/07
3575 <li>Jmol 11.0.2 integration</li>
3576 <li>PDB views stored in Jalview XML files</li>
3577 <li>Slide sequences</li>
3578 <li>Edit sequence in place</li>
3579 <li>EMBL CDS features</li>
3580 <li>DAS Feature mapping</li>
3581 <li>Feature ordering</li>
3582 <li>Alignment Properties</li>
3583 <li>Annotation Scores</li>
3584 <li>Sort by scores</li>
3585 <li>Feature/annotation editing in applet</li>
3590 <li>Headless state operation in 2.2.1</li>
3591 <li>Incorrect and unstable DNA pairwise alignment</li>
3592 <li>Cut and paste of sequences with annotation</li>
3593 <li>Feature group display state in XML</li>
3594 <li>Feature ordering in XML</li>
3595 <li>blc file iteration selection using filename # suffix</li>
3596 <li>Stockholm alignment properties</li>
3597 <li>Stockhom alignment secondary structure annotation</li>
3598 <li>2.2.1 applet had no feature transparency</li>
3599 <li>Number pad keys can be used in cursor mode</li>
3600 <li>Structure Viewer mirror image resolved</li>
3607 <div align="center">
3608 <strong>2.2.1</strong><br> 12/2/07
3613 <li>Non standard characters can be read and displayed
3614 <li>Annotations/Features can be imported/exported to the
3616 <li>Applet allows editing of sequence/annotation/group
3617 name & description
3618 <li>Preference setting to display sequence name in
3620 <li>Annotation file format extended to allow
3621 Sequence_groups to be defined
3622 <li>Default opening of alignment overview panel can be
3623 specified in preferences
3624 <li>PDB residue numbering annotation added to associated
3630 <li>Applet crash under certain Linux OS with Java 1.6
3632 <li>Annotation file export / import bugs fixed
3633 <li>PNG / EPS image output bugs fixed
3639 <div align="center">
3640 <strong>2.2</strong><br> 27/11/06
3645 <li>Multiple views on alignment
3646 <li>Sequence feature editing
3647 <li>"Reload" alignment
3648 <li>"Save" to current filename
3649 <li>Background dependent text colour
3650 <li>Right align sequence ids
3651 <li>User-defined lower case residue colours
3654 <li>Menu item accelerator keys
3655 <li>Control-V pastes to current alignment
3656 <li>Cancel button for DAS Feature Fetching
3657 <li>PCA and PDB Viewers zoom via mouse roller
3658 <li>User-defined sub-tree colours and sub-tree selection
3660 <li>'New Window' button on the 'Output to Text box'
3665 <li>New memory efficient Undo/Redo System
3666 <li>Optimised symbol lookups and conservation/consensus
3668 <li>Region Conservation/Consensus recalculated after
3670 <li>Fixed Remove Empty Columns Bug (empty columns at end
3672 <li>Slowed DAS Feature Fetching for increased robustness.
3674 <li>Made angle brackets in ASCII feature descriptions
3676 <li>Re-instated Zoom function for PCA
3677 <li>Sequence descriptions conserved in web service
3679 <li>UniProt ID discoverer uses any word separated by
3681 <li>WsDbFetch query/result association resolved
3682 <li>Tree leaf to sequence mapping improved
3683 <li>Smooth fonts switch moved to FontChooser dialog box.
3690 <div align="center">
3691 <strong>2.1.1</strong><br> 12/9/06
3696 <li>Copy consensus sequence to clipboard</li>
3701 <li>Image output - rightmost residues are rendered if
3702 sequence id panel has been resized</li>
3703 <li>Image output - all offscreen group boundaries are
3705 <li>Annotation files with sequence references - all
3706 elements in file are relative to sequence position</li>
3707 <li>Mac Applet users can use Alt key for group editing</li>
3713 <div align="center">
3714 <strong>2.1</strong><br> 22/8/06
3719 <li>MAFFT Multiple Alignment in default Web Service list</li>
3720 <li>DAS Feature fetching</li>
3721 <li>Hide sequences and columns</li>
3722 <li>Export Annotations and Features</li>
3723 <li>GFF file reading / writing</li>
3724 <li>Associate structures with sequences from local PDB
3726 <li>Add sequences to exisiting alignment</li>
3727 <li>Recently opened files / URL lists</li>
3728 <li>Applet can launch the full application</li>
3729 <li>Applet has transparency for features (Java 1.2
3731 <li>Applet has user defined colours parameter</li>
3732 <li>Applet can load sequences from parameter
3733 "sequence<em>x</em>"
3739 <li>Redundancy Panel reinstalled in the Applet</li>
3740 <li>Monospaced font - EPS / rescaling bug fixed</li>
3741 <li>Annotation files with sequence references bug fixed</li>
3747 <div align="center">
3748 <strong>2.08.1</strong><br> 2/5/06
3753 <li>Change case of selected region from Popup menu</li>
3754 <li>Choose to match case when searching</li>
3755 <li>Middle mouse button and mouse movement can compress /
3756 expand the visible width and height of the alignment</li>
3761 <li>Annotation Panel displays complete JNet results</li>
3767 <div align="center">
3768 <strong>2.08b</strong><br> 18/4/06
3774 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3775 <li>Righthand label on wrapped alignments shows correct
3782 <div align="center">
3783 <strong>2.08</strong><br> 10/4/06
3788 <li>Editing can be locked to the selection area</li>
3789 <li>Keyboard editing</li>
3790 <li>Create sequence features from searches</li>
3791 <li>Precalculated annotations can be loaded onto
3793 <li>Features file allows grouping of features</li>
3794 <li>Annotation Colouring scheme added</li>
3795 <li>Smooth fonts off by default - Faster rendering</li>
3796 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3801 <li>Drag & Drop fixed on Linux</li>
3802 <li>Jalview Archive file faster to load/save, sequence
3803 descriptions saved.</li>
3809 <div align="center">
3810 <strong>2.07</strong><br> 12/12/05
3815 <li>PDB Structure Viewer enhanced</li>
3816 <li>Sequence Feature retrieval and display enhanced</li>
3817 <li>Choose to output sequence start-end after sequence
3818 name for file output</li>
3819 <li>Sequence Fetcher WSDBFetch@EBI</li>
3820 <li>Applet can read feature files, PDB files and can be
3821 used for HTML form input</li>
3826 <li>HTML output writes groups and features</li>
3827 <li>Group editing is Control and mouse click</li>
3828 <li>File IO bugs</li>
3834 <div align="center">
3835 <strong>2.06</strong><br> 28/9/05
3840 <li>View annotations in wrapped mode</li>
3841 <li>More options for PCA viewer</li>
3846 <li>GUI bugs resolved</li>
3847 <li>Runs with -nodisplay from command line</li>
3853 <div align="center">
3854 <strong>2.05b</strong><br> 15/9/05
3859 <li>Choose EPS export as lineart or text</li>
3860 <li>Jar files are executable</li>
3861 <li>Can read in Uracil - maps to unknown residue</li>
3866 <li>Known OutOfMemory errors give warning message</li>
3867 <li>Overview window calculated more efficiently</li>
3868 <li>Several GUI bugs resolved</li>
3874 <div align="center">
3875 <strong>2.05</strong><br> 30/8/05
3880 <li>Edit and annotate in "Wrapped" view</li>
3885 <li>Several GUI bugs resolved</li>
3891 <div align="center">
3892 <strong>2.04</strong><br> 24/8/05
3897 <li>Hold down mouse wheel & scroll to change font
3903 <li>Improved JPred client reliability</li>
3904 <li>Improved loading of Jalview files</li>
3910 <div align="center">
3911 <strong>2.03</strong><br> 18/8/05
3916 <li>Set Proxy server name and port in preferences</li>
3917 <li>Multiple URL links from sequence ids</li>
3918 <li>User Defined Colours can have a scheme name and added
3920 <li>Choose to ignore gaps in consensus calculation</li>
3921 <li>Unix users can set default web browser</li>
3922 <li>Runs without GUI for batch processing</li>
3923 <li>Dynamically generated Web Service Menus</li>
3928 <li>InstallAnywhere download for Sparc Solaris</li>
3934 <div align="center">
3935 <strong>2.02</strong><br> 18/7/05
3941 <li>Copy & Paste order of sequences maintains
3942 alignment order.</li>
3948 <div align="center">
3949 <strong>2.01</strong><br> 12/7/05
3954 <li>Use delete key for deleting selection.</li>
3955 <li>Use Mouse wheel to scroll sequences.</li>
3956 <li>Help file updated to describe how to add alignment
3958 <li>Version and build date written to build properties
3960 <li>InstallAnywhere installation will check for updates
3961 at launch of Jalview.</li>
3966 <li>Delete gaps bug fixed.</li>
3967 <li>FileChooser sorts columns.</li>
3968 <li>Can remove groups one by one.</li>
3969 <li>Filechooser icons installed.</li>
3970 <li>Finder ignores return character when searching.
3971 Return key will initiate a search.<br>
3978 <div align="center">
3979 <strong>2.0</strong><br> 20/6/05
3984 <li>New codebase</li>