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-2920 -->Use HGVS nomenclature for variant
82 annotation retrieved from Uniprot
85 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
86 onto the Jalview Desktop
90 <td><div align="left">
94 <!-- JAL-3017 -->Cannot import features with multiple
95 variant elements (blocks import of some Uniprot records)
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-2993 -->F2/Keyboard mode edits work when Overview
107 window has input focus
110 <!-- JAL-2992 -->Annotation panel set too high when
111 annotation added to view (Windows)
114 <!-- JAL-3009 -->Jalview Desktop is slow to start up when network connectivity is poor
117 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
118 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
119 the currently open URL and links from a page viewed in
120 Firefox or Chrome on Windows is now fully supported. If
121 you are using Edge, only links in the page can be
122 dragged, and with Internet Explorer, only the currently
123 open URL in the browser can be dropped onto Jalview.</em>
129 <td width="60" nowrap>
131 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
134 <td><div align="left">
138 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
139 for disabling automatic superposition of multiple
140 structures and open structures in existing views
143 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
144 ID and annotation area margins can be click-dragged to
148 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
152 <!-- JAL-2759 -->Improved performance for large alignments
153 and lots of hidden columns
156 <!-- JAL-2593 -->Improved performance when rendering lots
157 of features (particularly when transparency is disabled)
162 <td><div align="left">
165 <!-- JAL-2899 -->Structure and Overview aren't updated
166 when Colour By Annotation threshold slider is adjusted
169 <!-- JAL-2778 -->Slow redraw when Overview panel shown
170 overlapping alignment panel
173 <!-- JAL-2929 -->Overview doesn't show end of unpadded
177 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
178 improved: CDS not handled correctly if transcript has no
182 <!-- JAL-2321 -->Secondary structure and temperature
183 factor annotation not added to sequence when local PDB
184 file associated with it by drag'n'drop or structure
188 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
189 dialog doesn't import PDB files dropped on an alignment
192 <!-- JAL-2666 -->Linked scrolling via protein horizontal
193 scroll bar doesn't work for some CDS/Protein views
196 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
197 Java 1.8u153 onwards and Java 1.9u4+.
200 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
201 columns in annotation row
204 <!-- JAL-2913 -->Preferences panel's ID Width control is not
205 honored in batch mode
208 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
209 for structures added to existing Jmol view
212 <!-- JAL-2223 -->'View Mappings' includes duplicate
213 entries after importing project with multiple views
216 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
217 protein sequences via SIFTS from associated PDB entries
218 with negative residue numbers or missing residues fails
221 <!-- JAL-2952 -->Exception when shading sequence with negative
222 Temperature Factor values from annotated PDB files (e.g.
223 as generated by CONSURF)
226 <!-- JAL-2920 -->Uniprot 'sequence variant' features
227 tooltip doesn't include a text description of mutation
230 <!-- JAL-2922 -->Invert displayed features very slow when
231 structure and/or overview windows are also shown
234 <!-- JAL-2954 -->Selecting columns from highlighted regions
235 very slow for alignments with large numbers of sequences
238 <!-- JAL-2925 -->Copy Consensus fails for group consensus
239 with 'StringIndexOutOfBounds'
242 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
243 platforms running Java 10
246 <!-- JAL-2960 -->Adding a structure to existing structure
247 view appears to do nothing because the view is hidden behind the alignment view
253 <!-- JAL-2926 -->Copy consensus sequence option in applet
254 should copy the group consensus when popup is opened on it
260 <!-- JAL-2913 -->Fixed ID width preference is not respected
263 <em>New Known Defects</em>
266 <!-- JAL-2973 --> Exceptions occasionally raised when
267 editing a large alignment and overview is displayed
270 <!-- JAL-2974 -->'Overview updating' progress bar is shown
271 repeatedly after a series of edits even when the overview
272 is no longer reflecting updates
275 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
276 structures for protein subsequence (if 'Trim Retrieved
277 Sequences' enabled) or Ensembl isoforms (Workaround in
278 2.10.4 is to fail back to N&W mapping)
285 <td width="60" nowrap>
287 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
290 <td><div align="left">
291 <ul><li>Updated Certum Codesigning Certificate
292 (Valid till 30th November 2018)</li></ul></div></td>
293 <td><div align="left">
296 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
297 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
298 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
299 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
300 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
301 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
302 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
308 <td width="60" nowrap>
310 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
313 <td><div align="left">
317 <!-- JAL-2446 -->Faster and more efficient management and
318 rendering of sequence features
321 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
322 429 rate limit request hander
325 <!-- JAL-2773 -->Structure views don't get updated unless
326 their colours have changed
329 <!-- JAL-2495 -->All linked sequences are highlighted for
330 a structure mousover (Jmol) or selection (Chimera)
333 <!-- JAL-2790 -->'Cancel' button in progress bar for
334 JABAWS AACon, RNAAliFold and Disorder prediction jobs
337 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
338 view from Ensembl locus cross-references
341 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
345 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
346 feature can be disabled
349 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
350 PDB easier retrieval of sequences for lists of IDs
353 <!-- JAL-2758 -->Short names for sequences retrieved from
359 <li>Groovy interpreter updated to 2.4.12</li>
360 <li>Example groovy script for generating a matrix of
361 percent identity scores for current alignment.</li>
363 <em>Testing and Deployment</em>
366 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
370 <td><div align="left">
374 <!-- JAL-2643 -->Pressing tab after updating the colour
375 threshold text field doesn't trigger an update to the
379 <!-- JAL-2682 -->Race condition when parsing sequence ID
383 <!-- JAL-2608 -->Overview windows are also closed when
384 alignment window is closed
387 <!-- JAL-2548 -->Export of features doesn't always respect
391 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
392 takes a long time in Cursor mode
398 <!-- JAL-2777 -->Structures with whitespace chainCode
399 cannot be viewed in Chimera
402 <!-- JAL-2728 -->Protein annotation panel too high in
406 <!-- JAL-2757 -->Can't edit the query after the server
407 error warning icon is shown in Uniprot and PDB Free Text
411 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
414 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
417 <!-- JAL-2739 -->Hidden column marker in last column not
418 rendered when switching back from Wrapped to normal view
421 <!-- JAL-2768 -->Annotation display corrupted when
422 scrolling right in unwapped alignment view
425 <!-- JAL-2542 -->Existing features on subsequence
426 incorrectly relocated when full sequence retrieved from
430 <!-- JAL-2733 -->Last reported memory still shown when
431 Desktop->Show Memory is unticked (OSX only)
434 <!-- JAL-2658 -->Amend Features dialog doesn't allow
435 features of same type and group to be selected for
439 <!-- JAL-2524 -->Jalview becomes sluggish in wide
440 alignments when hidden columns are present
443 <!-- JAL-2392 -->Jalview freezes when loading and
444 displaying several structures
447 <!-- JAL-2732 -->Black outlines left after resizing or
451 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
452 within the Jalview desktop on OSX
455 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
456 when in wrapped alignment mode
459 <!-- JAL-2636 -->Scale mark not shown when close to right
460 hand end of alignment
463 <!-- JAL-2684 -->Pairwise alignment of selected regions of
464 each selected sequence do not have correct start/end
468 <!-- JAL-2793 -->Alignment ruler height set incorrectly
469 after canceling the Alignment Window's Font dialog
472 <!-- JAL-2036 -->Show cross-references not enabled after
473 restoring project until a new view is created
476 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
477 URL links appears when only default EMBL-EBI link is
478 configured (since 2.10.2b2)
481 <!-- JAL-2775 -->Overview redraws whole window when box
485 <!-- JAL-2225 -->Structure viewer doesn't map all chains
486 in a multi-chain structure when viewing alignment
487 involving more than one chain (since 2.10)
490 <!-- JAL-2811 -->Double residue highlights in cursor mode
491 if new selection moves alignment window
494 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
495 arrow key in cursor mode to pass hidden column marker
498 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
499 that produces correctly annotated transcripts and products
502 <!-- JAL-2776 -->Toggling a feature group after first time
503 doesn't update associated structure view
506 <em>Applet</em><br />
509 <!-- JAL-2687 -->Concurrent modification exception when
510 closing alignment panel
513 <em>BioJSON</em><br />
516 <!-- JAL-2546 -->BioJSON export does not preserve
517 non-positional features
520 <em>New Known Issues</em>
523 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
524 sequence features correctly (for many previous versions of
528 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
529 using cursor in wrapped panel other than top
532 <!-- JAL-2791 -->Select columns containing feature ignores
533 graduated colour threshold
536 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
537 always preserve numbering and sequence features
540 <em>Known Java 9 Issues</em>
543 <!-- JAL-2902 -->Groovy Console very slow to open and is
544 not responsive when entering characters (Webstart, Java
551 <td width="60" nowrap>
553 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
554 <em>2/10/2017</em></strong>
557 <td><div align="left">
558 <em>New features in Jalview Desktop</em>
561 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
563 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
567 <td><div align="left">
571 <td width="60" nowrap>
573 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
574 <em>7/9/2017</em></strong>
577 <td><div align="left">
581 <!-- JAL-2588 -->Show gaps in overview window by colouring
582 in grey (sequences used to be coloured grey, and gaps were
586 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
590 <!-- JAL-2587 -->Overview updates immediately on increase
591 in size and progress bar shown as higher resolution
592 overview is recalculated
597 <td><div align="left">
601 <!-- JAL-2664 -->Overview window redraws every hidden
602 column region row by row
605 <!-- JAL-2681 -->duplicate protein sequences shown after
606 retrieving Ensembl crossrefs for sequences from Uniprot
609 <!-- JAL-2603 -->Overview window throws NPE if show boxes
610 format setting is unticked
613 <!-- JAL-2610 -->Groups are coloured wrongly in overview
614 if group has show boxes format setting unticked
617 <!-- JAL-2672,JAL-2665 -->Redraw problems when
618 autoscrolling whilst dragging current selection group to
619 include sequences and columns not currently displayed
622 <!-- JAL-2691 -->Not all chains are mapped when multimeric
623 assemblies are imported via CIF file
626 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
627 displayed when threshold or conservation colouring is also
631 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
635 <!-- JAL-2673 -->Jalview continues to scroll after
636 dragging a selected region off the visible region of the
640 <!-- JAL-2724 -->Cannot apply annotation based
641 colourscheme to all groups in a view
644 <!-- JAL-2511 -->IDs don't line up with sequences
645 initially after font size change using the Font chooser or
652 <td width="60" nowrap>
654 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
657 <td><div align="left">
658 <em>Calculations</em>
662 <!-- JAL-1933 -->Occupancy annotation row shows number of
663 ungapped positions in each column of the alignment.
666 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
667 a calculation dialog box
670 <!-- JAL-2379 -->Revised implementation of PCA for speed
671 and memory efficiency (~30x faster)
674 <!-- JAL-2403 -->Revised implementation of sequence
675 similarity scores as used by Tree, PCA, Shading Consensus
676 and other calculations
679 <!-- JAL-2416 -->Score matrices are stored as resource
680 files within the Jalview codebase
683 <!-- JAL-2500 -->Trees computed on Sequence Feature
684 Similarity may have different topology due to increased
691 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
692 model for alignments and groups
695 <!-- JAL-384 -->Custom shading schemes created via groovy
702 <!-- JAL-2526 -->Efficiency improvements for interacting
703 with alignment and overview windows
706 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
710 <!-- JAL-2388 -->Hidden columns and sequences can be
714 <!-- JAL-2611 -->Click-drag in visible area allows fine
715 adjustment of visible position
719 <em>Data import/export</em>
722 <!-- JAL-2535 -->Posterior probability annotation from
723 Stockholm files imported as sequence associated annotation
726 <!-- JAL-2507 -->More robust per-sequence positional
727 annotation input/output via stockholm flatfile
730 <!-- JAL-2533 -->Sequence names don't include file
731 extension when importing structure files without embedded
732 names or PDB accessions
735 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
736 format sequence substitution matrices
739 <em>User Interface</em>
742 <!-- JAL-2447 --> Experimental Features Checkbox in
743 Desktop's Tools menu to hide or show untested features in
747 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
748 via Overview or sequence motif search operations
751 <!-- JAL-2547 -->Amend sequence features dialog box can be
752 opened by double clicking gaps within sequence feature
756 <!-- JAL-1476 -->Status bar message shown when not enough
757 aligned positions were available to create a 3D structure
761 <em>3D Structure</em>
764 <!-- JAL-2430 -->Hidden regions in alignment views are not
765 coloured in linked structure views
768 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
769 file-based command exchange
772 <!-- JAL-2375 -->Structure chooser automatically shows
773 Cached Structures rather than querying the PDBe if
774 structures are already available for sequences
777 <!-- JAL-2520 -->Structures imported via URL are cached in
778 the Jalview project rather than downloaded again when the
782 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
783 to transfer Chimera's structure attributes as Jalview
784 features, and vice-versa (<strong>Experimental
788 <em>Web Services</em>
791 <!-- JAL-2549 -->Updated JABAWS client to v2.2
794 <!-- JAL-2335 -->Filter non-standard amino acids and
795 nucleotides when submitting to AACon and other MSA
799 <!-- JAL-2316, -->URLs for viewing database
800 cross-references provided by identifiers.org and the
808 <!-- JAL-2344 -->FileFormatI interface for describing and
809 identifying file formats (instead of String constants)
812 <!-- JAL-2228 -->FeatureCounter script refactored for
813 efficiency when counting all displayed features (not
814 backwards compatible with 2.10.1)
817 <em>Example files</em>
820 <!-- JAL-2631 -->Graduated feature colour style example
821 included in the example feature file
824 <em>Documentation</em>
827 <!-- JAL-2339 -->Release notes reformatted for readability
828 with the built-in Java help viewer
831 <!-- JAL-1644 -->Find documentation updated with 'search
832 sequence description' option
838 <!-- JAL-2485, -->External service integration tests for
839 Uniprot REST Free Text Search Client
842 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
845 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
850 <td><div align="left">
851 <em>Calculations</em>
854 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
855 matrix - C->R should be '-3'<br />Old matrix restored
856 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
858 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
859 Jalview's treatment of gaps in PCA and substitution matrix
860 based Tree calculations.<br /> <br />In earlier versions
861 of Jalview, gaps matching gaps were penalised, and gaps
862 matching non-gaps penalised even more. In the PCA
863 calculation, gaps were actually treated as non-gaps - so
864 different costs were applied, which meant Jalview's PCAs
865 were different to those produced by SeqSpace.<br />Jalview
866 now treats gaps in the same way as SeqSpace (ie it scores
867 them as 0). <br /> <br />Enter the following in the
868 Groovy console to restore pre-2.10.2 behaviour:<br />
869 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
870 // for 2.10.1 mode <br />
871 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
872 // to restore 2.10.2 mode <br /> <br /> <em>Note:
873 these settings will affect all subsequent tree and PCA
874 calculations (not recommended)</em></li>
876 <!-- JAL-2424 -->Fixed off-by-one bug that affected
877 scaling of branch lengths for trees computed using
878 Sequence Feature Similarity.
881 <!-- JAL-2377 -->PCA calculation could hang when
882 generating output report when working with highly
886 <!-- JAL-2544 --> Sort by features includes features to
887 right of selected region when gaps present on right-hand
891 <em>User Interface</em>
894 <!-- JAL-2346 -->Reopening Colour by annotation dialog
895 doesn't reselect a specific sequence's associated
896 annotation after it was used for colouring a view
899 <!-- JAL-2419 -->Current selection lost if popup menu
900 opened on a region of alignment without groups
903 <!-- JAL-2374 -->Popup menu not always shown for regions
904 of an alignment with overlapping groups
907 <!-- JAL-2310 -->Finder double counts if both a sequence's
908 name and description match
911 <!-- JAL-2370 -->Hiding column selection containing two
912 hidden regions results in incorrect hidden regions
915 <!-- JAL-2386 -->'Apply to all groups' setting when
916 changing colour does not apply Conservation slider value
920 <!-- JAL-2373 -->Percentage identity and conservation menu
921 items do not show a tick or allow shading to be disabled
924 <!-- JAL-2385 -->Conservation shading or PID threshold
925 lost when base colourscheme changed if slider not visible
928 <!-- JAL-2547 -->Sequence features shown in tooltip for
929 gaps before start of features
932 <!-- JAL-2623 -->Graduated feature colour threshold not
933 restored to UI when feature colour is edited
936 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
937 a time when scrolling vertically in wrapped mode.
940 <!-- JAL-2630 -->Structure and alignment overview update
941 as graduate feature colour settings are modified via the
945 <!-- JAL-2034 -->Overview window doesn't always update
946 when a group defined on the alignment is resized
949 <!-- JAL-2605 -->Mouseovers on left/right scale region in
950 wrapped view result in positional status updates
954 <!-- JAL-2563 -->Status bar doesn't show position for
955 ambiguous amino acid and nucleotide symbols
958 <!-- JAL-2602 -->Copy consensus sequence failed if
959 alignment included gapped columns
962 <!-- JAL-2473 -->Minimum size set for Jalview windows so
963 widgets don't permanently disappear
966 <!-- JAL-2503 -->Cannot select or filter quantitative
967 annotation that are shown only as column labels (e.g.
968 T-Coffee column reliability scores)
971 <!-- JAL-2594 -->Exception thrown if trying to create a
972 sequence feature on gaps only
975 <!-- JAL-2504 -->Features created with 'New feature'
976 button from a Find inherit previously defined feature type
977 rather than the Find query string
980 <!-- JAL-2423 -->incorrect title in output window when
981 exporting tree calculated in Jalview
984 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
985 and then revealing them reorders sequences on the
989 <!-- JAL-964 -->Group panel in sequence feature settings
990 doesn't update to reflect available set of groups after
991 interactively adding or modifying features
994 <!-- JAL-2225 -->Sequence Database chooser unusable on
998 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
999 only excluded gaps in current sequence and ignored
1006 <!-- JAL-2421 -->Overview window visible region moves
1007 erratically when hidden rows or columns are present
1010 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1011 Structure Viewer's colour menu don't correspond to
1015 <!-- JAL-2405 -->Protein specific colours only offered in
1016 colour and group colour menu for protein alignments
1019 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1020 reflect currently selected view or group's shading
1024 <!-- JAL-2624 -->Feature colour thresholds not respected
1025 when rendered on overview and structures when opacity at
1029 <!-- JAL-2589 -->User defined gap colour not shown in
1030 overview when features overlaid on alignment
1033 <em>Data import/export</em>
1036 <!-- JAL-2576 -->Very large alignments take a long time to
1040 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1041 added after a sequence was imported are not written to
1045 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1046 when importing RNA secondary structure via Stockholm
1049 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1050 not shown in correct direction for simple pseudoknots
1053 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1054 with lightGray or darkGray via features file (but can
1058 <!-- JAL-2383 -->Above PID colour threshold not recovered
1059 when alignment view imported from project
1062 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1063 structure and sequences extracted from structure files
1064 imported via URL and viewed in Jmol
1067 <!-- JAL-2520 -->Structures loaded via URL are saved in
1068 Jalview Projects rather than fetched via URL again when
1069 the project is loaded and the structure viewed
1072 <em>Web Services</em>
1075 <!-- JAL-2519 -->EnsemblGenomes example failing after
1076 release of Ensembl v.88
1079 <!-- JAL-2366 -->Proxy server address and port always
1080 appear enabled in Preferences->Connections
1083 <!-- JAL-2461 -->DAS registry not found exceptions
1084 removed from console output
1087 <!-- JAL-2582 -->Cannot retrieve protein products from
1088 Ensembl by Peptide ID
1091 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1092 created from SIFTs, and spurious 'Couldn't open structure
1093 in Chimera' errors raised after April 2017 update (problem
1094 due to 'null' string rather than empty string used for
1095 residues with no corresponding PDB mapping).
1098 <em>Application UI</em>
1101 <!-- JAL-2361 -->User Defined Colours not added to Colour
1105 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1106 case' residues (button in colourscheme editor debugged and
1107 new documentation and tooltips added)
1110 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1111 doesn't restore group-specific text colour thresholds
1114 <!-- JAL-2243 -->Feature settings panel does not update as
1115 new features are added to alignment
1118 <!-- JAL-2532 -->Cancel in feature settings reverts
1119 changes to feature colours via the Amend features dialog
1122 <!-- JAL-2506 -->Null pointer exception when attempting to
1123 edit graduated feature colour via amend features dialog
1127 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1128 selection menu changes colours of alignment views
1131 <!-- JAL-2426 -->Spurious exceptions in console raised
1132 from alignment calculation workers after alignment has
1136 <!-- JAL-1608 -->Typo in selection popup menu - Create
1137 groups now 'Create Group'
1140 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1141 Create/Undefine group doesn't always work
1144 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1145 shown again after pressing 'Cancel'
1148 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1149 adjusts start position in wrap mode
1152 <!-- JAL-2563 -->Status bar doesn't show positions for
1153 ambiguous amino acids
1156 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1157 CDS/Protein view after CDS sequences added for aligned
1161 <!-- JAL-2592 -->User defined colourschemes called 'User
1162 Defined' don't appear in Colours menu
1168 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1169 score models doesn't always result in an updated PCA plot
1172 <!-- JAL-2442 -->Features not rendered as transparent on
1173 overview or linked structure view
1176 <!-- JAL-2372 -->Colour group by conservation doesn't
1180 <!-- JAL-2517 -->Hitting Cancel after applying
1181 user-defined colourscheme doesn't restore original
1188 <!-- JAL-2314 -->Unit test failure:
1189 jalview.ws.jabaws.RNAStructExportImport setup fails
1192 <!-- JAL-2307 -->Unit test failure:
1193 jalview.ws.sifts.SiftsClientTest due to compatibility
1194 problems with deep array comparison equality asserts in
1195 successive versions of TestNG
1198 <!-- JAL-2479 -->Relocated StructureChooserTest and
1199 ParameterUtilsTest Unit tests to Network suite
1202 <em>New Known Issues</em>
1205 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1206 phase after a sequence motif find operation
1209 <!-- JAL-2550 -->Importing annotation file with rows
1210 containing just upper and lower case letters are
1211 interpreted as WUSS RNA secondary structure symbols
1214 <!-- JAL-2590 -->Cannot load and display Newick trees
1215 reliably from eggnog Ortholog database
1218 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1219 containing features of type Highlight' when 'B' is pressed
1220 to mark columns containing highlighted regions.
1223 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1224 doesn't always add secondary structure annotation.
1229 <td width="60" nowrap>
1230 <div align="center">
1231 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1234 <td><div align="left">
1238 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1239 for all consensus calculations
1242 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1245 <li>Updated Jalview's Certum code signing certificate
1248 <em>Application</em>
1251 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1252 set of database cross-references, sorted alphabetically
1255 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1256 from database cross references. Users with custom links
1257 will receive a <a href="webServices/urllinks.html#warning">warning
1258 dialog</a> asking them to update their preferences.
1261 <!-- JAL-2287-->Cancel button and escape listener on
1262 dialog warning user about disconnecting Jalview from a
1266 <!-- JAL-2320-->Jalview's Chimera control window closes if
1267 the Chimera it is connected to is shut down
1270 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1271 columns menu item to mark columns containing highlighted
1272 regions (e.g. from structure selections or results of a
1276 <!-- JAL-2284-->Command line option for batch-generation
1277 of HTML pages rendering alignment data with the BioJS
1287 <!-- JAL-2286 -->Columns with more than one modal residue
1288 are not coloured or thresholded according to percent
1289 identity (first observed in Jalview 2.8.2)
1292 <!-- JAL-2301 -->Threonine incorrectly reported as not
1296 <!-- JAL-2318 -->Updates to documentation pages (above PID
1297 threshold, amino acid properties)
1300 <!-- JAL-2292 -->Lower case residues in sequences are not
1301 reported as mapped to residues in a structure file in the
1305 <!--JAL-2324 -->Identical features with non-numeric scores
1306 could be added multiple times to a sequence
1309 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1310 bond features shown as two highlighted residues rather
1311 than a range in linked structure views, and treated
1312 correctly when selecting and computing trees from features
1315 <!-- JAL-2281-->Custom URL links for database
1316 cross-references are matched to database name regardless
1321 <em>Application</em>
1324 <!-- JAL-2282-->Custom URL links for specific database
1325 names without regular expressions also offer links from
1329 <!-- JAL-2315-->Removing a single configured link in the
1330 URL links pane in Connections preferences doesn't actually
1331 update Jalview configuration
1334 <!-- JAL-2272-->CTRL-Click on a selected region to open
1335 the alignment area popup menu doesn't work on El-Capitan
1338 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1339 files with similarly named sequences if dropped onto the
1343 <!-- JAL-2312 -->Additional mappings are shown for PDB
1344 entries where more chains exist in the PDB accession than
1345 are reported in the SIFTS file
1348 <!-- JAL-2317-->Certain structures do not get mapped to
1349 the structure view when displayed with Chimera
1352 <!-- JAL-2317-->No chains shown in the Chimera view
1353 panel's View->Show Chains submenu
1356 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1357 work for wrapped alignment views
1360 <!--JAL-2197 -->Rename UI components for running JPred
1361 predictions from 'JNet' to 'JPred'
1364 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1365 corrupted when annotation panel vertical scroll is not at
1366 first annotation row
1369 <!--JAL-2332 -->Attempting to view structure for Hen
1370 lysozyme results in a PDB Client error dialog box
1373 <!-- JAL-2319 -->Structure View's mapping report switched
1374 ranges for PDB and sequence for SIFTS
1377 SIFTS 'Not_Observed' residues mapped to non-existant
1381 <!-- <em>New Known Issues</em>
1388 <td width="60" nowrap>
1389 <div align="center">
1390 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1391 <em>25/10/2016</em></strong>
1394 <td><em>Application</em>
1396 <li>3D Structure chooser opens with 'Cached structures'
1397 view if structures already loaded</li>
1398 <li>Progress bar reports models as they are loaded to
1399 structure views</li>
1405 <li>Colour by conservation always enabled and no tick
1406 shown in menu when BLOSUM or PID shading applied</li>
1407 <li>FER1_ARATH and FER2_ARATH labels were switched in
1408 example sequences/projects/trees</li>
1410 <em>Application</em>
1412 <li>Jalview projects with views of local PDB structure
1413 files saved on Windows cannot be opened on OSX</li>
1414 <li>Multiple structure views can be opened and superposed
1415 without timeout for structures with multiple models or
1416 multiple sequences in alignment</li>
1417 <li>Cannot import or associated local PDB files without a
1418 PDB ID HEADER line</li>
1419 <li>RMSD is not output in Jmol console when superposition
1421 <li>Drag and drop of URL from Browser fails for Linux and
1422 OSX versions earlier than El Capitan</li>
1423 <li>ENA client ignores invalid content from ENA server</li>
1424 <li>Exceptions are not raised in console when ENA client
1425 attempts to fetch non-existent IDs via Fetch DB Refs UI
1427 <li>Exceptions are not raised in console when a new view
1428 is created on the alignment</li>
1429 <li>OSX right-click fixed for group selections: CMD-click
1430 to insert/remove gaps in groups and CTRL-click to open group
1433 <em>Build and deployment</em>
1435 <li>URL link checker now copes with multi-line anchor
1438 <em>New Known Issues</em>
1440 <li>Drag and drop from URL links in browsers do not work
1447 <td width="60" nowrap>
1448 <div align="center">
1449 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1452 <td><em>General</em>
1455 <!-- JAL-2124 -->Updated Spanish translations.
1458 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1459 for importing structure data to Jalview. Enables mmCIF and
1463 <!-- JAL-192 --->Alignment ruler shows positions relative to
1467 <!-- JAL-2202 -->Position/residue shown in status bar when
1468 mousing over sequence associated annotation
1471 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1475 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1476 '()', canonical '[]' and invalid '{}' base pair populations
1480 <!-- JAL-2092 -->Feature settings popup menu options for
1481 showing or hiding columns containing a feature
1484 <!-- JAL-1557 -->Edit selected group by double clicking on
1485 group and sequence associated annotation labels
1488 <!-- JAL-2236 -->Sequence name added to annotation label in
1489 select/hide columns by annotation and colour by annotation
1493 </ul> <em>Application</em>
1496 <!-- JAL-2050-->Automatically hide introns when opening a
1497 gene/transcript view
1500 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1504 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1505 structure mappings with the EMBL-EBI PDBe SIFTS database
1508 <!-- JAL-2079 -->Updated download sites used for Rfam and
1509 Pfam sources to xfam.org
1512 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1515 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1516 over sequences in Jalview
1519 <!-- JAL-2027-->Support for reverse-complement coding
1520 regions in ENA and EMBL
1523 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1524 for record retrieval via ENA rest API
1527 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1531 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1532 groovy script execution
1535 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1536 alignment window's Calculate menu
1539 <!-- JAL-1812 -->Allow groovy scripts that call
1540 Jalview.getAlignFrames() to run in headless mode
1543 <!-- JAL-2068 -->Support for creating new alignment
1544 calculation workers from groovy scripts
1547 <!-- JAL-1369 --->Store/restore reference sequence in
1551 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1552 associations are now saved/restored from project
1555 <!-- JAL-1993 -->Database selection dialog always shown
1556 before sequence fetcher is opened
1559 <!-- JAL-2183 -->Double click on an entry in Jalview's
1560 database chooser opens a sequence fetcher
1563 <!-- JAL-1563 -->Free-text search client for UniProt using
1564 the UniProt REST API
1567 <!-- JAL-2168 -->-nonews command line parameter to prevent
1568 the news reader opening
1571 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1572 querying stored in preferences
1575 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1579 <!-- JAL-1977-->Tooltips shown on database chooser
1582 <!-- JAL-391 -->Reverse complement function in calculate
1583 menu for nucleotide sequences
1586 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1587 and feature counts preserves alignment ordering (and
1588 debugged for complex feature sets).
1591 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1592 viewing structures with Jalview 2.10
1595 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1596 genome, transcript CCDS and gene ids via the Ensembl and
1597 Ensembl Genomes REST API
1600 <!-- JAL-2049 -->Protein sequence variant annotation
1601 computed for 'sequence_variant' annotation on CDS regions
1605 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1609 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1610 Ref Fetcher fails to match, or otherwise updates sequence
1611 data from external database records.
1614 <!-- JAL-2154 -->Revised Jalview Project format for
1615 efficient recovery of sequence coding and alignment
1616 annotation relationships.
1618 </ul> <!-- <em>Applet</em>
1629 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1633 <!-- JAL-2018-->Export features in Jalview format (again)
1634 includes graduated colourschemes
1637 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1638 working with big alignments and lots of hidden columns
1641 <!-- JAL-2053-->Hidden column markers not always rendered
1642 at right of alignment window
1645 <!-- JAL-2067 -->Tidied up links in help file table of
1649 <!-- JAL-2072 -->Feature based tree calculation not shown
1653 <!-- JAL-2075 -->Hidden columns ignored during feature
1654 based tree calculation
1657 <!-- JAL-2065 -->Alignment view stops updating when show
1658 unconserved enabled for group on alignment
1661 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1665 <!-- JAL-2146 -->Alignment column in status incorrectly
1666 shown as "Sequence position" when mousing over
1670 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1671 hidden columns present
1674 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1675 user created annotation added to alignment
1678 <!-- JAL-1841 -->RNA Structure consensus only computed for
1679 '()' base pair annotation
1682 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1683 in zero scores for all base pairs in RNA Structure
1687 <!-- JAL-2174-->Extend selection with columns containing
1691 <!-- JAL-2275 -->Pfam format writer puts extra space at
1692 beginning of sequence
1695 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1699 <!-- JAL-2238 -->Cannot create groups on an alignment from
1700 from a tree when t-coffee scores are shown
1703 <!-- JAL-1836,1967 -->Cannot import and view PDB
1704 structures with chains containing negative resnums (4q4h)
1707 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1711 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1712 to Clustal, PIR and PileUp output
1715 <!-- JAL-2008 -->Reordering sequence features that are
1716 not visible causes alignment window to repaint
1719 <!-- JAL-2006 -->Threshold sliders don't work in
1720 graduated colour and colour by annotation row for e-value
1721 scores associated with features and annotation rows
1724 <!-- JAL-1797 -->amino acid physicochemical conservation
1725 calculation should be case independent
1728 <!-- JAL-2173 -->Remove annotation also updates hidden
1732 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1733 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1734 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1737 <!-- JAL-2065 -->Null pointer exceptions and redraw
1738 problems when reference sequence defined and 'show
1739 non-conserved' enabled
1742 <!-- JAL-1306 -->Quality and Conservation are now shown on
1743 load even when Consensus calculation is disabled
1746 <!-- JAL-1932 -->Remove right on penultimate column of
1747 alignment does nothing
1750 <em>Application</em>
1753 <!-- JAL-1552-->URLs and links can't be imported by
1754 drag'n'drop on OSX when launched via webstart (note - not
1755 yet fixed for El Capitan)
1758 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1759 output when running on non-gb/us i18n platforms
1762 <!-- JAL-1944 -->Error thrown when exporting a view with
1763 hidden sequences as flat-file alignment
1766 <!-- JAL-2030-->InstallAnywhere distribution fails when
1770 <!-- JAL-2080-->Jalview very slow to launch via webstart
1771 (also hotfix for 2.9.0b2)
1774 <!-- JAL-2085 -->Cannot save project when view has a
1775 reference sequence defined
1778 <!-- JAL-1011 -->Columns are suddenly selected in other
1779 alignments and views when revealing hidden columns
1782 <!-- JAL-1989 -->Hide columns not mirrored in complement
1783 view in a cDNA/Protein splitframe
1786 <!-- JAL-1369 -->Cannot save/restore representative
1787 sequence from project when only one sequence is
1791 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1792 in Structure Chooser
1795 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1796 structure consensus didn't refresh annotation panel
1799 <!-- JAL-1962 -->View mapping in structure view shows
1800 mappings between sequence and all chains in a PDB file
1803 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1804 dialogs format columns correctly, don't display array
1805 data, sort columns according to type
1808 <!-- JAL-1975 -->Export complete shown after destination
1809 file chooser is cancelled during an image export
1812 <!-- JAL-2025 -->Error when querying PDB Service with
1813 sequence name containing special characters
1816 <!-- JAL-2024 -->Manual PDB structure querying should be
1820 <!-- JAL-2104 -->Large tooltips with broken HTML
1821 formatting don't wrap
1824 <!-- JAL-1128 -->Figures exported from wrapped view are
1825 truncated so L looks like I in consensus annotation
1828 <!-- JAL-2003 -->Export features should only export the
1829 currently displayed features for the current selection or
1833 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1834 after fetching cross-references, and restoring from
1838 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1839 followed in the structure viewer
1842 <!-- JAL-2163 -->Titles for individual alignments in
1843 splitframe not restored from project
1846 <!-- JAL-2145 -->missing autocalculated annotation at
1847 trailing end of protein alignment in transcript/product
1848 splitview when pad-gaps not enabled by default
1851 <!-- JAL-1797 -->amino acid physicochemical conservation
1855 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1856 article has been read (reopened issue due to
1857 internationalisation problems)
1860 <!-- JAL-1960 -->Only offer PDB structures in structure
1861 viewer based on sequence name, PDB and UniProt
1866 <!-- JAL-1976 -->No progress bar shown during export of
1870 <!-- JAL-2213 -->Structures not always superimposed after
1871 multiple structures are shown for one or more sequences.
1874 <!-- JAL-1370 -->Reference sequence characters should not
1875 be replaced with '.' when 'Show unconserved' format option
1879 <!-- JAL-1823 -->Cannot specify chain code when entering
1880 specific PDB id for sequence
1883 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1884 'Export hidden sequences' is enabled, but 'export hidden
1885 columns' is disabled.
1888 <!--JAL-2026-->Best Quality option in structure chooser
1889 selects lowest rather than highest resolution structures
1893 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1894 to sequence mapping in 'View Mappings' report
1897 <!-- JAL-2284 -->Unable to read old Jalview projects that
1898 contain non-XML data added after Jalvew wrote project.
1901 <!-- JAL-2118 -->Newly created annotation row reorders
1902 after clicking on it to create new annotation for a
1906 <!-- JAL-1980 -->Null Pointer Exception raised when
1907 pressing Add on an orphaned cut'n'paste window.
1909 <!-- may exclude, this is an external service stability issue JAL-1941
1910 -- > RNA 3D structure not added via DSSR service</li> -->
1915 <!-- JAL-2151 -->Incorrect columns are selected when
1916 hidden columns present before start of sequence
1919 <!-- JAL-1986 -->Missing dependencies on applet pages
1923 <!-- JAL-1947 -->Overview pixel size changes when
1924 sequences are hidden in applet
1927 <!-- JAL-1996 -->Updated instructions for applet
1928 deployment on examples pages.
1935 <td width="60" nowrap>
1936 <div align="center">
1937 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1938 <em>16/10/2015</em></strong>
1941 <td><em>General</em>
1943 <li>Time stamps for signed Jalview application and applet
1948 <em>Application</em>
1950 <li>Duplicate group consensus and conservation rows
1951 shown when tree is partitioned</li>
1952 <li>Erratic behaviour when tree partitions made with
1953 multiple cDNA/Protein split views</li>
1959 <td width="60" nowrap>
1960 <div align="center">
1961 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1962 <em>8/10/2015</em></strong>
1965 <td><em>General</em>
1967 <li>Updated Spanish translations of localized text for
1969 </ul> <em>Application</em>
1971 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1972 <li>Signed OSX InstallAnywhere installer<br></li>
1973 <li>Support for per-sequence based annotations in BioJSON</li>
1974 </ul> <em>Applet</em>
1976 <li>Split frame example added to applet examples page</li>
1977 </ul> <em>Build and Deployment</em>
1980 <!-- JAL-1888 -->New ant target for running Jalview's test
1988 <li>Mapping of cDNA to protein in split frames
1989 incorrect when sequence start > 1</li>
1990 <li>Broken images in filter column by annotation dialog
1992 <li>Feature colours not parsed from features file</li>
1993 <li>Exceptions and incomplete link URLs recovered when
1994 loading a features file containing HTML tags in feature
1998 <em>Application</em>
2000 <li>Annotations corrupted after BioJS export and
2002 <li>Incorrect sequence limits after Fetch DB References
2003 with 'trim retrieved sequences'</li>
2004 <li>Incorrect warning about deleting all data when
2005 deleting selected columns</li>
2006 <li>Patch to build system for shipping properly signed
2007 JNLP templates for webstart launch</li>
2008 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2009 unreleased structures for download or viewing</li>
2010 <li>Tab/space/return keystroke operation of EMBL-PDBe
2011 fetcher/viewer dialogs works correctly</li>
2012 <li>Disabled 'minimise' button on Jalview windows
2013 running on OSX to workaround redraw hang bug</li>
2014 <li>Split cDNA/Protein view position and geometry not
2015 recovered from jalview project</li>
2016 <li>Initial enabled/disabled state of annotation menu
2017 sorter 'show autocalculated first/last' corresponds to
2019 <li>Restoring of Clustal, RNA Helices and T-Coffee
2020 color schemes from BioJSON</li>
2024 <li>Reorder sequences mirrored in cDNA/Protein split
2026 <li>Applet with Jmol examples not loading correctly</li>
2032 <td><div align="center">
2033 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2035 <td><em>General</em>
2037 <li>Linked visualisation and analysis of DNA and Protein
2040 <li>Translated cDNA alignments shown as split protein
2041 and DNA alignment views</li>
2042 <li>Codon consensus annotation for linked protein and
2043 cDNA alignment views</li>
2044 <li>Link cDNA or Protein product sequences by loading
2045 them onto Protein or cDNA alignments</li>
2046 <li>Reconstruct linked cDNA alignment from aligned
2047 protein sequences</li>
2050 <li>Jmol integration updated to Jmol v14.2.14</li>
2051 <li>Import and export of Jalview alignment views as <a
2052 href="features/bioJsonFormat.html">BioJSON</a></li>
2053 <li>New alignment annotation file statements for
2054 reference sequences and marking hidden columns</li>
2055 <li>Reference sequence based alignment shading to
2056 highlight variation</li>
2057 <li>Select or hide columns according to alignment
2059 <li>Find option for locating sequences by description</li>
2060 <li>Conserved physicochemical properties shown in amino
2061 acid conservation row</li>
2062 <li>Alignments can be sorted by number of RNA helices</li>
2063 </ul> <em>Application</em>
2065 <li>New cDNA/Protein analysis capabilities
2067 <li>Get Cross-References should open a Split Frame
2068 view with cDNA/Protein</li>
2069 <li>Detect when nucleotide sequences and protein
2070 sequences are placed in the same alignment</li>
2071 <li>Split cDNA/Protein views are saved in Jalview
2076 <li>Use REST API to talk to Chimera</li>
2077 <li>Selected regions in Chimera are highlighted in linked
2078 Jalview windows</li>
2080 <li>VARNA RNA viewer updated to v3.93</li>
2081 <li>VARNA views are saved in Jalview Projects</li>
2082 <li>Pseudoknots displayed as Jalview RNA annotation can
2083 be shown in VARNA</li>
2085 <li>Make groups for selection uses marked columns as well
2086 as the active selected region</li>
2088 <li>Calculate UPGMA and NJ trees using sequence feature
2090 <li>New Export options
2092 <li>New Export Settings dialog to control hidden
2093 region export in flat file generation</li>
2095 <li>Export alignment views for display with the <a
2096 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2098 <li>Export scrollable SVG in HTML page</li>
2099 <li>Optional embedding of BioJSON data when exporting
2100 alignment figures to HTML</li>
2102 <li>3D structure retrieval and display
2104 <li>Free text and structured queries with the PDBe
2106 <li>PDBe Search API based discovery and selection of
2107 PDB structures for a sequence set</li>
2111 <li>JPred4 employed for protein secondary structure
2113 <li>Hide Insertions menu option to hide unaligned columns
2114 for one or a group of sequences</li>
2115 <li>Automatically hide insertions in alignments imported
2116 from the JPred4 web server</li>
2117 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2118 system on OSX<br />LGPL libraries courtesy of <a
2119 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2121 <li>changed 'View nucleotide structure' submenu to 'View
2122 VARNA 2D Structure'</li>
2123 <li>change "View protein structure" menu option to "3D
2126 </ul> <em>Applet</em>
2128 <li>New layout for applet example pages</li>
2129 <li>New parameters to enable SplitFrame view
2130 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2131 <li>New example demonstrating linked viewing of cDNA and
2132 Protein alignments</li>
2133 </ul> <em>Development and deployment</em>
2135 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2136 <li>Include installation type and git revision in build
2137 properties and console log output</li>
2138 <li>Jalview Github organisation, and new github site for
2139 storing BioJsMSA Templates</li>
2140 <li>Jalview's unit tests now managed with TestNG</li>
2143 <!-- <em>General</em>
2145 </ul> --> <!-- issues resolved --> <em>Application</em>
2147 <li>Escape should close any open find dialogs</li>
2148 <li>Typo in select-by-features status report</li>
2149 <li>Consensus RNA secondary secondary structure
2150 predictions are not highlighted in amber</li>
2151 <li>Missing gap character in v2.7 example file means
2152 alignment appears unaligned when pad-gaps is not enabled</li>
2153 <li>First switch to RNA Helices colouring doesn't colour
2154 associated structure views</li>
2155 <li>ID width preference option is greyed out when auto
2156 width checkbox not enabled</li>
2157 <li>Stopped a warning dialog from being shown when
2158 creating user defined colours</li>
2159 <li>'View Mapping' in structure viewer shows sequence
2160 mappings for just that viewer's sequences</li>
2161 <li>Workaround for superposing PDB files containing
2162 multiple models in Chimera</li>
2163 <li>Report sequence position in status bar when hovering
2164 over Jmol structure</li>
2165 <li>Cannot output gaps as '.' symbols with Selection ->
2166 output to text box</li>
2167 <li>Flat file exports of alignments with hidden columns
2168 have incorrect sequence start/end</li>
2169 <li>'Aligning' a second chain to a Chimera structure from
2171 <li>Colour schemes applied to structure viewers don't
2172 work for nucleotide</li>
2173 <li>Loading/cut'n'pasting an empty or invalid file leads
2174 to a grey/invisible alignment window</li>
2175 <li>Exported Jpred annotation from a sequence region
2176 imports to different position</li>
2177 <li>Space at beginning of sequence feature tooltips shown
2178 on some platforms</li>
2179 <li>Chimera viewer 'View | Show Chain' menu is not
2181 <li>'New View' fails with a Null Pointer Exception in
2182 console if Chimera has been opened</li>
2183 <li>Mouseover to Chimera not working</li>
2184 <li>Miscellaneous ENA XML feature qualifiers not
2186 <li>NPE in annotation renderer after 'Extract Scores'</li>
2187 <li>If two structures in one Chimera window, mouseover of
2188 either sequence shows on first structure</li>
2189 <li>'Show annotations' options should not make
2190 non-positional annotations visible</li>
2191 <li>Subsequence secondary structure annotation not shown
2192 in right place after 'view flanking regions'</li>
2193 <li>File Save As type unset when current file format is
2195 <li>Save as '.jar' option removed for saving Jalview
2197 <li>Colour by Sequence colouring in Chimera more
2199 <li>Cannot 'add reference annotation' for a sequence in
2200 several views on same alignment</li>
2201 <li>Cannot show linked products for EMBL / ENA records</li>
2202 <li>Jalview's tooltip wraps long texts containing no
2204 </ul> <em>Applet</em>
2206 <li>Jmol to JalviewLite mouseover/link not working</li>
2207 <li>JalviewLite can't import sequences with ID
2208 descriptions containing angle brackets</li>
2209 </ul> <em>General</em>
2211 <li>Cannot export and reimport RNA secondary structure
2212 via jalview annotation file</li>
2213 <li>Random helix colour palette for colour by annotation
2214 with RNA secondary structure</li>
2215 <li>Mouseover to cDNA from STOP residue in protein
2216 translation doesn't work.</li>
2217 <li>hints when using the select by annotation dialog box</li>
2218 <li>Jmol alignment incorrect if PDB file has alternate CA
2220 <li>FontChooser message dialog appears to hang after
2221 choosing 1pt font</li>
2222 <li>Peptide secondary structure incorrectly imported from
2223 annotation file when annotation display text includes 'e' or
2225 <li>Cannot set colour of new feature type whilst creating
2227 <li>cDNA translation alignment should not be sequence
2228 order dependent</li>
2229 <li>'Show unconserved' doesn't work for lower case
2231 <li>Nucleotide ambiguity codes involving R not recognised</li>
2232 </ul> <em>Deployment and Documentation</em>
2234 <li>Applet example pages appear different to the rest of
2235 www.jalview.org</li>
2236 </ul> <em>Application Known issues</em>
2238 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2239 <li>Misleading message appears after trying to delete
2241 <li>Jalview icon not shown in dock after InstallAnywhere
2242 version launches</li>
2243 <li>Fetching EMBL reference for an RNA sequence results
2244 fails with a sequence mismatch</li>
2245 <li>Corrupted or unreadable alignment display when
2246 scrolling alignment to right</li>
2247 <li>ArrayIndexOutOfBoundsException thrown when remove
2248 empty columns called on alignment with ragged gapped ends</li>
2249 <li>auto calculated alignment annotation rows do not get
2250 placed above or below non-autocalculated rows</li>
2251 <li>Jalview dekstop becomes sluggish at full screen in
2252 ultra-high resolution</li>
2253 <li>Cannot disable consensus calculation independently of
2254 quality and conservation</li>
2255 <li>Mouseover highlighting between cDNA and protein can
2256 become sluggish with more than one splitframe shown</li>
2257 </ul> <em>Applet Known Issues</em>
2259 <li>Core PDB parsing code requires Jmol</li>
2260 <li>Sequence canvas panel goes white when alignment
2261 window is being resized</li>
2267 <td><div align="center">
2268 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2270 <td><em>General</em>
2272 <li>Updated Java code signing certificate donated by
2274 <li>Features and annotation preserved when performing
2275 pairwise alignment</li>
2276 <li>RNA pseudoknot annotation can be
2277 imported/exported/displayed</li>
2278 <li>'colour by annotation' can colour by RNA and
2279 protein secondary structure</li>
2280 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2281 post-hoc with 2.9 release</em>)
2284 </ul> <em>Application</em>
2286 <li>Extract and display secondary structure for sequences
2287 with 3D structures</li>
2288 <li>Support for parsing RNAML</li>
2289 <li>Annotations menu for layout
2291 <li>sort sequence annotation rows by alignment</li>
2292 <li>place sequence annotation above/below alignment
2295 <li>Output in Stockholm format</li>
2296 <li>Internationalisation: improved Spanish (es)
2298 <li>Structure viewer preferences tab</li>
2299 <li>Disorder and Secondary Structure annotation tracks
2300 shared between alignments</li>
2301 <li>UCSF Chimera launch and linked highlighting from
2303 <li>Show/hide all sequence associated annotation rows for
2304 all or current selection</li>
2305 <li>disorder and secondary structure predictions
2306 available as dataset annotation</li>
2307 <li>Per-sequence rna helices colouring</li>
2310 <li>Sequence database accessions imported when fetching
2311 alignments from Rfam</li>
2312 <li>update VARNA version to 3.91</li>
2314 <li>New groovy scripts for exporting aligned positions,
2315 conservation values, and calculating sum of pairs scores.</li>
2316 <li>Command line argument to set default JABAWS server</li>
2317 <li>include installation type in build properties and
2318 console log output</li>
2319 <li>Updated Jalview project format to preserve dataset
2323 <!-- issues resolved --> <em>Application</em>
2325 <li>Distinguish alignment and sequence associated RNA
2326 structure in structure->view->VARNA</li>
2327 <li>Raise dialog box if user deletes all sequences in an
2329 <li>Pressing F1 results in documentation opening twice</li>
2330 <li>Sequence feature tooltip is wrapped</li>
2331 <li>Double click on sequence associated annotation
2332 selects only first column</li>
2333 <li>Redundancy removal doesn't result in unlinked
2334 leaves shown in tree</li>
2335 <li>Undos after several redundancy removals don't undo
2337 <li>Hide sequence doesn't hide associated annotation</li>
2338 <li>User defined colours dialog box too big to fit on
2339 screen and buttons not visible</li>
2340 <li>author list isn't updated if already written to
2341 Jalview properties</li>
2342 <li>Popup menu won't open after retrieving sequence
2344 <li>File open window for associate PDB doesn't open</li>
2345 <li>Left-then-right click on a sequence id opens a
2346 browser search window</li>
2347 <li>Cannot open sequence feature shading/sort popup menu
2348 in feature settings dialog</li>
2349 <li>better tooltip placement for some areas of Jalview
2351 <li>Allow addition of JABAWS Server which doesn't
2352 pass validation</li>
2353 <li>Web services parameters dialog box is too large to
2355 <li>Muscle nucleotide alignment preset obscured by
2357 <li>JABAWS preset submenus don't contain newly
2358 defined user preset</li>
2359 <li>MSA web services warns user if they were launched
2360 with invalid input</li>
2361 <li>Jalview cannot contact DAS Registy when running on
2364 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2365 'Superpose with' submenu not shown when new view
2369 </ul> <!-- <em>Applet</em>
2371 </ul> <em>General</em>
2373 </ul>--> <em>Deployment and Documentation</em>
2375 <li>2G and 1G options in launchApp have no effect on
2376 memory allocation</li>
2377 <li>launchApp service doesn't automatically open
2378 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2380 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2381 InstallAnywhere reports cannot find valid JVM when Java
2382 1.7_055 is available
2384 </ul> <em>Application Known issues</em>
2387 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2388 corrupted or unreadable alignment display when scrolling
2392 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2393 retrieval fails but progress bar continues for DAS retrieval
2394 with large number of ID
2397 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2398 flatfile output of visible region has incorrect sequence
2402 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2403 rna structure consensus doesn't update when secondary
2404 structure tracks are rearranged
2407 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2408 invalid rna structure positional highlighting does not
2409 highlight position of invalid base pairs
2412 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2413 out of memory errors are not raised when saving Jalview
2414 project from alignment window file menu
2417 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2418 Switching to RNA Helices colouring doesn't propagate to
2422 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2423 colour by RNA Helices not enabled when user created
2424 annotation added to alignment
2427 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2428 Jalview icon not shown on dock in Mountain Lion/Webstart
2430 </ul> <em>Applet Known Issues</em>
2433 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2434 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2437 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2438 Jalview and Jmol example not compatible with IE9
2441 <li>Sort by annotation score doesn't reverse order
2447 <td><div align="center">
2448 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2451 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2454 <li>Internationalisation of user interface (usually
2455 called i18n support) and translation for Spanish locale</li>
2456 <li>Define/Undefine group on current selection with
2457 Ctrl-G/Shift Ctrl-G</li>
2458 <li>Improved group creation/removal options in
2459 alignment/sequence Popup menu</li>
2460 <li>Sensible precision for symbol distribution
2461 percentages shown in logo tooltip.</li>
2462 <li>Annotation panel height set according to amount of
2463 annotation when alignment first opened</li>
2464 </ul> <em>Application</em>
2466 <li>Interactive consensus RNA secondary structure
2467 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2468 <li>Select columns containing particular features from
2469 Feature Settings dialog</li>
2470 <li>View all 'representative' PDB structures for selected
2472 <li>Update Jalview project format:
2474 <li>New file extension for Jalview projects '.jvp'</li>
2475 <li>Preserve sequence and annotation dataset (to
2476 store secondary structure annotation,etc)</li>
2477 <li>Per group and alignment annotation and RNA helix
2481 <li>New similarity measures for PCA and Tree calculation
2483 <li>Experimental support for retrieval and viewing of
2484 flanking regions for an alignment</li>
2488 <!-- issues resolved --> <em>Application</em>
2490 <li>logo keeps spinning and status remains at queued or
2491 running after job is cancelled</li>
2492 <li>cannot export features from alignments imported from
2493 Jalview/VAMSAS projects</li>
2494 <li>Buggy slider for web service parameters that take
2496 <li>Newly created RNA secondary structure line doesn't
2497 have 'display all symbols' flag set</li>
2498 <li>T-COFFEE alignment score shading scheme and other
2499 annotation shading not saved in Jalview project</li>
2500 <li>Local file cannot be loaded in freshly downloaded
2502 <li>Jalview icon not shown on dock in Mountain
2504 <li>Load file from desktop file browser fails</li>
2505 <li>Occasional NPE thrown when calculating large trees</li>
2506 <li>Cannot reorder or slide sequences after dragging an
2507 alignment onto desktop</li>
2508 <li>Colour by annotation dialog throws NPE after using
2509 'extract scores' function</li>
2510 <li>Loading/cut'n'pasting an empty file leads to a grey
2511 alignment window</li>
2512 <li>Disorder thresholds rendered incorrectly after
2513 performing IUPred disorder prediction</li>
2514 <li>Multiple group annotated consensus rows shown when
2515 changing 'normalise logo' display setting</li>
2516 <li>Find shows blank dialog after 'finished searching' if
2517 nothing matches query</li>
2518 <li>Null Pointer Exceptions raised when sorting by
2519 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2521 <li>Errors in Jmol console when structures in alignment
2522 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2524 <li>Not all working JABAWS services are shown in
2526 <li>JAVAWS version of Jalview fails to launch with
2527 'invalid literal/length code'</li>
2528 <li>Annotation/RNA Helix colourschemes cannot be applied
2529 to alignment with groups (actually fixed in 2.8.0b1)</li>
2530 <li>RNA Helices and T-Coffee Scores available as default
2533 </ul> <em>Applet</em>
2535 <li>Remove group option is shown even when selection is
2537 <li>Apply to all groups ticked but colourscheme changes
2538 don't affect groups</li>
2539 <li>Documented RNA Helices and T-Coffee Scores as valid
2540 colourscheme name</li>
2541 <li>Annotation labels drawn on sequence IDs when
2542 Annotation panel is not displayed</li>
2543 <li>Increased font size for dropdown menus on OSX and
2544 embedded windows</li>
2545 </ul> <em>Other</em>
2547 <li>Consensus sequence for alignments/groups with a
2548 single sequence were not calculated</li>
2549 <li>annotation files that contain only groups imported as
2550 annotation and junk sequences</li>
2551 <li>Fasta files with sequences containing '*' incorrectly
2552 recognised as PFAM or BLC</li>
2553 <li>conservation/PID slider apply all groups option
2554 doesn't affect background (2.8.0b1)
2556 <li>redundancy highlighting is erratic at 0% and 100%</li>
2557 <li>Remove gapped columns fails for sequences with ragged
2559 <li>AMSA annotation row with leading spaces is not
2560 registered correctly on import</li>
2561 <li>Jalview crashes when selecting PCA analysis for
2562 certain alignments</li>
2563 <li>Opening the colour by annotation dialog for an
2564 existing annotation based 'use original colours'
2565 colourscheme loses original colours setting</li>
2570 <td><div align="center">
2571 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2572 <em>30/1/2014</em></strong>
2576 <li>Trusted certificates for JalviewLite applet and
2577 Jalview Desktop application<br />Certificate was donated by
2578 <a href="https://www.certum.eu">Certum</a> to the Jalview
2579 open source project).
2581 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2582 <li>Output in Stockholm format</li>
2583 <li>Allow import of data from gzipped files</li>
2584 <li>Export/import group and sequence associated line
2585 graph thresholds</li>
2586 <li>Nucleotide substitution matrix that supports RNA and
2587 ambiguity codes</li>
2588 <li>Allow disorder predictions to be made on the current
2589 selection (or visible selection) in the same way that JPred
2591 <li>Groovy scripting for headless Jalview operation</li>
2592 </ul> <em>Other improvements</em>
2594 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2595 <li>COMBINE statement uses current SEQUENCE_REF and
2596 GROUP_REF scope to group annotation rows</li>
2597 <li>Support '' style escaping of quotes in Newick
2599 <li>Group options for JABAWS service by command line name</li>
2600 <li>Empty tooltip shown for JABA service options with a
2601 link but no description</li>
2602 <li>Select primary source when selecting authority in
2603 database fetcher GUI</li>
2604 <li>Add .mfa to FASTA file extensions recognised by
2606 <li>Annotation label tooltip text wrap</li>
2611 <li>Slow scrolling when lots of annotation rows are
2613 <li>Lots of NPE (and slowness) after creating RNA
2614 secondary structure annotation line</li>
2615 <li>Sequence database accessions not imported when
2616 fetching alignments from Rfam</li>
2617 <li>Incorrect SHMR submission for sequences with
2619 <li>View all structures does not always superpose
2621 <li>Option widgets in service parameters not updated to
2622 reflect user or preset settings</li>
2623 <li>Null pointer exceptions for some services without
2624 presets or adjustable parameters</li>
2625 <li>Discover PDB IDs entry in structure menu doesn't
2626 discover PDB xRefs</li>
2627 <li>Exception encountered while trying to retrieve
2628 features with DAS</li>
2629 <li>Lowest value in annotation row isn't coloured
2630 when colour by annotation (per sequence) is coloured</li>
2631 <li>Keyboard mode P jumps to start of gapped region when
2632 residue follows a gap</li>
2633 <li>Jalview appears to hang importing an alignment with
2634 Wrap as default or after enabling Wrap</li>
2635 <li>'Right click to add annotations' message
2636 shown in wrap mode when no annotations present</li>
2637 <li>Disorder predictions fail with NPE if no automatic
2638 annotation already exists on alignment</li>
2639 <li>oninit javascript function should be called after
2640 initialisation completes</li>
2641 <li>Remove redundancy after disorder prediction corrupts
2642 alignment window display</li>
2643 <li>Example annotation file in documentation is invalid</li>
2644 <li>Grouped line graph annotation rows are not exported
2645 to annotation file</li>
2646 <li>Multi-harmony analysis cannot be run when only two
2648 <li>Cannot create multiple groups of line graphs with
2649 several 'combine' statements in annotation file</li>
2650 <li>Pressing return several times causes Number Format
2651 exceptions in keyboard mode</li>
2652 <li>Multi-harmony (SHMMR) method doesn't submit
2653 correct partitions for input data</li>
2654 <li>Translation from DNA to Amino Acids fails</li>
2655 <li>Jalview fail to load newick tree with quoted label</li>
2656 <li>--headless flag isn't understood</li>
2657 <li>ClassCastException when generating EPS in headless
2659 <li>Adjusting sequence-associated shading threshold only
2660 changes one row's threshold</li>
2661 <li>Preferences and Feature settings panel panel
2662 doesn't open</li>
2663 <li>hide consensus histogram also hides conservation and
2664 quality histograms</li>
2669 <td><div align="center">
2670 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2672 <td><em>Application</em>
2674 <li>Support for JABAWS 2.0 Services (AACon alignment
2675 conservation, protein disorder and Clustal Omega)</li>
2676 <li>JABAWS server status indicator in Web Services
2678 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2679 in Jalview alignment window</li>
2680 <li>Updated Jalview build and deploy framework for OSX
2681 mountain lion, windows 7, and 8</li>
2682 <li>Nucleotide substitution matrix for PCA that supports
2683 RNA and ambiguity codes</li>
2685 <li>Improved sequence database retrieval GUI</li>
2686 <li>Support fetching and database reference look up
2687 against multiple DAS sources (Fetch all from in 'fetch db
2689 <li>Jalview project improvements
2691 <li>Store and retrieve the 'belowAlignment'
2692 flag for annotation</li>
2693 <li>calcId attribute to group annotation rows on the
2695 <li>Store AACon calculation settings for a view in
2696 Jalview project</li>
2700 <li>horizontal scrolling gesture support</li>
2701 <li>Visual progress indicator when PCA calculation is
2703 <li>Simpler JABA web services menus</li>
2704 <li>visual indication that web service results are still
2705 being retrieved from server</li>
2706 <li>Serialise the dialogs that are shown when Jalview
2707 starts up for first time</li>
2708 <li>Jalview user agent string for interacting with HTTP
2710 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2712 <li>Examples directory and Groovy library included in
2713 InstallAnywhere distribution</li>
2714 </ul> <em>Applet</em>
2716 <li>RNA alignment and secondary structure annotation
2717 visualization applet example</li>
2718 </ul> <em>General</em>
2720 <li>Normalise option for consensus sequence logo</li>
2721 <li>Reset button in PCA window to return dimensions to
2723 <li>Allow seqspace or Jalview variant of alignment PCA
2725 <li>PCA with either nucleic acid and protein substitution
2727 <li>Allow windows containing HTML reports to be exported
2729 <li>Interactive display and editing of RNA secondary
2730 structure contacts</li>
2731 <li>RNA Helix Alignment Colouring</li>
2732 <li>RNA base pair logo consensus</li>
2733 <li>Parse sequence associated secondary structure
2734 information in Stockholm files</li>
2735 <li>HTML Export database accessions and annotation
2736 information presented in tooltip for sequences</li>
2737 <li>Import secondary structure from LOCARNA clustalw
2738 style RNA alignment files</li>
2739 <li>import and visualise T-COFFEE quality scores for an
2741 <li>'colour by annotation' per sequence option to
2742 shade each sequence according to its associated alignment
2744 <li>New Jalview Logo</li>
2745 </ul> <em>Documentation and Development</em>
2747 <li>documentation for score matrices used in Jalview</li>
2748 <li>New Website!</li>
2750 <td><em>Application</em>
2752 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2753 wsdbfetch REST service</li>
2754 <li>Stop windows being moved outside desktop on OSX</li>
2755 <li>Filetype associations not installed for webstart
2757 <li>Jalview does not always retrieve progress of a JABAWS
2758 job execution in full once it is complete</li>
2759 <li>revise SHMR RSBS definition to ensure alignment is
2760 uploaded via ali_file parameter</li>
2761 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2762 <li>View all structures superposed fails with exception</li>
2763 <li>Jnet job queues forever if a very short sequence is
2764 submitted for prediction</li>
2765 <li>Cut and paste menu not opened when mouse clicked on
2767 <li>Putting fractional value into integer text box in
2768 alignment parameter dialog causes Jalview to hang</li>
2769 <li>Structure view highlighting doesn't work on
2771 <li>View all structures fails with exception shown in
2773 <li>Characters in filename associated with PDBEntry not
2774 escaped in a platform independent way</li>
2775 <li>Jalview desktop fails to launch with exception when
2777 <li>Tree calculation reports 'you must have 2 or more
2778 sequences selected' when selection is empty</li>
2779 <li>Jalview desktop fails to launch with jar signature
2780 failure when java web start temporary file caching is
2782 <li>DAS Sequence retrieval with range qualification
2783 results in sequence xref which includes range qualification</li>
2784 <li>Errors during processing of command line arguments
2785 cause progress bar (JAL-898) to be removed</li>
2786 <li>Replace comma for semi-colon option not disabled for
2787 DAS sources in sequence fetcher</li>
2788 <li>Cannot close news reader when JABAWS server warning
2789 dialog is shown</li>
2790 <li>Option widgets not updated to reflect user settings</li>
2791 <li>Edited sequence not submitted to web service</li>
2792 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2793 <li>InstallAnywhere installer doesn't unpack and run
2794 on OSX Mountain Lion</li>
2795 <li>Annotation panel not given a scroll bar when
2796 sequences with alignment annotation are pasted into the
2798 <li>Sequence associated annotation rows not associated
2799 when loaded from Jalview project</li>
2800 <li>Browser launch fails with NPE on java 1.7</li>
2801 <li>JABAWS alignment marked as finished when job was
2802 cancelled or job failed due to invalid input</li>
2803 <li>NPE with v2.7 example when clicking on Tree
2804 associated with all views</li>
2805 <li>Exceptions when copy/paste sequences with grouped
2806 annotation rows to new window</li>
2807 </ul> <em>Applet</em>
2809 <li>Sequence features are momentarily displayed before
2810 they are hidden using hidefeaturegroups applet parameter</li>
2811 <li>loading features via javascript API automatically
2812 enables feature display</li>
2813 <li>scrollToColumnIn javascript API method doesn't
2815 </ul> <em>General</em>
2817 <li>Redundancy removal fails for rna alignment</li>
2818 <li>PCA calculation fails when sequence has been selected
2819 and then deselected</li>
2820 <li>PCA window shows grey box when first opened on OSX</li>
2821 <li>Letters coloured pink in sequence logo when alignment
2822 coloured with clustalx</li>
2823 <li>Choosing fonts without letter symbols defined causes
2824 exceptions and redraw errors</li>
2825 <li>Initial PCA plot view is not same as manually
2826 reconfigured view</li>
2827 <li>Grouped annotation graph label has incorrect line
2829 <li>Grouped annotation graph label display is corrupted
2830 for lots of labels</li>
2835 <div align="center">
2836 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2839 <td><em>Application</em>
2841 <li>Jalview Desktop News Reader</li>
2842 <li>Tweaked default layout of web services menu</li>
2843 <li>View/alignment association menu to enable user to
2844 easily specify which alignment a multi-structure view takes
2845 its colours/correspondences from</li>
2846 <li>Allow properties file location to be specified as URL</li>
2847 <li>Extend Jalview project to preserve associations
2848 between many alignment views and a single Jmol display</li>
2849 <li>Store annotation row height in Jalview project file</li>
2850 <li>Annotation row column label formatting attributes
2851 stored in project file</li>
2852 <li>Annotation row order for auto-calculated annotation
2853 rows preserved in Jalview project file</li>
2854 <li>Visual progress indication when Jalview state is
2855 saved using Desktop window menu</li>
2856 <li>Visual indication that command line arguments are
2857 still being processed</li>
2858 <li>Groovy script execution from URL</li>
2859 <li>Colour by annotation default min and max colours in
2861 <li>Automatically associate PDB files dragged onto an
2862 alignment with sequences that have high similarity and
2864 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2865 <li>'view structures' option to open many
2866 structures in same window</li>
2867 <li>Sort associated views menu option for tree panel</li>
2868 <li>Group all JABA and non-JABA services for a particular
2869 analysis function in its own submenu</li>
2870 </ul> <em>Applet</em>
2872 <li>Userdefined and autogenerated annotation rows for
2874 <li>Adjustment of alignment annotation pane height</li>
2875 <li>Annotation scrollbar for annotation panel</li>
2876 <li>Drag to reorder annotation rows in annotation panel</li>
2877 <li>'automaticScrolling' parameter</li>
2878 <li>Allow sequences with partial ID string matches to be
2879 annotated from GFF/Jalview features files</li>
2880 <li>Sequence logo annotation row in applet</li>
2881 <li>Absolute paths relative to host server in applet
2882 parameters are treated as such</li>
2883 <li>New in the JalviewLite javascript API:
2885 <li>JalviewLite.js javascript library</li>
2886 <li>Javascript callbacks for
2888 <li>Applet initialisation</li>
2889 <li>Sequence/alignment mouse-overs and selections</li>
2892 <li>scrollTo row and column alignment scrolling
2894 <li>Select sequence/alignment regions from javascript</li>
2895 <li>javascript structure viewer harness to pass
2896 messages between Jmol and Jalview when running as
2897 distinct applets</li>
2898 <li>sortBy method</li>
2899 <li>Set of applet and application examples shipped
2900 with documentation</li>
2901 <li>New example to demonstrate JalviewLite and Jmol
2902 javascript message exchange</li>
2904 </ul> <em>General</em>
2906 <li>Enable Jmol displays to be associated with multiple
2907 multiple alignments</li>
2908 <li>Option to automatically sort alignment with new tree</li>
2909 <li>User configurable link to enable redirects to a
2910 www.Jalview.org mirror</li>
2911 <li>Jmol colours option for Jmol displays</li>
2912 <li>Configurable newline string when writing alignment
2913 and other flat files</li>
2914 <li>Allow alignment annotation description lines to
2915 contain html tags</li>
2916 </ul> <em>Documentation and Development</em>
2918 <li>Add groovy test harness for bulk load testing to
2920 <li>Groovy script to load and align a set of sequences
2921 using a web service before displaying the result in the
2922 Jalview desktop</li>
2923 <li>Restructured javascript and applet api documentation</li>
2924 <li>Ant target to publish example html files with applet
2926 <li>Netbeans project for building Jalview from source</li>
2927 <li>ant task to create online javadoc for Jalview source</li>
2929 <td><em>Application</em>
2931 <li>User defined colourscheme throws exception when
2932 current built in colourscheme is saved as new scheme</li>
2933 <li>AlignFrame->Save in application pops up save
2934 dialog for valid filename/format</li>
2935 <li>Cannot view associated structure for UniProt sequence</li>
2936 <li>PDB file association breaks for UniProt sequence
2938 <li>Associate PDB from file dialog does not tell you
2939 which sequence is to be associated with the file</li>
2940 <li>Find All raises null pointer exception when query
2941 only matches sequence IDs</li>
2942 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2943 <li>Jalview project with Jmol views created with Jalview
2944 2.4 cannot be loaded</li>
2945 <li>Filetype associations not installed for webstart
2947 <li>Two or more chains in a single PDB file associated
2948 with sequences in different alignments do not get coloured
2949 by their associated sequence</li>
2950 <li>Visibility status of autocalculated annotation row
2951 not preserved when project is loaded</li>
2952 <li>Annotation row height and visibility attributes not
2953 stored in Jalview project</li>
2954 <li>Tree bootstraps are not preserved when saved as a
2955 Jalview project</li>
2956 <li>Envision2 workflow tooltips are corrupted</li>
2957 <li>Enabling show group conservation also enables colour
2958 by conservation</li>
2959 <li>Duplicate group associated conservation or consensus
2960 created on new view</li>
2961 <li>Annotation scrollbar not displayed after 'show
2962 all hidden annotation rows' option selected</li>
2963 <li>Alignment quality not updated after alignment
2964 annotation row is hidden then shown</li>
2965 <li>Preserve colouring of structures coloured by
2966 sequences in pre Jalview 2.7 projects</li>
2967 <li>Web service job parameter dialog is not laid out
2969 <li>Web services menu not refreshed after 'reset
2970 services' button is pressed in preferences</li>
2971 <li>Annotation off by one in Jalview v2_3 example project</li>
2972 <li>Structures imported from file and saved in project
2973 get name like jalview_pdb1234.txt when reloaded</li>
2974 <li>Jalview does not always retrieve progress of a JABAWS
2975 job execution in full once it is complete</li>
2976 </ul> <em>Applet</em>
2978 <li>Alignment height set incorrectly when lots of
2979 annotation rows are displayed</li>
2980 <li>Relative URLs in feature HTML text not resolved to
2982 <li>View follows highlighting does not work for positions
2984 <li><= shown as = in tooltip</li>
2985 <li>Export features raises exception when no features
2987 <li>Separator string used for serialising lists of IDs
2988 for javascript api is modified when separator string
2989 provided as parameter</li>
2990 <li>Null pointer exception when selecting tree leaves for
2991 alignment with no existing selection</li>
2992 <li>Relative URLs for datasources assumed to be relative
2993 to applet's codebase</li>
2994 <li>Status bar not updated after finished searching and
2995 search wraps around to first result</li>
2996 <li>StructureSelectionManager instance shared between
2997 several Jalview applets causes race conditions and memory
2999 <li>Hover tooltip and mouseover of position on structure
3000 not sent from Jmol in applet</li>
3001 <li>Certain sequences of javascript method calls to
3002 applet API fatally hang browser</li>
3003 </ul> <em>General</em>
3005 <li>View follows structure mouseover scrolls beyond
3006 position with wrapped view and hidden regions</li>
3007 <li>Find sequence position moves to wrong residue
3008 with/without hidden columns</li>
3009 <li>Sequence length given in alignment properties window
3011 <li>InvalidNumberFormat exceptions thrown when trying to
3012 import PDB like structure files</li>
3013 <li>Positional search results are only highlighted
3014 between user-supplied sequence start/end bounds</li>
3015 <li>End attribute of sequence is not validated</li>
3016 <li>Find dialog only finds first sequence containing a
3017 given sequence position</li>
3018 <li>Sequence numbering not preserved in MSF alignment
3020 <li>Jalview PDB file reader does not extract sequence
3021 from nucleotide chains correctly</li>
3022 <li>Structure colours not updated when tree partition
3023 changed in alignment</li>
3024 <li>Sequence associated secondary structure not correctly
3025 parsed in interleaved stockholm</li>
3026 <li>Colour by annotation dialog does not restore current
3028 <li>Hiding (nearly) all sequences doesn't work
3030 <li>Sequences containing lowercase letters are not
3031 properly associated with their pdb files</li>
3032 </ul> <em>Documentation and Development</em>
3034 <li>schemas/JalviewWsParamSet.xsd corrupted by
3035 ApplyCopyright tool</li>
3040 <div align="center">
3041 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3044 <td><em>Application</em>
3046 <li>New warning dialog when the Jalview Desktop cannot
3047 contact web services</li>
3048 <li>JABA service parameters for a preset are shown in
3049 service job window</li>
3050 <li>JABA Service menu entries reworded</li>
3054 <li>Modeller PIR IO broken - cannot correctly import a
3055 pir file emitted by Jalview</li>
3056 <li>Existing feature settings transferred to new
3057 alignment view created from cut'n'paste</li>
3058 <li>Improved test for mixed amino/nucleotide chains when
3059 parsing PDB files</li>
3060 <li>Consensus and conservation annotation rows
3061 occasionally become blank for all new windows</li>
3062 <li>Exception raised when right clicking above sequences
3063 in wrapped view mode</li>
3064 </ul> <em>Application</em>
3066 <li>multiple multiply aligned structure views cause cpu
3067 usage to hit 100% and computer to hang</li>
3068 <li>Web Service parameter layout breaks for long user
3069 parameter names</li>
3070 <li>Jaba service discovery hangs desktop if Jaba server
3077 <div align="center">
3078 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3081 <td><em>Application</em>
3083 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3084 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3087 <li>Web Services preference tab</li>
3088 <li>Analysis parameters dialog box and user defined
3090 <li>Improved speed and layout of Envision2 service menu</li>
3091 <li>Superpose structures using associated sequence
3093 <li>Export coordinates and projection as CSV from PCA
3095 </ul> <em>Applet</em>
3097 <li>enable javascript: execution by the applet via the
3098 link out mechanism</li>
3099 </ul> <em>Other</em>
3101 <li>Updated the Jmol Jalview interface to work with Jmol
3103 <li>The Jalview Desktop and JalviewLite applet now
3104 require Java 1.5</li>
3105 <li>Allow Jalview feature colour specification for GFF
3106 sequence annotation files</li>
3107 <li>New 'colour by label' keword in Jalview feature file
3108 type colour specification</li>
3109 <li>New Jalview Desktop Groovy API method that allows a
3110 script to check if it being run in an interactive session or
3111 in a batch operation from the Jalview command line</li>
3115 <li>clustalx colourscheme colours Ds preferentially when
3116 both D+E are present in over 50% of the column</li>
3117 </ul> <em>Application</em>
3119 <li>typo in AlignmentFrame->View->Hide->all but
3120 selected Regions menu item</li>
3121 <li>sequence fetcher replaces ',' for ';' when the ',' is
3122 part of a valid accession ID</li>
3123 <li>fatal OOM if object retrieved by sequence fetcher
3124 runs out of memory</li>
3125 <li>unhandled Out of Memory Error when viewing pca
3126 analysis results</li>
3127 <li>InstallAnywhere builds fail to launch on OS X java
3128 10.5 update 4 (due to apple Java 1.6 update)</li>
3129 <li>Installanywhere Jalview silently fails to launch</li>
3130 </ul> <em>Applet</em>
3132 <li>Jalview.getFeatureGroups() raises an
3133 ArrayIndexOutOfBoundsException if no feature groups are
3140 <div align="center">
3141 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3147 <li>Alignment prettyprinter doesn't cope with long
3149 <li>clustalx colourscheme colours Ds preferentially when
3150 both D+E are present in over 50% of the column</li>
3151 <li>nucleic acid structures retrieved from PDB do not
3152 import correctly</li>
3153 <li>More columns get selected than were clicked on when a
3154 number of columns are hidden</li>
3155 <li>annotation label popup menu not providing correct
3156 add/hide/show options when rows are hidden or none are
3158 <li>Stockholm format shown in list of readable formats,
3159 and parser copes better with alignments from RFAM.</li>
3160 <li>CSV output of consensus only includes the percentage
3161 of all symbols if sequence logo display is enabled</li>
3163 </ul> <em>Applet</em>
3165 <li>annotation panel disappears when annotation is
3167 </ul> <em>Application</em>
3169 <li>Alignment view not redrawn properly when new
3170 alignment opened where annotation panel is visible but no
3171 annotations are present on alignment</li>
3172 <li>pasted region containing hidden columns is
3173 incorrectly displayed in new alignment window</li>
3174 <li>Jalview slow to complete operations when stdout is
3175 flooded (fix is to close the Jalview console)</li>
3176 <li>typo in AlignmentFrame->View->Hide->all but
3177 selected Rregions menu item.</li>
3178 <li>inconsistent group submenu and Format submenu entry
3179 'Un' or 'Non'conserved</li>
3180 <li>Sequence feature settings are being shared by
3181 multiple distinct alignments</li>
3182 <li>group annotation not recreated when tree partition is
3184 <li>double click on group annotation to select sequences
3185 does not propagate to associated trees</li>
3186 <li>Mac OSX specific issues:
3188 <li>exception raised when mouse clicked on desktop
3189 window background</li>
3190 <li>Desktop menu placed on menu bar and application
3191 name set correctly</li>
3192 <li>sequence feature settings not wide enough for the
3193 save feature colourscheme button</li>
3202 <div align="center">
3203 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3206 <td><em>New Capabilities</em>
3208 <li>URL links generated from description line for
3209 regular-expression based URL links (applet and application)
3211 <li>Non-positional feature URL links are shown in link
3213 <li>Linked viewing of nucleic acid sequences and
3215 <li>Automatic Scrolling option in View menu to display
3216 the currently highlighted region of an alignment.</li>
3217 <li>Order an alignment by sequence length, or using the
3218 average score or total feature count for each sequence.</li>
3219 <li>Shading features by score or associated description</li>
3220 <li>Subdivide alignment and groups based on identity of
3221 selected subsequence (Make Groups from Selection).</li>
3222 <li>New hide/show options including Shift+Control+H to
3223 hide everything but the currently selected region.</li>
3224 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3225 </ul> <em>Application</em>
3227 <li>Fetch DB References capabilities and UI expanded to
3228 support retrieval from DAS sequence sources</li>
3229 <li>Local DAS Sequence sources can be added via the
3230 command line or via the Add local source dialog box.</li>
3231 <li>DAS Dbref and DbxRef feature types are parsed as
3232 database references and protein_name is parsed as
3233 description line (BioSapiens terms).</li>
3234 <li>Enable or disable non-positional feature and database
3235 references in sequence ID tooltip from View menu in
3237 <!-- <li>New hidden columns and rows and representatives capabilities
3238 in annotations file (in progress - not yet fully implemented)</li> -->
3239 <li>Group-associated consensus, sequence logos and
3240 conservation plots</li>
3241 <li>Symbol distributions for each column can be exported
3242 and visualized as sequence logos</li>
3243 <li>Optionally scale multi-character column labels to fit
3244 within each column of annotation row<!-- todo for applet -->
3246 <li>Optional automatic sort of associated alignment view
3247 when a new tree is opened.</li>
3248 <li>Jalview Java Console</li>
3249 <li>Better placement of desktop window when moving
3250 between different screens.</li>
3251 <li>New preference items for sequence ID tooltip and
3252 consensus annotation</li>
3253 <li>Client to submit sequences and IDs to Envision2
3255 <li><em>Vamsas Capabilities</em>
3257 <li>Improved VAMSAS synchronization (Jalview archive
3258 used to preserve views, structures, and tree display
3260 <li>Import of vamsas documents from disk or URL via
3262 <li>Sharing of selected regions between views and
3263 with other VAMSAS applications (Experimental feature!)</li>
3264 <li>Updated API to VAMSAS version 0.2</li>
3266 </ul> <em>Applet</em>
3268 <li>Middle button resizes annotation row height</li>
3271 <li>sortByTree (true/false) - automatically sort the
3272 associated alignment view by the tree when a new tree is
3274 <li>showTreeBootstraps (true/false) - show or hide
3275 branch bootstraps (default is to show them if available)</li>
3276 <li>showTreeDistances (true/false) - show or hide
3277 branch lengths (default is to show them if available)</li>
3278 <li>showUnlinkedTreeNodes (true/false) - indicate if
3279 unassociated nodes should be highlighted in the tree
3281 <li>heightScale and widthScale (1.0 or more) -
3282 increase the height or width of a cell in the alignment
3283 grid relative to the current font size.</li>
3286 <li>Non-positional features displayed in sequence ID
3288 </ul> <em>Other</em>
3290 <li>Features format: graduated colour definitions and
3291 specification of feature scores</li>
3292 <li>Alignment Annotations format: new keywords for group
3293 associated annotation (GROUP_REF) and annotation row display
3294 properties (ROW_PROPERTIES)</li>
3295 <li>XML formats extended to support graduated feature
3296 colourschemes, group associated annotation, and profile
3297 visualization settings.</li></td>
3300 <li>Source field in GFF files parsed as feature source
3301 rather than description</li>
3302 <li>Non-positional features are now included in sequence
3303 feature and gff files (controlled via non-positional feature
3304 visibility in tooltip).</li>
3305 <li>URL links generated for all feature links (bugfix)</li>
3306 <li>Added URL embedding instructions to features file
3308 <li>Codons containing ambiguous nucleotides translated as
3309 'X' in peptide product</li>
3310 <li>Match case switch in find dialog box works for both
3311 sequence ID and sequence string and query strings do not
3312 have to be in upper case to match case-insensitively.</li>
3313 <li>AMSA files only contain first column of
3314 multi-character column annotation labels</li>
3315 <li>Jalview Annotation File generation/parsing consistent
3316 with documentation (e.g. Stockholm annotation can be
3317 exported and re-imported)</li>
3318 <li>PDB files without embedded PDB IDs given a friendly
3320 <li>Find incrementally searches ID string matches as well
3321 as subsequence matches, and correctly reports total number
3325 <li>Better handling of exceptions during sequence
3327 <li>Dasobert generated non-positional feature URL
3328 link text excludes the start_end suffix</li>
3329 <li>DAS feature and source retrieval buttons disabled
3330 when fetch or registry operations in progress.</li>
3331 <li>PDB files retrieved from URLs are cached properly</li>
3332 <li>Sequence description lines properly shared via
3334 <li>Sequence fetcher fetches multiple records for all
3336 <li>Ensured that command line das feature retrieval
3337 completes before alignment figures are generated.</li>
3338 <li>Reduced time taken when opening file browser for
3340 <li>isAligned check prior to calculating tree, PCA or
3341 submitting an MSA to JNet now excludes hidden sequences.</li>
3342 <li>User defined group colours properly recovered
3343 from Jalview projects.</li>
3352 <div align="center">
3353 <strong>2.4.0.b2</strong><br> 28/10/2009
3358 <li>Experimental support for google analytics usage
3360 <li>Jalview privacy settings (user preferences and docs).</li>
3365 <li>Race condition in applet preventing startup in
3367 <li>Exception when feature created from selection beyond
3368 length of sequence.</li>
3369 <li>Allow synthetic PDB files to be imported gracefully</li>
3370 <li>Sequence associated annotation rows associate with
3371 all sequences with a given id</li>
3372 <li>Find function matches case-insensitively for sequence
3373 ID string searches</li>
3374 <li>Non-standard characters do not cause pairwise
3375 alignment to fail with exception</li>
3376 </ul> <em>Application Issues</em>
3378 <li>Sequences are now validated against EMBL database</li>
3379 <li>Sequence fetcher fetches multiple records for all
3381 </ul> <em>InstallAnywhere Issues</em>
3383 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3384 issue with installAnywhere mechanism)</li>
3385 <li>Command line launching of JARs from InstallAnywhere
3386 version (java class versioning error fixed)</li>
3393 <div align="center">
3394 <strong>2.4</strong><br> 27/8/2008
3397 <td><em>User Interface</em>
3399 <li>Linked highlighting of codon and amino acid from
3400 translation and protein products</li>
3401 <li>Linked highlighting of structure associated with
3402 residue mapping to codon position</li>
3403 <li>Sequence Fetcher provides example accession numbers
3404 and 'clear' button</li>
3405 <li>MemoryMonitor added as an option under Desktop's
3407 <li>Extract score function to parse whitespace separated
3408 numeric data in description line</li>
3409 <li>Column labels in alignment annotation can be centred.</li>
3410 <li>Tooltip for sequence associated annotation give name
3412 </ul> <em>Web Services and URL fetching</em>
3414 <li>JPred3 web service</li>
3415 <li>Prototype sequence search client (no public services
3417 <li>Fetch either seed alignment or full alignment from
3419 <li>URL Links created for matching database cross
3420 references as well as sequence ID</li>
3421 <li>URL Links can be created using regular-expressions</li>
3422 </ul> <em>Sequence Database Connectivity</em>
3424 <li>Retrieval of cross-referenced sequences from other
3426 <li>Generalised database reference retrieval and
3427 validation to all fetchable databases</li>
3428 <li>Fetch sequences from DAS sources supporting the
3429 sequence command</li>
3430 </ul> <em>Import and Export</em>
3431 <li>export annotation rows as CSV for spreadsheet import</li>
3432 <li>Jalview projects record alignment dataset associations,
3433 EMBL products, and cDNA sequence mappings</li>
3434 <li>Sequence Group colour can be specified in Annotation
3436 <li>Ad-hoc colouring of group in Annotation File using RGB
3437 triplet as name of colourscheme</li>
3438 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3440 <li>treenode binding for VAMSAS tree exchange</li>
3441 <li>local editing and update of sequences in VAMSAS
3442 alignments (experimental)</li>
3443 <li>Create new or select existing session to join</li>
3444 <li>load and save of vamsas documents</li>
3445 </ul> <em>Application command line</em>
3447 <li>-tree parameter to open trees (introduced for passing
3449 <li>-fetchfrom command line argument to specify nicknames
3450 of DAS servers to query for alignment features</li>
3451 <li>-dasserver command line argument to add new servers
3452 that are also automatically queried for features</li>
3453 <li>-groovy command line argument executes a given groovy
3454 script after all input data has been loaded and parsed</li>
3455 </ul> <em>Applet-Application data exchange</em>
3457 <li>Trees passed as applet parameters can be passed to
3458 application (when using "View in full
3459 application")</li>
3460 </ul> <em>Applet Parameters</em>
3462 <li>feature group display control parameter</li>
3463 <li>debug parameter</li>
3464 <li>showbutton parameter</li>
3465 </ul> <em>Applet API methods</em>
3467 <li>newView public method</li>
3468 <li>Window (current view) specific get/set public methods</li>
3469 <li>Feature display control methods</li>
3470 <li>get list of currently selected sequences</li>
3471 </ul> <em>New Jalview distribution features</em>
3473 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3474 <li>RELEASE file gives build properties for the latest
3475 Jalview release.</li>
3476 <li>Java 1.1 Applet build made easier and donotobfuscate
3477 property controls execution of obfuscator</li>
3478 <li>Build target for generating source distribution</li>
3479 <li>Debug flag for javacc</li>
3480 <li>.jalview_properties file is documented (slightly) in
3481 jalview.bin.Cache</li>
3482 <li>Continuous Build Integration for stable and
3483 development version of Application, Applet and source
3488 <li>selected region output includes visible annotations
3489 (for certain formats)</li>
3490 <li>edit label/displaychar contains existing label/char
3492 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3493 <li>shorter peptide product names from EMBL records</li>
3494 <li>Newick string generator makes compact representations</li>
3495 <li>bootstrap values parsed correctly for tree files with
3497 <li>pathological filechooser bug avoided by not allowing
3498 filenames containing a ':'</li>
3499 <li>Fixed exception when parsing GFF files containing
3500 global sequence features</li>
3501 <li>Alignment datasets are finalized only when number of
3502 references from alignment sequences goes to zero</li>
3503 <li>Close of tree branch colour box without colour
3504 selection causes cascading exceptions</li>
3505 <li>occasional negative imgwidth exceptions</li>
3506 <li>better reporting of non-fatal warnings to user when
3507 file parsing fails.</li>
3508 <li>Save works when Jalview project is default format</li>
3509 <li>Save as dialog opened if current alignment format is
3510 not a valid output format</li>
3511 <li>UniProt canonical names introduced for both das and
3513 <li>Histidine should be midblue (not pink!) in Zappo</li>
3514 <li>error messages passed up and output when data read
3516 <li>edit undo recovers previous dataset sequence when
3517 sequence is edited</li>
3518 <li>allow PDB files without pdb ID HEADER lines (like
3519 those generated by MODELLER) to be read in properly</li>
3520 <li>allow reading of JPred concise files as a normal
3522 <li>Stockholm annotation parsing and alignment properties
3523 import fixed for PFAM records</li>
3524 <li>Structure view windows have correct name in Desktop
3526 <li>annotation consisting of sequence associated scores
3527 can be read and written correctly to annotation file</li>
3528 <li>Aligned cDNA translation to aligned peptide works
3530 <li>Fixed display of hidden sequence markers and
3531 non-italic font for representatives in Applet</li>
3532 <li>Applet Menus are always embedded in applet window on
3534 <li>Newly shown features appear at top of stack (in
3536 <li>Annotations added via parameter not drawn properly
3537 due to null pointer exceptions</li>
3538 <li>Secondary structure lines are drawn starting from
3539 first column of alignment</li>
3540 <li>UniProt XML import updated for new schema release in
3542 <li>Sequence feature to sequence ID match for Features
3543 file is case-insensitive</li>
3544 <li>Sequence features read from Features file appended to
3545 all sequences with matching IDs</li>
3546 <li>PDB structure coloured correctly for associated views
3547 containing a sub-sequence</li>
3548 <li>PDB files can be retrieved by applet from Jar files</li>
3549 <li>feature and annotation file applet parameters
3550 referring to different directories are retrieved correctly</li>
3551 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3552 <li>Fixed application hang whilst waiting for
3553 splash-screen version check to complete</li>
3554 <li>Applet properly URLencodes input parameter values
3555 when passing them to the launchApp service</li>
3556 <li>display name and local features preserved in results
3557 retrieved from web service</li>
3558 <li>Visual delay indication for sequence retrieval and
3559 sequence fetcher initialisation</li>
3560 <li>updated Application to use DAS 1.53e version of
3561 dasobert DAS client</li>
3562 <li>Re-instated Full AMSA support and .amsa file
3564 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3572 <div align="center">
3573 <strong>2.3</strong><br> 9/5/07
3578 <li>Jmol 11.0.2 integration</li>
3579 <li>PDB views stored in Jalview XML files</li>
3580 <li>Slide sequences</li>
3581 <li>Edit sequence in place</li>
3582 <li>EMBL CDS features</li>
3583 <li>DAS Feature mapping</li>
3584 <li>Feature ordering</li>
3585 <li>Alignment Properties</li>
3586 <li>Annotation Scores</li>
3587 <li>Sort by scores</li>
3588 <li>Feature/annotation editing in applet</li>
3593 <li>Headless state operation in 2.2.1</li>
3594 <li>Incorrect and unstable DNA pairwise alignment</li>
3595 <li>Cut and paste of sequences with annotation</li>
3596 <li>Feature group display state in XML</li>
3597 <li>Feature ordering in XML</li>
3598 <li>blc file iteration selection using filename # suffix</li>
3599 <li>Stockholm alignment properties</li>
3600 <li>Stockhom alignment secondary structure annotation</li>
3601 <li>2.2.1 applet had no feature transparency</li>
3602 <li>Number pad keys can be used in cursor mode</li>
3603 <li>Structure Viewer mirror image resolved</li>
3610 <div align="center">
3611 <strong>2.2.1</strong><br> 12/2/07
3616 <li>Non standard characters can be read and displayed
3617 <li>Annotations/Features can be imported/exported to the
3619 <li>Applet allows editing of sequence/annotation/group
3620 name & description
3621 <li>Preference setting to display sequence name in
3623 <li>Annotation file format extended to allow
3624 Sequence_groups to be defined
3625 <li>Default opening of alignment overview panel can be
3626 specified in preferences
3627 <li>PDB residue numbering annotation added to associated
3633 <li>Applet crash under certain Linux OS with Java 1.6
3635 <li>Annotation file export / import bugs fixed
3636 <li>PNG / EPS image output bugs fixed
3642 <div align="center">
3643 <strong>2.2</strong><br> 27/11/06
3648 <li>Multiple views on alignment
3649 <li>Sequence feature editing
3650 <li>"Reload" alignment
3651 <li>"Save" to current filename
3652 <li>Background dependent text colour
3653 <li>Right align sequence ids
3654 <li>User-defined lower case residue colours
3657 <li>Menu item accelerator keys
3658 <li>Control-V pastes to current alignment
3659 <li>Cancel button for DAS Feature Fetching
3660 <li>PCA and PDB Viewers zoom via mouse roller
3661 <li>User-defined sub-tree colours and sub-tree selection
3663 <li>'New Window' button on the 'Output to Text box'
3668 <li>New memory efficient Undo/Redo System
3669 <li>Optimised symbol lookups and conservation/consensus
3671 <li>Region Conservation/Consensus recalculated after
3673 <li>Fixed Remove Empty Columns Bug (empty columns at end
3675 <li>Slowed DAS Feature Fetching for increased robustness.
3677 <li>Made angle brackets in ASCII feature descriptions
3679 <li>Re-instated Zoom function for PCA
3680 <li>Sequence descriptions conserved in web service
3682 <li>UniProt ID discoverer uses any word separated by
3684 <li>WsDbFetch query/result association resolved
3685 <li>Tree leaf to sequence mapping improved
3686 <li>Smooth fonts switch moved to FontChooser dialog box.
3693 <div align="center">
3694 <strong>2.1.1</strong><br> 12/9/06
3699 <li>Copy consensus sequence to clipboard</li>
3704 <li>Image output - rightmost residues are rendered if
3705 sequence id panel has been resized</li>
3706 <li>Image output - all offscreen group boundaries are
3708 <li>Annotation files with sequence references - all
3709 elements in file are relative to sequence position</li>
3710 <li>Mac Applet users can use Alt key for group editing</li>
3716 <div align="center">
3717 <strong>2.1</strong><br> 22/8/06
3722 <li>MAFFT Multiple Alignment in default Web Service list</li>
3723 <li>DAS Feature fetching</li>
3724 <li>Hide sequences and columns</li>
3725 <li>Export Annotations and Features</li>
3726 <li>GFF file reading / writing</li>
3727 <li>Associate structures with sequences from local PDB
3729 <li>Add sequences to exisiting alignment</li>
3730 <li>Recently opened files / URL lists</li>
3731 <li>Applet can launch the full application</li>
3732 <li>Applet has transparency for features (Java 1.2
3734 <li>Applet has user defined colours parameter</li>
3735 <li>Applet can load sequences from parameter
3736 "sequence<em>x</em>"
3742 <li>Redundancy Panel reinstalled in the Applet</li>
3743 <li>Monospaced font - EPS / rescaling bug fixed</li>
3744 <li>Annotation files with sequence references bug fixed</li>
3750 <div align="center">
3751 <strong>2.08.1</strong><br> 2/5/06
3756 <li>Change case of selected region from Popup menu</li>
3757 <li>Choose to match case when searching</li>
3758 <li>Middle mouse button and mouse movement can compress /
3759 expand the visible width and height of the alignment</li>
3764 <li>Annotation Panel displays complete JNet results</li>
3770 <div align="center">
3771 <strong>2.08b</strong><br> 18/4/06
3777 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3778 <li>Righthand label on wrapped alignments shows correct
3785 <div align="center">
3786 <strong>2.08</strong><br> 10/4/06
3791 <li>Editing can be locked to the selection area</li>
3792 <li>Keyboard editing</li>
3793 <li>Create sequence features from searches</li>
3794 <li>Precalculated annotations can be loaded onto
3796 <li>Features file allows grouping of features</li>
3797 <li>Annotation Colouring scheme added</li>
3798 <li>Smooth fonts off by default - Faster rendering</li>
3799 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3804 <li>Drag & Drop fixed on Linux</li>
3805 <li>Jalview Archive file faster to load/save, sequence
3806 descriptions saved.</li>
3812 <div align="center">
3813 <strong>2.07</strong><br> 12/12/05
3818 <li>PDB Structure Viewer enhanced</li>
3819 <li>Sequence Feature retrieval and display enhanced</li>
3820 <li>Choose to output sequence start-end after sequence
3821 name for file output</li>
3822 <li>Sequence Fetcher WSDBFetch@EBI</li>
3823 <li>Applet can read feature files, PDB files and can be
3824 used for HTML form input</li>
3829 <li>HTML output writes groups and features</li>
3830 <li>Group editing is Control and mouse click</li>
3831 <li>File IO bugs</li>
3837 <div align="center">
3838 <strong>2.06</strong><br> 28/9/05
3843 <li>View annotations in wrapped mode</li>
3844 <li>More options for PCA viewer</li>
3849 <li>GUI bugs resolved</li>
3850 <li>Runs with -nodisplay from command line</li>
3856 <div align="center">
3857 <strong>2.05b</strong><br> 15/9/05
3862 <li>Choose EPS export as lineart or text</li>
3863 <li>Jar files are executable</li>
3864 <li>Can read in Uracil - maps to unknown residue</li>
3869 <li>Known OutOfMemory errors give warning message</li>
3870 <li>Overview window calculated more efficiently</li>
3871 <li>Several GUI bugs resolved</li>
3877 <div align="center">
3878 <strong>2.05</strong><br> 30/8/05
3883 <li>Edit and annotate in "Wrapped" view</li>
3888 <li>Several GUI bugs resolved</li>
3894 <div align="center">
3895 <strong>2.04</strong><br> 24/8/05
3900 <li>Hold down mouse wheel & scroll to change font
3906 <li>Improved JPred client reliability</li>
3907 <li>Improved loading of Jalview files</li>
3913 <div align="center">
3914 <strong>2.03</strong><br> 18/8/05
3919 <li>Set Proxy server name and port in preferences</li>
3920 <li>Multiple URL links from sequence ids</li>
3921 <li>User Defined Colours can have a scheme name and added
3923 <li>Choose to ignore gaps in consensus calculation</li>
3924 <li>Unix users can set default web browser</li>
3925 <li>Runs without GUI for batch processing</li>
3926 <li>Dynamically generated Web Service Menus</li>
3931 <li>InstallAnywhere download for Sparc Solaris</li>
3937 <div align="center">
3938 <strong>2.02</strong><br> 18/7/05
3944 <li>Copy & Paste order of sequences maintains
3945 alignment order.</li>
3951 <div align="center">
3952 <strong>2.01</strong><br> 12/7/05
3957 <li>Use delete key for deleting selection.</li>
3958 <li>Use Mouse wheel to scroll sequences.</li>
3959 <li>Help file updated to describe how to add alignment
3961 <li>Version and build date written to build properties
3963 <li>InstallAnywhere installation will check for updates
3964 at launch of Jalview.</li>
3969 <li>Delete gaps bug fixed.</li>
3970 <li>FileChooser sorts columns.</li>
3971 <li>Can remove groups one by one.</li>
3972 <li>Filechooser icons installed.</li>
3973 <li>Finder ignores return character when searching.
3974 Return key will initiate a search.<br>
3981 <div align="center">
3982 <strong>2.0</strong><br> 20/6/05
3987 <li>New codebase</li>