3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
81 control superposition of multiple structures and open
82 structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
98 <!-- JAL-2593 -->Improved performance when rendering lots
104 <td><div align="left">
107 <!-- JAL-2899 -->Structure and Overview aren't updated
108 when Colour By Annotation threshold slider is adjusted
111 <!-- JAL-2778 -->Slow redraw when Overview panel shown
112 overlapping alignment panel
115 <!-- JAL-2666 -->Linked scrolling via protein horizontal
116 scroll bar doesn't work for some CDS/Protein views
119 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
120 Java 1.8u153 onwards and Java 1.9u4+.
123 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
124 columns in annotation row
127 <!-- JAL-2913 -->Preferences panel's ID Width control is
128 honored in interactive and batch mode
131 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
132 for structures added to existing Jmol view
135 <!-- JAL-2223 -->'View Mappings' includes duplicate
136 entries after importing project with multiple views
139 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
140 protein sequences via SIFTS from associated PDB entries
141 with negative residue numbers or missing residues fails
144 <!-- JAL-2952 -->Exception when shading sequence with negative
145 Temperature Factor values from annotated PDB files (e.g.
146 as generated by CONSURF)
149 <!-- JAL-2954 -->Selecting columns from highlighted regions
150 very slow for alignments with large numbers of sequences
153 <!-- JAL-2925 -->Copy Consensus fails for group consensus
154 with 'StringIndexOutOfBounds'
157 <!-- JAL-2976 -->VAqua(4) (<a
158 href="http://violetlib.org/vaqua/overview.html">download
159 here</a>) provided as fallback Look and Feel for OSX
160 platforms running Java 10
166 <!-- JAL-2926 -->Copy consensus sequence option in applet
167 should copy the group consensus when popup is opened on it
171 <em>New Known Defects</em>
174 <!-- JAL-2973 --> Exceptions occasionally raised when
175 editing a large alignment and overview is displayed
178 <!-- JAL-2974 -->'Overview updating' progress bar is shown
179 repeatedly after a series of edits even when the overview
180 is no longer reflecting updates
183 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
184 structures for protein subsequence (if 'Trim Retrieved
185 Sequences' enabled) or Ensembl isoforms (Workaround in
186 2.10.4 is to fail back to N&W mapping)
193 <td width="60" nowrap>
195 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
198 <td><div align="left">
199 <ul><li>Updated Certum Codesigning Certificate
200 (Valid till 30th November 2018)</li></ul></div></td>
201 <td><div align="left">
204 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
205 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
206 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
207 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
208 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
209 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
210 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
216 <td width="60" nowrap>
218 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
221 <td><div align="left">
225 <!-- JAL-2446 -->Faster and more efficient management and
226 rendering of sequence features
229 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
230 429 rate limit request hander
233 <!-- JAL-2773 -->Structure views don't get updated unless
234 their colours have changed
237 <!-- JAL-2495 -->All linked sequences are highlighted for
238 a structure mousover (Jmol) or selection (Chimera)
241 <!-- JAL-2790 -->'Cancel' button in progress bar for
242 JABAWS AACon, RNAAliFold and Disorder prediction jobs
245 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
246 view from Ensembl locus cross-references
249 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
253 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
254 feature can be disabled
257 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
258 PDB easier retrieval of sequences for lists of IDs
261 <!-- JAL-2758 -->Short names for sequences retrieved from
267 <li>Groovy interpreter updated to 2.4.12</li>
268 <li>Example groovy script for generating a matrix of
269 percent identity scores for current alignment.</li>
271 <em>Testing and Deployment</em>
274 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
278 <td><div align="left">
282 <!-- JAL-2643 -->Pressing tab after updating the colour
283 threshold text field doesn't trigger an update to the
287 <!-- JAL-2682 -->Race condition when parsing sequence ID
291 <!-- JAL-2608 -->Overview windows are also closed when
292 alignment window is closed
295 <!-- JAL-2548 -->Export of features doesn't always respect
299 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
300 takes a long time in Cursor mode
306 <!-- JAL-2777 -->Structures with whitespace chainCode
307 cannot be viewed in Chimera
310 <!-- JAL-2728 -->Protein annotation panel too high in
314 <!-- JAL-2757 -->Can't edit the query after the server
315 error warning icon is shown in Uniprot and PDB Free Text
319 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
322 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
325 <!-- JAL-2739 -->Hidden column marker in last column not
326 rendered when switching back from Wrapped to normal view
329 <!-- JAL-2768 -->Annotation display corrupted when
330 scrolling right in unwapped alignment view
333 <!-- JAL-2542 -->Existing features on subsequence
334 incorrectly relocated when full sequence retrieved from
338 <!-- JAL-2733 -->Last reported memory still shown when
339 Desktop->Show Memory is unticked (OSX only)
342 <!-- JAL-2658 -->Amend Features dialog doesn't allow
343 features of same type and group to be selected for
347 <!-- JAL-2524 -->Jalview becomes sluggish in wide
348 alignments when hidden columns are present
351 <!-- JAL-2392 -->Jalview freezes when loading and
352 displaying several structures
355 <!-- JAL-2732 -->Black outlines left after resizing or
359 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
360 within the Jalview desktop on OSX
363 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
364 when in wrapped alignment mode
367 <!-- JAL-2636 -->Scale mark not shown when close to right
368 hand end of alignment
371 <!-- JAL-2684 -->Pairwise alignment of selected regions of
372 each selected sequence do not have correct start/end
376 <!-- JAL-2793 -->Alignment ruler height set incorrectly
377 after canceling the Alignment Window's Font dialog
380 <!-- JAL-2036 -->Show cross-references not enabled after
381 restoring project until a new view is created
384 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
385 URL links appears when only default EMBL-EBI link is
386 configured (since 2.10.2b2)
389 <!-- JAL-2775 -->Overview redraws whole window when box
393 <!-- JAL-2225 -->Structure viewer doesn't map all chains
394 in a multi-chain structure when viewing alignment
395 involving more than one chain (since 2.10)
398 <!-- JAL-2811 -->Double residue highlights in cursor mode
399 if new selection moves alignment window
402 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
403 arrow key in cursor mode to pass hidden column marker
406 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
407 that produces correctly annotated transcripts and products
410 <!-- JAL-2776 -->Toggling a feature group after first time
411 doesn't update associated structure view
414 <em>Applet</em><br />
417 <!-- JAL-2687 -->Concurrent modification exception when
418 closing alignment panel
421 <em>BioJSON</em><br />
424 <!-- JAL-2546 -->BioJSON export does not preserve
425 non-positional features
428 <em>New Known Issues</em>
431 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
432 sequence features correctly (for many previous versions of
436 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
437 using cursor in wrapped panel other than top
440 <!-- JAL-2791 -->Select columns containing feature ignores
441 graduated colour threshold
444 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
445 always preserve numbering and sequence features
448 <em>Known Java 9 Issues</em>
451 <!-- JAL-2902 -->Groovy Console very slow to open and is
452 not responsive when entering characters (Webstart, Java
459 <td width="60" nowrap>
461 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
462 <em>2/10/2017</em></strong>
465 <td><div align="left">
466 <em>New features in Jalview Desktop</em>
469 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
471 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
475 <td><div align="left">
479 <td width="60" nowrap>
481 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
482 <em>7/9/2017</em></strong>
485 <td><div align="left">
489 <!-- JAL-2588 -->Show gaps in overview window by colouring
490 in grey (sequences used to be coloured grey, and gaps were
494 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
498 <!-- JAL-2587 -->Overview updates immediately on increase
499 in size and progress bar shown as higher resolution
500 overview is recalculated
505 <td><div align="left">
509 <!-- JAL-2664 -->Overview window redraws every hidden
510 column region row by row
513 <!-- JAL-2681 -->duplicate protein sequences shown after
514 retrieving Ensembl crossrefs for sequences from Uniprot
517 <!-- JAL-2603 -->Overview window throws NPE if show boxes
518 format setting is unticked
521 <!-- JAL-2610 -->Groups are coloured wrongly in overview
522 if group has show boxes format setting unticked
525 <!-- JAL-2672,JAL-2665 -->Redraw problems when
526 autoscrolling whilst dragging current selection group to
527 include sequences and columns not currently displayed
530 <!-- JAL-2691 -->Not all chains are mapped when multimeric
531 assemblies are imported via CIF file
534 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
535 displayed when threshold or conservation colouring is also
539 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
543 <!-- JAL-2673 -->Jalview continues to scroll after
544 dragging a selected region off the visible region of the
548 <!-- JAL-2724 -->Cannot apply annotation based
549 colourscheme to all groups in a view
552 <!-- JAL-2511 -->IDs don't line up with sequences
553 initially after font size change using the Font chooser or
560 <td width="60" nowrap>
562 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
565 <td><div align="left">
566 <em>Calculations</em>
570 <!-- JAL-1933 -->Occupancy annotation row shows number of
571 ungapped positions in each column of the alignment.
574 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
575 a calculation dialog box
578 <!-- JAL-2379 -->Revised implementation of PCA for speed
579 and memory efficiency (~30x faster)
582 <!-- JAL-2403 -->Revised implementation of sequence
583 similarity scores as used by Tree, PCA, Shading Consensus
584 and other calculations
587 <!-- JAL-2416 -->Score matrices are stored as resource
588 files within the Jalview codebase
591 <!-- JAL-2500 -->Trees computed on Sequence Feature
592 Similarity may have different topology due to increased
599 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
600 model for alignments and groups
603 <!-- JAL-384 -->Custom shading schemes created via groovy
610 <!-- JAL-2526 -->Efficiency improvements for interacting
611 with alignment and overview windows
614 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
618 <!-- JAL-2388 -->Hidden columns and sequences can be
622 <!-- JAL-2611 -->Click-drag in visible area allows fine
623 adjustment of visible position
627 <em>Data import/export</em>
630 <!-- JAL-2535 -->Posterior probability annotation from
631 Stockholm files imported as sequence associated annotation
634 <!-- JAL-2507 -->More robust per-sequence positional
635 annotation input/output via stockholm flatfile
638 <!-- JAL-2533 -->Sequence names don't include file
639 extension when importing structure files without embedded
640 names or PDB accessions
643 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
644 format sequence substitution matrices
647 <em>User Interface</em>
650 <!-- JAL-2447 --> Experimental Features Checkbox in
651 Desktop's Tools menu to hide or show untested features in
655 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
656 via Overview or sequence motif search operations
659 <!-- JAL-2547 -->Amend sequence features dialog box can be
660 opened by double clicking gaps within sequence feature
664 <!-- JAL-1476 -->Status bar message shown when not enough
665 aligned positions were available to create a 3D structure
669 <em>3D Structure</em>
672 <!-- JAL-2430 -->Hidden regions in alignment views are not
673 coloured in linked structure views
676 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
677 file-based command exchange
680 <!-- JAL-2375 -->Structure chooser automatically shows
681 Cached Structures rather than querying the PDBe if
682 structures are already available for sequences
685 <!-- JAL-2520 -->Structures imported via URL are cached in
686 the Jalview project rather than downloaded again when the
690 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
691 to transfer Chimera's structure attributes as Jalview
692 features, and vice-versa (<strong>Experimental
696 <em>Web Services</em>
699 <!-- JAL-2549 -->Updated JABAWS client to v2.2
702 <!-- JAL-2335 -->Filter non-standard amino acids and
703 nucleotides when submitting to AACon and other MSA
707 <!-- JAL-2316, -->URLs for viewing database
708 cross-references provided by identifiers.org and the
716 <!-- JAL-2344 -->FileFormatI interface for describing and
717 identifying file formats (instead of String constants)
720 <!-- JAL-2228 -->FeatureCounter script refactored for
721 efficiency when counting all displayed features (not
722 backwards compatible with 2.10.1)
725 <em>Example files</em>
728 <!-- JAL-2631 -->Graduated feature colour style example
729 included in the example feature file
732 <em>Documentation</em>
735 <!-- JAL-2339 -->Release notes reformatted for readability
736 with the built-in Java help viewer
739 <!-- JAL-1644 -->Find documentation updated with 'search
740 sequence description' option
746 <!-- JAL-2485, -->External service integration tests for
747 Uniprot REST Free Text Search Client
750 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
753 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
758 <td><div align="left">
759 <em>Calculations</em>
762 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
763 matrix - C->R should be '-3'<br />Old matrix restored
764 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
766 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
767 Jalview's treatment of gaps in PCA and substitution matrix
768 based Tree calculations.<br /> <br />In earlier versions
769 of Jalview, gaps matching gaps were penalised, and gaps
770 matching non-gaps penalised even more. In the PCA
771 calculation, gaps were actually treated as non-gaps - so
772 different costs were applied, which meant Jalview's PCAs
773 were different to those produced by SeqSpace.<br />Jalview
774 now treats gaps in the same way as SeqSpace (ie it scores
775 them as 0). <br /> <br />Enter the following in the
776 Groovy console to restore pre-2.10.2 behaviour:<br />
777 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
778 // for 2.10.1 mode <br />
779 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
780 // to restore 2.10.2 mode <br /> <br /> <em>Note:
781 these settings will affect all subsequent tree and PCA
782 calculations (not recommended)</em></li>
784 <!-- JAL-2424 -->Fixed off-by-one bug that affected
785 scaling of branch lengths for trees computed using
786 Sequence Feature Similarity.
789 <!-- JAL-2377 -->PCA calculation could hang when
790 generating output report when working with highly
794 <!-- JAL-2544 --> Sort by features includes features to
795 right of selected region when gaps present on right-hand
799 <em>User Interface</em>
802 <!-- JAL-2346 -->Reopening Colour by annotation dialog
803 doesn't reselect a specific sequence's associated
804 annotation after it was used for colouring a view
807 <!-- JAL-2419 -->Current selection lost if popup menu
808 opened on a region of alignment without groups
811 <!-- JAL-2374 -->Popup menu not always shown for regions
812 of an alignment with overlapping groups
815 <!-- JAL-2310 -->Finder double counts if both a sequence's
816 name and description match
819 <!-- JAL-2370 -->Hiding column selection containing two
820 hidden regions results in incorrect hidden regions
823 <!-- JAL-2386 -->'Apply to all groups' setting when
824 changing colour does not apply Conservation slider value
828 <!-- JAL-2373 -->Percentage identity and conservation menu
829 items do not show a tick or allow shading to be disabled
832 <!-- JAL-2385 -->Conservation shading or PID threshold
833 lost when base colourscheme changed if slider not visible
836 <!-- JAL-2547 -->Sequence features shown in tooltip for
837 gaps before start of features
840 <!-- JAL-2623 -->Graduated feature colour threshold not
841 restored to UI when feature colour is edited
844 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
845 a time when scrolling vertically in wrapped mode.
848 <!-- JAL-2630 -->Structure and alignment overview update
849 as graduate feature colour settings are modified via the
853 <!-- JAL-2034 -->Overview window doesn't always update
854 when a group defined on the alignment is resized
857 <!-- JAL-2605 -->Mouseovers on left/right scale region in
858 wrapped view result in positional status updates
862 <!-- JAL-2563 -->Status bar doesn't show position for
863 ambiguous amino acid and nucleotide symbols
866 <!-- JAL-2602 -->Copy consensus sequence failed if
867 alignment included gapped columns
870 <!-- JAL-2473 -->Minimum size set for Jalview windows so
871 widgets don't permanently disappear
874 <!-- JAL-2503 -->Cannot select or filter quantitative
875 annotation that are shown only as column labels (e.g.
876 T-Coffee column reliability scores)
879 <!-- JAL-2594 -->Exception thrown if trying to create a
880 sequence feature on gaps only
883 <!-- JAL-2504 -->Features created with 'New feature'
884 button from a Find inherit previously defined feature type
885 rather than the Find query string
888 <!-- JAL-2423 -->incorrect title in output window when
889 exporting tree calculated in Jalview
892 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
893 and then revealing them reorders sequences on the
897 <!-- JAL-964 -->Group panel in sequence feature settings
898 doesn't update to reflect available set of groups after
899 interactively adding or modifying features
902 <!-- JAL-2225 -->Sequence Database chooser unusable on
906 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
907 only excluded gaps in current sequence and ignored
914 <!-- JAL-2421 -->Overview window visible region moves
915 erratically when hidden rows or columns are present
918 <!-- JAL-2362 -->Per-residue colourschemes applied via the
919 Structure Viewer's colour menu don't correspond to
923 <!-- JAL-2405 -->Protein specific colours only offered in
924 colour and group colour menu for protein alignments
927 <!-- JAL-2385 -->Colour threshold slider doesn't update to
928 reflect currently selected view or group's shading
932 <!-- JAL-2624 -->Feature colour thresholds not respected
933 when rendered on overview and structures when opacity at
937 <!-- JAL-2589 -->User defined gap colour not shown in
938 overview when features overlaid on alignment
941 <em>Data import/export</em>
944 <!-- JAL-2576 -->Very large alignments take a long time to
948 <!-- JAL-2507 -->Per-sequence RNA secondary structures
949 added after a sequence was imported are not written to
953 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
954 when importing RNA secondary structure via Stockholm
957 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
958 not shown in correct direction for simple pseudoknots
961 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
962 with lightGray or darkGray via features file (but can
966 <!-- JAL-2383 -->Above PID colour threshold not recovered
967 when alignment view imported from project
970 <!-- JAL-2520,JAL-2465 -->No mappings generated between
971 structure and sequences extracted from structure files
972 imported via URL and viewed in Jmol
975 <!-- JAL-2520 -->Structures loaded via URL are saved in
976 Jalview Projects rather than fetched via URL again when
977 the project is loaded and the structure viewed
980 <em>Web Services</em>
983 <!-- JAL-2519 -->EnsemblGenomes example failing after
984 release of Ensembl v.88
987 <!-- JAL-2366 -->Proxy server address and port always
988 appear enabled in Preferences->Connections
991 <!-- JAL-2461 -->DAS registry not found exceptions
992 removed from console output
995 <!-- JAL-2582 -->Cannot retrieve protein products from
996 Ensembl by Peptide ID
999 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1000 created from SIFTs, and spurious 'Couldn't open structure
1001 in Chimera' errors raised after April 2017 update (problem
1002 due to 'null' string rather than empty string used for
1003 residues with no corresponding PDB mapping).
1006 <em>Application UI</em>
1009 <!-- JAL-2361 -->User Defined Colours not added to Colour
1013 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1014 case' residues (button in colourscheme editor debugged and
1015 new documentation and tooltips added)
1018 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1019 doesn't restore group-specific text colour thresholds
1022 <!-- JAL-2243 -->Feature settings panel does not update as
1023 new features are added to alignment
1026 <!-- JAL-2532 -->Cancel in feature settings reverts
1027 changes to feature colours via the Amend features dialog
1030 <!-- JAL-2506 -->Null pointer exception when attempting to
1031 edit graduated feature colour via amend features dialog
1035 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1036 selection menu changes colours of alignment views
1039 <!-- JAL-2426 -->Spurious exceptions in console raised
1040 from alignment calculation workers after alignment has
1044 <!-- JAL-1608 -->Typo in selection popup menu - Create
1045 groups now 'Create Group'
1048 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1049 Create/Undefine group doesn't always work
1052 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1053 shown again after pressing 'Cancel'
1056 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1057 adjusts start position in wrap mode
1060 <!-- JAL-2563 -->Status bar doesn't show positions for
1061 ambiguous amino acids
1064 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1065 CDS/Protein view after CDS sequences added for aligned
1069 <!-- JAL-2592 -->User defined colourschemes called 'User
1070 Defined' don't appear in Colours menu
1076 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1077 score models doesn't always result in an updated PCA plot
1080 <!-- JAL-2442 -->Features not rendered as transparent on
1081 overview or linked structure view
1084 <!-- JAL-2372 -->Colour group by conservation doesn't
1088 <!-- JAL-2517 -->Hitting Cancel after applying
1089 user-defined colourscheme doesn't restore original
1096 <!-- JAL-2314 -->Unit test failure:
1097 jalview.ws.jabaws.RNAStructExportImport setup fails
1100 <!-- JAL-2307 -->Unit test failure:
1101 jalview.ws.sifts.SiftsClientTest due to compatibility
1102 problems with deep array comparison equality asserts in
1103 successive versions of TestNG
1106 <!-- JAL-2479 -->Relocated StructureChooserTest and
1107 ParameterUtilsTest Unit tests to Network suite
1110 <em>New Known Issues</em>
1113 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1114 phase after a sequence motif find operation
1117 <!-- JAL-2550 -->Importing annotation file with rows
1118 containing just upper and lower case letters are
1119 interpreted as WUSS RNA secondary structure symbols
1122 <!-- JAL-2590 -->Cannot load and display Newick trees
1123 reliably from eggnog Ortholog database
1126 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1127 containing features of type Highlight' when 'B' is pressed
1128 to mark columns containing highlighted regions.
1131 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1132 doesn't always add secondary structure annotation.
1137 <td width="60" nowrap>
1138 <div align="center">
1139 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1142 <td><div align="left">
1146 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1147 for all consensus calculations
1150 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1153 <li>Updated Jalview's Certum code signing certificate
1156 <em>Application</em>
1159 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1160 set of database cross-references, sorted alphabetically
1163 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1164 from database cross references. Users with custom links
1165 will receive a <a href="webServices/urllinks.html#warning">warning
1166 dialog</a> asking them to update their preferences.
1169 <!-- JAL-2287-->Cancel button and escape listener on
1170 dialog warning user about disconnecting Jalview from a
1174 <!-- JAL-2320-->Jalview's Chimera control window closes if
1175 the Chimera it is connected to is shut down
1178 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1179 columns menu item to mark columns containing highlighted
1180 regions (e.g. from structure selections or results of a
1184 <!-- JAL-2284-->Command line option for batch-generation
1185 of HTML pages rendering alignment data with the BioJS
1195 <!-- JAL-2286 -->Columns with more than one modal residue
1196 are not coloured or thresholded according to percent
1197 identity (first observed in Jalview 2.8.2)
1200 <!-- JAL-2301 -->Threonine incorrectly reported as not
1204 <!-- JAL-2318 -->Updates to documentation pages (above PID
1205 threshold, amino acid properties)
1208 <!-- JAL-2292 -->Lower case residues in sequences are not
1209 reported as mapped to residues in a structure file in the
1213 <!--JAL-2324 -->Identical features with non-numeric scores
1214 could be added multiple times to a sequence
1217 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1218 bond features shown as two highlighted residues rather
1219 than a range in linked structure views, and treated
1220 correctly when selecting and computing trees from features
1223 <!-- JAL-2281-->Custom URL links for database
1224 cross-references are matched to database name regardless
1229 <em>Application</em>
1232 <!-- JAL-2282-->Custom URL links for specific database
1233 names without regular expressions also offer links from
1237 <!-- JAL-2315-->Removing a single configured link in the
1238 URL links pane in Connections preferences doesn't actually
1239 update Jalview configuration
1242 <!-- JAL-2272-->CTRL-Click on a selected region to open
1243 the alignment area popup menu doesn't work on El-Capitan
1246 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1247 files with similarly named sequences if dropped onto the
1251 <!-- JAL-2312 -->Additional mappings are shown for PDB
1252 entries where more chains exist in the PDB accession than
1253 are reported in the SIFTS file
1256 <!-- JAL-2317-->Certain structures do not get mapped to
1257 the structure view when displayed with Chimera
1260 <!-- JAL-2317-->No chains shown in the Chimera view
1261 panel's View->Show Chains submenu
1264 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1265 work for wrapped alignment views
1268 <!--JAL-2197 -->Rename UI components for running JPred
1269 predictions from 'JNet' to 'JPred'
1272 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1273 corrupted when annotation panel vertical scroll is not at
1274 first annotation row
1277 <!--JAL-2332 -->Attempting to view structure for Hen
1278 lysozyme results in a PDB Client error dialog box
1281 <!-- JAL-2319 -->Structure View's mapping report switched
1282 ranges for PDB and sequence for SIFTS
1285 SIFTS 'Not_Observed' residues mapped to non-existant
1289 <!-- <em>New Known Issues</em>
1296 <td width="60" nowrap>
1297 <div align="center">
1298 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1299 <em>25/10/2016</em></strong>
1302 <td><em>Application</em>
1304 <li>3D Structure chooser opens with 'Cached structures'
1305 view if structures already loaded</li>
1306 <li>Progress bar reports models as they are loaded to
1307 structure views</li>
1313 <li>Colour by conservation always enabled and no tick
1314 shown in menu when BLOSUM or PID shading applied</li>
1315 <li>FER1_ARATH and FER2_ARATH labels were switched in
1316 example sequences/projects/trees</li>
1318 <em>Application</em>
1320 <li>Jalview projects with views of local PDB structure
1321 files saved on Windows cannot be opened on OSX</li>
1322 <li>Multiple structure views can be opened and superposed
1323 without timeout for structures with multiple models or
1324 multiple sequences in alignment</li>
1325 <li>Cannot import or associated local PDB files without a
1326 PDB ID HEADER line</li>
1327 <li>RMSD is not output in Jmol console when superposition
1329 <li>Drag and drop of URL from Browser fails for Linux and
1330 OSX versions earlier than El Capitan</li>
1331 <li>ENA client ignores invalid content from ENA server</li>
1332 <li>Exceptions are not raised in console when ENA client
1333 attempts to fetch non-existent IDs via Fetch DB Refs UI
1335 <li>Exceptions are not raised in console when a new view
1336 is created on the alignment</li>
1337 <li>OSX right-click fixed for group selections: CMD-click
1338 to insert/remove gaps in groups and CTRL-click to open group
1341 <em>Build and deployment</em>
1343 <li>URL link checker now copes with multi-line anchor
1346 <em>New Known Issues</em>
1348 <li>Drag and drop from URL links in browsers do not work
1355 <td width="60" nowrap>
1356 <div align="center">
1357 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1360 <td><em>General</em>
1363 <!-- JAL-2124 -->Updated Spanish translations.
1366 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1367 for importing structure data to Jalview. Enables mmCIF and
1371 <!-- JAL-192 --->Alignment ruler shows positions relative to
1375 <!-- JAL-2202 -->Position/residue shown in status bar when
1376 mousing over sequence associated annotation
1379 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1383 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1384 '()', canonical '[]' and invalid '{}' base pair populations
1388 <!-- JAL-2092 -->Feature settings popup menu options for
1389 showing or hiding columns containing a feature
1392 <!-- JAL-1557 -->Edit selected group by double clicking on
1393 group and sequence associated annotation labels
1396 <!-- JAL-2236 -->Sequence name added to annotation label in
1397 select/hide columns by annotation and colour by annotation
1401 </ul> <em>Application</em>
1404 <!-- JAL-2050-->Automatically hide introns when opening a
1405 gene/transcript view
1408 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1412 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1413 structure mappings with the EMBL-EBI PDBe SIFTS database
1416 <!-- JAL-2079 -->Updated download sites used for Rfam and
1417 Pfam sources to xfam.org
1420 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1423 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1424 over sequences in Jalview
1427 <!-- JAL-2027-->Support for reverse-complement coding
1428 regions in ENA and EMBL
1431 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1432 for record retrieval via ENA rest API
1435 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1439 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1440 groovy script execution
1443 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1444 alignment window's Calculate menu
1447 <!-- JAL-1812 -->Allow groovy scripts that call
1448 Jalview.getAlignFrames() to run in headless mode
1451 <!-- JAL-2068 -->Support for creating new alignment
1452 calculation workers from groovy scripts
1455 <!-- JAL-1369 --->Store/restore reference sequence in
1459 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1460 associations are now saved/restored from project
1463 <!-- JAL-1993 -->Database selection dialog always shown
1464 before sequence fetcher is opened
1467 <!-- JAL-2183 -->Double click on an entry in Jalview's
1468 database chooser opens a sequence fetcher
1471 <!-- JAL-1563 -->Free-text search client for UniProt using
1472 the UniProt REST API
1475 <!-- JAL-2168 -->-nonews command line parameter to prevent
1476 the news reader opening
1479 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1480 querying stored in preferences
1483 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1487 <!-- JAL-1977-->Tooltips shown on database chooser
1490 <!-- JAL-391 -->Reverse complement function in calculate
1491 menu for nucleotide sequences
1494 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1495 and feature counts preserves alignment ordering (and
1496 debugged for complex feature sets).
1499 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1500 viewing structures with Jalview 2.10
1503 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1504 genome, transcript CCDS and gene ids via the Ensembl and
1505 Ensembl Genomes REST API
1508 <!-- JAL-2049 -->Protein sequence variant annotation
1509 computed for 'sequence_variant' annotation on CDS regions
1513 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1517 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1518 Ref Fetcher fails to match, or otherwise updates sequence
1519 data from external database records.
1522 <!-- JAL-2154 -->Revised Jalview Project format for
1523 efficient recovery of sequence coding and alignment
1524 annotation relationships.
1526 </ul> <!-- <em>Applet</em>
1537 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1541 <!-- JAL-2018-->Export features in Jalview format (again)
1542 includes graduated colourschemes
1545 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1546 working with big alignments and lots of hidden columns
1549 <!-- JAL-2053-->Hidden column markers not always rendered
1550 at right of alignment window
1553 <!-- JAL-2067 -->Tidied up links in help file table of
1557 <!-- JAL-2072 -->Feature based tree calculation not shown
1561 <!-- JAL-2075 -->Hidden columns ignored during feature
1562 based tree calculation
1565 <!-- JAL-2065 -->Alignment view stops updating when show
1566 unconserved enabled for group on alignment
1569 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1573 <!-- JAL-2146 -->Alignment column in status incorrectly
1574 shown as "Sequence position" when mousing over
1578 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1579 hidden columns present
1582 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1583 user created annotation added to alignment
1586 <!-- JAL-1841 -->RNA Structure consensus only computed for
1587 '()' base pair annotation
1590 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1591 in zero scores for all base pairs in RNA Structure
1595 <!-- JAL-2174-->Extend selection with columns containing
1599 <!-- JAL-2275 -->Pfam format writer puts extra space at
1600 beginning of sequence
1603 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1607 <!-- JAL-2238 -->Cannot create groups on an alignment from
1608 from a tree when t-coffee scores are shown
1611 <!-- JAL-1836,1967 -->Cannot import and view PDB
1612 structures with chains containing negative resnums (4q4h)
1615 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1619 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1620 to Clustal, PIR and PileUp output
1623 <!-- JAL-2008 -->Reordering sequence features that are
1624 not visible causes alignment window to repaint
1627 <!-- JAL-2006 -->Threshold sliders don't work in
1628 graduated colour and colour by annotation row for e-value
1629 scores associated with features and annotation rows
1632 <!-- JAL-1797 -->amino acid physicochemical conservation
1633 calculation should be case independent
1636 <!-- JAL-2173 -->Remove annotation also updates hidden
1640 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1641 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1642 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1645 <!-- JAL-2065 -->Null pointer exceptions and redraw
1646 problems when reference sequence defined and 'show
1647 non-conserved' enabled
1650 <!-- JAL-1306 -->Quality and Conservation are now shown on
1651 load even when Consensus calculation is disabled
1654 <!-- JAL-1932 -->Remove right on penultimate column of
1655 alignment does nothing
1658 <em>Application</em>
1661 <!-- JAL-1552-->URLs and links can't be imported by
1662 drag'n'drop on OSX when launched via webstart (note - not
1663 yet fixed for El Capitan)
1666 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1667 output when running on non-gb/us i18n platforms
1670 <!-- JAL-1944 -->Error thrown when exporting a view with
1671 hidden sequences as flat-file alignment
1674 <!-- JAL-2030-->InstallAnywhere distribution fails when
1678 <!-- JAL-2080-->Jalview very slow to launch via webstart
1679 (also hotfix for 2.9.0b2)
1682 <!-- JAL-2085 -->Cannot save project when view has a
1683 reference sequence defined
1686 <!-- JAL-1011 -->Columns are suddenly selected in other
1687 alignments and views when revealing hidden columns
1690 <!-- JAL-1989 -->Hide columns not mirrored in complement
1691 view in a cDNA/Protein splitframe
1694 <!-- JAL-1369 -->Cannot save/restore representative
1695 sequence from project when only one sequence is
1699 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1700 in Structure Chooser
1703 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1704 structure consensus didn't refresh annotation panel
1707 <!-- JAL-1962 -->View mapping in structure view shows
1708 mappings between sequence and all chains in a PDB file
1711 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1712 dialogs format columns correctly, don't display array
1713 data, sort columns according to type
1716 <!-- JAL-1975 -->Export complete shown after destination
1717 file chooser is cancelled during an image export
1720 <!-- JAL-2025 -->Error when querying PDB Service with
1721 sequence name containing special characters
1724 <!-- JAL-2024 -->Manual PDB structure querying should be
1728 <!-- JAL-2104 -->Large tooltips with broken HTML
1729 formatting don't wrap
1732 <!-- JAL-1128 -->Figures exported from wrapped view are
1733 truncated so L looks like I in consensus annotation
1736 <!-- JAL-2003 -->Export features should only export the
1737 currently displayed features for the current selection or
1741 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1742 after fetching cross-references, and restoring from
1746 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1747 followed in the structure viewer
1750 <!-- JAL-2163 -->Titles for individual alignments in
1751 splitframe not restored from project
1754 <!-- JAL-2145 -->missing autocalculated annotation at
1755 trailing end of protein alignment in transcript/product
1756 splitview when pad-gaps not enabled by default
1759 <!-- JAL-1797 -->amino acid physicochemical conservation
1763 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1764 article has been read (reopened issue due to
1765 internationalisation problems)
1768 <!-- JAL-1960 -->Only offer PDB structures in structure
1769 viewer based on sequence name, PDB and UniProt
1774 <!-- JAL-1976 -->No progress bar shown during export of
1778 <!-- JAL-2213 -->Structures not always superimposed after
1779 multiple structures are shown for one or more sequences.
1782 <!-- JAL-1370 -->Reference sequence characters should not
1783 be replaced with '.' when 'Show unconserved' format option
1787 <!-- JAL-1823 -->Cannot specify chain code when entering
1788 specific PDB id for sequence
1791 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1792 'Export hidden sequences' is enabled, but 'export hidden
1793 columns' is disabled.
1796 <!--JAL-2026-->Best Quality option in structure chooser
1797 selects lowest rather than highest resolution structures
1801 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1802 to sequence mapping in 'View Mappings' report
1805 <!-- JAL-2284 -->Unable to read old Jalview projects that
1806 contain non-XML data added after Jalvew wrote project.
1809 <!-- JAL-2118 -->Newly created annotation row reorders
1810 after clicking on it to create new annotation for a
1814 <!-- JAL-1980 -->Null Pointer Exception raised when
1815 pressing Add on an orphaned cut'n'paste window.
1817 <!-- may exclude, this is an external service stability issue JAL-1941
1818 -- > RNA 3D structure not added via DSSR service</li> -->
1823 <!-- JAL-2151 -->Incorrect columns are selected when
1824 hidden columns present before start of sequence
1827 <!-- JAL-1986 -->Missing dependencies on applet pages
1831 <!-- JAL-1947 -->Overview pixel size changes when
1832 sequences are hidden in applet
1835 <!-- JAL-1996 -->Updated instructions for applet
1836 deployment on examples pages.
1843 <td width="60" nowrap>
1844 <div align="center">
1845 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1846 <em>16/10/2015</em></strong>
1849 <td><em>General</em>
1851 <li>Time stamps for signed Jalview application and applet
1856 <em>Application</em>
1858 <li>Duplicate group consensus and conservation rows
1859 shown when tree is partitioned</li>
1860 <li>Erratic behaviour when tree partitions made with
1861 multiple cDNA/Protein split views</li>
1867 <td width="60" nowrap>
1868 <div align="center">
1869 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1870 <em>8/10/2015</em></strong>
1873 <td><em>General</em>
1875 <li>Updated Spanish translations of localized text for
1877 </ul> <em>Application</em>
1879 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1880 <li>Signed OSX InstallAnywhere installer<br></li>
1881 <li>Support for per-sequence based annotations in BioJSON</li>
1882 </ul> <em>Applet</em>
1884 <li>Split frame example added to applet examples page</li>
1885 </ul> <em>Build and Deployment</em>
1888 <!-- JAL-1888 -->New ant target for running Jalview's test
1896 <li>Mapping of cDNA to protein in split frames
1897 incorrect when sequence start > 1</li>
1898 <li>Broken images in filter column by annotation dialog
1900 <li>Feature colours not parsed from features file</li>
1901 <li>Exceptions and incomplete link URLs recovered when
1902 loading a features file containing HTML tags in feature
1906 <em>Application</em>
1908 <li>Annotations corrupted after BioJS export and
1910 <li>Incorrect sequence limits after Fetch DB References
1911 with 'trim retrieved sequences'</li>
1912 <li>Incorrect warning about deleting all data when
1913 deleting selected columns</li>
1914 <li>Patch to build system for shipping properly signed
1915 JNLP templates for webstart launch</li>
1916 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1917 unreleased structures for download or viewing</li>
1918 <li>Tab/space/return keystroke operation of EMBL-PDBe
1919 fetcher/viewer dialogs works correctly</li>
1920 <li>Disabled 'minimise' button on Jalview windows
1921 running on OSX to workaround redraw hang bug</li>
1922 <li>Split cDNA/Protein view position and geometry not
1923 recovered from jalview project</li>
1924 <li>Initial enabled/disabled state of annotation menu
1925 sorter 'show autocalculated first/last' corresponds to
1927 <li>Restoring of Clustal, RNA Helices and T-Coffee
1928 color schemes from BioJSON</li>
1932 <li>Reorder sequences mirrored in cDNA/Protein split
1934 <li>Applet with Jmol examples not loading correctly</li>
1940 <td><div align="center">
1941 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1943 <td><em>General</em>
1945 <li>Linked visualisation and analysis of DNA and Protein
1948 <li>Translated cDNA alignments shown as split protein
1949 and DNA alignment views</li>
1950 <li>Codon consensus annotation for linked protein and
1951 cDNA alignment views</li>
1952 <li>Link cDNA or Protein product sequences by loading
1953 them onto Protein or cDNA alignments</li>
1954 <li>Reconstruct linked cDNA alignment from aligned
1955 protein sequences</li>
1958 <li>Jmol integration updated to Jmol v14.2.14</li>
1959 <li>Import and export of Jalview alignment views as <a
1960 href="features/bioJsonFormat.html">BioJSON</a></li>
1961 <li>New alignment annotation file statements for
1962 reference sequences and marking hidden columns</li>
1963 <li>Reference sequence based alignment shading to
1964 highlight variation</li>
1965 <li>Select or hide columns according to alignment
1967 <li>Find option for locating sequences by description</li>
1968 <li>Conserved physicochemical properties shown in amino
1969 acid conservation row</li>
1970 <li>Alignments can be sorted by number of RNA helices</li>
1971 </ul> <em>Application</em>
1973 <li>New cDNA/Protein analysis capabilities
1975 <li>Get Cross-References should open a Split Frame
1976 view with cDNA/Protein</li>
1977 <li>Detect when nucleotide sequences and protein
1978 sequences are placed in the same alignment</li>
1979 <li>Split cDNA/Protein views are saved in Jalview
1984 <li>Use REST API to talk to Chimera</li>
1985 <li>Selected regions in Chimera are highlighted in linked
1986 Jalview windows</li>
1988 <li>VARNA RNA viewer updated to v3.93</li>
1989 <li>VARNA views are saved in Jalview Projects</li>
1990 <li>Pseudoknots displayed as Jalview RNA annotation can
1991 be shown in VARNA</li>
1993 <li>Make groups for selection uses marked columns as well
1994 as the active selected region</li>
1996 <li>Calculate UPGMA and NJ trees using sequence feature
1998 <li>New Export options
2000 <li>New Export Settings dialog to control hidden
2001 region export in flat file generation</li>
2003 <li>Export alignment views for display with the <a
2004 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2006 <li>Export scrollable SVG in HTML page</li>
2007 <li>Optional embedding of BioJSON data when exporting
2008 alignment figures to HTML</li>
2010 <li>3D structure retrieval and display
2012 <li>Free text and structured queries with the PDBe
2014 <li>PDBe Search API based discovery and selection of
2015 PDB structures for a sequence set</li>
2019 <li>JPred4 employed for protein secondary structure
2021 <li>Hide Insertions menu option to hide unaligned columns
2022 for one or a group of sequences</li>
2023 <li>Automatically hide insertions in alignments imported
2024 from the JPred4 web server</li>
2025 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2026 system on OSX<br />LGPL libraries courtesy of <a
2027 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2029 <li>changed 'View nucleotide structure' submenu to 'View
2030 VARNA 2D Structure'</li>
2031 <li>change "View protein structure" menu option to "3D
2034 </ul> <em>Applet</em>
2036 <li>New layout for applet example pages</li>
2037 <li>New parameters to enable SplitFrame view
2038 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2039 <li>New example demonstrating linked viewing of cDNA and
2040 Protein alignments</li>
2041 </ul> <em>Development and deployment</em>
2043 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2044 <li>Include installation type and git revision in build
2045 properties and console log output</li>
2046 <li>Jalview Github organisation, and new github site for
2047 storing BioJsMSA Templates</li>
2048 <li>Jalview's unit tests now managed with TestNG</li>
2051 <!-- <em>General</em>
2053 </ul> --> <!-- issues resolved --> <em>Application</em>
2055 <li>Escape should close any open find dialogs</li>
2056 <li>Typo in select-by-features status report</li>
2057 <li>Consensus RNA secondary secondary structure
2058 predictions are not highlighted in amber</li>
2059 <li>Missing gap character in v2.7 example file means
2060 alignment appears unaligned when pad-gaps is not enabled</li>
2061 <li>First switch to RNA Helices colouring doesn't colour
2062 associated structure views</li>
2063 <li>ID width preference option is greyed out when auto
2064 width checkbox not enabled</li>
2065 <li>Stopped a warning dialog from being shown when
2066 creating user defined colours</li>
2067 <li>'View Mapping' in structure viewer shows sequence
2068 mappings for just that viewer's sequences</li>
2069 <li>Workaround for superposing PDB files containing
2070 multiple models in Chimera</li>
2071 <li>Report sequence position in status bar when hovering
2072 over Jmol structure</li>
2073 <li>Cannot output gaps as '.' symbols with Selection ->
2074 output to text box</li>
2075 <li>Flat file exports of alignments with hidden columns
2076 have incorrect sequence start/end</li>
2077 <li>'Aligning' a second chain to a Chimera structure from
2079 <li>Colour schemes applied to structure viewers don't
2080 work for nucleotide</li>
2081 <li>Loading/cut'n'pasting an empty or invalid file leads
2082 to a grey/invisible alignment window</li>
2083 <li>Exported Jpred annotation from a sequence region
2084 imports to different position</li>
2085 <li>Space at beginning of sequence feature tooltips shown
2086 on some platforms</li>
2087 <li>Chimera viewer 'View | Show Chain' menu is not
2089 <li>'New View' fails with a Null Pointer Exception in
2090 console if Chimera has been opened</li>
2091 <li>Mouseover to Chimera not working</li>
2092 <li>Miscellaneous ENA XML feature qualifiers not
2094 <li>NPE in annotation renderer after 'Extract Scores'</li>
2095 <li>If two structures in one Chimera window, mouseover of
2096 either sequence shows on first structure</li>
2097 <li>'Show annotations' options should not make
2098 non-positional annotations visible</li>
2099 <li>Subsequence secondary structure annotation not shown
2100 in right place after 'view flanking regions'</li>
2101 <li>File Save As type unset when current file format is
2103 <li>Save as '.jar' option removed for saving Jalview
2105 <li>Colour by Sequence colouring in Chimera more
2107 <li>Cannot 'add reference annotation' for a sequence in
2108 several views on same alignment</li>
2109 <li>Cannot show linked products for EMBL / ENA records</li>
2110 <li>Jalview's tooltip wraps long texts containing no
2112 </ul> <em>Applet</em>
2114 <li>Jmol to JalviewLite mouseover/link not working</li>
2115 <li>JalviewLite can't import sequences with ID
2116 descriptions containing angle brackets</li>
2117 </ul> <em>General</em>
2119 <li>Cannot export and reimport RNA secondary structure
2120 via jalview annotation file</li>
2121 <li>Random helix colour palette for colour by annotation
2122 with RNA secondary structure</li>
2123 <li>Mouseover to cDNA from STOP residue in protein
2124 translation doesn't work.</li>
2125 <li>hints when using the select by annotation dialog box</li>
2126 <li>Jmol alignment incorrect if PDB file has alternate CA
2128 <li>FontChooser message dialog appears to hang after
2129 choosing 1pt font</li>
2130 <li>Peptide secondary structure incorrectly imported from
2131 annotation file when annotation display text includes 'e' or
2133 <li>Cannot set colour of new feature type whilst creating
2135 <li>cDNA translation alignment should not be sequence
2136 order dependent</li>
2137 <li>'Show unconserved' doesn't work for lower case
2139 <li>Nucleotide ambiguity codes involving R not recognised</li>
2140 </ul> <em>Deployment and Documentation</em>
2142 <li>Applet example pages appear different to the rest of
2143 www.jalview.org</li>
2144 </ul> <em>Application Known issues</em>
2146 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2147 <li>Misleading message appears after trying to delete
2149 <li>Jalview icon not shown in dock after InstallAnywhere
2150 version launches</li>
2151 <li>Fetching EMBL reference for an RNA sequence results
2152 fails with a sequence mismatch</li>
2153 <li>Corrupted or unreadable alignment display when
2154 scrolling alignment to right</li>
2155 <li>ArrayIndexOutOfBoundsException thrown when remove
2156 empty columns called on alignment with ragged gapped ends</li>
2157 <li>auto calculated alignment annotation rows do not get
2158 placed above or below non-autocalculated rows</li>
2159 <li>Jalview dekstop becomes sluggish at full screen in
2160 ultra-high resolution</li>
2161 <li>Cannot disable consensus calculation independently of
2162 quality and conservation</li>
2163 <li>Mouseover highlighting between cDNA and protein can
2164 become sluggish with more than one splitframe shown</li>
2165 </ul> <em>Applet Known Issues</em>
2167 <li>Core PDB parsing code requires Jmol</li>
2168 <li>Sequence canvas panel goes white when alignment
2169 window is being resized</li>
2175 <td><div align="center">
2176 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2178 <td><em>General</em>
2180 <li>Updated Java code signing certificate donated by
2182 <li>Features and annotation preserved when performing
2183 pairwise alignment</li>
2184 <li>RNA pseudoknot annotation can be
2185 imported/exported/displayed</li>
2186 <li>'colour by annotation' can colour by RNA and
2187 protein secondary structure</li>
2188 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2189 post-hoc with 2.9 release</em>)
2192 </ul> <em>Application</em>
2194 <li>Extract and display secondary structure for sequences
2195 with 3D structures</li>
2196 <li>Support for parsing RNAML</li>
2197 <li>Annotations menu for layout
2199 <li>sort sequence annotation rows by alignment</li>
2200 <li>place sequence annotation above/below alignment
2203 <li>Output in Stockholm format</li>
2204 <li>Internationalisation: improved Spanish (es)
2206 <li>Structure viewer preferences tab</li>
2207 <li>Disorder and Secondary Structure annotation tracks
2208 shared between alignments</li>
2209 <li>UCSF Chimera launch and linked highlighting from
2211 <li>Show/hide all sequence associated annotation rows for
2212 all or current selection</li>
2213 <li>disorder and secondary structure predictions
2214 available as dataset annotation</li>
2215 <li>Per-sequence rna helices colouring</li>
2218 <li>Sequence database accessions imported when fetching
2219 alignments from Rfam</li>
2220 <li>update VARNA version to 3.91</li>
2222 <li>New groovy scripts for exporting aligned positions,
2223 conservation values, and calculating sum of pairs scores.</li>
2224 <li>Command line argument to set default JABAWS server</li>
2225 <li>include installation type in build properties and
2226 console log output</li>
2227 <li>Updated Jalview project format to preserve dataset
2231 <!-- issues resolved --> <em>Application</em>
2233 <li>Distinguish alignment and sequence associated RNA
2234 structure in structure->view->VARNA</li>
2235 <li>Raise dialog box if user deletes all sequences in an
2237 <li>Pressing F1 results in documentation opening twice</li>
2238 <li>Sequence feature tooltip is wrapped</li>
2239 <li>Double click on sequence associated annotation
2240 selects only first column</li>
2241 <li>Redundancy removal doesn't result in unlinked
2242 leaves shown in tree</li>
2243 <li>Undos after several redundancy removals don't undo
2245 <li>Hide sequence doesn't hide associated annotation</li>
2246 <li>User defined colours dialog box too big to fit on
2247 screen and buttons not visible</li>
2248 <li>author list isn't updated if already written to
2249 Jalview properties</li>
2250 <li>Popup menu won't open after retrieving sequence
2252 <li>File open window for associate PDB doesn't open</li>
2253 <li>Left-then-right click on a sequence id opens a
2254 browser search window</li>
2255 <li>Cannot open sequence feature shading/sort popup menu
2256 in feature settings dialog</li>
2257 <li>better tooltip placement for some areas of Jalview
2259 <li>Allow addition of JABAWS Server which doesn't
2260 pass validation</li>
2261 <li>Web services parameters dialog box is too large to
2263 <li>Muscle nucleotide alignment preset obscured by
2265 <li>JABAWS preset submenus don't contain newly
2266 defined user preset</li>
2267 <li>MSA web services warns user if they were launched
2268 with invalid input</li>
2269 <li>Jalview cannot contact DAS Registy when running on
2272 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2273 'Superpose with' submenu not shown when new view
2277 </ul> <!-- <em>Applet</em>
2279 </ul> <em>General</em>
2281 </ul>--> <em>Deployment and Documentation</em>
2283 <li>2G and 1G options in launchApp have no effect on
2284 memory allocation</li>
2285 <li>launchApp service doesn't automatically open
2286 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2288 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2289 InstallAnywhere reports cannot find valid JVM when Java
2290 1.7_055 is available
2292 </ul> <em>Application Known issues</em>
2295 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2296 corrupted or unreadable alignment display when scrolling
2300 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2301 retrieval fails but progress bar continues for DAS retrieval
2302 with large number of ID
2305 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2306 flatfile output of visible region has incorrect sequence
2310 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2311 rna structure consensus doesn't update when secondary
2312 structure tracks are rearranged
2315 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2316 invalid rna structure positional highlighting does not
2317 highlight position of invalid base pairs
2320 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2321 out of memory errors are not raised when saving Jalview
2322 project from alignment window file menu
2325 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2326 Switching to RNA Helices colouring doesn't propagate to
2330 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2331 colour by RNA Helices not enabled when user created
2332 annotation added to alignment
2335 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2336 Jalview icon not shown on dock in Mountain Lion/Webstart
2338 </ul> <em>Applet Known Issues</em>
2341 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2342 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2345 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2346 Jalview and Jmol example not compatible with IE9
2349 <li>Sort by annotation score doesn't reverse order
2355 <td><div align="center">
2356 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2359 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2362 <li>Internationalisation of user interface (usually
2363 called i18n support) and translation for Spanish locale</li>
2364 <li>Define/Undefine group on current selection with
2365 Ctrl-G/Shift Ctrl-G</li>
2366 <li>Improved group creation/removal options in
2367 alignment/sequence Popup menu</li>
2368 <li>Sensible precision for symbol distribution
2369 percentages shown in logo tooltip.</li>
2370 <li>Annotation panel height set according to amount of
2371 annotation when alignment first opened</li>
2372 </ul> <em>Application</em>
2374 <li>Interactive consensus RNA secondary structure
2375 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2376 <li>Select columns containing particular features from
2377 Feature Settings dialog</li>
2378 <li>View all 'representative' PDB structures for selected
2380 <li>Update Jalview project format:
2382 <li>New file extension for Jalview projects '.jvp'</li>
2383 <li>Preserve sequence and annotation dataset (to
2384 store secondary structure annotation,etc)</li>
2385 <li>Per group and alignment annotation and RNA helix
2389 <li>New similarity measures for PCA and Tree calculation
2391 <li>Experimental support for retrieval and viewing of
2392 flanking regions for an alignment</li>
2396 <!-- issues resolved --> <em>Application</em>
2398 <li>logo keeps spinning and status remains at queued or
2399 running after job is cancelled</li>
2400 <li>cannot export features from alignments imported from
2401 Jalview/VAMSAS projects</li>
2402 <li>Buggy slider for web service parameters that take
2404 <li>Newly created RNA secondary structure line doesn't
2405 have 'display all symbols' flag set</li>
2406 <li>T-COFFEE alignment score shading scheme and other
2407 annotation shading not saved in Jalview project</li>
2408 <li>Local file cannot be loaded in freshly downloaded
2410 <li>Jalview icon not shown on dock in Mountain
2412 <li>Load file from desktop file browser fails</li>
2413 <li>Occasional NPE thrown when calculating large trees</li>
2414 <li>Cannot reorder or slide sequences after dragging an
2415 alignment onto desktop</li>
2416 <li>Colour by annotation dialog throws NPE after using
2417 'extract scores' function</li>
2418 <li>Loading/cut'n'pasting an empty file leads to a grey
2419 alignment window</li>
2420 <li>Disorder thresholds rendered incorrectly after
2421 performing IUPred disorder prediction</li>
2422 <li>Multiple group annotated consensus rows shown when
2423 changing 'normalise logo' display setting</li>
2424 <li>Find shows blank dialog after 'finished searching' if
2425 nothing matches query</li>
2426 <li>Null Pointer Exceptions raised when sorting by
2427 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2429 <li>Errors in Jmol console when structures in alignment
2430 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2432 <li>Not all working JABAWS services are shown in
2434 <li>JAVAWS version of Jalview fails to launch with
2435 'invalid literal/length code'</li>
2436 <li>Annotation/RNA Helix colourschemes cannot be applied
2437 to alignment with groups (actually fixed in 2.8.0b1)</li>
2438 <li>RNA Helices and T-Coffee Scores available as default
2441 </ul> <em>Applet</em>
2443 <li>Remove group option is shown even when selection is
2445 <li>Apply to all groups ticked but colourscheme changes
2446 don't affect groups</li>
2447 <li>Documented RNA Helices and T-Coffee Scores as valid
2448 colourscheme name</li>
2449 <li>Annotation labels drawn on sequence IDs when
2450 Annotation panel is not displayed</li>
2451 <li>Increased font size for dropdown menus on OSX and
2452 embedded windows</li>
2453 </ul> <em>Other</em>
2455 <li>Consensus sequence for alignments/groups with a
2456 single sequence were not calculated</li>
2457 <li>annotation files that contain only groups imported as
2458 annotation and junk sequences</li>
2459 <li>Fasta files with sequences containing '*' incorrectly
2460 recognised as PFAM or BLC</li>
2461 <li>conservation/PID slider apply all groups option
2462 doesn't affect background (2.8.0b1)
2464 <li>redundancy highlighting is erratic at 0% and 100%</li>
2465 <li>Remove gapped columns fails for sequences with ragged
2467 <li>AMSA annotation row with leading spaces is not
2468 registered correctly on import</li>
2469 <li>Jalview crashes when selecting PCA analysis for
2470 certain alignments</li>
2471 <li>Opening the colour by annotation dialog for an
2472 existing annotation based 'use original colours'
2473 colourscheme loses original colours setting</li>
2478 <td><div align="center">
2479 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2480 <em>30/1/2014</em></strong>
2484 <li>Trusted certificates for JalviewLite applet and
2485 Jalview Desktop application<br />Certificate was donated by
2486 <a href="https://www.certum.eu">Certum</a> to the Jalview
2487 open source project).
2489 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2490 <li>Output in Stockholm format</li>
2491 <li>Allow import of data from gzipped files</li>
2492 <li>Export/import group and sequence associated line
2493 graph thresholds</li>
2494 <li>Nucleotide substitution matrix that supports RNA and
2495 ambiguity codes</li>
2496 <li>Allow disorder predictions to be made on the current
2497 selection (or visible selection) in the same way that JPred
2499 <li>Groovy scripting for headless Jalview operation</li>
2500 </ul> <em>Other improvements</em>
2502 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2503 <li>COMBINE statement uses current SEQUENCE_REF and
2504 GROUP_REF scope to group annotation rows</li>
2505 <li>Support '' style escaping of quotes in Newick
2507 <li>Group options for JABAWS service by command line name</li>
2508 <li>Empty tooltip shown for JABA service options with a
2509 link but no description</li>
2510 <li>Select primary source when selecting authority in
2511 database fetcher GUI</li>
2512 <li>Add .mfa to FASTA file extensions recognised by
2514 <li>Annotation label tooltip text wrap</li>
2519 <li>Slow scrolling when lots of annotation rows are
2521 <li>Lots of NPE (and slowness) after creating RNA
2522 secondary structure annotation line</li>
2523 <li>Sequence database accessions not imported when
2524 fetching alignments from Rfam</li>
2525 <li>Incorrect SHMR submission for sequences with
2527 <li>View all structures does not always superpose
2529 <li>Option widgets in service parameters not updated to
2530 reflect user or preset settings</li>
2531 <li>Null pointer exceptions for some services without
2532 presets or adjustable parameters</li>
2533 <li>Discover PDB IDs entry in structure menu doesn't
2534 discover PDB xRefs</li>
2535 <li>Exception encountered while trying to retrieve
2536 features with DAS</li>
2537 <li>Lowest value in annotation row isn't coloured
2538 when colour by annotation (per sequence) is coloured</li>
2539 <li>Keyboard mode P jumps to start of gapped region when
2540 residue follows a gap</li>
2541 <li>Jalview appears to hang importing an alignment with
2542 Wrap as default or after enabling Wrap</li>
2543 <li>'Right click to add annotations' message
2544 shown in wrap mode when no annotations present</li>
2545 <li>Disorder predictions fail with NPE if no automatic
2546 annotation already exists on alignment</li>
2547 <li>oninit javascript function should be called after
2548 initialisation completes</li>
2549 <li>Remove redundancy after disorder prediction corrupts
2550 alignment window display</li>
2551 <li>Example annotation file in documentation is invalid</li>
2552 <li>Grouped line graph annotation rows are not exported
2553 to annotation file</li>
2554 <li>Multi-harmony analysis cannot be run when only two
2556 <li>Cannot create multiple groups of line graphs with
2557 several 'combine' statements in annotation file</li>
2558 <li>Pressing return several times causes Number Format
2559 exceptions in keyboard mode</li>
2560 <li>Multi-harmony (SHMMR) method doesn't submit
2561 correct partitions for input data</li>
2562 <li>Translation from DNA to Amino Acids fails</li>
2563 <li>Jalview fail to load newick tree with quoted label</li>
2564 <li>--headless flag isn't understood</li>
2565 <li>ClassCastException when generating EPS in headless
2567 <li>Adjusting sequence-associated shading threshold only
2568 changes one row's threshold</li>
2569 <li>Preferences and Feature settings panel panel
2570 doesn't open</li>
2571 <li>hide consensus histogram also hides conservation and
2572 quality histograms</li>
2577 <td><div align="center">
2578 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2580 <td><em>Application</em>
2582 <li>Support for JABAWS 2.0 Services (AACon alignment
2583 conservation, protein disorder and Clustal Omega)</li>
2584 <li>JABAWS server status indicator in Web Services
2586 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2587 in Jalview alignment window</li>
2588 <li>Updated Jalview build and deploy framework for OSX
2589 mountain lion, windows 7, and 8</li>
2590 <li>Nucleotide substitution matrix for PCA that supports
2591 RNA and ambiguity codes</li>
2593 <li>Improved sequence database retrieval GUI</li>
2594 <li>Support fetching and database reference look up
2595 against multiple DAS sources (Fetch all from in 'fetch db
2597 <li>Jalview project improvements
2599 <li>Store and retrieve the 'belowAlignment'
2600 flag for annotation</li>
2601 <li>calcId attribute to group annotation rows on the
2603 <li>Store AACon calculation settings for a view in
2604 Jalview project</li>
2608 <li>horizontal scrolling gesture support</li>
2609 <li>Visual progress indicator when PCA calculation is
2611 <li>Simpler JABA web services menus</li>
2612 <li>visual indication that web service results are still
2613 being retrieved from server</li>
2614 <li>Serialise the dialogs that are shown when Jalview
2615 starts up for first time</li>
2616 <li>Jalview user agent string for interacting with HTTP
2618 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2620 <li>Examples directory and Groovy library included in
2621 InstallAnywhere distribution</li>
2622 </ul> <em>Applet</em>
2624 <li>RNA alignment and secondary structure annotation
2625 visualization applet example</li>
2626 </ul> <em>General</em>
2628 <li>Normalise option for consensus sequence logo</li>
2629 <li>Reset button in PCA window to return dimensions to
2631 <li>Allow seqspace or Jalview variant of alignment PCA
2633 <li>PCA with either nucleic acid and protein substitution
2635 <li>Allow windows containing HTML reports to be exported
2637 <li>Interactive display and editing of RNA secondary
2638 structure contacts</li>
2639 <li>RNA Helix Alignment Colouring</li>
2640 <li>RNA base pair logo consensus</li>
2641 <li>Parse sequence associated secondary structure
2642 information in Stockholm files</li>
2643 <li>HTML Export database accessions and annotation
2644 information presented in tooltip for sequences</li>
2645 <li>Import secondary structure from LOCARNA clustalw
2646 style RNA alignment files</li>
2647 <li>import and visualise T-COFFEE quality scores for an
2649 <li>'colour by annotation' per sequence option to
2650 shade each sequence according to its associated alignment
2652 <li>New Jalview Logo</li>
2653 </ul> <em>Documentation and Development</em>
2655 <li>documentation for score matrices used in Jalview</li>
2656 <li>New Website!</li>
2658 <td><em>Application</em>
2660 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2661 wsdbfetch REST service</li>
2662 <li>Stop windows being moved outside desktop on OSX</li>
2663 <li>Filetype associations not installed for webstart
2665 <li>Jalview does not always retrieve progress of a JABAWS
2666 job execution in full once it is complete</li>
2667 <li>revise SHMR RSBS definition to ensure alignment is
2668 uploaded via ali_file parameter</li>
2669 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2670 <li>View all structures superposed fails with exception</li>
2671 <li>Jnet job queues forever if a very short sequence is
2672 submitted for prediction</li>
2673 <li>Cut and paste menu not opened when mouse clicked on
2675 <li>Putting fractional value into integer text box in
2676 alignment parameter dialog causes Jalview to hang</li>
2677 <li>Structure view highlighting doesn't work on
2679 <li>View all structures fails with exception shown in
2681 <li>Characters in filename associated with PDBEntry not
2682 escaped in a platform independent way</li>
2683 <li>Jalview desktop fails to launch with exception when
2685 <li>Tree calculation reports 'you must have 2 or more
2686 sequences selected' when selection is empty</li>
2687 <li>Jalview desktop fails to launch with jar signature
2688 failure when java web start temporary file caching is
2690 <li>DAS Sequence retrieval with range qualification
2691 results in sequence xref which includes range qualification</li>
2692 <li>Errors during processing of command line arguments
2693 cause progress bar (JAL-898) to be removed</li>
2694 <li>Replace comma for semi-colon option not disabled for
2695 DAS sources in sequence fetcher</li>
2696 <li>Cannot close news reader when JABAWS server warning
2697 dialog is shown</li>
2698 <li>Option widgets not updated to reflect user settings</li>
2699 <li>Edited sequence not submitted to web service</li>
2700 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2701 <li>InstallAnywhere installer doesn't unpack and run
2702 on OSX Mountain Lion</li>
2703 <li>Annotation panel not given a scroll bar when
2704 sequences with alignment annotation are pasted into the
2706 <li>Sequence associated annotation rows not associated
2707 when loaded from Jalview project</li>
2708 <li>Browser launch fails with NPE on java 1.7</li>
2709 <li>JABAWS alignment marked as finished when job was
2710 cancelled or job failed due to invalid input</li>
2711 <li>NPE with v2.7 example when clicking on Tree
2712 associated with all views</li>
2713 <li>Exceptions when copy/paste sequences with grouped
2714 annotation rows to new window</li>
2715 </ul> <em>Applet</em>
2717 <li>Sequence features are momentarily displayed before
2718 they are hidden using hidefeaturegroups applet parameter</li>
2719 <li>loading features via javascript API automatically
2720 enables feature display</li>
2721 <li>scrollToColumnIn javascript API method doesn't
2723 </ul> <em>General</em>
2725 <li>Redundancy removal fails for rna alignment</li>
2726 <li>PCA calculation fails when sequence has been selected
2727 and then deselected</li>
2728 <li>PCA window shows grey box when first opened on OSX</li>
2729 <li>Letters coloured pink in sequence logo when alignment
2730 coloured with clustalx</li>
2731 <li>Choosing fonts without letter symbols defined causes
2732 exceptions and redraw errors</li>
2733 <li>Initial PCA plot view is not same as manually
2734 reconfigured view</li>
2735 <li>Grouped annotation graph label has incorrect line
2737 <li>Grouped annotation graph label display is corrupted
2738 for lots of labels</li>
2743 <div align="center">
2744 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2747 <td><em>Application</em>
2749 <li>Jalview Desktop News Reader</li>
2750 <li>Tweaked default layout of web services menu</li>
2751 <li>View/alignment association menu to enable user to
2752 easily specify which alignment a multi-structure view takes
2753 its colours/correspondences from</li>
2754 <li>Allow properties file location to be specified as URL</li>
2755 <li>Extend Jalview project to preserve associations
2756 between many alignment views and a single Jmol display</li>
2757 <li>Store annotation row height in Jalview project file</li>
2758 <li>Annotation row column label formatting attributes
2759 stored in project file</li>
2760 <li>Annotation row order for auto-calculated annotation
2761 rows preserved in Jalview project file</li>
2762 <li>Visual progress indication when Jalview state is
2763 saved using Desktop window menu</li>
2764 <li>Visual indication that command line arguments are
2765 still being processed</li>
2766 <li>Groovy script execution from URL</li>
2767 <li>Colour by annotation default min and max colours in
2769 <li>Automatically associate PDB files dragged onto an
2770 alignment with sequences that have high similarity and
2772 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2773 <li>'view structures' option to open many
2774 structures in same window</li>
2775 <li>Sort associated views menu option for tree panel</li>
2776 <li>Group all JABA and non-JABA services for a particular
2777 analysis function in its own submenu</li>
2778 </ul> <em>Applet</em>
2780 <li>Userdefined and autogenerated annotation rows for
2782 <li>Adjustment of alignment annotation pane height</li>
2783 <li>Annotation scrollbar for annotation panel</li>
2784 <li>Drag to reorder annotation rows in annotation panel</li>
2785 <li>'automaticScrolling' parameter</li>
2786 <li>Allow sequences with partial ID string matches to be
2787 annotated from GFF/Jalview features files</li>
2788 <li>Sequence logo annotation row in applet</li>
2789 <li>Absolute paths relative to host server in applet
2790 parameters are treated as such</li>
2791 <li>New in the JalviewLite javascript API:
2793 <li>JalviewLite.js javascript library</li>
2794 <li>Javascript callbacks for
2796 <li>Applet initialisation</li>
2797 <li>Sequence/alignment mouse-overs and selections</li>
2800 <li>scrollTo row and column alignment scrolling
2802 <li>Select sequence/alignment regions from javascript</li>
2803 <li>javascript structure viewer harness to pass
2804 messages between Jmol and Jalview when running as
2805 distinct applets</li>
2806 <li>sortBy method</li>
2807 <li>Set of applet and application examples shipped
2808 with documentation</li>
2809 <li>New example to demonstrate JalviewLite and Jmol
2810 javascript message exchange</li>
2812 </ul> <em>General</em>
2814 <li>Enable Jmol displays to be associated with multiple
2815 multiple alignments</li>
2816 <li>Option to automatically sort alignment with new tree</li>
2817 <li>User configurable link to enable redirects to a
2818 www.Jalview.org mirror</li>
2819 <li>Jmol colours option for Jmol displays</li>
2820 <li>Configurable newline string when writing alignment
2821 and other flat files</li>
2822 <li>Allow alignment annotation description lines to
2823 contain html tags</li>
2824 </ul> <em>Documentation and Development</em>
2826 <li>Add groovy test harness for bulk load testing to
2828 <li>Groovy script to load and align a set of sequences
2829 using a web service before displaying the result in the
2830 Jalview desktop</li>
2831 <li>Restructured javascript and applet api documentation</li>
2832 <li>Ant target to publish example html files with applet
2834 <li>Netbeans project for building Jalview from source</li>
2835 <li>ant task to create online javadoc for Jalview source</li>
2837 <td><em>Application</em>
2839 <li>User defined colourscheme throws exception when
2840 current built in colourscheme is saved as new scheme</li>
2841 <li>AlignFrame->Save in application pops up save
2842 dialog for valid filename/format</li>
2843 <li>Cannot view associated structure for UniProt sequence</li>
2844 <li>PDB file association breaks for UniProt sequence
2846 <li>Associate PDB from file dialog does not tell you
2847 which sequence is to be associated with the file</li>
2848 <li>Find All raises null pointer exception when query
2849 only matches sequence IDs</li>
2850 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2851 <li>Jalview project with Jmol views created with Jalview
2852 2.4 cannot be loaded</li>
2853 <li>Filetype associations not installed for webstart
2855 <li>Two or more chains in a single PDB file associated
2856 with sequences in different alignments do not get coloured
2857 by their associated sequence</li>
2858 <li>Visibility status of autocalculated annotation row
2859 not preserved when project is loaded</li>
2860 <li>Annotation row height and visibility attributes not
2861 stored in Jalview project</li>
2862 <li>Tree bootstraps are not preserved when saved as a
2863 Jalview project</li>
2864 <li>Envision2 workflow tooltips are corrupted</li>
2865 <li>Enabling show group conservation also enables colour
2866 by conservation</li>
2867 <li>Duplicate group associated conservation or consensus
2868 created on new view</li>
2869 <li>Annotation scrollbar not displayed after 'show
2870 all hidden annotation rows' option selected</li>
2871 <li>Alignment quality not updated after alignment
2872 annotation row is hidden then shown</li>
2873 <li>Preserve colouring of structures coloured by
2874 sequences in pre Jalview 2.7 projects</li>
2875 <li>Web service job parameter dialog is not laid out
2877 <li>Web services menu not refreshed after 'reset
2878 services' button is pressed in preferences</li>
2879 <li>Annotation off by one in Jalview v2_3 example project</li>
2880 <li>Structures imported from file and saved in project
2881 get name like jalview_pdb1234.txt when reloaded</li>
2882 <li>Jalview does not always retrieve progress of a JABAWS
2883 job execution in full once it is complete</li>
2884 </ul> <em>Applet</em>
2886 <li>Alignment height set incorrectly when lots of
2887 annotation rows are displayed</li>
2888 <li>Relative URLs in feature HTML text not resolved to
2890 <li>View follows highlighting does not work for positions
2892 <li><= shown as = in tooltip</li>
2893 <li>Export features raises exception when no features
2895 <li>Separator string used for serialising lists of IDs
2896 for javascript api is modified when separator string
2897 provided as parameter</li>
2898 <li>Null pointer exception when selecting tree leaves for
2899 alignment with no existing selection</li>
2900 <li>Relative URLs for datasources assumed to be relative
2901 to applet's codebase</li>
2902 <li>Status bar not updated after finished searching and
2903 search wraps around to first result</li>
2904 <li>StructureSelectionManager instance shared between
2905 several Jalview applets causes race conditions and memory
2907 <li>Hover tooltip and mouseover of position on structure
2908 not sent from Jmol in applet</li>
2909 <li>Certain sequences of javascript method calls to
2910 applet API fatally hang browser</li>
2911 </ul> <em>General</em>
2913 <li>View follows structure mouseover scrolls beyond
2914 position with wrapped view and hidden regions</li>
2915 <li>Find sequence position moves to wrong residue
2916 with/without hidden columns</li>
2917 <li>Sequence length given in alignment properties window
2919 <li>InvalidNumberFormat exceptions thrown when trying to
2920 import PDB like structure files</li>
2921 <li>Positional search results are only highlighted
2922 between user-supplied sequence start/end bounds</li>
2923 <li>End attribute of sequence is not validated</li>
2924 <li>Find dialog only finds first sequence containing a
2925 given sequence position</li>
2926 <li>Sequence numbering not preserved in MSF alignment
2928 <li>Jalview PDB file reader does not extract sequence
2929 from nucleotide chains correctly</li>
2930 <li>Structure colours not updated when tree partition
2931 changed in alignment</li>
2932 <li>Sequence associated secondary structure not correctly
2933 parsed in interleaved stockholm</li>
2934 <li>Colour by annotation dialog does not restore current
2936 <li>Hiding (nearly) all sequences doesn't work
2938 <li>Sequences containing lowercase letters are not
2939 properly associated with their pdb files</li>
2940 </ul> <em>Documentation and Development</em>
2942 <li>schemas/JalviewWsParamSet.xsd corrupted by
2943 ApplyCopyright tool</li>
2948 <div align="center">
2949 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2952 <td><em>Application</em>
2954 <li>New warning dialog when the Jalview Desktop cannot
2955 contact web services</li>
2956 <li>JABA service parameters for a preset are shown in
2957 service job window</li>
2958 <li>JABA Service menu entries reworded</li>
2962 <li>Modeller PIR IO broken - cannot correctly import a
2963 pir file emitted by Jalview</li>
2964 <li>Existing feature settings transferred to new
2965 alignment view created from cut'n'paste</li>
2966 <li>Improved test for mixed amino/nucleotide chains when
2967 parsing PDB files</li>
2968 <li>Consensus and conservation annotation rows
2969 occasionally become blank for all new windows</li>
2970 <li>Exception raised when right clicking above sequences
2971 in wrapped view mode</li>
2972 </ul> <em>Application</em>
2974 <li>multiple multiply aligned structure views cause cpu
2975 usage to hit 100% and computer to hang</li>
2976 <li>Web Service parameter layout breaks for long user
2977 parameter names</li>
2978 <li>Jaba service discovery hangs desktop if Jaba server
2985 <div align="center">
2986 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2989 <td><em>Application</em>
2991 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2992 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2995 <li>Web Services preference tab</li>
2996 <li>Analysis parameters dialog box and user defined
2998 <li>Improved speed and layout of Envision2 service menu</li>
2999 <li>Superpose structures using associated sequence
3001 <li>Export coordinates and projection as CSV from PCA
3003 </ul> <em>Applet</em>
3005 <li>enable javascript: execution by the applet via the
3006 link out mechanism</li>
3007 </ul> <em>Other</em>
3009 <li>Updated the Jmol Jalview interface to work with Jmol
3011 <li>The Jalview Desktop and JalviewLite applet now
3012 require Java 1.5</li>
3013 <li>Allow Jalview feature colour specification for GFF
3014 sequence annotation files</li>
3015 <li>New 'colour by label' keword in Jalview feature file
3016 type colour specification</li>
3017 <li>New Jalview Desktop Groovy API method that allows a
3018 script to check if it being run in an interactive session or
3019 in a batch operation from the Jalview command line</li>
3023 <li>clustalx colourscheme colours Ds preferentially when
3024 both D+E are present in over 50% of the column</li>
3025 </ul> <em>Application</em>
3027 <li>typo in AlignmentFrame->View->Hide->all but
3028 selected Regions menu item</li>
3029 <li>sequence fetcher replaces ',' for ';' when the ',' is
3030 part of a valid accession ID</li>
3031 <li>fatal OOM if object retrieved by sequence fetcher
3032 runs out of memory</li>
3033 <li>unhandled Out of Memory Error when viewing pca
3034 analysis results</li>
3035 <li>InstallAnywhere builds fail to launch on OS X java
3036 10.5 update 4 (due to apple Java 1.6 update)</li>
3037 <li>Installanywhere Jalview silently fails to launch</li>
3038 </ul> <em>Applet</em>
3040 <li>Jalview.getFeatureGroups() raises an
3041 ArrayIndexOutOfBoundsException if no feature groups are
3048 <div align="center">
3049 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3055 <li>Alignment prettyprinter doesn't cope with long
3057 <li>clustalx colourscheme colours Ds preferentially when
3058 both D+E are present in over 50% of the column</li>
3059 <li>nucleic acid structures retrieved from PDB do not
3060 import correctly</li>
3061 <li>More columns get selected than were clicked on when a
3062 number of columns are hidden</li>
3063 <li>annotation label popup menu not providing correct
3064 add/hide/show options when rows are hidden or none are
3066 <li>Stockholm format shown in list of readable formats,
3067 and parser copes better with alignments from RFAM.</li>
3068 <li>CSV output of consensus only includes the percentage
3069 of all symbols if sequence logo display is enabled</li>
3071 </ul> <em>Applet</em>
3073 <li>annotation panel disappears when annotation is
3075 </ul> <em>Application</em>
3077 <li>Alignment view not redrawn properly when new
3078 alignment opened where annotation panel is visible but no
3079 annotations are present on alignment</li>
3080 <li>pasted region containing hidden columns is
3081 incorrectly displayed in new alignment window</li>
3082 <li>Jalview slow to complete operations when stdout is
3083 flooded (fix is to close the Jalview console)</li>
3084 <li>typo in AlignmentFrame->View->Hide->all but
3085 selected Rregions menu item.</li>
3086 <li>inconsistent group submenu and Format submenu entry
3087 'Un' or 'Non'conserved</li>
3088 <li>Sequence feature settings are being shared by
3089 multiple distinct alignments</li>
3090 <li>group annotation not recreated when tree partition is
3092 <li>double click on group annotation to select sequences
3093 does not propagate to associated trees</li>
3094 <li>Mac OSX specific issues:
3096 <li>exception raised when mouse clicked on desktop
3097 window background</li>
3098 <li>Desktop menu placed on menu bar and application
3099 name set correctly</li>
3100 <li>sequence feature settings not wide enough for the
3101 save feature colourscheme button</li>
3110 <div align="center">
3111 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3114 <td><em>New Capabilities</em>
3116 <li>URL links generated from description line for
3117 regular-expression based URL links (applet and application)
3119 <li>Non-positional feature URL links are shown in link
3121 <li>Linked viewing of nucleic acid sequences and
3123 <li>Automatic Scrolling option in View menu to display
3124 the currently highlighted region of an alignment.</li>
3125 <li>Order an alignment by sequence length, or using the
3126 average score or total feature count for each sequence.</li>
3127 <li>Shading features by score or associated description</li>
3128 <li>Subdivide alignment and groups based on identity of
3129 selected subsequence (Make Groups from Selection).</li>
3130 <li>New hide/show options including Shift+Control+H to
3131 hide everything but the currently selected region.</li>
3132 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3133 </ul> <em>Application</em>
3135 <li>Fetch DB References capabilities and UI expanded to
3136 support retrieval from DAS sequence sources</li>
3137 <li>Local DAS Sequence sources can be added via the
3138 command line or via the Add local source dialog box.</li>
3139 <li>DAS Dbref and DbxRef feature types are parsed as
3140 database references and protein_name is parsed as
3141 description line (BioSapiens terms).</li>
3142 <li>Enable or disable non-positional feature and database
3143 references in sequence ID tooltip from View menu in
3145 <!-- <li>New hidden columns and rows and representatives capabilities
3146 in annotations file (in progress - not yet fully implemented)</li> -->
3147 <li>Group-associated consensus, sequence logos and
3148 conservation plots</li>
3149 <li>Symbol distributions for each column can be exported
3150 and visualized as sequence logos</li>
3151 <li>Optionally scale multi-character column labels to fit
3152 within each column of annotation row<!-- todo for applet -->
3154 <li>Optional automatic sort of associated alignment view
3155 when a new tree is opened.</li>
3156 <li>Jalview Java Console</li>
3157 <li>Better placement of desktop window when moving
3158 between different screens.</li>
3159 <li>New preference items for sequence ID tooltip and
3160 consensus annotation</li>
3161 <li>Client to submit sequences and IDs to Envision2
3163 <li><em>Vamsas Capabilities</em>
3165 <li>Improved VAMSAS synchronization (Jalview archive
3166 used to preserve views, structures, and tree display
3168 <li>Import of vamsas documents from disk or URL via
3170 <li>Sharing of selected regions between views and
3171 with other VAMSAS applications (Experimental feature!)</li>
3172 <li>Updated API to VAMSAS version 0.2</li>
3174 </ul> <em>Applet</em>
3176 <li>Middle button resizes annotation row height</li>
3179 <li>sortByTree (true/false) - automatically sort the
3180 associated alignment view by the tree when a new tree is
3182 <li>showTreeBootstraps (true/false) - show or hide
3183 branch bootstraps (default is to show them if available)</li>
3184 <li>showTreeDistances (true/false) - show or hide
3185 branch lengths (default is to show them if available)</li>
3186 <li>showUnlinkedTreeNodes (true/false) - indicate if
3187 unassociated nodes should be highlighted in the tree
3189 <li>heightScale and widthScale (1.0 or more) -
3190 increase the height or width of a cell in the alignment
3191 grid relative to the current font size.</li>
3194 <li>Non-positional features displayed in sequence ID
3196 </ul> <em>Other</em>
3198 <li>Features format: graduated colour definitions and
3199 specification of feature scores</li>
3200 <li>Alignment Annotations format: new keywords for group
3201 associated annotation (GROUP_REF) and annotation row display
3202 properties (ROW_PROPERTIES)</li>
3203 <li>XML formats extended to support graduated feature
3204 colourschemes, group associated annotation, and profile
3205 visualization settings.</li></td>
3208 <li>Source field in GFF files parsed as feature source
3209 rather than description</li>
3210 <li>Non-positional features are now included in sequence
3211 feature and gff files (controlled via non-positional feature
3212 visibility in tooltip).</li>
3213 <li>URL links generated for all feature links (bugfix)</li>
3214 <li>Added URL embedding instructions to features file
3216 <li>Codons containing ambiguous nucleotides translated as
3217 'X' in peptide product</li>
3218 <li>Match case switch in find dialog box works for both
3219 sequence ID and sequence string and query strings do not
3220 have to be in upper case to match case-insensitively.</li>
3221 <li>AMSA files only contain first column of
3222 multi-character column annotation labels</li>
3223 <li>Jalview Annotation File generation/parsing consistent
3224 with documentation (e.g. Stockholm annotation can be
3225 exported and re-imported)</li>
3226 <li>PDB files without embedded PDB IDs given a friendly
3228 <li>Find incrementally searches ID string matches as well
3229 as subsequence matches, and correctly reports total number
3233 <li>Better handling of exceptions during sequence
3235 <li>Dasobert generated non-positional feature URL
3236 link text excludes the start_end suffix</li>
3237 <li>DAS feature and source retrieval buttons disabled
3238 when fetch or registry operations in progress.</li>
3239 <li>PDB files retrieved from URLs are cached properly</li>
3240 <li>Sequence description lines properly shared via
3242 <li>Sequence fetcher fetches multiple records for all
3244 <li>Ensured that command line das feature retrieval
3245 completes before alignment figures are generated.</li>
3246 <li>Reduced time taken when opening file browser for
3248 <li>isAligned check prior to calculating tree, PCA or
3249 submitting an MSA to JNet now excludes hidden sequences.</li>
3250 <li>User defined group colours properly recovered
3251 from Jalview projects.</li>
3260 <div align="center">
3261 <strong>2.4.0.b2</strong><br> 28/10/2009
3266 <li>Experimental support for google analytics usage
3268 <li>Jalview privacy settings (user preferences and docs).</li>
3273 <li>Race condition in applet preventing startup in
3275 <li>Exception when feature created from selection beyond
3276 length of sequence.</li>
3277 <li>Allow synthetic PDB files to be imported gracefully</li>
3278 <li>Sequence associated annotation rows associate with
3279 all sequences with a given id</li>
3280 <li>Find function matches case-insensitively for sequence
3281 ID string searches</li>
3282 <li>Non-standard characters do not cause pairwise
3283 alignment to fail with exception</li>
3284 </ul> <em>Application Issues</em>
3286 <li>Sequences are now validated against EMBL database</li>
3287 <li>Sequence fetcher fetches multiple records for all
3289 </ul> <em>InstallAnywhere Issues</em>
3291 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3292 issue with installAnywhere mechanism)</li>
3293 <li>Command line launching of JARs from InstallAnywhere
3294 version (java class versioning error fixed)</li>
3301 <div align="center">
3302 <strong>2.4</strong><br> 27/8/2008
3305 <td><em>User Interface</em>
3307 <li>Linked highlighting of codon and amino acid from
3308 translation and protein products</li>
3309 <li>Linked highlighting of structure associated with
3310 residue mapping to codon position</li>
3311 <li>Sequence Fetcher provides example accession numbers
3312 and 'clear' button</li>
3313 <li>MemoryMonitor added as an option under Desktop's
3315 <li>Extract score function to parse whitespace separated
3316 numeric data in description line</li>
3317 <li>Column labels in alignment annotation can be centred.</li>
3318 <li>Tooltip for sequence associated annotation give name
3320 </ul> <em>Web Services and URL fetching</em>
3322 <li>JPred3 web service</li>
3323 <li>Prototype sequence search client (no public services
3325 <li>Fetch either seed alignment or full alignment from
3327 <li>URL Links created for matching database cross
3328 references as well as sequence ID</li>
3329 <li>URL Links can be created using regular-expressions</li>
3330 </ul> <em>Sequence Database Connectivity</em>
3332 <li>Retrieval of cross-referenced sequences from other
3334 <li>Generalised database reference retrieval and
3335 validation to all fetchable databases</li>
3336 <li>Fetch sequences from DAS sources supporting the
3337 sequence command</li>
3338 </ul> <em>Import and Export</em>
3339 <li>export annotation rows as CSV for spreadsheet import</li>
3340 <li>Jalview projects record alignment dataset associations,
3341 EMBL products, and cDNA sequence mappings</li>
3342 <li>Sequence Group colour can be specified in Annotation
3344 <li>Ad-hoc colouring of group in Annotation File using RGB
3345 triplet as name of colourscheme</li>
3346 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3348 <li>treenode binding for VAMSAS tree exchange</li>
3349 <li>local editing and update of sequences in VAMSAS
3350 alignments (experimental)</li>
3351 <li>Create new or select existing session to join</li>
3352 <li>load and save of vamsas documents</li>
3353 </ul> <em>Application command line</em>
3355 <li>-tree parameter to open trees (introduced for passing
3357 <li>-fetchfrom command line argument to specify nicknames
3358 of DAS servers to query for alignment features</li>
3359 <li>-dasserver command line argument to add new servers
3360 that are also automatically queried for features</li>
3361 <li>-groovy command line argument executes a given groovy
3362 script after all input data has been loaded and parsed</li>
3363 </ul> <em>Applet-Application data exchange</em>
3365 <li>Trees passed as applet parameters can be passed to
3366 application (when using "View in full
3367 application")</li>
3368 </ul> <em>Applet Parameters</em>
3370 <li>feature group display control parameter</li>
3371 <li>debug parameter</li>
3372 <li>showbutton parameter</li>
3373 </ul> <em>Applet API methods</em>
3375 <li>newView public method</li>
3376 <li>Window (current view) specific get/set public methods</li>
3377 <li>Feature display control methods</li>
3378 <li>get list of currently selected sequences</li>
3379 </ul> <em>New Jalview distribution features</em>
3381 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3382 <li>RELEASE file gives build properties for the latest
3383 Jalview release.</li>
3384 <li>Java 1.1 Applet build made easier and donotobfuscate
3385 property controls execution of obfuscator</li>
3386 <li>Build target for generating source distribution</li>
3387 <li>Debug flag for javacc</li>
3388 <li>.jalview_properties file is documented (slightly) in
3389 jalview.bin.Cache</li>
3390 <li>Continuous Build Integration for stable and
3391 development version of Application, Applet and source
3396 <li>selected region output includes visible annotations
3397 (for certain formats)</li>
3398 <li>edit label/displaychar contains existing label/char
3400 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3401 <li>shorter peptide product names from EMBL records</li>
3402 <li>Newick string generator makes compact representations</li>
3403 <li>bootstrap values parsed correctly for tree files with
3405 <li>pathological filechooser bug avoided by not allowing
3406 filenames containing a ':'</li>
3407 <li>Fixed exception when parsing GFF files containing
3408 global sequence features</li>
3409 <li>Alignment datasets are finalized only when number of
3410 references from alignment sequences goes to zero</li>
3411 <li>Close of tree branch colour box without colour
3412 selection causes cascading exceptions</li>
3413 <li>occasional negative imgwidth exceptions</li>
3414 <li>better reporting of non-fatal warnings to user when
3415 file parsing fails.</li>
3416 <li>Save works when Jalview project is default format</li>
3417 <li>Save as dialog opened if current alignment format is
3418 not a valid output format</li>
3419 <li>UniProt canonical names introduced for both das and
3421 <li>Histidine should be midblue (not pink!) in Zappo</li>
3422 <li>error messages passed up and output when data read
3424 <li>edit undo recovers previous dataset sequence when
3425 sequence is edited</li>
3426 <li>allow PDB files without pdb ID HEADER lines (like
3427 those generated by MODELLER) to be read in properly</li>
3428 <li>allow reading of JPred concise files as a normal
3430 <li>Stockholm annotation parsing and alignment properties
3431 import fixed for PFAM records</li>
3432 <li>Structure view windows have correct name in Desktop
3434 <li>annotation consisting of sequence associated scores
3435 can be read and written correctly to annotation file</li>
3436 <li>Aligned cDNA translation to aligned peptide works
3438 <li>Fixed display of hidden sequence markers and
3439 non-italic font for representatives in Applet</li>
3440 <li>Applet Menus are always embedded in applet window on
3442 <li>Newly shown features appear at top of stack (in
3444 <li>Annotations added via parameter not drawn properly
3445 due to null pointer exceptions</li>
3446 <li>Secondary structure lines are drawn starting from
3447 first column of alignment</li>
3448 <li>UniProt XML import updated for new schema release in
3450 <li>Sequence feature to sequence ID match for Features
3451 file is case-insensitive</li>
3452 <li>Sequence features read from Features file appended to
3453 all sequences with matching IDs</li>
3454 <li>PDB structure coloured correctly for associated views
3455 containing a sub-sequence</li>
3456 <li>PDB files can be retrieved by applet from Jar files</li>
3457 <li>feature and annotation file applet parameters
3458 referring to different directories are retrieved correctly</li>
3459 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3460 <li>Fixed application hang whilst waiting for
3461 splash-screen version check to complete</li>
3462 <li>Applet properly URLencodes input parameter values
3463 when passing them to the launchApp service</li>
3464 <li>display name and local features preserved in results
3465 retrieved from web service</li>
3466 <li>Visual delay indication for sequence retrieval and
3467 sequence fetcher initialisation</li>
3468 <li>updated Application to use DAS 1.53e version of
3469 dasobert DAS client</li>
3470 <li>Re-instated Full AMSA support and .amsa file
3472 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3480 <div align="center">
3481 <strong>2.3</strong><br> 9/5/07
3486 <li>Jmol 11.0.2 integration</li>
3487 <li>PDB views stored in Jalview XML files</li>
3488 <li>Slide sequences</li>
3489 <li>Edit sequence in place</li>
3490 <li>EMBL CDS features</li>
3491 <li>DAS Feature mapping</li>
3492 <li>Feature ordering</li>
3493 <li>Alignment Properties</li>
3494 <li>Annotation Scores</li>
3495 <li>Sort by scores</li>
3496 <li>Feature/annotation editing in applet</li>
3501 <li>Headless state operation in 2.2.1</li>
3502 <li>Incorrect and unstable DNA pairwise alignment</li>
3503 <li>Cut and paste of sequences with annotation</li>
3504 <li>Feature group display state in XML</li>
3505 <li>Feature ordering in XML</li>
3506 <li>blc file iteration selection using filename # suffix</li>
3507 <li>Stockholm alignment properties</li>
3508 <li>Stockhom alignment secondary structure annotation</li>
3509 <li>2.2.1 applet had no feature transparency</li>
3510 <li>Number pad keys can be used in cursor mode</li>
3511 <li>Structure Viewer mirror image resolved</li>
3518 <div align="center">
3519 <strong>2.2.1</strong><br> 12/2/07
3524 <li>Non standard characters can be read and displayed
3525 <li>Annotations/Features can be imported/exported to the
3527 <li>Applet allows editing of sequence/annotation/group
3528 name & description
3529 <li>Preference setting to display sequence name in
3531 <li>Annotation file format extended to allow
3532 Sequence_groups to be defined
3533 <li>Default opening of alignment overview panel can be
3534 specified in preferences
3535 <li>PDB residue numbering annotation added to associated
3541 <li>Applet crash under certain Linux OS with Java 1.6
3543 <li>Annotation file export / import bugs fixed
3544 <li>PNG / EPS image output bugs fixed
3550 <div align="center">
3551 <strong>2.2</strong><br> 27/11/06
3556 <li>Multiple views on alignment
3557 <li>Sequence feature editing
3558 <li>"Reload" alignment
3559 <li>"Save" to current filename
3560 <li>Background dependent text colour
3561 <li>Right align sequence ids
3562 <li>User-defined lower case residue colours
3565 <li>Menu item accelerator keys
3566 <li>Control-V pastes to current alignment
3567 <li>Cancel button for DAS Feature Fetching
3568 <li>PCA and PDB Viewers zoom via mouse roller
3569 <li>User-defined sub-tree colours and sub-tree selection
3571 <li>'New Window' button on the 'Output to Text box'
3576 <li>New memory efficient Undo/Redo System
3577 <li>Optimised symbol lookups and conservation/consensus
3579 <li>Region Conservation/Consensus recalculated after
3581 <li>Fixed Remove Empty Columns Bug (empty columns at end
3583 <li>Slowed DAS Feature Fetching for increased robustness.
3585 <li>Made angle brackets in ASCII feature descriptions
3587 <li>Re-instated Zoom function for PCA
3588 <li>Sequence descriptions conserved in web service
3590 <li>UniProt ID discoverer uses any word separated by
3592 <li>WsDbFetch query/result association resolved
3593 <li>Tree leaf to sequence mapping improved
3594 <li>Smooth fonts switch moved to FontChooser dialog box.
3601 <div align="center">
3602 <strong>2.1.1</strong><br> 12/9/06
3607 <li>Copy consensus sequence to clipboard</li>
3612 <li>Image output - rightmost residues are rendered if
3613 sequence id panel has been resized</li>
3614 <li>Image output - all offscreen group boundaries are
3616 <li>Annotation files with sequence references - all
3617 elements in file are relative to sequence position</li>
3618 <li>Mac Applet users can use Alt key for group editing</li>
3624 <div align="center">
3625 <strong>2.1</strong><br> 22/8/06
3630 <li>MAFFT Multiple Alignment in default Web Service list</li>
3631 <li>DAS Feature fetching</li>
3632 <li>Hide sequences and columns</li>
3633 <li>Export Annotations and Features</li>
3634 <li>GFF file reading / writing</li>
3635 <li>Associate structures with sequences from local PDB
3637 <li>Add sequences to exisiting alignment</li>
3638 <li>Recently opened files / URL lists</li>
3639 <li>Applet can launch the full application</li>
3640 <li>Applet has transparency for features (Java 1.2
3642 <li>Applet has user defined colours parameter</li>
3643 <li>Applet can load sequences from parameter
3644 "sequence<em>x</em>"
3650 <li>Redundancy Panel reinstalled in the Applet</li>
3651 <li>Monospaced font - EPS / rescaling bug fixed</li>
3652 <li>Annotation files with sequence references bug fixed</li>
3658 <div align="center">
3659 <strong>2.08.1</strong><br> 2/5/06
3664 <li>Change case of selected region from Popup menu</li>
3665 <li>Choose to match case when searching</li>
3666 <li>Middle mouse button and mouse movement can compress /
3667 expand the visible width and height of the alignment</li>
3672 <li>Annotation Panel displays complete JNet results</li>
3678 <div align="center">
3679 <strong>2.08b</strong><br> 18/4/06
3685 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3686 <li>Righthand label on wrapped alignments shows correct
3693 <div align="center">
3694 <strong>2.08</strong><br> 10/4/06
3699 <li>Editing can be locked to the selection area</li>
3700 <li>Keyboard editing</li>
3701 <li>Create sequence features from searches</li>
3702 <li>Precalculated annotations can be loaded onto
3704 <li>Features file allows grouping of features</li>
3705 <li>Annotation Colouring scheme added</li>
3706 <li>Smooth fonts off by default - Faster rendering</li>
3707 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3712 <li>Drag & Drop fixed on Linux</li>
3713 <li>Jalview Archive file faster to load/save, sequence
3714 descriptions saved.</li>
3720 <div align="center">
3721 <strong>2.07</strong><br> 12/12/05
3726 <li>PDB Structure Viewer enhanced</li>
3727 <li>Sequence Feature retrieval and display enhanced</li>
3728 <li>Choose to output sequence start-end after sequence
3729 name for file output</li>
3730 <li>Sequence Fetcher WSDBFetch@EBI</li>
3731 <li>Applet can read feature files, PDB files and can be
3732 used for HTML form input</li>
3737 <li>HTML output writes groups and features</li>
3738 <li>Group editing is Control and mouse click</li>
3739 <li>File IO bugs</li>
3745 <div align="center">
3746 <strong>2.06</strong><br> 28/9/05
3751 <li>View annotations in wrapped mode</li>
3752 <li>More options for PCA viewer</li>
3757 <li>GUI bugs resolved</li>
3758 <li>Runs with -nodisplay from command line</li>
3764 <div align="center">
3765 <strong>2.05b</strong><br> 15/9/05
3770 <li>Choose EPS export as lineart or text</li>
3771 <li>Jar files are executable</li>
3772 <li>Can read in Uracil - maps to unknown residue</li>
3777 <li>Known OutOfMemory errors give warning message</li>
3778 <li>Overview window calculated more efficiently</li>
3779 <li>Several GUI bugs resolved</li>
3785 <div align="center">
3786 <strong>2.05</strong><br> 30/8/05
3791 <li>Edit and annotate in "Wrapped" view</li>
3796 <li>Several GUI bugs resolved</li>
3802 <div align="center">
3803 <strong>2.04</strong><br> 24/8/05
3808 <li>Hold down mouse wheel & scroll to change font
3814 <li>Improved JPred client reliability</li>
3815 <li>Improved loading of Jalview files</li>
3821 <div align="center">
3822 <strong>2.03</strong><br> 18/8/05
3827 <li>Set Proxy server name and port in preferences</li>
3828 <li>Multiple URL links from sequence ids</li>
3829 <li>User Defined Colours can have a scheme name and added
3831 <li>Choose to ignore gaps in consensus calculation</li>
3832 <li>Unix users can set default web browser</li>
3833 <li>Runs without GUI for batch processing</li>
3834 <li>Dynamically generated Web Service Menus</li>
3839 <li>InstallAnywhere download for Sparc Solaris</li>
3845 <div align="center">
3846 <strong>2.02</strong><br> 18/7/05
3852 <li>Copy & Paste order of sequences maintains
3853 alignment order.</li>
3859 <div align="center">
3860 <strong>2.01</strong><br> 12/7/05
3865 <li>Use delete key for deleting selection.</li>
3866 <li>Use Mouse wheel to scroll sequences.</li>
3867 <li>Help file updated to describe how to add alignment
3869 <li>Version and build date written to build properties
3871 <li>InstallAnywhere installation will check for updates
3872 at launch of Jalview.</li>
3877 <li>Delete gaps bug fixed.</li>
3878 <li>FileChooser sorts columns.</li>
3879 <li>Can remove groups one by one.</li>
3880 <li>Filechooser icons installed.</li>
3881 <li>Finder ignores return character when searching.
3882 Return key will initiate a search.<br>
3889 <div align="center">
3890 <strong>2.0</strong><br> 20/6/05
3895 <li>New codebase</li>