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>8/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
81 for disabling automatic superposition of multiple
82 structures and open structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
98 <!-- JAL-2593 -->Improved performance when rendering lots
99 of features (particularly when transparency is disabled)
104 <td><div align="left">
107 <!-- JAL-2899 -->Structure and Overview aren't updated
108 when Colour By Annotation threshold slider is adjusted
111 <!-- JAL-2778 -->Slow redraw when Overview panel shown
112 overlapping alignment panel
115 <!-- JAL-2929 -->overview doesn't show end of unpadded
119 <!-- JAL-2789, JAL-2893 -->Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
125 <!-- JAL-2666 -->Linked scrolling via protein horizontal
126 scroll bar doesn't work for some CDS/Protein views
129 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
130 Java 1.8u153 onwards and Java 1.9u4+.
133 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
134 columns in annotation row
137 <!-- JAL-2913 -->Preferences panel's ID Width control is
138 honored in interactive and batch mode
141 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
142 for structures added to existing Jmol view
145 <!-- JAL-2223 -->'View Mappings' includes duplicate
146 entries after importing project with multiple views
149 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
150 protein sequences via SIFTS from associated PDB entries
151 with negative residue numbers or missing residues fails
154 <!-- JAL-2952 -->Exception when shading sequence with negative
155 Temperature Factor values from annotated PDB files (e.g.
156 as generated by CONSURF)
159 <!-- JAL-2922 -->Invert displayed features very slow when
160 structure and/or overview windows are also shown
163 <!-- JAL-2954 -->Selecting columns from highlighted regions
164 very slow for alignments with large numbers of sequences
167 <!-- JAL-2925 -->Copy Consensus fails for group consensus
168 with 'StringIndexOutOfBounds'
171 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
172 platforms running Java 10
175 <!-- JAL-2960 -->Adding a structure to existing structure
176 view appears to do nothing because the view is hidden behind the alignment view
182 <!-- JAL-2926 -->Copy consensus sequence option in applet
183 should copy the group consensus when popup is opened on it
189 <!-- JAL-2913 -->Fixed ID width preference is not respected
192 <em>New Known Defects</em>
195 <!-- JAL-2973 --> Exceptions occasionally raised when
196 editing a large alignment and overview is displayed
199 <!-- JAL-2974 -->'Overview updating' progress bar is shown
200 repeatedly after a series of edits even when the overview
201 is no longer reflecting updates
204 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
205 structures for protein subsequence (if 'Trim Retrieved
206 Sequences' enabled) or Ensembl isoforms (Workaround in
207 2.10.4 is to fail back to N&W mapping)
214 <td width="60" nowrap>
216 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
219 <td><div align="left">
220 <ul><li>Updated Certum Codesigning Certificate
221 (Valid till 30th November 2018)</li></ul></div></td>
222 <td><div align="left">
225 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
226 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
227 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
228 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
229 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
230 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
231 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
237 <td width="60" nowrap>
239 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
242 <td><div align="left">
246 <!-- JAL-2446 -->Faster and more efficient management and
247 rendering of sequence features
250 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
251 429 rate limit request hander
254 <!-- JAL-2773 -->Structure views don't get updated unless
255 their colours have changed
258 <!-- JAL-2495 -->All linked sequences are highlighted for
259 a structure mousover (Jmol) or selection (Chimera)
262 <!-- JAL-2790 -->'Cancel' button in progress bar for
263 JABAWS AACon, RNAAliFold and Disorder prediction jobs
266 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
267 view from Ensembl locus cross-references
270 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
274 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
275 feature can be disabled
278 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
279 PDB easier retrieval of sequences for lists of IDs
282 <!-- JAL-2758 -->Short names for sequences retrieved from
288 <li>Groovy interpreter updated to 2.4.12</li>
289 <li>Example groovy script for generating a matrix of
290 percent identity scores for current alignment.</li>
292 <em>Testing and Deployment</em>
295 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
299 <td><div align="left">
303 <!-- JAL-2643 -->Pressing tab after updating the colour
304 threshold text field doesn't trigger an update to the
308 <!-- JAL-2682 -->Race condition when parsing sequence ID
312 <!-- JAL-2608 -->Overview windows are also closed when
313 alignment window is closed
316 <!-- JAL-2548 -->Export of features doesn't always respect
320 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
321 takes a long time in Cursor mode
327 <!-- JAL-2777 -->Structures with whitespace chainCode
328 cannot be viewed in Chimera
331 <!-- JAL-2728 -->Protein annotation panel too high in
335 <!-- JAL-2757 -->Can't edit the query after the server
336 error warning icon is shown in Uniprot and PDB Free Text
340 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
343 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
346 <!-- JAL-2739 -->Hidden column marker in last column not
347 rendered when switching back from Wrapped to normal view
350 <!-- JAL-2768 -->Annotation display corrupted when
351 scrolling right in unwapped alignment view
354 <!-- JAL-2542 -->Existing features on subsequence
355 incorrectly relocated when full sequence retrieved from
359 <!-- JAL-2733 -->Last reported memory still shown when
360 Desktop->Show Memory is unticked (OSX only)
363 <!-- JAL-2658 -->Amend Features dialog doesn't allow
364 features of same type and group to be selected for
368 <!-- JAL-2524 -->Jalview becomes sluggish in wide
369 alignments when hidden columns are present
372 <!-- JAL-2392 -->Jalview freezes when loading and
373 displaying several structures
376 <!-- JAL-2732 -->Black outlines left after resizing or
380 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
381 within the Jalview desktop on OSX
384 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
385 when in wrapped alignment mode
388 <!-- JAL-2636 -->Scale mark not shown when close to right
389 hand end of alignment
392 <!-- JAL-2684 -->Pairwise alignment of selected regions of
393 each selected sequence do not have correct start/end
397 <!-- JAL-2793 -->Alignment ruler height set incorrectly
398 after canceling the Alignment Window's Font dialog
401 <!-- JAL-2036 -->Show cross-references not enabled after
402 restoring project until a new view is created
405 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
406 URL links appears when only default EMBL-EBI link is
407 configured (since 2.10.2b2)
410 <!-- JAL-2775 -->Overview redraws whole window when box
414 <!-- JAL-2225 -->Structure viewer doesn't map all chains
415 in a multi-chain structure when viewing alignment
416 involving more than one chain (since 2.10)
419 <!-- JAL-2811 -->Double residue highlights in cursor mode
420 if new selection moves alignment window
423 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
424 arrow key in cursor mode to pass hidden column marker
427 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
428 that produces correctly annotated transcripts and products
431 <!-- JAL-2776 -->Toggling a feature group after first time
432 doesn't update associated structure view
435 <em>Applet</em><br />
438 <!-- JAL-2687 -->Concurrent modification exception when
439 closing alignment panel
442 <em>BioJSON</em><br />
445 <!-- JAL-2546 -->BioJSON export does not preserve
446 non-positional features
449 <em>New Known Issues</em>
452 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
453 sequence features correctly (for many previous versions of
457 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
458 using cursor in wrapped panel other than top
461 <!-- JAL-2791 -->Select columns containing feature ignores
462 graduated colour threshold
465 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
466 always preserve numbering and sequence features
469 <em>Known Java 9 Issues</em>
472 <!-- JAL-2902 -->Groovy Console very slow to open and is
473 not responsive when entering characters (Webstart, Java
480 <td width="60" nowrap>
482 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
483 <em>2/10/2017</em></strong>
486 <td><div align="left">
487 <em>New features in Jalview Desktop</em>
490 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
492 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
496 <td><div align="left">
500 <td width="60" nowrap>
502 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
503 <em>7/9/2017</em></strong>
506 <td><div align="left">
510 <!-- JAL-2588 -->Show gaps in overview window by colouring
511 in grey (sequences used to be coloured grey, and gaps were
515 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
519 <!-- JAL-2587 -->Overview updates immediately on increase
520 in size and progress bar shown as higher resolution
521 overview is recalculated
526 <td><div align="left">
530 <!-- JAL-2664 -->Overview window redraws every hidden
531 column region row by row
534 <!-- JAL-2681 -->duplicate protein sequences shown after
535 retrieving Ensembl crossrefs for sequences from Uniprot
538 <!-- JAL-2603 -->Overview window throws NPE if show boxes
539 format setting is unticked
542 <!-- JAL-2610 -->Groups are coloured wrongly in overview
543 if group has show boxes format setting unticked
546 <!-- JAL-2672,JAL-2665 -->Redraw problems when
547 autoscrolling whilst dragging current selection group to
548 include sequences and columns not currently displayed
551 <!-- JAL-2691 -->Not all chains are mapped when multimeric
552 assemblies are imported via CIF file
555 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
556 displayed when threshold or conservation colouring is also
560 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
564 <!-- JAL-2673 -->Jalview continues to scroll after
565 dragging a selected region off the visible region of the
569 <!-- JAL-2724 -->Cannot apply annotation based
570 colourscheme to all groups in a view
573 <!-- JAL-2511 -->IDs don't line up with sequences
574 initially after font size change using the Font chooser or
581 <td width="60" nowrap>
583 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
586 <td><div align="left">
587 <em>Calculations</em>
591 <!-- JAL-1933 -->Occupancy annotation row shows number of
592 ungapped positions in each column of the alignment.
595 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
596 a calculation dialog box
599 <!-- JAL-2379 -->Revised implementation of PCA for speed
600 and memory efficiency (~30x faster)
603 <!-- JAL-2403 -->Revised implementation of sequence
604 similarity scores as used by Tree, PCA, Shading Consensus
605 and other calculations
608 <!-- JAL-2416 -->Score matrices are stored as resource
609 files within the Jalview codebase
612 <!-- JAL-2500 -->Trees computed on Sequence Feature
613 Similarity may have different topology due to increased
620 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
621 model for alignments and groups
624 <!-- JAL-384 -->Custom shading schemes created via groovy
631 <!-- JAL-2526 -->Efficiency improvements for interacting
632 with alignment and overview windows
635 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
639 <!-- JAL-2388 -->Hidden columns and sequences can be
643 <!-- JAL-2611 -->Click-drag in visible area allows fine
644 adjustment of visible position
648 <em>Data import/export</em>
651 <!-- JAL-2535 -->Posterior probability annotation from
652 Stockholm files imported as sequence associated annotation
655 <!-- JAL-2507 -->More robust per-sequence positional
656 annotation input/output via stockholm flatfile
659 <!-- JAL-2533 -->Sequence names don't include file
660 extension when importing structure files without embedded
661 names or PDB accessions
664 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
665 format sequence substitution matrices
668 <em>User Interface</em>
671 <!-- JAL-2447 --> Experimental Features Checkbox in
672 Desktop's Tools menu to hide or show untested features in
676 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
677 via Overview or sequence motif search operations
680 <!-- JAL-2547 -->Amend sequence features dialog box can be
681 opened by double clicking gaps within sequence feature
685 <!-- JAL-1476 -->Status bar message shown when not enough
686 aligned positions were available to create a 3D structure
690 <em>3D Structure</em>
693 <!-- JAL-2430 -->Hidden regions in alignment views are not
694 coloured in linked structure views
697 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
698 file-based command exchange
701 <!-- JAL-2375 -->Structure chooser automatically shows
702 Cached Structures rather than querying the PDBe if
703 structures are already available for sequences
706 <!-- JAL-2520 -->Structures imported via URL are cached in
707 the Jalview project rather than downloaded again when the
711 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
712 to transfer Chimera's structure attributes as Jalview
713 features, and vice-versa (<strong>Experimental
717 <em>Web Services</em>
720 <!-- JAL-2549 -->Updated JABAWS client to v2.2
723 <!-- JAL-2335 -->Filter non-standard amino acids and
724 nucleotides when submitting to AACon and other MSA
728 <!-- JAL-2316, -->URLs for viewing database
729 cross-references provided by identifiers.org and the
737 <!-- JAL-2344 -->FileFormatI interface for describing and
738 identifying file formats (instead of String constants)
741 <!-- JAL-2228 -->FeatureCounter script refactored for
742 efficiency when counting all displayed features (not
743 backwards compatible with 2.10.1)
746 <em>Example files</em>
749 <!-- JAL-2631 -->Graduated feature colour style example
750 included in the example feature file
753 <em>Documentation</em>
756 <!-- JAL-2339 -->Release notes reformatted for readability
757 with the built-in Java help viewer
760 <!-- JAL-1644 -->Find documentation updated with 'search
761 sequence description' option
767 <!-- JAL-2485, -->External service integration tests for
768 Uniprot REST Free Text Search Client
771 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
774 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
779 <td><div align="left">
780 <em>Calculations</em>
783 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
784 matrix - C->R should be '-3'<br />Old matrix restored
785 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
787 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
788 Jalview's treatment of gaps in PCA and substitution matrix
789 based Tree calculations.<br /> <br />In earlier versions
790 of Jalview, gaps matching gaps were penalised, and gaps
791 matching non-gaps penalised even more. In the PCA
792 calculation, gaps were actually treated as non-gaps - so
793 different costs were applied, which meant Jalview's PCAs
794 were different to those produced by SeqSpace.<br />Jalview
795 now treats gaps in the same way as SeqSpace (ie it scores
796 them as 0). <br /> <br />Enter the following in the
797 Groovy console to restore pre-2.10.2 behaviour:<br />
798 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
799 // for 2.10.1 mode <br />
800 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
801 // to restore 2.10.2 mode <br /> <br /> <em>Note:
802 these settings will affect all subsequent tree and PCA
803 calculations (not recommended)</em></li>
805 <!-- JAL-2424 -->Fixed off-by-one bug that affected
806 scaling of branch lengths for trees computed using
807 Sequence Feature Similarity.
810 <!-- JAL-2377 -->PCA calculation could hang when
811 generating output report when working with highly
815 <!-- JAL-2544 --> Sort by features includes features to
816 right of selected region when gaps present on right-hand
820 <em>User Interface</em>
823 <!-- JAL-2346 -->Reopening Colour by annotation dialog
824 doesn't reselect a specific sequence's associated
825 annotation after it was used for colouring a view
828 <!-- JAL-2419 -->Current selection lost if popup menu
829 opened on a region of alignment without groups
832 <!-- JAL-2374 -->Popup menu not always shown for regions
833 of an alignment with overlapping groups
836 <!-- JAL-2310 -->Finder double counts if both a sequence's
837 name and description match
840 <!-- JAL-2370 -->Hiding column selection containing two
841 hidden regions results in incorrect hidden regions
844 <!-- JAL-2386 -->'Apply to all groups' setting when
845 changing colour does not apply Conservation slider value
849 <!-- JAL-2373 -->Percentage identity and conservation menu
850 items do not show a tick or allow shading to be disabled
853 <!-- JAL-2385 -->Conservation shading or PID threshold
854 lost when base colourscheme changed if slider not visible
857 <!-- JAL-2547 -->Sequence features shown in tooltip for
858 gaps before start of features
861 <!-- JAL-2623 -->Graduated feature colour threshold not
862 restored to UI when feature colour is edited
865 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
866 a time when scrolling vertically in wrapped mode.
869 <!-- JAL-2630 -->Structure and alignment overview update
870 as graduate feature colour settings are modified via the
874 <!-- JAL-2034 -->Overview window doesn't always update
875 when a group defined on the alignment is resized
878 <!-- JAL-2605 -->Mouseovers on left/right scale region in
879 wrapped view result in positional status updates
883 <!-- JAL-2563 -->Status bar doesn't show position for
884 ambiguous amino acid and nucleotide symbols
887 <!-- JAL-2602 -->Copy consensus sequence failed if
888 alignment included gapped columns
891 <!-- JAL-2473 -->Minimum size set for Jalview windows so
892 widgets don't permanently disappear
895 <!-- JAL-2503 -->Cannot select or filter quantitative
896 annotation that are shown only as column labels (e.g.
897 T-Coffee column reliability scores)
900 <!-- JAL-2594 -->Exception thrown if trying to create a
901 sequence feature on gaps only
904 <!-- JAL-2504 -->Features created with 'New feature'
905 button from a Find inherit previously defined feature type
906 rather than the Find query string
909 <!-- JAL-2423 -->incorrect title in output window when
910 exporting tree calculated in Jalview
913 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
914 and then revealing them reorders sequences on the
918 <!-- JAL-964 -->Group panel in sequence feature settings
919 doesn't update to reflect available set of groups after
920 interactively adding or modifying features
923 <!-- JAL-2225 -->Sequence Database chooser unusable on
927 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
928 only excluded gaps in current sequence and ignored
935 <!-- JAL-2421 -->Overview window visible region moves
936 erratically when hidden rows or columns are present
939 <!-- JAL-2362 -->Per-residue colourschemes applied via the
940 Structure Viewer's colour menu don't correspond to
944 <!-- JAL-2405 -->Protein specific colours only offered in
945 colour and group colour menu for protein alignments
948 <!-- JAL-2385 -->Colour threshold slider doesn't update to
949 reflect currently selected view or group's shading
953 <!-- JAL-2624 -->Feature colour thresholds not respected
954 when rendered on overview and structures when opacity at
958 <!-- JAL-2589 -->User defined gap colour not shown in
959 overview when features overlaid on alignment
962 <em>Data import/export</em>
965 <!-- JAL-2576 -->Very large alignments take a long time to
969 <!-- JAL-2507 -->Per-sequence RNA secondary structures
970 added after a sequence was imported are not written to
974 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
975 when importing RNA secondary structure via Stockholm
978 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
979 not shown in correct direction for simple pseudoknots
982 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
983 with lightGray or darkGray via features file (but can
987 <!-- JAL-2383 -->Above PID colour threshold not recovered
988 when alignment view imported from project
991 <!-- JAL-2520,JAL-2465 -->No mappings generated between
992 structure and sequences extracted from structure files
993 imported via URL and viewed in Jmol
996 <!-- JAL-2520 -->Structures loaded via URL are saved in
997 Jalview Projects rather than fetched via URL again when
998 the project is loaded and the structure viewed
1001 <em>Web Services</em>
1004 <!-- JAL-2519 -->EnsemblGenomes example failing after
1005 release of Ensembl v.88
1008 <!-- JAL-2366 -->Proxy server address and port always
1009 appear enabled in Preferences->Connections
1012 <!-- JAL-2461 -->DAS registry not found exceptions
1013 removed from console output
1016 <!-- JAL-2582 -->Cannot retrieve protein products from
1017 Ensembl by Peptide ID
1020 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1021 created from SIFTs, and spurious 'Couldn't open structure
1022 in Chimera' errors raised after April 2017 update (problem
1023 due to 'null' string rather than empty string used for
1024 residues with no corresponding PDB mapping).
1027 <em>Application UI</em>
1030 <!-- JAL-2361 -->User Defined Colours not added to Colour
1034 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1035 case' residues (button in colourscheme editor debugged and
1036 new documentation and tooltips added)
1039 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1040 doesn't restore group-specific text colour thresholds
1043 <!-- JAL-2243 -->Feature settings panel does not update as
1044 new features are added to alignment
1047 <!-- JAL-2532 -->Cancel in feature settings reverts
1048 changes to feature colours via the Amend features dialog
1051 <!-- JAL-2506 -->Null pointer exception when attempting to
1052 edit graduated feature colour via amend features dialog
1056 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1057 selection menu changes colours of alignment views
1060 <!-- JAL-2426 -->Spurious exceptions in console raised
1061 from alignment calculation workers after alignment has
1065 <!-- JAL-1608 -->Typo in selection popup menu - Create
1066 groups now 'Create Group'
1069 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1070 Create/Undefine group doesn't always work
1073 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1074 shown again after pressing 'Cancel'
1077 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1078 adjusts start position in wrap mode
1081 <!-- JAL-2563 -->Status bar doesn't show positions for
1082 ambiguous amino acids
1085 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1086 CDS/Protein view after CDS sequences added for aligned
1090 <!-- JAL-2592 -->User defined colourschemes called 'User
1091 Defined' don't appear in Colours menu
1097 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1098 score models doesn't always result in an updated PCA plot
1101 <!-- JAL-2442 -->Features not rendered as transparent on
1102 overview or linked structure view
1105 <!-- JAL-2372 -->Colour group by conservation doesn't
1109 <!-- JAL-2517 -->Hitting Cancel after applying
1110 user-defined colourscheme doesn't restore original
1117 <!-- JAL-2314 -->Unit test failure:
1118 jalview.ws.jabaws.RNAStructExportImport setup fails
1121 <!-- JAL-2307 -->Unit test failure:
1122 jalview.ws.sifts.SiftsClientTest due to compatibility
1123 problems with deep array comparison equality asserts in
1124 successive versions of TestNG
1127 <!-- JAL-2479 -->Relocated StructureChooserTest and
1128 ParameterUtilsTest Unit tests to Network suite
1131 <em>New Known Issues</em>
1134 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1135 phase after a sequence motif find operation
1138 <!-- JAL-2550 -->Importing annotation file with rows
1139 containing just upper and lower case letters are
1140 interpreted as WUSS RNA secondary structure symbols
1143 <!-- JAL-2590 -->Cannot load and display Newick trees
1144 reliably from eggnog Ortholog database
1147 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1148 containing features of type Highlight' when 'B' is pressed
1149 to mark columns containing highlighted regions.
1152 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1153 doesn't always add secondary structure annotation.
1158 <td width="60" nowrap>
1159 <div align="center">
1160 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1163 <td><div align="left">
1167 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1168 for all consensus calculations
1171 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1174 <li>Updated Jalview's Certum code signing certificate
1177 <em>Application</em>
1180 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1181 set of database cross-references, sorted alphabetically
1184 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1185 from database cross references. Users with custom links
1186 will receive a <a href="webServices/urllinks.html#warning">warning
1187 dialog</a> asking them to update their preferences.
1190 <!-- JAL-2287-->Cancel button and escape listener on
1191 dialog warning user about disconnecting Jalview from a
1195 <!-- JAL-2320-->Jalview's Chimera control window closes if
1196 the Chimera it is connected to is shut down
1199 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1200 columns menu item to mark columns containing highlighted
1201 regions (e.g. from structure selections or results of a
1205 <!-- JAL-2284-->Command line option for batch-generation
1206 of HTML pages rendering alignment data with the BioJS
1216 <!-- JAL-2286 -->Columns with more than one modal residue
1217 are not coloured or thresholded according to percent
1218 identity (first observed in Jalview 2.8.2)
1221 <!-- JAL-2301 -->Threonine incorrectly reported as not
1225 <!-- JAL-2318 -->Updates to documentation pages (above PID
1226 threshold, amino acid properties)
1229 <!-- JAL-2292 -->Lower case residues in sequences are not
1230 reported as mapped to residues in a structure file in the
1234 <!--JAL-2324 -->Identical features with non-numeric scores
1235 could be added multiple times to a sequence
1238 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1239 bond features shown as two highlighted residues rather
1240 than a range in linked structure views, and treated
1241 correctly when selecting and computing trees from features
1244 <!-- JAL-2281-->Custom URL links for database
1245 cross-references are matched to database name regardless
1250 <em>Application</em>
1253 <!-- JAL-2282-->Custom URL links for specific database
1254 names without regular expressions also offer links from
1258 <!-- JAL-2315-->Removing a single configured link in the
1259 URL links pane in Connections preferences doesn't actually
1260 update Jalview configuration
1263 <!-- JAL-2272-->CTRL-Click on a selected region to open
1264 the alignment area popup menu doesn't work on El-Capitan
1267 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1268 files with similarly named sequences if dropped onto the
1272 <!-- JAL-2312 -->Additional mappings are shown for PDB
1273 entries where more chains exist in the PDB accession than
1274 are reported in the SIFTS file
1277 <!-- JAL-2317-->Certain structures do not get mapped to
1278 the structure view when displayed with Chimera
1281 <!-- JAL-2317-->No chains shown in the Chimera view
1282 panel's View->Show Chains submenu
1285 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1286 work for wrapped alignment views
1289 <!--JAL-2197 -->Rename UI components for running JPred
1290 predictions from 'JNet' to 'JPred'
1293 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1294 corrupted when annotation panel vertical scroll is not at
1295 first annotation row
1298 <!--JAL-2332 -->Attempting to view structure for Hen
1299 lysozyme results in a PDB Client error dialog box
1302 <!-- JAL-2319 -->Structure View's mapping report switched
1303 ranges for PDB and sequence for SIFTS
1306 SIFTS 'Not_Observed' residues mapped to non-existant
1310 <!-- <em>New Known Issues</em>
1317 <td width="60" nowrap>
1318 <div align="center">
1319 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1320 <em>25/10/2016</em></strong>
1323 <td><em>Application</em>
1325 <li>3D Structure chooser opens with 'Cached structures'
1326 view if structures already loaded</li>
1327 <li>Progress bar reports models as they are loaded to
1328 structure views</li>
1334 <li>Colour by conservation always enabled and no tick
1335 shown in menu when BLOSUM or PID shading applied</li>
1336 <li>FER1_ARATH and FER2_ARATH labels were switched in
1337 example sequences/projects/trees</li>
1339 <em>Application</em>
1341 <li>Jalview projects with views of local PDB structure
1342 files saved on Windows cannot be opened on OSX</li>
1343 <li>Multiple structure views can be opened and superposed
1344 without timeout for structures with multiple models or
1345 multiple sequences in alignment</li>
1346 <li>Cannot import or associated local PDB files without a
1347 PDB ID HEADER line</li>
1348 <li>RMSD is not output in Jmol console when superposition
1350 <li>Drag and drop of URL from Browser fails for Linux and
1351 OSX versions earlier than El Capitan</li>
1352 <li>ENA client ignores invalid content from ENA server</li>
1353 <li>Exceptions are not raised in console when ENA client
1354 attempts to fetch non-existent IDs via Fetch DB Refs UI
1356 <li>Exceptions are not raised in console when a new view
1357 is created on the alignment</li>
1358 <li>OSX right-click fixed for group selections: CMD-click
1359 to insert/remove gaps in groups and CTRL-click to open group
1362 <em>Build and deployment</em>
1364 <li>URL link checker now copes with multi-line anchor
1367 <em>New Known Issues</em>
1369 <li>Drag and drop from URL links in browsers do not work
1376 <td width="60" nowrap>
1377 <div align="center">
1378 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1381 <td><em>General</em>
1384 <!-- JAL-2124 -->Updated Spanish translations.
1387 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1388 for importing structure data to Jalview. Enables mmCIF and
1392 <!-- JAL-192 --->Alignment ruler shows positions relative to
1396 <!-- JAL-2202 -->Position/residue shown in status bar when
1397 mousing over sequence associated annotation
1400 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1404 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1405 '()', canonical '[]' and invalid '{}' base pair populations
1409 <!-- JAL-2092 -->Feature settings popup menu options for
1410 showing or hiding columns containing a feature
1413 <!-- JAL-1557 -->Edit selected group by double clicking on
1414 group and sequence associated annotation labels
1417 <!-- JAL-2236 -->Sequence name added to annotation label in
1418 select/hide columns by annotation and colour by annotation
1422 </ul> <em>Application</em>
1425 <!-- JAL-2050-->Automatically hide introns when opening a
1426 gene/transcript view
1429 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1433 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1434 structure mappings with the EMBL-EBI PDBe SIFTS database
1437 <!-- JAL-2079 -->Updated download sites used for Rfam and
1438 Pfam sources to xfam.org
1441 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1444 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1445 over sequences in Jalview
1448 <!-- JAL-2027-->Support for reverse-complement coding
1449 regions in ENA and EMBL
1452 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1453 for record retrieval via ENA rest API
1456 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1460 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1461 groovy script execution
1464 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1465 alignment window's Calculate menu
1468 <!-- JAL-1812 -->Allow groovy scripts that call
1469 Jalview.getAlignFrames() to run in headless mode
1472 <!-- JAL-2068 -->Support for creating new alignment
1473 calculation workers from groovy scripts
1476 <!-- JAL-1369 --->Store/restore reference sequence in
1480 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1481 associations are now saved/restored from project
1484 <!-- JAL-1993 -->Database selection dialog always shown
1485 before sequence fetcher is opened
1488 <!-- JAL-2183 -->Double click on an entry in Jalview's
1489 database chooser opens a sequence fetcher
1492 <!-- JAL-1563 -->Free-text search client for UniProt using
1493 the UniProt REST API
1496 <!-- JAL-2168 -->-nonews command line parameter to prevent
1497 the news reader opening
1500 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1501 querying stored in preferences
1504 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1508 <!-- JAL-1977-->Tooltips shown on database chooser
1511 <!-- JAL-391 -->Reverse complement function in calculate
1512 menu for nucleotide sequences
1515 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1516 and feature counts preserves alignment ordering (and
1517 debugged for complex feature sets).
1520 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1521 viewing structures with Jalview 2.10
1524 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1525 genome, transcript CCDS and gene ids via the Ensembl and
1526 Ensembl Genomes REST API
1529 <!-- JAL-2049 -->Protein sequence variant annotation
1530 computed for 'sequence_variant' annotation on CDS regions
1534 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1538 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1539 Ref Fetcher fails to match, or otherwise updates sequence
1540 data from external database records.
1543 <!-- JAL-2154 -->Revised Jalview Project format for
1544 efficient recovery of sequence coding and alignment
1545 annotation relationships.
1547 </ul> <!-- <em>Applet</em>
1558 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1562 <!-- JAL-2018-->Export features in Jalview format (again)
1563 includes graduated colourschemes
1566 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1567 working with big alignments and lots of hidden columns
1570 <!-- JAL-2053-->Hidden column markers not always rendered
1571 at right of alignment window
1574 <!-- JAL-2067 -->Tidied up links in help file table of
1578 <!-- JAL-2072 -->Feature based tree calculation not shown
1582 <!-- JAL-2075 -->Hidden columns ignored during feature
1583 based tree calculation
1586 <!-- JAL-2065 -->Alignment view stops updating when show
1587 unconserved enabled for group on alignment
1590 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1594 <!-- JAL-2146 -->Alignment column in status incorrectly
1595 shown as "Sequence position" when mousing over
1599 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1600 hidden columns present
1603 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1604 user created annotation added to alignment
1607 <!-- JAL-1841 -->RNA Structure consensus only computed for
1608 '()' base pair annotation
1611 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1612 in zero scores for all base pairs in RNA Structure
1616 <!-- JAL-2174-->Extend selection with columns containing
1620 <!-- JAL-2275 -->Pfam format writer puts extra space at
1621 beginning of sequence
1624 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1628 <!-- JAL-2238 -->Cannot create groups on an alignment from
1629 from a tree when t-coffee scores are shown
1632 <!-- JAL-1836,1967 -->Cannot import and view PDB
1633 structures with chains containing negative resnums (4q4h)
1636 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1640 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1641 to Clustal, PIR and PileUp output
1644 <!-- JAL-2008 -->Reordering sequence features that are
1645 not visible causes alignment window to repaint
1648 <!-- JAL-2006 -->Threshold sliders don't work in
1649 graduated colour and colour by annotation row for e-value
1650 scores associated with features and annotation rows
1653 <!-- JAL-1797 -->amino acid physicochemical conservation
1654 calculation should be case independent
1657 <!-- JAL-2173 -->Remove annotation also updates hidden
1661 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1662 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1663 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1666 <!-- JAL-2065 -->Null pointer exceptions and redraw
1667 problems when reference sequence defined and 'show
1668 non-conserved' enabled
1671 <!-- JAL-1306 -->Quality and Conservation are now shown on
1672 load even when Consensus calculation is disabled
1675 <!-- JAL-1932 -->Remove right on penultimate column of
1676 alignment does nothing
1679 <em>Application</em>
1682 <!-- JAL-1552-->URLs and links can't be imported by
1683 drag'n'drop on OSX when launched via webstart (note - not
1684 yet fixed for El Capitan)
1687 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1688 output when running on non-gb/us i18n platforms
1691 <!-- JAL-1944 -->Error thrown when exporting a view with
1692 hidden sequences as flat-file alignment
1695 <!-- JAL-2030-->InstallAnywhere distribution fails when
1699 <!-- JAL-2080-->Jalview very slow to launch via webstart
1700 (also hotfix for 2.9.0b2)
1703 <!-- JAL-2085 -->Cannot save project when view has a
1704 reference sequence defined
1707 <!-- JAL-1011 -->Columns are suddenly selected in other
1708 alignments and views when revealing hidden columns
1711 <!-- JAL-1989 -->Hide columns not mirrored in complement
1712 view in a cDNA/Protein splitframe
1715 <!-- JAL-1369 -->Cannot save/restore representative
1716 sequence from project when only one sequence is
1720 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1721 in Structure Chooser
1724 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1725 structure consensus didn't refresh annotation panel
1728 <!-- JAL-1962 -->View mapping in structure view shows
1729 mappings between sequence and all chains in a PDB file
1732 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1733 dialogs format columns correctly, don't display array
1734 data, sort columns according to type
1737 <!-- JAL-1975 -->Export complete shown after destination
1738 file chooser is cancelled during an image export
1741 <!-- JAL-2025 -->Error when querying PDB Service with
1742 sequence name containing special characters
1745 <!-- JAL-2024 -->Manual PDB structure querying should be
1749 <!-- JAL-2104 -->Large tooltips with broken HTML
1750 formatting don't wrap
1753 <!-- JAL-1128 -->Figures exported from wrapped view are
1754 truncated so L looks like I in consensus annotation
1757 <!-- JAL-2003 -->Export features should only export the
1758 currently displayed features for the current selection or
1762 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1763 after fetching cross-references, and restoring from
1767 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1768 followed in the structure viewer
1771 <!-- JAL-2163 -->Titles for individual alignments in
1772 splitframe not restored from project
1775 <!-- JAL-2145 -->missing autocalculated annotation at
1776 trailing end of protein alignment in transcript/product
1777 splitview when pad-gaps not enabled by default
1780 <!-- JAL-1797 -->amino acid physicochemical conservation
1784 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1785 article has been read (reopened issue due to
1786 internationalisation problems)
1789 <!-- JAL-1960 -->Only offer PDB structures in structure
1790 viewer based on sequence name, PDB and UniProt
1795 <!-- JAL-1976 -->No progress bar shown during export of
1799 <!-- JAL-2213 -->Structures not always superimposed after
1800 multiple structures are shown for one or more sequences.
1803 <!-- JAL-1370 -->Reference sequence characters should not
1804 be replaced with '.' when 'Show unconserved' format option
1808 <!-- JAL-1823 -->Cannot specify chain code when entering
1809 specific PDB id for sequence
1812 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1813 'Export hidden sequences' is enabled, but 'export hidden
1814 columns' is disabled.
1817 <!--JAL-2026-->Best Quality option in structure chooser
1818 selects lowest rather than highest resolution structures
1822 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1823 to sequence mapping in 'View Mappings' report
1826 <!-- JAL-2284 -->Unable to read old Jalview projects that
1827 contain non-XML data added after Jalvew wrote project.
1830 <!-- JAL-2118 -->Newly created annotation row reorders
1831 after clicking on it to create new annotation for a
1835 <!-- JAL-1980 -->Null Pointer Exception raised when
1836 pressing Add on an orphaned cut'n'paste window.
1838 <!-- may exclude, this is an external service stability issue JAL-1941
1839 -- > RNA 3D structure not added via DSSR service</li> -->
1844 <!-- JAL-2151 -->Incorrect columns are selected when
1845 hidden columns present before start of sequence
1848 <!-- JAL-1986 -->Missing dependencies on applet pages
1852 <!-- JAL-1947 -->Overview pixel size changes when
1853 sequences are hidden in applet
1856 <!-- JAL-1996 -->Updated instructions for applet
1857 deployment on examples pages.
1864 <td width="60" nowrap>
1865 <div align="center">
1866 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1867 <em>16/10/2015</em></strong>
1870 <td><em>General</em>
1872 <li>Time stamps for signed Jalview application and applet
1877 <em>Application</em>
1879 <li>Duplicate group consensus and conservation rows
1880 shown when tree is partitioned</li>
1881 <li>Erratic behaviour when tree partitions made with
1882 multiple cDNA/Protein split views</li>
1888 <td width="60" nowrap>
1889 <div align="center">
1890 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1891 <em>8/10/2015</em></strong>
1894 <td><em>General</em>
1896 <li>Updated Spanish translations of localized text for
1898 </ul> <em>Application</em>
1900 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1901 <li>Signed OSX InstallAnywhere installer<br></li>
1902 <li>Support for per-sequence based annotations in BioJSON</li>
1903 </ul> <em>Applet</em>
1905 <li>Split frame example added to applet examples page</li>
1906 </ul> <em>Build and Deployment</em>
1909 <!-- JAL-1888 -->New ant target for running Jalview's test
1917 <li>Mapping of cDNA to protein in split frames
1918 incorrect when sequence start > 1</li>
1919 <li>Broken images in filter column by annotation dialog
1921 <li>Feature colours not parsed from features file</li>
1922 <li>Exceptions and incomplete link URLs recovered when
1923 loading a features file containing HTML tags in feature
1927 <em>Application</em>
1929 <li>Annotations corrupted after BioJS export and
1931 <li>Incorrect sequence limits after Fetch DB References
1932 with 'trim retrieved sequences'</li>
1933 <li>Incorrect warning about deleting all data when
1934 deleting selected columns</li>
1935 <li>Patch to build system for shipping properly signed
1936 JNLP templates for webstart launch</li>
1937 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1938 unreleased structures for download or viewing</li>
1939 <li>Tab/space/return keystroke operation of EMBL-PDBe
1940 fetcher/viewer dialogs works correctly</li>
1941 <li>Disabled 'minimise' button on Jalview windows
1942 running on OSX to workaround redraw hang bug</li>
1943 <li>Split cDNA/Protein view position and geometry not
1944 recovered from jalview project</li>
1945 <li>Initial enabled/disabled state of annotation menu
1946 sorter 'show autocalculated first/last' corresponds to
1948 <li>Restoring of Clustal, RNA Helices and T-Coffee
1949 color schemes from BioJSON</li>
1953 <li>Reorder sequences mirrored in cDNA/Protein split
1955 <li>Applet with Jmol examples not loading correctly</li>
1961 <td><div align="center">
1962 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1964 <td><em>General</em>
1966 <li>Linked visualisation and analysis of DNA and Protein
1969 <li>Translated cDNA alignments shown as split protein
1970 and DNA alignment views</li>
1971 <li>Codon consensus annotation for linked protein and
1972 cDNA alignment views</li>
1973 <li>Link cDNA or Protein product sequences by loading
1974 them onto Protein or cDNA alignments</li>
1975 <li>Reconstruct linked cDNA alignment from aligned
1976 protein sequences</li>
1979 <li>Jmol integration updated to Jmol v14.2.14</li>
1980 <li>Import and export of Jalview alignment views as <a
1981 href="features/bioJsonFormat.html">BioJSON</a></li>
1982 <li>New alignment annotation file statements for
1983 reference sequences and marking hidden columns</li>
1984 <li>Reference sequence based alignment shading to
1985 highlight variation</li>
1986 <li>Select or hide columns according to alignment
1988 <li>Find option for locating sequences by description</li>
1989 <li>Conserved physicochemical properties shown in amino
1990 acid conservation row</li>
1991 <li>Alignments can be sorted by number of RNA helices</li>
1992 </ul> <em>Application</em>
1994 <li>New cDNA/Protein analysis capabilities
1996 <li>Get Cross-References should open a Split Frame
1997 view with cDNA/Protein</li>
1998 <li>Detect when nucleotide sequences and protein
1999 sequences are placed in the same alignment</li>
2000 <li>Split cDNA/Protein views are saved in Jalview
2005 <li>Use REST API to talk to Chimera</li>
2006 <li>Selected regions in Chimera are highlighted in linked
2007 Jalview windows</li>
2009 <li>VARNA RNA viewer updated to v3.93</li>
2010 <li>VARNA views are saved in Jalview Projects</li>
2011 <li>Pseudoknots displayed as Jalview RNA annotation can
2012 be shown in VARNA</li>
2014 <li>Make groups for selection uses marked columns as well
2015 as the active selected region</li>
2017 <li>Calculate UPGMA and NJ trees using sequence feature
2019 <li>New Export options
2021 <li>New Export Settings dialog to control hidden
2022 region export in flat file generation</li>
2024 <li>Export alignment views for display with the <a
2025 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2027 <li>Export scrollable SVG in HTML page</li>
2028 <li>Optional embedding of BioJSON data when exporting
2029 alignment figures to HTML</li>
2031 <li>3D structure retrieval and display
2033 <li>Free text and structured queries with the PDBe
2035 <li>PDBe Search API based discovery and selection of
2036 PDB structures for a sequence set</li>
2040 <li>JPred4 employed for protein secondary structure
2042 <li>Hide Insertions menu option to hide unaligned columns
2043 for one or a group of sequences</li>
2044 <li>Automatically hide insertions in alignments imported
2045 from the JPred4 web server</li>
2046 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2047 system on OSX<br />LGPL libraries courtesy of <a
2048 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2050 <li>changed 'View nucleotide structure' submenu to 'View
2051 VARNA 2D Structure'</li>
2052 <li>change "View protein structure" menu option to "3D
2055 </ul> <em>Applet</em>
2057 <li>New layout for applet example pages</li>
2058 <li>New parameters to enable SplitFrame view
2059 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2060 <li>New example demonstrating linked viewing of cDNA and
2061 Protein alignments</li>
2062 </ul> <em>Development and deployment</em>
2064 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2065 <li>Include installation type and git revision in build
2066 properties and console log output</li>
2067 <li>Jalview Github organisation, and new github site for
2068 storing BioJsMSA Templates</li>
2069 <li>Jalview's unit tests now managed with TestNG</li>
2072 <!-- <em>General</em>
2074 </ul> --> <!-- issues resolved --> <em>Application</em>
2076 <li>Escape should close any open find dialogs</li>
2077 <li>Typo in select-by-features status report</li>
2078 <li>Consensus RNA secondary secondary structure
2079 predictions are not highlighted in amber</li>
2080 <li>Missing gap character in v2.7 example file means
2081 alignment appears unaligned when pad-gaps is not enabled</li>
2082 <li>First switch to RNA Helices colouring doesn't colour
2083 associated structure views</li>
2084 <li>ID width preference option is greyed out when auto
2085 width checkbox not enabled</li>
2086 <li>Stopped a warning dialog from being shown when
2087 creating user defined colours</li>
2088 <li>'View Mapping' in structure viewer shows sequence
2089 mappings for just that viewer's sequences</li>
2090 <li>Workaround for superposing PDB files containing
2091 multiple models in Chimera</li>
2092 <li>Report sequence position in status bar when hovering
2093 over Jmol structure</li>
2094 <li>Cannot output gaps as '.' symbols with Selection ->
2095 output to text box</li>
2096 <li>Flat file exports of alignments with hidden columns
2097 have incorrect sequence start/end</li>
2098 <li>'Aligning' a second chain to a Chimera structure from
2100 <li>Colour schemes applied to structure viewers don't
2101 work for nucleotide</li>
2102 <li>Loading/cut'n'pasting an empty or invalid file leads
2103 to a grey/invisible alignment window</li>
2104 <li>Exported Jpred annotation from a sequence region
2105 imports to different position</li>
2106 <li>Space at beginning of sequence feature tooltips shown
2107 on some platforms</li>
2108 <li>Chimera viewer 'View | Show Chain' menu is not
2110 <li>'New View' fails with a Null Pointer Exception in
2111 console if Chimera has been opened</li>
2112 <li>Mouseover to Chimera not working</li>
2113 <li>Miscellaneous ENA XML feature qualifiers not
2115 <li>NPE in annotation renderer after 'Extract Scores'</li>
2116 <li>If two structures in one Chimera window, mouseover of
2117 either sequence shows on first structure</li>
2118 <li>'Show annotations' options should not make
2119 non-positional annotations visible</li>
2120 <li>Subsequence secondary structure annotation not shown
2121 in right place after 'view flanking regions'</li>
2122 <li>File Save As type unset when current file format is
2124 <li>Save as '.jar' option removed for saving Jalview
2126 <li>Colour by Sequence colouring in Chimera more
2128 <li>Cannot 'add reference annotation' for a sequence in
2129 several views on same alignment</li>
2130 <li>Cannot show linked products for EMBL / ENA records</li>
2131 <li>Jalview's tooltip wraps long texts containing no
2133 </ul> <em>Applet</em>
2135 <li>Jmol to JalviewLite mouseover/link not working</li>
2136 <li>JalviewLite can't import sequences with ID
2137 descriptions containing angle brackets</li>
2138 </ul> <em>General</em>
2140 <li>Cannot export and reimport RNA secondary structure
2141 via jalview annotation file</li>
2142 <li>Random helix colour palette for colour by annotation
2143 with RNA secondary structure</li>
2144 <li>Mouseover to cDNA from STOP residue in protein
2145 translation doesn't work.</li>
2146 <li>hints when using the select by annotation dialog box</li>
2147 <li>Jmol alignment incorrect if PDB file has alternate CA
2149 <li>FontChooser message dialog appears to hang after
2150 choosing 1pt font</li>
2151 <li>Peptide secondary structure incorrectly imported from
2152 annotation file when annotation display text includes 'e' or
2154 <li>Cannot set colour of new feature type whilst creating
2156 <li>cDNA translation alignment should not be sequence
2157 order dependent</li>
2158 <li>'Show unconserved' doesn't work for lower case
2160 <li>Nucleotide ambiguity codes involving R not recognised</li>
2161 </ul> <em>Deployment and Documentation</em>
2163 <li>Applet example pages appear different to the rest of
2164 www.jalview.org</li>
2165 </ul> <em>Application Known issues</em>
2167 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2168 <li>Misleading message appears after trying to delete
2170 <li>Jalview icon not shown in dock after InstallAnywhere
2171 version launches</li>
2172 <li>Fetching EMBL reference for an RNA sequence results
2173 fails with a sequence mismatch</li>
2174 <li>Corrupted or unreadable alignment display when
2175 scrolling alignment to right</li>
2176 <li>ArrayIndexOutOfBoundsException thrown when remove
2177 empty columns called on alignment with ragged gapped ends</li>
2178 <li>auto calculated alignment annotation rows do not get
2179 placed above or below non-autocalculated rows</li>
2180 <li>Jalview dekstop becomes sluggish at full screen in
2181 ultra-high resolution</li>
2182 <li>Cannot disable consensus calculation independently of
2183 quality and conservation</li>
2184 <li>Mouseover highlighting between cDNA and protein can
2185 become sluggish with more than one splitframe shown</li>
2186 </ul> <em>Applet Known Issues</em>
2188 <li>Core PDB parsing code requires Jmol</li>
2189 <li>Sequence canvas panel goes white when alignment
2190 window is being resized</li>
2196 <td><div align="center">
2197 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2199 <td><em>General</em>
2201 <li>Updated Java code signing certificate donated by
2203 <li>Features and annotation preserved when performing
2204 pairwise alignment</li>
2205 <li>RNA pseudoknot annotation can be
2206 imported/exported/displayed</li>
2207 <li>'colour by annotation' can colour by RNA and
2208 protein secondary structure</li>
2209 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2210 post-hoc with 2.9 release</em>)
2213 </ul> <em>Application</em>
2215 <li>Extract and display secondary structure for sequences
2216 with 3D structures</li>
2217 <li>Support for parsing RNAML</li>
2218 <li>Annotations menu for layout
2220 <li>sort sequence annotation rows by alignment</li>
2221 <li>place sequence annotation above/below alignment
2224 <li>Output in Stockholm format</li>
2225 <li>Internationalisation: improved Spanish (es)
2227 <li>Structure viewer preferences tab</li>
2228 <li>Disorder and Secondary Structure annotation tracks
2229 shared between alignments</li>
2230 <li>UCSF Chimera launch and linked highlighting from
2232 <li>Show/hide all sequence associated annotation rows for
2233 all or current selection</li>
2234 <li>disorder and secondary structure predictions
2235 available as dataset annotation</li>
2236 <li>Per-sequence rna helices colouring</li>
2239 <li>Sequence database accessions imported when fetching
2240 alignments from Rfam</li>
2241 <li>update VARNA version to 3.91</li>
2243 <li>New groovy scripts for exporting aligned positions,
2244 conservation values, and calculating sum of pairs scores.</li>
2245 <li>Command line argument to set default JABAWS server</li>
2246 <li>include installation type in build properties and
2247 console log output</li>
2248 <li>Updated Jalview project format to preserve dataset
2252 <!-- issues resolved --> <em>Application</em>
2254 <li>Distinguish alignment and sequence associated RNA
2255 structure in structure->view->VARNA</li>
2256 <li>Raise dialog box if user deletes all sequences in an
2258 <li>Pressing F1 results in documentation opening twice</li>
2259 <li>Sequence feature tooltip is wrapped</li>
2260 <li>Double click on sequence associated annotation
2261 selects only first column</li>
2262 <li>Redundancy removal doesn't result in unlinked
2263 leaves shown in tree</li>
2264 <li>Undos after several redundancy removals don't undo
2266 <li>Hide sequence doesn't hide associated annotation</li>
2267 <li>User defined colours dialog box too big to fit on
2268 screen and buttons not visible</li>
2269 <li>author list isn't updated if already written to
2270 Jalview properties</li>
2271 <li>Popup menu won't open after retrieving sequence
2273 <li>File open window for associate PDB doesn't open</li>
2274 <li>Left-then-right click on a sequence id opens a
2275 browser search window</li>
2276 <li>Cannot open sequence feature shading/sort popup menu
2277 in feature settings dialog</li>
2278 <li>better tooltip placement for some areas of Jalview
2280 <li>Allow addition of JABAWS Server which doesn't
2281 pass validation</li>
2282 <li>Web services parameters dialog box is too large to
2284 <li>Muscle nucleotide alignment preset obscured by
2286 <li>JABAWS preset submenus don't contain newly
2287 defined user preset</li>
2288 <li>MSA web services warns user if they were launched
2289 with invalid input</li>
2290 <li>Jalview cannot contact DAS Registy when running on
2293 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2294 'Superpose with' submenu not shown when new view
2298 </ul> <!-- <em>Applet</em>
2300 </ul> <em>General</em>
2302 </ul>--> <em>Deployment and Documentation</em>
2304 <li>2G and 1G options in launchApp have no effect on
2305 memory allocation</li>
2306 <li>launchApp service doesn't automatically open
2307 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2309 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2310 InstallAnywhere reports cannot find valid JVM when Java
2311 1.7_055 is available
2313 </ul> <em>Application Known issues</em>
2316 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2317 corrupted or unreadable alignment display when scrolling
2321 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2322 retrieval fails but progress bar continues for DAS retrieval
2323 with large number of ID
2326 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2327 flatfile output of visible region has incorrect sequence
2331 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2332 rna structure consensus doesn't update when secondary
2333 structure tracks are rearranged
2336 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2337 invalid rna structure positional highlighting does not
2338 highlight position of invalid base pairs
2341 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2342 out of memory errors are not raised when saving Jalview
2343 project from alignment window file menu
2346 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2347 Switching to RNA Helices colouring doesn't propagate to
2351 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2352 colour by RNA Helices not enabled when user created
2353 annotation added to alignment
2356 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2357 Jalview icon not shown on dock in Mountain Lion/Webstart
2359 </ul> <em>Applet Known Issues</em>
2362 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2363 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2366 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2367 Jalview and Jmol example not compatible with IE9
2370 <li>Sort by annotation score doesn't reverse order
2376 <td><div align="center">
2377 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2380 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2383 <li>Internationalisation of user interface (usually
2384 called i18n support) and translation for Spanish locale</li>
2385 <li>Define/Undefine group on current selection with
2386 Ctrl-G/Shift Ctrl-G</li>
2387 <li>Improved group creation/removal options in
2388 alignment/sequence Popup menu</li>
2389 <li>Sensible precision for symbol distribution
2390 percentages shown in logo tooltip.</li>
2391 <li>Annotation panel height set according to amount of
2392 annotation when alignment first opened</li>
2393 </ul> <em>Application</em>
2395 <li>Interactive consensus RNA secondary structure
2396 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2397 <li>Select columns containing particular features from
2398 Feature Settings dialog</li>
2399 <li>View all 'representative' PDB structures for selected
2401 <li>Update Jalview project format:
2403 <li>New file extension for Jalview projects '.jvp'</li>
2404 <li>Preserve sequence and annotation dataset (to
2405 store secondary structure annotation,etc)</li>
2406 <li>Per group and alignment annotation and RNA helix
2410 <li>New similarity measures for PCA and Tree calculation
2412 <li>Experimental support for retrieval and viewing of
2413 flanking regions for an alignment</li>
2417 <!-- issues resolved --> <em>Application</em>
2419 <li>logo keeps spinning and status remains at queued or
2420 running after job is cancelled</li>
2421 <li>cannot export features from alignments imported from
2422 Jalview/VAMSAS projects</li>
2423 <li>Buggy slider for web service parameters that take
2425 <li>Newly created RNA secondary structure line doesn't
2426 have 'display all symbols' flag set</li>
2427 <li>T-COFFEE alignment score shading scheme and other
2428 annotation shading not saved in Jalview project</li>
2429 <li>Local file cannot be loaded in freshly downloaded
2431 <li>Jalview icon not shown on dock in Mountain
2433 <li>Load file from desktop file browser fails</li>
2434 <li>Occasional NPE thrown when calculating large trees</li>
2435 <li>Cannot reorder or slide sequences after dragging an
2436 alignment onto desktop</li>
2437 <li>Colour by annotation dialog throws NPE after using
2438 'extract scores' function</li>
2439 <li>Loading/cut'n'pasting an empty file leads to a grey
2440 alignment window</li>
2441 <li>Disorder thresholds rendered incorrectly after
2442 performing IUPred disorder prediction</li>
2443 <li>Multiple group annotated consensus rows shown when
2444 changing 'normalise logo' display setting</li>
2445 <li>Find shows blank dialog after 'finished searching' if
2446 nothing matches query</li>
2447 <li>Null Pointer Exceptions raised when sorting by
2448 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2450 <li>Errors in Jmol console when structures in alignment
2451 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2453 <li>Not all working JABAWS services are shown in
2455 <li>JAVAWS version of Jalview fails to launch with
2456 'invalid literal/length code'</li>
2457 <li>Annotation/RNA Helix colourschemes cannot be applied
2458 to alignment with groups (actually fixed in 2.8.0b1)</li>
2459 <li>RNA Helices and T-Coffee Scores available as default
2462 </ul> <em>Applet</em>
2464 <li>Remove group option is shown even when selection is
2466 <li>Apply to all groups ticked but colourscheme changes
2467 don't affect groups</li>
2468 <li>Documented RNA Helices and T-Coffee Scores as valid
2469 colourscheme name</li>
2470 <li>Annotation labels drawn on sequence IDs when
2471 Annotation panel is not displayed</li>
2472 <li>Increased font size for dropdown menus on OSX and
2473 embedded windows</li>
2474 </ul> <em>Other</em>
2476 <li>Consensus sequence for alignments/groups with a
2477 single sequence were not calculated</li>
2478 <li>annotation files that contain only groups imported as
2479 annotation and junk sequences</li>
2480 <li>Fasta files with sequences containing '*' incorrectly
2481 recognised as PFAM or BLC</li>
2482 <li>conservation/PID slider apply all groups option
2483 doesn't affect background (2.8.0b1)
2485 <li>redundancy highlighting is erratic at 0% and 100%</li>
2486 <li>Remove gapped columns fails for sequences with ragged
2488 <li>AMSA annotation row with leading spaces is not
2489 registered correctly on import</li>
2490 <li>Jalview crashes when selecting PCA analysis for
2491 certain alignments</li>
2492 <li>Opening the colour by annotation dialog for an
2493 existing annotation based 'use original colours'
2494 colourscheme loses original colours setting</li>
2499 <td><div align="center">
2500 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2501 <em>30/1/2014</em></strong>
2505 <li>Trusted certificates for JalviewLite applet and
2506 Jalview Desktop application<br />Certificate was donated by
2507 <a href="https://www.certum.eu">Certum</a> to the Jalview
2508 open source project).
2510 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2511 <li>Output in Stockholm format</li>
2512 <li>Allow import of data from gzipped files</li>
2513 <li>Export/import group and sequence associated line
2514 graph thresholds</li>
2515 <li>Nucleotide substitution matrix that supports RNA and
2516 ambiguity codes</li>
2517 <li>Allow disorder predictions to be made on the current
2518 selection (or visible selection) in the same way that JPred
2520 <li>Groovy scripting for headless Jalview operation</li>
2521 </ul> <em>Other improvements</em>
2523 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2524 <li>COMBINE statement uses current SEQUENCE_REF and
2525 GROUP_REF scope to group annotation rows</li>
2526 <li>Support '' style escaping of quotes in Newick
2528 <li>Group options for JABAWS service by command line name</li>
2529 <li>Empty tooltip shown for JABA service options with a
2530 link but no description</li>
2531 <li>Select primary source when selecting authority in
2532 database fetcher GUI</li>
2533 <li>Add .mfa to FASTA file extensions recognised by
2535 <li>Annotation label tooltip text wrap</li>
2540 <li>Slow scrolling when lots of annotation rows are
2542 <li>Lots of NPE (and slowness) after creating RNA
2543 secondary structure annotation line</li>
2544 <li>Sequence database accessions not imported when
2545 fetching alignments from Rfam</li>
2546 <li>Incorrect SHMR submission for sequences with
2548 <li>View all structures does not always superpose
2550 <li>Option widgets in service parameters not updated to
2551 reflect user or preset settings</li>
2552 <li>Null pointer exceptions for some services without
2553 presets or adjustable parameters</li>
2554 <li>Discover PDB IDs entry in structure menu doesn't
2555 discover PDB xRefs</li>
2556 <li>Exception encountered while trying to retrieve
2557 features with DAS</li>
2558 <li>Lowest value in annotation row isn't coloured
2559 when colour by annotation (per sequence) is coloured</li>
2560 <li>Keyboard mode P jumps to start of gapped region when
2561 residue follows a gap</li>
2562 <li>Jalview appears to hang importing an alignment with
2563 Wrap as default or after enabling Wrap</li>
2564 <li>'Right click to add annotations' message
2565 shown in wrap mode when no annotations present</li>
2566 <li>Disorder predictions fail with NPE if no automatic
2567 annotation already exists on alignment</li>
2568 <li>oninit javascript function should be called after
2569 initialisation completes</li>
2570 <li>Remove redundancy after disorder prediction corrupts
2571 alignment window display</li>
2572 <li>Example annotation file in documentation is invalid</li>
2573 <li>Grouped line graph annotation rows are not exported
2574 to annotation file</li>
2575 <li>Multi-harmony analysis cannot be run when only two
2577 <li>Cannot create multiple groups of line graphs with
2578 several 'combine' statements in annotation file</li>
2579 <li>Pressing return several times causes Number Format
2580 exceptions in keyboard mode</li>
2581 <li>Multi-harmony (SHMMR) method doesn't submit
2582 correct partitions for input data</li>
2583 <li>Translation from DNA to Amino Acids fails</li>
2584 <li>Jalview fail to load newick tree with quoted label</li>
2585 <li>--headless flag isn't understood</li>
2586 <li>ClassCastException when generating EPS in headless
2588 <li>Adjusting sequence-associated shading threshold only
2589 changes one row's threshold</li>
2590 <li>Preferences and Feature settings panel panel
2591 doesn't open</li>
2592 <li>hide consensus histogram also hides conservation and
2593 quality histograms</li>
2598 <td><div align="center">
2599 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2601 <td><em>Application</em>
2603 <li>Support for JABAWS 2.0 Services (AACon alignment
2604 conservation, protein disorder and Clustal Omega)</li>
2605 <li>JABAWS server status indicator in Web Services
2607 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2608 in Jalview alignment window</li>
2609 <li>Updated Jalview build and deploy framework for OSX
2610 mountain lion, windows 7, and 8</li>
2611 <li>Nucleotide substitution matrix for PCA that supports
2612 RNA and ambiguity codes</li>
2614 <li>Improved sequence database retrieval GUI</li>
2615 <li>Support fetching and database reference look up
2616 against multiple DAS sources (Fetch all from in 'fetch db
2618 <li>Jalview project improvements
2620 <li>Store and retrieve the 'belowAlignment'
2621 flag for annotation</li>
2622 <li>calcId attribute to group annotation rows on the
2624 <li>Store AACon calculation settings for a view in
2625 Jalview project</li>
2629 <li>horizontal scrolling gesture support</li>
2630 <li>Visual progress indicator when PCA calculation is
2632 <li>Simpler JABA web services menus</li>
2633 <li>visual indication that web service results are still
2634 being retrieved from server</li>
2635 <li>Serialise the dialogs that are shown when Jalview
2636 starts up for first time</li>
2637 <li>Jalview user agent string for interacting with HTTP
2639 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2641 <li>Examples directory and Groovy library included in
2642 InstallAnywhere distribution</li>
2643 </ul> <em>Applet</em>
2645 <li>RNA alignment and secondary structure annotation
2646 visualization applet example</li>
2647 </ul> <em>General</em>
2649 <li>Normalise option for consensus sequence logo</li>
2650 <li>Reset button in PCA window to return dimensions to
2652 <li>Allow seqspace or Jalview variant of alignment PCA
2654 <li>PCA with either nucleic acid and protein substitution
2656 <li>Allow windows containing HTML reports to be exported
2658 <li>Interactive display and editing of RNA secondary
2659 structure contacts</li>
2660 <li>RNA Helix Alignment Colouring</li>
2661 <li>RNA base pair logo consensus</li>
2662 <li>Parse sequence associated secondary structure
2663 information in Stockholm files</li>
2664 <li>HTML Export database accessions and annotation
2665 information presented in tooltip for sequences</li>
2666 <li>Import secondary structure from LOCARNA clustalw
2667 style RNA alignment files</li>
2668 <li>import and visualise T-COFFEE quality scores for an
2670 <li>'colour by annotation' per sequence option to
2671 shade each sequence according to its associated alignment
2673 <li>New Jalview Logo</li>
2674 </ul> <em>Documentation and Development</em>
2676 <li>documentation for score matrices used in Jalview</li>
2677 <li>New Website!</li>
2679 <td><em>Application</em>
2681 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2682 wsdbfetch REST service</li>
2683 <li>Stop windows being moved outside desktop on OSX</li>
2684 <li>Filetype associations not installed for webstart
2686 <li>Jalview does not always retrieve progress of a JABAWS
2687 job execution in full once it is complete</li>
2688 <li>revise SHMR RSBS definition to ensure alignment is
2689 uploaded via ali_file parameter</li>
2690 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2691 <li>View all structures superposed fails with exception</li>
2692 <li>Jnet job queues forever if a very short sequence is
2693 submitted for prediction</li>
2694 <li>Cut and paste menu not opened when mouse clicked on
2696 <li>Putting fractional value into integer text box in
2697 alignment parameter dialog causes Jalview to hang</li>
2698 <li>Structure view highlighting doesn't work on
2700 <li>View all structures fails with exception shown in
2702 <li>Characters in filename associated with PDBEntry not
2703 escaped in a platform independent way</li>
2704 <li>Jalview desktop fails to launch with exception when
2706 <li>Tree calculation reports 'you must have 2 or more
2707 sequences selected' when selection is empty</li>
2708 <li>Jalview desktop fails to launch with jar signature
2709 failure when java web start temporary file caching is
2711 <li>DAS Sequence retrieval with range qualification
2712 results in sequence xref which includes range qualification</li>
2713 <li>Errors during processing of command line arguments
2714 cause progress bar (JAL-898) to be removed</li>
2715 <li>Replace comma for semi-colon option not disabled for
2716 DAS sources in sequence fetcher</li>
2717 <li>Cannot close news reader when JABAWS server warning
2718 dialog is shown</li>
2719 <li>Option widgets not updated to reflect user settings</li>
2720 <li>Edited sequence not submitted to web service</li>
2721 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2722 <li>InstallAnywhere installer doesn't unpack and run
2723 on OSX Mountain Lion</li>
2724 <li>Annotation panel not given a scroll bar when
2725 sequences with alignment annotation are pasted into the
2727 <li>Sequence associated annotation rows not associated
2728 when loaded from Jalview project</li>
2729 <li>Browser launch fails with NPE on java 1.7</li>
2730 <li>JABAWS alignment marked as finished when job was
2731 cancelled or job failed due to invalid input</li>
2732 <li>NPE with v2.7 example when clicking on Tree
2733 associated with all views</li>
2734 <li>Exceptions when copy/paste sequences with grouped
2735 annotation rows to new window</li>
2736 </ul> <em>Applet</em>
2738 <li>Sequence features are momentarily displayed before
2739 they are hidden using hidefeaturegroups applet parameter</li>
2740 <li>loading features via javascript API automatically
2741 enables feature display</li>
2742 <li>scrollToColumnIn javascript API method doesn't
2744 </ul> <em>General</em>
2746 <li>Redundancy removal fails for rna alignment</li>
2747 <li>PCA calculation fails when sequence has been selected
2748 and then deselected</li>
2749 <li>PCA window shows grey box when first opened on OSX</li>
2750 <li>Letters coloured pink in sequence logo when alignment
2751 coloured with clustalx</li>
2752 <li>Choosing fonts without letter symbols defined causes
2753 exceptions and redraw errors</li>
2754 <li>Initial PCA plot view is not same as manually
2755 reconfigured view</li>
2756 <li>Grouped annotation graph label has incorrect line
2758 <li>Grouped annotation graph label display is corrupted
2759 for lots of labels</li>
2764 <div align="center">
2765 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2768 <td><em>Application</em>
2770 <li>Jalview Desktop News Reader</li>
2771 <li>Tweaked default layout of web services menu</li>
2772 <li>View/alignment association menu to enable user to
2773 easily specify which alignment a multi-structure view takes
2774 its colours/correspondences from</li>
2775 <li>Allow properties file location to be specified as URL</li>
2776 <li>Extend Jalview project to preserve associations
2777 between many alignment views and a single Jmol display</li>
2778 <li>Store annotation row height in Jalview project file</li>
2779 <li>Annotation row column label formatting attributes
2780 stored in project file</li>
2781 <li>Annotation row order for auto-calculated annotation
2782 rows preserved in Jalview project file</li>
2783 <li>Visual progress indication when Jalview state is
2784 saved using Desktop window menu</li>
2785 <li>Visual indication that command line arguments are
2786 still being processed</li>
2787 <li>Groovy script execution from URL</li>
2788 <li>Colour by annotation default min and max colours in
2790 <li>Automatically associate PDB files dragged onto an
2791 alignment with sequences that have high similarity and
2793 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2794 <li>'view structures' option to open many
2795 structures in same window</li>
2796 <li>Sort associated views menu option for tree panel</li>
2797 <li>Group all JABA and non-JABA services for a particular
2798 analysis function in its own submenu</li>
2799 </ul> <em>Applet</em>
2801 <li>Userdefined and autogenerated annotation rows for
2803 <li>Adjustment of alignment annotation pane height</li>
2804 <li>Annotation scrollbar for annotation panel</li>
2805 <li>Drag to reorder annotation rows in annotation panel</li>
2806 <li>'automaticScrolling' parameter</li>
2807 <li>Allow sequences with partial ID string matches to be
2808 annotated from GFF/Jalview features files</li>
2809 <li>Sequence logo annotation row in applet</li>
2810 <li>Absolute paths relative to host server in applet
2811 parameters are treated as such</li>
2812 <li>New in the JalviewLite javascript API:
2814 <li>JalviewLite.js javascript library</li>
2815 <li>Javascript callbacks for
2817 <li>Applet initialisation</li>
2818 <li>Sequence/alignment mouse-overs and selections</li>
2821 <li>scrollTo row and column alignment scrolling
2823 <li>Select sequence/alignment regions from javascript</li>
2824 <li>javascript structure viewer harness to pass
2825 messages between Jmol and Jalview when running as
2826 distinct applets</li>
2827 <li>sortBy method</li>
2828 <li>Set of applet and application examples shipped
2829 with documentation</li>
2830 <li>New example to demonstrate JalviewLite and Jmol
2831 javascript message exchange</li>
2833 </ul> <em>General</em>
2835 <li>Enable Jmol displays to be associated with multiple
2836 multiple alignments</li>
2837 <li>Option to automatically sort alignment with new tree</li>
2838 <li>User configurable link to enable redirects to a
2839 www.Jalview.org mirror</li>
2840 <li>Jmol colours option for Jmol displays</li>
2841 <li>Configurable newline string when writing alignment
2842 and other flat files</li>
2843 <li>Allow alignment annotation description lines to
2844 contain html tags</li>
2845 </ul> <em>Documentation and Development</em>
2847 <li>Add groovy test harness for bulk load testing to
2849 <li>Groovy script to load and align a set of sequences
2850 using a web service before displaying the result in the
2851 Jalview desktop</li>
2852 <li>Restructured javascript and applet api documentation</li>
2853 <li>Ant target to publish example html files with applet
2855 <li>Netbeans project for building Jalview from source</li>
2856 <li>ant task to create online javadoc for Jalview source</li>
2858 <td><em>Application</em>
2860 <li>User defined colourscheme throws exception when
2861 current built in colourscheme is saved as new scheme</li>
2862 <li>AlignFrame->Save in application pops up save
2863 dialog for valid filename/format</li>
2864 <li>Cannot view associated structure for UniProt sequence</li>
2865 <li>PDB file association breaks for UniProt sequence
2867 <li>Associate PDB from file dialog does not tell you
2868 which sequence is to be associated with the file</li>
2869 <li>Find All raises null pointer exception when query
2870 only matches sequence IDs</li>
2871 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2872 <li>Jalview project with Jmol views created with Jalview
2873 2.4 cannot be loaded</li>
2874 <li>Filetype associations not installed for webstart
2876 <li>Two or more chains in a single PDB file associated
2877 with sequences in different alignments do not get coloured
2878 by their associated sequence</li>
2879 <li>Visibility status of autocalculated annotation row
2880 not preserved when project is loaded</li>
2881 <li>Annotation row height and visibility attributes not
2882 stored in Jalview project</li>
2883 <li>Tree bootstraps are not preserved when saved as a
2884 Jalview project</li>
2885 <li>Envision2 workflow tooltips are corrupted</li>
2886 <li>Enabling show group conservation also enables colour
2887 by conservation</li>
2888 <li>Duplicate group associated conservation or consensus
2889 created on new view</li>
2890 <li>Annotation scrollbar not displayed after 'show
2891 all hidden annotation rows' option selected</li>
2892 <li>Alignment quality not updated after alignment
2893 annotation row is hidden then shown</li>
2894 <li>Preserve colouring of structures coloured by
2895 sequences in pre Jalview 2.7 projects</li>
2896 <li>Web service job parameter dialog is not laid out
2898 <li>Web services menu not refreshed after 'reset
2899 services' button is pressed in preferences</li>
2900 <li>Annotation off by one in Jalview v2_3 example project</li>
2901 <li>Structures imported from file and saved in project
2902 get name like jalview_pdb1234.txt when reloaded</li>
2903 <li>Jalview does not always retrieve progress of a JABAWS
2904 job execution in full once it is complete</li>
2905 </ul> <em>Applet</em>
2907 <li>Alignment height set incorrectly when lots of
2908 annotation rows are displayed</li>
2909 <li>Relative URLs in feature HTML text not resolved to
2911 <li>View follows highlighting does not work for positions
2913 <li><= shown as = in tooltip</li>
2914 <li>Export features raises exception when no features
2916 <li>Separator string used for serialising lists of IDs
2917 for javascript api is modified when separator string
2918 provided as parameter</li>
2919 <li>Null pointer exception when selecting tree leaves for
2920 alignment with no existing selection</li>
2921 <li>Relative URLs for datasources assumed to be relative
2922 to applet's codebase</li>
2923 <li>Status bar not updated after finished searching and
2924 search wraps around to first result</li>
2925 <li>StructureSelectionManager instance shared between
2926 several Jalview applets causes race conditions and memory
2928 <li>Hover tooltip and mouseover of position on structure
2929 not sent from Jmol in applet</li>
2930 <li>Certain sequences of javascript method calls to
2931 applet API fatally hang browser</li>
2932 </ul> <em>General</em>
2934 <li>View follows structure mouseover scrolls beyond
2935 position with wrapped view and hidden regions</li>
2936 <li>Find sequence position moves to wrong residue
2937 with/without hidden columns</li>
2938 <li>Sequence length given in alignment properties window
2940 <li>InvalidNumberFormat exceptions thrown when trying to
2941 import PDB like structure files</li>
2942 <li>Positional search results are only highlighted
2943 between user-supplied sequence start/end bounds</li>
2944 <li>End attribute of sequence is not validated</li>
2945 <li>Find dialog only finds first sequence containing a
2946 given sequence position</li>
2947 <li>Sequence numbering not preserved in MSF alignment
2949 <li>Jalview PDB file reader does not extract sequence
2950 from nucleotide chains correctly</li>
2951 <li>Structure colours not updated when tree partition
2952 changed in alignment</li>
2953 <li>Sequence associated secondary structure not correctly
2954 parsed in interleaved stockholm</li>
2955 <li>Colour by annotation dialog does not restore current
2957 <li>Hiding (nearly) all sequences doesn't work
2959 <li>Sequences containing lowercase letters are not
2960 properly associated with their pdb files</li>
2961 </ul> <em>Documentation and Development</em>
2963 <li>schemas/JalviewWsParamSet.xsd corrupted by
2964 ApplyCopyright tool</li>
2969 <div align="center">
2970 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2973 <td><em>Application</em>
2975 <li>New warning dialog when the Jalview Desktop cannot
2976 contact web services</li>
2977 <li>JABA service parameters for a preset are shown in
2978 service job window</li>
2979 <li>JABA Service menu entries reworded</li>
2983 <li>Modeller PIR IO broken - cannot correctly import a
2984 pir file emitted by Jalview</li>
2985 <li>Existing feature settings transferred to new
2986 alignment view created from cut'n'paste</li>
2987 <li>Improved test for mixed amino/nucleotide chains when
2988 parsing PDB files</li>
2989 <li>Consensus and conservation annotation rows
2990 occasionally become blank for all new windows</li>
2991 <li>Exception raised when right clicking above sequences
2992 in wrapped view mode</li>
2993 </ul> <em>Application</em>
2995 <li>multiple multiply aligned structure views cause cpu
2996 usage to hit 100% and computer to hang</li>
2997 <li>Web Service parameter layout breaks for long user
2998 parameter names</li>
2999 <li>Jaba service discovery hangs desktop if Jaba server
3006 <div align="center">
3007 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3010 <td><em>Application</em>
3012 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3013 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3016 <li>Web Services preference tab</li>
3017 <li>Analysis parameters dialog box and user defined
3019 <li>Improved speed and layout of Envision2 service menu</li>
3020 <li>Superpose structures using associated sequence
3022 <li>Export coordinates and projection as CSV from PCA
3024 </ul> <em>Applet</em>
3026 <li>enable javascript: execution by the applet via the
3027 link out mechanism</li>
3028 </ul> <em>Other</em>
3030 <li>Updated the Jmol Jalview interface to work with Jmol
3032 <li>The Jalview Desktop and JalviewLite applet now
3033 require Java 1.5</li>
3034 <li>Allow Jalview feature colour specification for GFF
3035 sequence annotation files</li>
3036 <li>New 'colour by label' keword in Jalview feature file
3037 type colour specification</li>
3038 <li>New Jalview Desktop Groovy API method that allows a
3039 script to check if it being run in an interactive session or
3040 in a batch operation from the Jalview command line</li>
3044 <li>clustalx colourscheme colours Ds preferentially when
3045 both D+E are present in over 50% of the column</li>
3046 </ul> <em>Application</em>
3048 <li>typo in AlignmentFrame->View->Hide->all but
3049 selected Regions menu item</li>
3050 <li>sequence fetcher replaces ',' for ';' when the ',' is
3051 part of a valid accession ID</li>
3052 <li>fatal OOM if object retrieved by sequence fetcher
3053 runs out of memory</li>
3054 <li>unhandled Out of Memory Error when viewing pca
3055 analysis results</li>
3056 <li>InstallAnywhere builds fail to launch on OS X java
3057 10.5 update 4 (due to apple Java 1.6 update)</li>
3058 <li>Installanywhere Jalview silently fails to launch</li>
3059 </ul> <em>Applet</em>
3061 <li>Jalview.getFeatureGroups() raises an
3062 ArrayIndexOutOfBoundsException if no feature groups are
3069 <div align="center">
3070 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3076 <li>Alignment prettyprinter doesn't cope with long
3078 <li>clustalx colourscheme colours Ds preferentially when
3079 both D+E are present in over 50% of the column</li>
3080 <li>nucleic acid structures retrieved from PDB do not
3081 import correctly</li>
3082 <li>More columns get selected than were clicked on when a
3083 number of columns are hidden</li>
3084 <li>annotation label popup menu not providing correct
3085 add/hide/show options when rows are hidden or none are
3087 <li>Stockholm format shown in list of readable formats,
3088 and parser copes better with alignments from RFAM.</li>
3089 <li>CSV output of consensus only includes the percentage
3090 of all symbols if sequence logo display is enabled</li>
3092 </ul> <em>Applet</em>
3094 <li>annotation panel disappears when annotation is
3096 </ul> <em>Application</em>
3098 <li>Alignment view not redrawn properly when new
3099 alignment opened where annotation panel is visible but no
3100 annotations are present on alignment</li>
3101 <li>pasted region containing hidden columns is
3102 incorrectly displayed in new alignment window</li>
3103 <li>Jalview slow to complete operations when stdout is
3104 flooded (fix is to close the Jalview console)</li>
3105 <li>typo in AlignmentFrame->View->Hide->all but
3106 selected Rregions menu item.</li>
3107 <li>inconsistent group submenu and Format submenu entry
3108 'Un' or 'Non'conserved</li>
3109 <li>Sequence feature settings are being shared by
3110 multiple distinct alignments</li>
3111 <li>group annotation not recreated when tree partition is
3113 <li>double click on group annotation to select sequences
3114 does not propagate to associated trees</li>
3115 <li>Mac OSX specific issues:
3117 <li>exception raised when mouse clicked on desktop
3118 window background</li>
3119 <li>Desktop menu placed on menu bar and application
3120 name set correctly</li>
3121 <li>sequence feature settings not wide enough for the
3122 save feature colourscheme button</li>
3131 <div align="center">
3132 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3135 <td><em>New Capabilities</em>
3137 <li>URL links generated from description line for
3138 regular-expression based URL links (applet and application)
3140 <li>Non-positional feature URL links are shown in link
3142 <li>Linked viewing of nucleic acid sequences and
3144 <li>Automatic Scrolling option in View menu to display
3145 the currently highlighted region of an alignment.</li>
3146 <li>Order an alignment by sequence length, or using the
3147 average score or total feature count for each sequence.</li>
3148 <li>Shading features by score or associated description</li>
3149 <li>Subdivide alignment and groups based on identity of
3150 selected subsequence (Make Groups from Selection).</li>
3151 <li>New hide/show options including Shift+Control+H to
3152 hide everything but the currently selected region.</li>
3153 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3154 </ul> <em>Application</em>
3156 <li>Fetch DB References capabilities and UI expanded to
3157 support retrieval from DAS sequence sources</li>
3158 <li>Local DAS Sequence sources can be added via the
3159 command line or via the Add local source dialog box.</li>
3160 <li>DAS Dbref and DbxRef feature types are parsed as
3161 database references and protein_name is parsed as
3162 description line (BioSapiens terms).</li>
3163 <li>Enable or disable non-positional feature and database
3164 references in sequence ID tooltip from View menu in
3166 <!-- <li>New hidden columns and rows and representatives capabilities
3167 in annotations file (in progress - not yet fully implemented)</li> -->
3168 <li>Group-associated consensus, sequence logos and
3169 conservation plots</li>
3170 <li>Symbol distributions for each column can be exported
3171 and visualized as sequence logos</li>
3172 <li>Optionally scale multi-character column labels to fit
3173 within each column of annotation row<!-- todo for applet -->
3175 <li>Optional automatic sort of associated alignment view
3176 when a new tree is opened.</li>
3177 <li>Jalview Java Console</li>
3178 <li>Better placement of desktop window when moving
3179 between different screens.</li>
3180 <li>New preference items for sequence ID tooltip and
3181 consensus annotation</li>
3182 <li>Client to submit sequences and IDs to Envision2
3184 <li><em>Vamsas Capabilities</em>
3186 <li>Improved VAMSAS synchronization (Jalview archive
3187 used to preserve views, structures, and tree display
3189 <li>Import of vamsas documents from disk or URL via
3191 <li>Sharing of selected regions between views and
3192 with other VAMSAS applications (Experimental feature!)</li>
3193 <li>Updated API to VAMSAS version 0.2</li>
3195 </ul> <em>Applet</em>
3197 <li>Middle button resizes annotation row height</li>
3200 <li>sortByTree (true/false) - automatically sort the
3201 associated alignment view by the tree when a new tree is
3203 <li>showTreeBootstraps (true/false) - show or hide
3204 branch bootstraps (default is to show them if available)</li>
3205 <li>showTreeDistances (true/false) - show or hide
3206 branch lengths (default is to show them if available)</li>
3207 <li>showUnlinkedTreeNodes (true/false) - indicate if
3208 unassociated nodes should be highlighted in the tree
3210 <li>heightScale and widthScale (1.0 or more) -
3211 increase the height or width of a cell in the alignment
3212 grid relative to the current font size.</li>
3215 <li>Non-positional features displayed in sequence ID
3217 </ul> <em>Other</em>
3219 <li>Features format: graduated colour definitions and
3220 specification of feature scores</li>
3221 <li>Alignment Annotations format: new keywords for group
3222 associated annotation (GROUP_REF) and annotation row display
3223 properties (ROW_PROPERTIES)</li>
3224 <li>XML formats extended to support graduated feature
3225 colourschemes, group associated annotation, and profile
3226 visualization settings.</li></td>
3229 <li>Source field in GFF files parsed as feature source
3230 rather than description</li>
3231 <li>Non-positional features are now included in sequence
3232 feature and gff files (controlled via non-positional feature
3233 visibility in tooltip).</li>
3234 <li>URL links generated for all feature links (bugfix)</li>
3235 <li>Added URL embedding instructions to features file
3237 <li>Codons containing ambiguous nucleotides translated as
3238 'X' in peptide product</li>
3239 <li>Match case switch in find dialog box works for both
3240 sequence ID and sequence string and query strings do not
3241 have to be in upper case to match case-insensitively.</li>
3242 <li>AMSA files only contain first column of
3243 multi-character column annotation labels</li>
3244 <li>Jalview Annotation File generation/parsing consistent
3245 with documentation (e.g. Stockholm annotation can be
3246 exported and re-imported)</li>
3247 <li>PDB files without embedded PDB IDs given a friendly
3249 <li>Find incrementally searches ID string matches as well
3250 as subsequence matches, and correctly reports total number
3254 <li>Better handling of exceptions during sequence
3256 <li>Dasobert generated non-positional feature URL
3257 link text excludes the start_end suffix</li>
3258 <li>DAS feature and source retrieval buttons disabled
3259 when fetch or registry operations in progress.</li>
3260 <li>PDB files retrieved from URLs are cached properly</li>
3261 <li>Sequence description lines properly shared via
3263 <li>Sequence fetcher fetches multiple records for all
3265 <li>Ensured that command line das feature retrieval
3266 completes before alignment figures are generated.</li>
3267 <li>Reduced time taken when opening file browser for
3269 <li>isAligned check prior to calculating tree, PCA or
3270 submitting an MSA to JNet now excludes hidden sequences.</li>
3271 <li>User defined group colours properly recovered
3272 from Jalview projects.</li>
3281 <div align="center">
3282 <strong>2.4.0.b2</strong><br> 28/10/2009
3287 <li>Experimental support for google analytics usage
3289 <li>Jalview privacy settings (user preferences and docs).</li>
3294 <li>Race condition in applet preventing startup in
3296 <li>Exception when feature created from selection beyond
3297 length of sequence.</li>
3298 <li>Allow synthetic PDB files to be imported gracefully</li>
3299 <li>Sequence associated annotation rows associate with
3300 all sequences with a given id</li>
3301 <li>Find function matches case-insensitively for sequence
3302 ID string searches</li>
3303 <li>Non-standard characters do not cause pairwise
3304 alignment to fail with exception</li>
3305 </ul> <em>Application Issues</em>
3307 <li>Sequences are now validated against EMBL database</li>
3308 <li>Sequence fetcher fetches multiple records for all
3310 </ul> <em>InstallAnywhere Issues</em>
3312 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3313 issue with installAnywhere mechanism)</li>
3314 <li>Command line launching of JARs from InstallAnywhere
3315 version (java class versioning error fixed)</li>
3322 <div align="center">
3323 <strong>2.4</strong><br> 27/8/2008
3326 <td><em>User Interface</em>
3328 <li>Linked highlighting of codon and amino acid from
3329 translation and protein products</li>
3330 <li>Linked highlighting of structure associated with
3331 residue mapping to codon position</li>
3332 <li>Sequence Fetcher provides example accession numbers
3333 and 'clear' button</li>
3334 <li>MemoryMonitor added as an option under Desktop's
3336 <li>Extract score function to parse whitespace separated
3337 numeric data in description line</li>
3338 <li>Column labels in alignment annotation can be centred.</li>
3339 <li>Tooltip for sequence associated annotation give name
3341 </ul> <em>Web Services and URL fetching</em>
3343 <li>JPred3 web service</li>
3344 <li>Prototype sequence search client (no public services
3346 <li>Fetch either seed alignment or full alignment from
3348 <li>URL Links created for matching database cross
3349 references as well as sequence ID</li>
3350 <li>URL Links can be created using regular-expressions</li>
3351 </ul> <em>Sequence Database Connectivity</em>
3353 <li>Retrieval of cross-referenced sequences from other
3355 <li>Generalised database reference retrieval and
3356 validation to all fetchable databases</li>
3357 <li>Fetch sequences from DAS sources supporting the
3358 sequence command</li>
3359 </ul> <em>Import and Export</em>
3360 <li>export annotation rows as CSV for spreadsheet import</li>
3361 <li>Jalview projects record alignment dataset associations,
3362 EMBL products, and cDNA sequence mappings</li>
3363 <li>Sequence Group colour can be specified in Annotation
3365 <li>Ad-hoc colouring of group in Annotation File using RGB
3366 triplet as name of colourscheme</li>
3367 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3369 <li>treenode binding for VAMSAS tree exchange</li>
3370 <li>local editing and update of sequences in VAMSAS
3371 alignments (experimental)</li>
3372 <li>Create new or select existing session to join</li>
3373 <li>load and save of vamsas documents</li>
3374 </ul> <em>Application command line</em>
3376 <li>-tree parameter to open trees (introduced for passing
3378 <li>-fetchfrom command line argument to specify nicknames
3379 of DAS servers to query for alignment features</li>
3380 <li>-dasserver command line argument to add new servers
3381 that are also automatically queried for features</li>
3382 <li>-groovy command line argument executes a given groovy
3383 script after all input data has been loaded and parsed</li>
3384 </ul> <em>Applet-Application data exchange</em>
3386 <li>Trees passed as applet parameters can be passed to
3387 application (when using "View in full
3388 application")</li>
3389 </ul> <em>Applet Parameters</em>
3391 <li>feature group display control parameter</li>
3392 <li>debug parameter</li>
3393 <li>showbutton parameter</li>
3394 </ul> <em>Applet API methods</em>
3396 <li>newView public method</li>
3397 <li>Window (current view) specific get/set public methods</li>
3398 <li>Feature display control methods</li>
3399 <li>get list of currently selected sequences</li>
3400 </ul> <em>New Jalview distribution features</em>
3402 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3403 <li>RELEASE file gives build properties for the latest
3404 Jalview release.</li>
3405 <li>Java 1.1 Applet build made easier and donotobfuscate
3406 property controls execution of obfuscator</li>
3407 <li>Build target for generating source distribution</li>
3408 <li>Debug flag for javacc</li>
3409 <li>.jalview_properties file is documented (slightly) in
3410 jalview.bin.Cache</li>
3411 <li>Continuous Build Integration for stable and
3412 development version of Application, Applet and source
3417 <li>selected region output includes visible annotations
3418 (for certain formats)</li>
3419 <li>edit label/displaychar contains existing label/char
3421 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3422 <li>shorter peptide product names from EMBL records</li>
3423 <li>Newick string generator makes compact representations</li>
3424 <li>bootstrap values parsed correctly for tree files with
3426 <li>pathological filechooser bug avoided by not allowing
3427 filenames containing a ':'</li>
3428 <li>Fixed exception when parsing GFF files containing
3429 global sequence features</li>
3430 <li>Alignment datasets are finalized only when number of
3431 references from alignment sequences goes to zero</li>
3432 <li>Close of tree branch colour box without colour
3433 selection causes cascading exceptions</li>
3434 <li>occasional negative imgwidth exceptions</li>
3435 <li>better reporting of non-fatal warnings to user when
3436 file parsing fails.</li>
3437 <li>Save works when Jalview project is default format</li>
3438 <li>Save as dialog opened if current alignment format is
3439 not a valid output format</li>
3440 <li>UniProt canonical names introduced for both das and
3442 <li>Histidine should be midblue (not pink!) in Zappo</li>
3443 <li>error messages passed up and output when data read
3445 <li>edit undo recovers previous dataset sequence when
3446 sequence is edited</li>
3447 <li>allow PDB files without pdb ID HEADER lines (like
3448 those generated by MODELLER) to be read in properly</li>
3449 <li>allow reading of JPred concise files as a normal
3451 <li>Stockholm annotation parsing and alignment properties
3452 import fixed for PFAM records</li>
3453 <li>Structure view windows have correct name in Desktop
3455 <li>annotation consisting of sequence associated scores
3456 can be read and written correctly to annotation file</li>
3457 <li>Aligned cDNA translation to aligned peptide works
3459 <li>Fixed display of hidden sequence markers and
3460 non-italic font for representatives in Applet</li>
3461 <li>Applet Menus are always embedded in applet window on
3463 <li>Newly shown features appear at top of stack (in
3465 <li>Annotations added via parameter not drawn properly
3466 due to null pointer exceptions</li>
3467 <li>Secondary structure lines are drawn starting from
3468 first column of alignment</li>
3469 <li>UniProt XML import updated for new schema release in
3471 <li>Sequence feature to sequence ID match for Features
3472 file is case-insensitive</li>
3473 <li>Sequence features read from Features file appended to
3474 all sequences with matching IDs</li>
3475 <li>PDB structure coloured correctly for associated views
3476 containing a sub-sequence</li>
3477 <li>PDB files can be retrieved by applet from Jar files</li>
3478 <li>feature and annotation file applet parameters
3479 referring to different directories are retrieved correctly</li>
3480 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3481 <li>Fixed application hang whilst waiting for
3482 splash-screen version check to complete</li>
3483 <li>Applet properly URLencodes input parameter values
3484 when passing them to the launchApp service</li>
3485 <li>display name and local features preserved in results
3486 retrieved from web service</li>
3487 <li>Visual delay indication for sequence retrieval and
3488 sequence fetcher initialisation</li>
3489 <li>updated Application to use DAS 1.53e version of
3490 dasobert DAS client</li>
3491 <li>Re-instated Full AMSA support and .amsa file
3493 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3501 <div align="center">
3502 <strong>2.3</strong><br> 9/5/07
3507 <li>Jmol 11.0.2 integration</li>
3508 <li>PDB views stored in Jalview XML files</li>
3509 <li>Slide sequences</li>
3510 <li>Edit sequence in place</li>
3511 <li>EMBL CDS features</li>
3512 <li>DAS Feature mapping</li>
3513 <li>Feature ordering</li>
3514 <li>Alignment Properties</li>
3515 <li>Annotation Scores</li>
3516 <li>Sort by scores</li>
3517 <li>Feature/annotation editing in applet</li>
3522 <li>Headless state operation in 2.2.1</li>
3523 <li>Incorrect and unstable DNA pairwise alignment</li>
3524 <li>Cut and paste of sequences with annotation</li>
3525 <li>Feature group display state in XML</li>
3526 <li>Feature ordering in XML</li>
3527 <li>blc file iteration selection using filename # suffix</li>
3528 <li>Stockholm alignment properties</li>
3529 <li>Stockhom alignment secondary structure annotation</li>
3530 <li>2.2.1 applet had no feature transparency</li>
3531 <li>Number pad keys can be used in cursor mode</li>
3532 <li>Structure Viewer mirror image resolved</li>
3539 <div align="center">
3540 <strong>2.2.1</strong><br> 12/2/07
3545 <li>Non standard characters can be read and displayed
3546 <li>Annotations/Features can be imported/exported to the
3548 <li>Applet allows editing of sequence/annotation/group
3549 name & description
3550 <li>Preference setting to display sequence name in
3552 <li>Annotation file format extended to allow
3553 Sequence_groups to be defined
3554 <li>Default opening of alignment overview panel can be
3555 specified in preferences
3556 <li>PDB residue numbering annotation added to associated
3562 <li>Applet crash under certain Linux OS with Java 1.6
3564 <li>Annotation file export / import bugs fixed
3565 <li>PNG / EPS image output bugs fixed
3571 <div align="center">
3572 <strong>2.2</strong><br> 27/11/06
3577 <li>Multiple views on alignment
3578 <li>Sequence feature editing
3579 <li>"Reload" alignment
3580 <li>"Save" to current filename
3581 <li>Background dependent text colour
3582 <li>Right align sequence ids
3583 <li>User-defined lower case residue colours
3586 <li>Menu item accelerator keys
3587 <li>Control-V pastes to current alignment
3588 <li>Cancel button for DAS Feature Fetching
3589 <li>PCA and PDB Viewers zoom via mouse roller
3590 <li>User-defined sub-tree colours and sub-tree selection
3592 <li>'New Window' button on the 'Output to Text box'
3597 <li>New memory efficient Undo/Redo System
3598 <li>Optimised symbol lookups and conservation/consensus
3600 <li>Region Conservation/Consensus recalculated after
3602 <li>Fixed Remove Empty Columns Bug (empty columns at end
3604 <li>Slowed DAS Feature Fetching for increased robustness.
3606 <li>Made angle brackets in ASCII feature descriptions
3608 <li>Re-instated Zoom function for PCA
3609 <li>Sequence descriptions conserved in web service
3611 <li>UniProt ID discoverer uses any word separated by
3613 <li>WsDbFetch query/result association resolved
3614 <li>Tree leaf to sequence mapping improved
3615 <li>Smooth fonts switch moved to FontChooser dialog box.
3622 <div align="center">
3623 <strong>2.1.1</strong><br> 12/9/06
3628 <li>Copy consensus sequence to clipboard</li>
3633 <li>Image output - rightmost residues are rendered if
3634 sequence id panel has been resized</li>
3635 <li>Image output - all offscreen group boundaries are
3637 <li>Annotation files with sequence references - all
3638 elements in file are relative to sequence position</li>
3639 <li>Mac Applet users can use Alt key for group editing</li>
3645 <div align="center">
3646 <strong>2.1</strong><br> 22/8/06
3651 <li>MAFFT Multiple Alignment in default Web Service list</li>
3652 <li>DAS Feature fetching</li>
3653 <li>Hide sequences and columns</li>
3654 <li>Export Annotations and Features</li>
3655 <li>GFF file reading / writing</li>
3656 <li>Associate structures with sequences from local PDB
3658 <li>Add sequences to exisiting alignment</li>
3659 <li>Recently opened files / URL lists</li>
3660 <li>Applet can launch the full application</li>
3661 <li>Applet has transparency for features (Java 1.2
3663 <li>Applet has user defined colours parameter</li>
3664 <li>Applet can load sequences from parameter
3665 "sequence<em>x</em>"
3671 <li>Redundancy Panel reinstalled in the Applet</li>
3672 <li>Monospaced font - EPS / rescaling bug fixed</li>
3673 <li>Annotation files with sequence references bug fixed</li>
3679 <div align="center">
3680 <strong>2.08.1</strong><br> 2/5/06
3685 <li>Change case of selected region from Popup menu</li>
3686 <li>Choose to match case when searching</li>
3687 <li>Middle mouse button and mouse movement can compress /
3688 expand the visible width and height of the alignment</li>
3693 <li>Annotation Panel displays complete JNet results</li>
3699 <div align="center">
3700 <strong>2.08b</strong><br> 18/4/06
3706 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3707 <li>Righthand label on wrapped alignments shows correct
3714 <div align="center">
3715 <strong>2.08</strong><br> 10/4/06
3720 <li>Editing can be locked to the selection area</li>
3721 <li>Keyboard editing</li>
3722 <li>Create sequence features from searches</li>
3723 <li>Precalculated annotations can be loaded onto
3725 <li>Features file allows grouping of features</li>
3726 <li>Annotation Colouring scheme added</li>
3727 <li>Smooth fonts off by default - Faster rendering</li>
3728 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3733 <li>Drag & Drop fixed on Linux</li>
3734 <li>Jalview Archive file faster to load/save, sequence
3735 descriptions saved.</li>
3741 <div align="center">
3742 <strong>2.07</strong><br> 12/12/05
3747 <li>PDB Structure Viewer enhanced</li>
3748 <li>Sequence Feature retrieval and display enhanced</li>
3749 <li>Choose to output sequence start-end after sequence
3750 name for file output</li>
3751 <li>Sequence Fetcher WSDBFetch@EBI</li>
3752 <li>Applet can read feature files, PDB files and can be
3753 used for HTML form input</li>
3758 <li>HTML output writes groups and features</li>
3759 <li>Group editing is Control and mouse click</li>
3760 <li>File IO bugs</li>
3766 <div align="center">
3767 <strong>2.06</strong><br> 28/9/05
3772 <li>View annotations in wrapped mode</li>
3773 <li>More options for PCA viewer</li>
3778 <li>GUI bugs resolved</li>
3779 <li>Runs with -nodisplay from command line</li>
3785 <div align="center">
3786 <strong>2.05b</strong><br> 15/9/05
3791 <li>Choose EPS export as lineart or text</li>
3792 <li>Jar files are executable</li>
3793 <li>Can read in Uracil - maps to unknown residue</li>
3798 <li>Known OutOfMemory errors give warning message</li>
3799 <li>Overview window calculated more efficiently</li>
3800 <li>Several GUI bugs resolved</li>
3806 <div align="center">
3807 <strong>2.05</strong><br> 30/8/05
3812 <li>Edit and annotate in "Wrapped" view</li>
3817 <li>Several GUI bugs resolved</li>
3823 <div align="center">
3824 <strong>2.04</strong><br> 24/8/05
3829 <li>Hold down mouse wheel & scroll to change font
3835 <li>Improved JPred client reliability</li>
3836 <li>Improved loading of Jalview files</li>
3842 <div align="center">
3843 <strong>2.03</strong><br> 18/8/05
3848 <li>Set Proxy server name and port in preferences</li>
3849 <li>Multiple URL links from sequence ids</li>
3850 <li>User Defined Colours can have a scheme name and added
3852 <li>Choose to ignore gaps in consensus calculation</li>
3853 <li>Unix users can set default web browser</li>
3854 <li>Runs without GUI for batch processing</li>
3855 <li>Dynamically generated Web Service Menus</li>
3860 <li>InstallAnywhere download for Sparc Solaris</li>
3866 <div align="center">
3867 <strong>2.02</strong><br> 18/7/05
3873 <li>Copy & Paste order of sequences maintains
3874 alignment order.</li>
3880 <div align="center">
3881 <strong>2.01</strong><br> 12/7/05
3886 <li>Use delete key for deleting selection.</li>
3887 <li>Use Mouse wheel to scroll sequences.</li>
3888 <li>Help file updated to describe how to add alignment
3890 <li>Version and build date written to build properties
3892 <li>InstallAnywhere installation will check for updates
3893 at launch of Jalview.</li>
3898 <li>Delete gaps bug fixed.</li>
3899 <li>FileChooser sorts columns.</li>
3900 <li>Can remove groups one by one.</li>
3901 <li>Filechooser icons installed.</li>
3902 <li>Finder ignores return character when searching.
3903 Return key will initiate a search.<br>
3910 <div align="center">
3911 <strong>2.0</strong><br> 20/6/05
3916 <li>New codebase</li>