3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->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) (<a
172 href="http://violetlib.org/vaqua/overview.html">download
173 here</a>) provided as fallback Look and Feel for OSX
174 platforms running Java 10
177 <!-- JAL-2960 -->Adding a structure to existing structure
178 view appears to do nothing because the view is hidden behind the alignment view
184 <!-- JAL-2926 -->Copy consensus sequence option in applet
185 should copy the group consensus when popup is opened on it
191 <!-- JAL-2913 -->Fixed ID width preference is not respected
194 <em>New Known Defects</em>
197 <!-- JAL-2973 --> Exceptions occasionally raised when
198 editing a large alignment and overview is displayed
201 <!-- JAL-2974 -->'Overview updating' progress bar is shown
202 repeatedly after a series of edits even when the overview
203 is no longer reflecting updates
206 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
207 structures for protein subsequence (if 'Trim Retrieved
208 Sequences' enabled) or Ensembl isoforms (Workaround in
209 2.10.4 is to fail back to N&W mapping)
216 <td width="60" nowrap>
218 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
221 <td><div align="left">
222 <ul><li>Updated Certum Codesigning Certificate
223 (Valid till 30th November 2018)</li></ul></div></td>
224 <td><div align="left">
227 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
228 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
229 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
230 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
231 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
232 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
233 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
239 <td width="60" nowrap>
241 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
244 <td><div align="left">
248 <!-- JAL-2446 -->Faster and more efficient management and
249 rendering of sequence features
252 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
253 429 rate limit request hander
256 <!-- JAL-2773 -->Structure views don't get updated unless
257 their colours have changed
260 <!-- JAL-2495 -->All linked sequences are highlighted for
261 a structure mousover (Jmol) or selection (Chimera)
264 <!-- JAL-2790 -->'Cancel' button in progress bar for
265 JABAWS AACon, RNAAliFold and Disorder prediction jobs
268 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
269 view from Ensembl locus cross-references
272 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
276 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
277 feature can be disabled
280 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
281 PDB easier retrieval of sequences for lists of IDs
284 <!-- JAL-2758 -->Short names for sequences retrieved from
290 <li>Groovy interpreter updated to 2.4.12</li>
291 <li>Example groovy script for generating a matrix of
292 percent identity scores for current alignment.</li>
294 <em>Testing and Deployment</em>
297 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
301 <td><div align="left">
305 <!-- JAL-2643 -->Pressing tab after updating the colour
306 threshold text field doesn't trigger an update to the
310 <!-- JAL-2682 -->Race condition when parsing sequence ID
314 <!-- JAL-2608 -->Overview windows are also closed when
315 alignment window is closed
318 <!-- JAL-2548 -->Export of features doesn't always respect
322 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
323 takes a long time in Cursor mode
329 <!-- JAL-2777 -->Structures with whitespace chainCode
330 cannot be viewed in Chimera
333 <!-- JAL-2728 -->Protein annotation panel too high in
337 <!-- JAL-2757 -->Can't edit the query after the server
338 error warning icon is shown in Uniprot and PDB Free Text
342 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
345 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
348 <!-- JAL-2739 -->Hidden column marker in last column not
349 rendered when switching back from Wrapped to normal view
352 <!-- JAL-2768 -->Annotation display corrupted when
353 scrolling right in unwapped alignment view
356 <!-- JAL-2542 -->Existing features on subsequence
357 incorrectly relocated when full sequence retrieved from
361 <!-- JAL-2733 -->Last reported memory still shown when
362 Desktop->Show Memory is unticked (OSX only)
365 <!-- JAL-2658 -->Amend Features dialog doesn't allow
366 features of same type and group to be selected for
370 <!-- JAL-2524 -->Jalview becomes sluggish in wide
371 alignments when hidden columns are present
374 <!-- JAL-2392 -->Jalview freezes when loading and
375 displaying several structures
378 <!-- JAL-2732 -->Black outlines left after resizing or
382 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
383 within the Jalview desktop on OSX
386 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
387 when in wrapped alignment mode
390 <!-- JAL-2636 -->Scale mark not shown when close to right
391 hand end of alignment
394 <!-- JAL-2684 -->Pairwise alignment of selected regions of
395 each selected sequence do not have correct start/end
399 <!-- JAL-2793 -->Alignment ruler height set incorrectly
400 after canceling the Alignment Window's Font dialog
403 <!-- JAL-2036 -->Show cross-references not enabled after
404 restoring project until a new view is created
407 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
408 URL links appears when only default EMBL-EBI link is
409 configured (since 2.10.2b2)
412 <!-- JAL-2775 -->Overview redraws whole window when box
416 <!-- JAL-2225 -->Structure viewer doesn't map all chains
417 in a multi-chain structure when viewing alignment
418 involving more than one chain (since 2.10)
421 <!-- JAL-2811 -->Double residue highlights in cursor mode
422 if new selection moves alignment window
425 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
426 arrow key in cursor mode to pass hidden column marker
429 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
430 that produces correctly annotated transcripts and products
433 <!-- JAL-2776 -->Toggling a feature group after first time
434 doesn't update associated structure view
437 <em>Applet</em><br />
440 <!-- JAL-2687 -->Concurrent modification exception when
441 closing alignment panel
444 <em>BioJSON</em><br />
447 <!-- JAL-2546 -->BioJSON export does not preserve
448 non-positional features
451 <em>New Known Issues</em>
454 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
455 sequence features correctly (for many previous versions of
459 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
460 using cursor in wrapped panel other than top
463 <!-- JAL-2791 -->Select columns containing feature ignores
464 graduated colour threshold
467 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
468 always preserve numbering and sequence features
471 <em>Known Java 9 Issues</em>
474 <!-- JAL-2902 -->Groovy Console very slow to open and is
475 not responsive when entering characters (Webstart, Java
482 <td width="60" nowrap>
484 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
485 <em>2/10/2017</em></strong>
488 <td><div align="left">
489 <em>New features in Jalview Desktop</em>
492 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
494 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
498 <td><div align="left">
502 <td width="60" nowrap>
504 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
505 <em>7/9/2017</em></strong>
508 <td><div align="left">
512 <!-- JAL-2588 -->Show gaps in overview window by colouring
513 in grey (sequences used to be coloured grey, and gaps were
517 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
521 <!-- JAL-2587 -->Overview updates immediately on increase
522 in size and progress bar shown as higher resolution
523 overview is recalculated
528 <td><div align="left">
532 <!-- JAL-2664 -->Overview window redraws every hidden
533 column region row by row
536 <!-- JAL-2681 -->duplicate protein sequences shown after
537 retrieving Ensembl crossrefs for sequences from Uniprot
540 <!-- JAL-2603 -->Overview window throws NPE if show boxes
541 format setting is unticked
544 <!-- JAL-2610 -->Groups are coloured wrongly in overview
545 if group has show boxes format setting unticked
548 <!-- JAL-2672,JAL-2665 -->Redraw problems when
549 autoscrolling whilst dragging current selection group to
550 include sequences and columns not currently displayed
553 <!-- JAL-2691 -->Not all chains are mapped when multimeric
554 assemblies are imported via CIF file
557 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
558 displayed when threshold or conservation colouring is also
562 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
566 <!-- JAL-2673 -->Jalview continues to scroll after
567 dragging a selected region off the visible region of the
571 <!-- JAL-2724 -->Cannot apply annotation based
572 colourscheme to all groups in a view
575 <!-- JAL-2511 -->IDs don't line up with sequences
576 initially after font size change using the Font chooser or
583 <td width="60" nowrap>
585 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
588 <td><div align="left">
589 <em>Calculations</em>
593 <!-- JAL-1933 -->Occupancy annotation row shows number of
594 ungapped positions in each column of the alignment.
597 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
598 a calculation dialog box
601 <!-- JAL-2379 -->Revised implementation of PCA for speed
602 and memory efficiency (~30x faster)
605 <!-- JAL-2403 -->Revised implementation of sequence
606 similarity scores as used by Tree, PCA, Shading Consensus
607 and other calculations
610 <!-- JAL-2416 -->Score matrices are stored as resource
611 files within the Jalview codebase
614 <!-- JAL-2500 -->Trees computed on Sequence Feature
615 Similarity may have different topology due to increased
622 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
623 model for alignments and groups
626 <!-- JAL-384 -->Custom shading schemes created via groovy
633 <!-- JAL-2526 -->Efficiency improvements for interacting
634 with alignment and overview windows
637 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
641 <!-- JAL-2388 -->Hidden columns and sequences can be
645 <!-- JAL-2611 -->Click-drag in visible area allows fine
646 adjustment of visible position
650 <em>Data import/export</em>
653 <!-- JAL-2535 -->Posterior probability annotation from
654 Stockholm files imported as sequence associated annotation
657 <!-- JAL-2507 -->More robust per-sequence positional
658 annotation input/output via stockholm flatfile
661 <!-- JAL-2533 -->Sequence names don't include file
662 extension when importing structure files without embedded
663 names or PDB accessions
666 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
667 format sequence substitution matrices
670 <em>User Interface</em>
673 <!-- JAL-2447 --> Experimental Features Checkbox in
674 Desktop's Tools menu to hide or show untested features in
678 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
679 via Overview or sequence motif search operations
682 <!-- JAL-2547 -->Amend sequence features dialog box can be
683 opened by double clicking gaps within sequence feature
687 <!-- JAL-1476 -->Status bar message shown when not enough
688 aligned positions were available to create a 3D structure
692 <em>3D Structure</em>
695 <!-- JAL-2430 -->Hidden regions in alignment views are not
696 coloured in linked structure views
699 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
700 file-based command exchange
703 <!-- JAL-2375 -->Structure chooser automatically shows
704 Cached Structures rather than querying the PDBe if
705 structures are already available for sequences
708 <!-- JAL-2520 -->Structures imported via URL are cached in
709 the Jalview project rather than downloaded again when the
713 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
714 to transfer Chimera's structure attributes as Jalview
715 features, and vice-versa (<strong>Experimental
719 <em>Web Services</em>
722 <!-- JAL-2549 -->Updated JABAWS client to v2.2
725 <!-- JAL-2335 -->Filter non-standard amino acids and
726 nucleotides when submitting to AACon and other MSA
730 <!-- JAL-2316, -->URLs for viewing database
731 cross-references provided by identifiers.org and the
739 <!-- JAL-2344 -->FileFormatI interface for describing and
740 identifying file formats (instead of String constants)
743 <!-- JAL-2228 -->FeatureCounter script refactored for
744 efficiency when counting all displayed features (not
745 backwards compatible with 2.10.1)
748 <em>Example files</em>
751 <!-- JAL-2631 -->Graduated feature colour style example
752 included in the example feature file
755 <em>Documentation</em>
758 <!-- JAL-2339 -->Release notes reformatted for readability
759 with the built-in Java help viewer
762 <!-- JAL-1644 -->Find documentation updated with 'search
763 sequence description' option
769 <!-- JAL-2485, -->External service integration tests for
770 Uniprot REST Free Text Search Client
773 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
776 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
781 <td><div align="left">
782 <em>Calculations</em>
785 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
786 matrix - C->R should be '-3'<br />Old matrix restored
787 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
789 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
790 Jalview's treatment of gaps in PCA and substitution matrix
791 based Tree calculations.<br /> <br />In earlier versions
792 of Jalview, gaps matching gaps were penalised, and gaps
793 matching non-gaps penalised even more. In the PCA
794 calculation, gaps were actually treated as non-gaps - so
795 different costs were applied, which meant Jalview's PCAs
796 were different to those produced by SeqSpace.<br />Jalview
797 now treats gaps in the same way as SeqSpace (ie it scores
798 them as 0). <br /> <br />Enter the following in the
799 Groovy console to restore pre-2.10.2 behaviour:<br />
800 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
801 // for 2.10.1 mode <br />
802 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
803 // to restore 2.10.2 mode <br /> <br /> <em>Note:
804 these settings will affect all subsequent tree and PCA
805 calculations (not recommended)</em></li>
807 <!-- JAL-2424 -->Fixed off-by-one bug that affected
808 scaling of branch lengths for trees computed using
809 Sequence Feature Similarity.
812 <!-- JAL-2377 -->PCA calculation could hang when
813 generating output report when working with highly
817 <!-- JAL-2544 --> Sort by features includes features to
818 right of selected region when gaps present on right-hand
822 <em>User Interface</em>
825 <!-- JAL-2346 -->Reopening Colour by annotation dialog
826 doesn't reselect a specific sequence's associated
827 annotation after it was used for colouring a view
830 <!-- JAL-2419 -->Current selection lost if popup menu
831 opened on a region of alignment without groups
834 <!-- JAL-2374 -->Popup menu not always shown for regions
835 of an alignment with overlapping groups
838 <!-- JAL-2310 -->Finder double counts if both a sequence's
839 name and description match
842 <!-- JAL-2370 -->Hiding column selection containing two
843 hidden regions results in incorrect hidden regions
846 <!-- JAL-2386 -->'Apply to all groups' setting when
847 changing colour does not apply Conservation slider value
851 <!-- JAL-2373 -->Percentage identity and conservation menu
852 items do not show a tick or allow shading to be disabled
855 <!-- JAL-2385 -->Conservation shading or PID threshold
856 lost when base colourscheme changed if slider not visible
859 <!-- JAL-2547 -->Sequence features shown in tooltip for
860 gaps before start of features
863 <!-- JAL-2623 -->Graduated feature colour threshold not
864 restored to UI when feature colour is edited
867 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
868 a time when scrolling vertically in wrapped mode.
871 <!-- JAL-2630 -->Structure and alignment overview update
872 as graduate feature colour settings are modified via the
876 <!-- JAL-2034 -->Overview window doesn't always update
877 when a group defined on the alignment is resized
880 <!-- JAL-2605 -->Mouseovers on left/right scale region in
881 wrapped view result in positional status updates
885 <!-- JAL-2563 -->Status bar doesn't show position for
886 ambiguous amino acid and nucleotide symbols
889 <!-- JAL-2602 -->Copy consensus sequence failed if
890 alignment included gapped columns
893 <!-- JAL-2473 -->Minimum size set for Jalview windows so
894 widgets don't permanently disappear
897 <!-- JAL-2503 -->Cannot select or filter quantitative
898 annotation that are shown only as column labels (e.g.
899 T-Coffee column reliability scores)
902 <!-- JAL-2594 -->Exception thrown if trying to create a
903 sequence feature on gaps only
906 <!-- JAL-2504 -->Features created with 'New feature'
907 button from a Find inherit previously defined feature type
908 rather than the Find query string
911 <!-- JAL-2423 -->incorrect title in output window when
912 exporting tree calculated in Jalview
915 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
916 and then revealing them reorders sequences on the
920 <!-- JAL-964 -->Group panel in sequence feature settings
921 doesn't update to reflect available set of groups after
922 interactively adding or modifying features
925 <!-- JAL-2225 -->Sequence Database chooser unusable on
929 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
930 only excluded gaps in current sequence and ignored
937 <!-- JAL-2421 -->Overview window visible region moves
938 erratically when hidden rows or columns are present
941 <!-- JAL-2362 -->Per-residue colourschemes applied via the
942 Structure Viewer's colour menu don't correspond to
946 <!-- JAL-2405 -->Protein specific colours only offered in
947 colour and group colour menu for protein alignments
950 <!-- JAL-2385 -->Colour threshold slider doesn't update to
951 reflect currently selected view or group's shading
955 <!-- JAL-2624 -->Feature colour thresholds not respected
956 when rendered on overview and structures when opacity at
960 <!-- JAL-2589 -->User defined gap colour not shown in
961 overview when features overlaid on alignment
964 <em>Data import/export</em>
967 <!-- JAL-2576 -->Very large alignments take a long time to
971 <!-- JAL-2507 -->Per-sequence RNA secondary structures
972 added after a sequence was imported are not written to
976 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
977 when importing RNA secondary structure via Stockholm
980 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
981 not shown in correct direction for simple pseudoknots
984 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
985 with lightGray or darkGray via features file (but can
989 <!-- JAL-2383 -->Above PID colour threshold not recovered
990 when alignment view imported from project
993 <!-- JAL-2520,JAL-2465 -->No mappings generated between
994 structure and sequences extracted from structure files
995 imported via URL and viewed in Jmol
998 <!-- JAL-2520 -->Structures loaded via URL are saved in
999 Jalview Projects rather than fetched via URL again when
1000 the project is loaded and the structure viewed
1003 <em>Web Services</em>
1006 <!-- JAL-2519 -->EnsemblGenomes example failing after
1007 release of Ensembl v.88
1010 <!-- JAL-2366 -->Proxy server address and port always
1011 appear enabled in Preferences->Connections
1014 <!-- JAL-2461 -->DAS registry not found exceptions
1015 removed from console output
1018 <!-- JAL-2582 -->Cannot retrieve protein products from
1019 Ensembl by Peptide ID
1022 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1023 created from SIFTs, and spurious 'Couldn't open structure
1024 in Chimera' errors raised after April 2017 update (problem
1025 due to 'null' string rather than empty string used for
1026 residues with no corresponding PDB mapping).
1029 <em>Application UI</em>
1032 <!-- JAL-2361 -->User Defined Colours not added to Colour
1036 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1037 case' residues (button in colourscheme editor debugged and
1038 new documentation and tooltips added)
1041 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1042 doesn't restore group-specific text colour thresholds
1045 <!-- JAL-2243 -->Feature settings panel does not update as
1046 new features are added to alignment
1049 <!-- JAL-2532 -->Cancel in feature settings reverts
1050 changes to feature colours via the Amend features dialog
1053 <!-- JAL-2506 -->Null pointer exception when attempting to
1054 edit graduated feature colour via amend features dialog
1058 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1059 selection menu changes colours of alignment views
1062 <!-- JAL-2426 -->Spurious exceptions in console raised
1063 from alignment calculation workers after alignment has
1067 <!-- JAL-1608 -->Typo in selection popup menu - Create
1068 groups now 'Create Group'
1071 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1072 Create/Undefine group doesn't always work
1075 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1076 shown again after pressing 'Cancel'
1079 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1080 adjusts start position in wrap mode
1083 <!-- JAL-2563 -->Status bar doesn't show positions for
1084 ambiguous amino acids
1087 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1088 CDS/Protein view after CDS sequences added for aligned
1092 <!-- JAL-2592 -->User defined colourschemes called 'User
1093 Defined' don't appear in Colours menu
1099 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1100 score models doesn't always result in an updated PCA plot
1103 <!-- JAL-2442 -->Features not rendered as transparent on
1104 overview or linked structure view
1107 <!-- JAL-2372 -->Colour group by conservation doesn't
1111 <!-- JAL-2517 -->Hitting Cancel after applying
1112 user-defined colourscheme doesn't restore original
1119 <!-- JAL-2314 -->Unit test failure:
1120 jalview.ws.jabaws.RNAStructExportImport setup fails
1123 <!-- JAL-2307 -->Unit test failure:
1124 jalview.ws.sifts.SiftsClientTest due to compatibility
1125 problems with deep array comparison equality asserts in
1126 successive versions of TestNG
1129 <!-- JAL-2479 -->Relocated StructureChooserTest and
1130 ParameterUtilsTest Unit tests to Network suite
1133 <em>New Known Issues</em>
1136 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1137 phase after a sequence motif find operation
1140 <!-- JAL-2550 -->Importing annotation file with rows
1141 containing just upper and lower case letters are
1142 interpreted as WUSS RNA secondary structure symbols
1145 <!-- JAL-2590 -->Cannot load and display Newick trees
1146 reliably from eggnog Ortholog database
1149 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1150 containing features of type Highlight' when 'B' is pressed
1151 to mark columns containing highlighted regions.
1154 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1155 doesn't always add secondary structure annotation.
1160 <td width="60" nowrap>
1161 <div align="center">
1162 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1165 <td><div align="left">
1169 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1170 for all consensus calculations
1173 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1176 <li>Updated Jalview's Certum code signing certificate
1179 <em>Application</em>
1182 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1183 set of database cross-references, sorted alphabetically
1186 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1187 from database cross references. Users with custom links
1188 will receive a <a href="webServices/urllinks.html#warning">warning
1189 dialog</a> asking them to update their preferences.
1192 <!-- JAL-2287-->Cancel button and escape listener on
1193 dialog warning user about disconnecting Jalview from a
1197 <!-- JAL-2320-->Jalview's Chimera control window closes if
1198 the Chimera it is connected to is shut down
1201 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1202 columns menu item to mark columns containing highlighted
1203 regions (e.g. from structure selections or results of a
1207 <!-- JAL-2284-->Command line option for batch-generation
1208 of HTML pages rendering alignment data with the BioJS
1218 <!-- JAL-2286 -->Columns with more than one modal residue
1219 are not coloured or thresholded according to percent
1220 identity (first observed in Jalview 2.8.2)
1223 <!-- JAL-2301 -->Threonine incorrectly reported as not
1227 <!-- JAL-2318 -->Updates to documentation pages (above PID
1228 threshold, amino acid properties)
1231 <!-- JAL-2292 -->Lower case residues in sequences are not
1232 reported as mapped to residues in a structure file in the
1236 <!--JAL-2324 -->Identical features with non-numeric scores
1237 could be added multiple times to a sequence
1240 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1241 bond features shown as two highlighted residues rather
1242 than a range in linked structure views, and treated
1243 correctly when selecting and computing trees from features
1246 <!-- JAL-2281-->Custom URL links for database
1247 cross-references are matched to database name regardless
1252 <em>Application</em>
1255 <!-- JAL-2282-->Custom URL links for specific database
1256 names without regular expressions also offer links from
1260 <!-- JAL-2315-->Removing a single configured link in the
1261 URL links pane in Connections preferences doesn't actually
1262 update Jalview configuration
1265 <!-- JAL-2272-->CTRL-Click on a selected region to open
1266 the alignment area popup menu doesn't work on El-Capitan
1269 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1270 files with similarly named sequences if dropped onto the
1274 <!-- JAL-2312 -->Additional mappings are shown for PDB
1275 entries where more chains exist in the PDB accession than
1276 are reported in the SIFTS file
1279 <!-- JAL-2317-->Certain structures do not get mapped to
1280 the structure view when displayed with Chimera
1283 <!-- JAL-2317-->No chains shown in the Chimera view
1284 panel's View->Show Chains submenu
1287 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1288 work for wrapped alignment views
1291 <!--JAL-2197 -->Rename UI components for running JPred
1292 predictions from 'JNet' to 'JPred'
1295 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1296 corrupted when annotation panel vertical scroll is not at
1297 first annotation row
1300 <!--JAL-2332 -->Attempting to view structure for Hen
1301 lysozyme results in a PDB Client error dialog box
1304 <!-- JAL-2319 -->Structure View's mapping report switched
1305 ranges for PDB and sequence for SIFTS
1308 SIFTS 'Not_Observed' residues mapped to non-existant
1312 <!-- <em>New Known Issues</em>
1319 <td width="60" nowrap>
1320 <div align="center">
1321 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1322 <em>25/10/2016</em></strong>
1325 <td><em>Application</em>
1327 <li>3D Structure chooser opens with 'Cached structures'
1328 view if structures already loaded</li>
1329 <li>Progress bar reports models as they are loaded to
1330 structure views</li>
1336 <li>Colour by conservation always enabled and no tick
1337 shown in menu when BLOSUM or PID shading applied</li>
1338 <li>FER1_ARATH and FER2_ARATH labels were switched in
1339 example sequences/projects/trees</li>
1341 <em>Application</em>
1343 <li>Jalview projects with views of local PDB structure
1344 files saved on Windows cannot be opened on OSX</li>
1345 <li>Multiple structure views can be opened and superposed
1346 without timeout for structures with multiple models or
1347 multiple sequences in alignment</li>
1348 <li>Cannot import or associated local PDB files without a
1349 PDB ID HEADER line</li>
1350 <li>RMSD is not output in Jmol console when superposition
1352 <li>Drag and drop of URL from Browser fails for Linux and
1353 OSX versions earlier than El Capitan</li>
1354 <li>ENA client ignores invalid content from ENA server</li>
1355 <li>Exceptions are not raised in console when ENA client
1356 attempts to fetch non-existent IDs via Fetch DB Refs UI
1358 <li>Exceptions are not raised in console when a new view
1359 is created on the alignment</li>
1360 <li>OSX right-click fixed for group selections: CMD-click
1361 to insert/remove gaps in groups and CTRL-click to open group
1364 <em>Build and deployment</em>
1366 <li>URL link checker now copes with multi-line anchor
1369 <em>New Known Issues</em>
1371 <li>Drag and drop from URL links in browsers do not work
1378 <td width="60" nowrap>
1379 <div align="center">
1380 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1383 <td><em>General</em>
1386 <!-- JAL-2124 -->Updated Spanish translations.
1389 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1390 for importing structure data to Jalview. Enables mmCIF and
1394 <!-- JAL-192 --->Alignment ruler shows positions relative to
1398 <!-- JAL-2202 -->Position/residue shown in status bar when
1399 mousing over sequence associated annotation
1402 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1406 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1407 '()', canonical '[]' and invalid '{}' base pair populations
1411 <!-- JAL-2092 -->Feature settings popup menu options for
1412 showing or hiding columns containing a feature
1415 <!-- JAL-1557 -->Edit selected group by double clicking on
1416 group and sequence associated annotation labels
1419 <!-- JAL-2236 -->Sequence name added to annotation label in
1420 select/hide columns by annotation and colour by annotation
1424 </ul> <em>Application</em>
1427 <!-- JAL-2050-->Automatically hide introns when opening a
1428 gene/transcript view
1431 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1435 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1436 structure mappings with the EMBL-EBI PDBe SIFTS database
1439 <!-- JAL-2079 -->Updated download sites used for Rfam and
1440 Pfam sources to xfam.org
1443 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1446 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1447 over sequences in Jalview
1450 <!-- JAL-2027-->Support for reverse-complement coding
1451 regions in ENA and EMBL
1454 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1455 for record retrieval via ENA rest API
1458 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1462 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1463 groovy script execution
1466 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1467 alignment window's Calculate menu
1470 <!-- JAL-1812 -->Allow groovy scripts that call
1471 Jalview.getAlignFrames() to run in headless mode
1474 <!-- JAL-2068 -->Support for creating new alignment
1475 calculation workers from groovy scripts
1478 <!-- JAL-1369 --->Store/restore reference sequence in
1482 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1483 associations are now saved/restored from project
1486 <!-- JAL-1993 -->Database selection dialog always shown
1487 before sequence fetcher is opened
1490 <!-- JAL-2183 -->Double click on an entry in Jalview's
1491 database chooser opens a sequence fetcher
1494 <!-- JAL-1563 -->Free-text search client for UniProt using
1495 the UniProt REST API
1498 <!-- JAL-2168 -->-nonews command line parameter to prevent
1499 the news reader opening
1502 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1503 querying stored in preferences
1506 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1510 <!-- JAL-1977-->Tooltips shown on database chooser
1513 <!-- JAL-391 -->Reverse complement function in calculate
1514 menu for nucleotide sequences
1517 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1518 and feature counts preserves alignment ordering (and
1519 debugged for complex feature sets).
1522 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1523 viewing structures with Jalview 2.10
1526 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1527 genome, transcript CCDS and gene ids via the Ensembl and
1528 Ensembl Genomes REST API
1531 <!-- JAL-2049 -->Protein sequence variant annotation
1532 computed for 'sequence_variant' annotation on CDS regions
1536 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1540 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1541 Ref Fetcher fails to match, or otherwise updates sequence
1542 data from external database records.
1545 <!-- JAL-2154 -->Revised Jalview Project format for
1546 efficient recovery of sequence coding and alignment
1547 annotation relationships.
1549 </ul> <!-- <em>Applet</em>
1560 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1564 <!-- JAL-2018-->Export features in Jalview format (again)
1565 includes graduated colourschemes
1568 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1569 working with big alignments and lots of hidden columns
1572 <!-- JAL-2053-->Hidden column markers not always rendered
1573 at right of alignment window
1576 <!-- JAL-2067 -->Tidied up links in help file table of
1580 <!-- JAL-2072 -->Feature based tree calculation not shown
1584 <!-- JAL-2075 -->Hidden columns ignored during feature
1585 based tree calculation
1588 <!-- JAL-2065 -->Alignment view stops updating when show
1589 unconserved enabled for group on alignment
1592 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1596 <!-- JAL-2146 -->Alignment column in status incorrectly
1597 shown as "Sequence position" when mousing over
1601 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1602 hidden columns present
1605 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1606 user created annotation added to alignment
1609 <!-- JAL-1841 -->RNA Structure consensus only computed for
1610 '()' base pair annotation
1613 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1614 in zero scores for all base pairs in RNA Structure
1618 <!-- JAL-2174-->Extend selection with columns containing
1622 <!-- JAL-2275 -->Pfam format writer puts extra space at
1623 beginning of sequence
1626 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1630 <!-- JAL-2238 -->Cannot create groups on an alignment from
1631 from a tree when t-coffee scores are shown
1634 <!-- JAL-1836,1967 -->Cannot import and view PDB
1635 structures with chains containing negative resnums (4q4h)
1638 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1642 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1643 to Clustal, PIR and PileUp output
1646 <!-- JAL-2008 -->Reordering sequence features that are
1647 not visible causes alignment window to repaint
1650 <!-- JAL-2006 -->Threshold sliders don't work in
1651 graduated colour and colour by annotation row for e-value
1652 scores associated with features and annotation rows
1655 <!-- JAL-1797 -->amino acid physicochemical conservation
1656 calculation should be case independent
1659 <!-- JAL-2173 -->Remove annotation also updates hidden
1663 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1664 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1665 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1668 <!-- JAL-2065 -->Null pointer exceptions and redraw
1669 problems when reference sequence defined and 'show
1670 non-conserved' enabled
1673 <!-- JAL-1306 -->Quality and Conservation are now shown on
1674 load even when Consensus calculation is disabled
1677 <!-- JAL-1932 -->Remove right on penultimate column of
1678 alignment does nothing
1681 <em>Application</em>
1684 <!-- JAL-1552-->URLs and links can't be imported by
1685 drag'n'drop on OSX when launched via webstart (note - not
1686 yet fixed for El Capitan)
1689 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1690 output when running on non-gb/us i18n platforms
1693 <!-- JAL-1944 -->Error thrown when exporting a view with
1694 hidden sequences as flat-file alignment
1697 <!-- JAL-2030-->InstallAnywhere distribution fails when
1701 <!-- JAL-2080-->Jalview very slow to launch via webstart
1702 (also hotfix for 2.9.0b2)
1705 <!-- JAL-2085 -->Cannot save project when view has a
1706 reference sequence defined
1709 <!-- JAL-1011 -->Columns are suddenly selected in other
1710 alignments and views when revealing hidden columns
1713 <!-- JAL-1989 -->Hide columns not mirrored in complement
1714 view in a cDNA/Protein splitframe
1717 <!-- JAL-1369 -->Cannot save/restore representative
1718 sequence from project when only one sequence is
1722 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1723 in Structure Chooser
1726 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1727 structure consensus didn't refresh annotation panel
1730 <!-- JAL-1962 -->View mapping in structure view shows
1731 mappings between sequence and all chains in a PDB file
1734 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1735 dialogs format columns correctly, don't display array
1736 data, sort columns according to type
1739 <!-- JAL-1975 -->Export complete shown after destination
1740 file chooser is cancelled during an image export
1743 <!-- JAL-2025 -->Error when querying PDB Service with
1744 sequence name containing special characters
1747 <!-- JAL-2024 -->Manual PDB structure querying should be
1751 <!-- JAL-2104 -->Large tooltips with broken HTML
1752 formatting don't wrap
1755 <!-- JAL-1128 -->Figures exported from wrapped view are
1756 truncated so L looks like I in consensus annotation
1759 <!-- JAL-2003 -->Export features should only export the
1760 currently displayed features for the current selection or
1764 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1765 after fetching cross-references, and restoring from
1769 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1770 followed in the structure viewer
1773 <!-- JAL-2163 -->Titles for individual alignments in
1774 splitframe not restored from project
1777 <!-- JAL-2145 -->missing autocalculated annotation at
1778 trailing end of protein alignment in transcript/product
1779 splitview when pad-gaps not enabled by default
1782 <!-- JAL-1797 -->amino acid physicochemical conservation
1786 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1787 article has been read (reopened issue due to
1788 internationalisation problems)
1791 <!-- JAL-1960 -->Only offer PDB structures in structure
1792 viewer based on sequence name, PDB and UniProt
1797 <!-- JAL-1976 -->No progress bar shown during export of
1801 <!-- JAL-2213 -->Structures not always superimposed after
1802 multiple structures are shown for one or more sequences.
1805 <!-- JAL-1370 -->Reference sequence characters should not
1806 be replaced with '.' when 'Show unconserved' format option
1810 <!-- JAL-1823 -->Cannot specify chain code when entering
1811 specific PDB id for sequence
1814 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1815 'Export hidden sequences' is enabled, but 'export hidden
1816 columns' is disabled.
1819 <!--JAL-2026-->Best Quality option in structure chooser
1820 selects lowest rather than highest resolution structures
1824 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1825 to sequence mapping in 'View Mappings' report
1828 <!-- JAL-2284 -->Unable to read old Jalview projects that
1829 contain non-XML data added after Jalvew wrote project.
1832 <!-- JAL-2118 -->Newly created annotation row reorders
1833 after clicking on it to create new annotation for a
1837 <!-- JAL-1980 -->Null Pointer Exception raised when
1838 pressing Add on an orphaned cut'n'paste window.
1840 <!-- may exclude, this is an external service stability issue JAL-1941
1841 -- > RNA 3D structure not added via DSSR service</li> -->
1846 <!-- JAL-2151 -->Incorrect columns are selected when
1847 hidden columns present before start of sequence
1850 <!-- JAL-1986 -->Missing dependencies on applet pages
1854 <!-- JAL-1947 -->Overview pixel size changes when
1855 sequences are hidden in applet
1858 <!-- JAL-1996 -->Updated instructions for applet
1859 deployment on examples pages.
1866 <td width="60" nowrap>
1867 <div align="center">
1868 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1869 <em>16/10/2015</em></strong>
1872 <td><em>General</em>
1874 <li>Time stamps for signed Jalview application and applet
1879 <em>Application</em>
1881 <li>Duplicate group consensus and conservation rows
1882 shown when tree is partitioned</li>
1883 <li>Erratic behaviour when tree partitions made with
1884 multiple cDNA/Protein split views</li>
1890 <td width="60" nowrap>
1891 <div align="center">
1892 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1893 <em>8/10/2015</em></strong>
1896 <td><em>General</em>
1898 <li>Updated Spanish translations of localized text for
1900 </ul> <em>Application</em>
1902 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1903 <li>Signed OSX InstallAnywhere installer<br></li>
1904 <li>Support for per-sequence based annotations in BioJSON</li>
1905 </ul> <em>Applet</em>
1907 <li>Split frame example added to applet examples page</li>
1908 </ul> <em>Build and Deployment</em>
1911 <!-- JAL-1888 -->New ant target for running Jalview's test
1919 <li>Mapping of cDNA to protein in split frames
1920 incorrect when sequence start > 1</li>
1921 <li>Broken images in filter column by annotation dialog
1923 <li>Feature colours not parsed from features file</li>
1924 <li>Exceptions and incomplete link URLs recovered when
1925 loading a features file containing HTML tags in feature
1929 <em>Application</em>
1931 <li>Annotations corrupted after BioJS export and
1933 <li>Incorrect sequence limits after Fetch DB References
1934 with 'trim retrieved sequences'</li>
1935 <li>Incorrect warning about deleting all data when
1936 deleting selected columns</li>
1937 <li>Patch to build system for shipping properly signed
1938 JNLP templates for webstart launch</li>
1939 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1940 unreleased structures for download or viewing</li>
1941 <li>Tab/space/return keystroke operation of EMBL-PDBe
1942 fetcher/viewer dialogs works correctly</li>
1943 <li>Disabled 'minimise' button on Jalview windows
1944 running on OSX to workaround redraw hang bug</li>
1945 <li>Split cDNA/Protein view position and geometry not
1946 recovered from jalview project</li>
1947 <li>Initial enabled/disabled state of annotation menu
1948 sorter 'show autocalculated first/last' corresponds to
1950 <li>Restoring of Clustal, RNA Helices and T-Coffee
1951 color schemes from BioJSON</li>
1955 <li>Reorder sequences mirrored in cDNA/Protein split
1957 <li>Applet with Jmol examples not loading correctly</li>
1963 <td><div align="center">
1964 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1966 <td><em>General</em>
1968 <li>Linked visualisation and analysis of DNA and Protein
1971 <li>Translated cDNA alignments shown as split protein
1972 and DNA alignment views</li>
1973 <li>Codon consensus annotation for linked protein and
1974 cDNA alignment views</li>
1975 <li>Link cDNA or Protein product sequences by loading
1976 them onto Protein or cDNA alignments</li>
1977 <li>Reconstruct linked cDNA alignment from aligned
1978 protein sequences</li>
1981 <li>Jmol integration updated to Jmol v14.2.14</li>
1982 <li>Import and export of Jalview alignment views as <a
1983 href="features/bioJsonFormat.html">BioJSON</a></li>
1984 <li>New alignment annotation file statements for
1985 reference sequences and marking hidden columns</li>
1986 <li>Reference sequence based alignment shading to
1987 highlight variation</li>
1988 <li>Select or hide columns according to alignment
1990 <li>Find option for locating sequences by description</li>
1991 <li>Conserved physicochemical properties shown in amino
1992 acid conservation row</li>
1993 <li>Alignments can be sorted by number of RNA helices</li>
1994 </ul> <em>Application</em>
1996 <li>New cDNA/Protein analysis capabilities
1998 <li>Get Cross-References should open a Split Frame
1999 view with cDNA/Protein</li>
2000 <li>Detect when nucleotide sequences and protein
2001 sequences are placed in the same alignment</li>
2002 <li>Split cDNA/Protein views are saved in Jalview
2007 <li>Use REST API to talk to Chimera</li>
2008 <li>Selected regions in Chimera are highlighted in linked
2009 Jalview windows</li>
2011 <li>VARNA RNA viewer updated to v3.93</li>
2012 <li>VARNA views are saved in Jalview Projects</li>
2013 <li>Pseudoknots displayed as Jalview RNA annotation can
2014 be shown in VARNA</li>
2016 <li>Make groups for selection uses marked columns as well
2017 as the active selected region</li>
2019 <li>Calculate UPGMA and NJ trees using sequence feature
2021 <li>New Export options
2023 <li>New Export Settings dialog to control hidden
2024 region export in flat file generation</li>
2026 <li>Export alignment views for display with the <a
2027 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2029 <li>Export scrollable SVG in HTML page</li>
2030 <li>Optional embedding of BioJSON data when exporting
2031 alignment figures to HTML</li>
2033 <li>3D structure retrieval and display
2035 <li>Free text and structured queries with the PDBe
2037 <li>PDBe Search API based discovery and selection of
2038 PDB structures for a sequence set</li>
2042 <li>JPred4 employed for protein secondary structure
2044 <li>Hide Insertions menu option to hide unaligned columns
2045 for one or a group of sequences</li>
2046 <li>Automatically hide insertions in alignments imported
2047 from the JPred4 web server</li>
2048 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2049 system on OSX<br />LGPL libraries courtesy of <a
2050 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2052 <li>changed 'View nucleotide structure' submenu to 'View
2053 VARNA 2D Structure'</li>
2054 <li>change "View protein structure" menu option to "3D
2057 </ul> <em>Applet</em>
2059 <li>New layout for applet example pages</li>
2060 <li>New parameters to enable SplitFrame view
2061 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2062 <li>New example demonstrating linked viewing of cDNA and
2063 Protein alignments</li>
2064 </ul> <em>Development and deployment</em>
2066 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2067 <li>Include installation type and git revision in build
2068 properties and console log output</li>
2069 <li>Jalview Github organisation, and new github site for
2070 storing BioJsMSA Templates</li>
2071 <li>Jalview's unit tests now managed with TestNG</li>
2074 <!-- <em>General</em>
2076 </ul> --> <!-- issues resolved --> <em>Application</em>
2078 <li>Escape should close any open find dialogs</li>
2079 <li>Typo in select-by-features status report</li>
2080 <li>Consensus RNA secondary secondary structure
2081 predictions are not highlighted in amber</li>
2082 <li>Missing gap character in v2.7 example file means
2083 alignment appears unaligned when pad-gaps is not enabled</li>
2084 <li>First switch to RNA Helices colouring doesn't colour
2085 associated structure views</li>
2086 <li>ID width preference option is greyed out when auto
2087 width checkbox not enabled</li>
2088 <li>Stopped a warning dialog from being shown when
2089 creating user defined colours</li>
2090 <li>'View Mapping' in structure viewer shows sequence
2091 mappings for just that viewer's sequences</li>
2092 <li>Workaround for superposing PDB files containing
2093 multiple models in Chimera</li>
2094 <li>Report sequence position in status bar when hovering
2095 over Jmol structure</li>
2096 <li>Cannot output gaps as '.' symbols with Selection ->
2097 output to text box</li>
2098 <li>Flat file exports of alignments with hidden columns
2099 have incorrect sequence start/end</li>
2100 <li>'Aligning' a second chain to a Chimera structure from
2102 <li>Colour schemes applied to structure viewers don't
2103 work for nucleotide</li>
2104 <li>Loading/cut'n'pasting an empty or invalid file leads
2105 to a grey/invisible alignment window</li>
2106 <li>Exported Jpred annotation from a sequence region
2107 imports to different position</li>
2108 <li>Space at beginning of sequence feature tooltips shown
2109 on some platforms</li>
2110 <li>Chimera viewer 'View | Show Chain' menu is not
2112 <li>'New View' fails with a Null Pointer Exception in
2113 console if Chimera has been opened</li>
2114 <li>Mouseover to Chimera not working</li>
2115 <li>Miscellaneous ENA XML feature qualifiers not
2117 <li>NPE in annotation renderer after 'Extract Scores'</li>
2118 <li>If two structures in one Chimera window, mouseover of
2119 either sequence shows on first structure</li>
2120 <li>'Show annotations' options should not make
2121 non-positional annotations visible</li>
2122 <li>Subsequence secondary structure annotation not shown
2123 in right place after 'view flanking regions'</li>
2124 <li>File Save As type unset when current file format is
2126 <li>Save as '.jar' option removed for saving Jalview
2128 <li>Colour by Sequence colouring in Chimera more
2130 <li>Cannot 'add reference annotation' for a sequence in
2131 several views on same alignment</li>
2132 <li>Cannot show linked products for EMBL / ENA records</li>
2133 <li>Jalview's tooltip wraps long texts containing no
2135 </ul> <em>Applet</em>
2137 <li>Jmol to JalviewLite mouseover/link not working</li>
2138 <li>JalviewLite can't import sequences with ID
2139 descriptions containing angle brackets</li>
2140 </ul> <em>General</em>
2142 <li>Cannot export and reimport RNA secondary structure
2143 via jalview annotation file</li>
2144 <li>Random helix colour palette for colour by annotation
2145 with RNA secondary structure</li>
2146 <li>Mouseover to cDNA from STOP residue in protein
2147 translation doesn't work.</li>
2148 <li>hints when using the select by annotation dialog box</li>
2149 <li>Jmol alignment incorrect if PDB file has alternate CA
2151 <li>FontChooser message dialog appears to hang after
2152 choosing 1pt font</li>
2153 <li>Peptide secondary structure incorrectly imported from
2154 annotation file when annotation display text includes 'e' or
2156 <li>Cannot set colour of new feature type whilst creating
2158 <li>cDNA translation alignment should not be sequence
2159 order dependent</li>
2160 <li>'Show unconserved' doesn't work for lower case
2162 <li>Nucleotide ambiguity codes involving R not recognised</li>
2163 </ul> <em>Deployment and Documentation</em>
2165 <li>Applet example pages appear different to the rest of
2166 www.jalview.org</li>
2167 </ul> <em>Application Known issues</em>
2169 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2170 <li>Misleading message appears after trying to delete
2172 <li>Jalview icon not shown in dock after InstallAnywhere
2173 version launches</li>
2174 <li>Fetching EMBL reference for an RNA sequence results
2175 fails with a sequence mismatch</li>
2176 <li>Corrupted or unreadable alignment display when
2177 scrolling alignment to right</li>
2178 <li>ArrayIndexOutOfBoundsException thrown when remove
2179 empty columns called on alignment with ragged gapped ends</li>
2180 <li>auto calculated alignment annotation rows do not get
2181 placed above or below non-autocalculated rows</li>
2182 <li>Jalview dekstop becomes sluggish at full screen in
2183 ultra-high resolution</li>
2184 <li>Cannot disable consensus calculation independently of
2185 quality and conservation</li>
2186 <li>Mouseover highlighting between cDNA and protein can
2187 become sluggish with more than one splitframe shown</li>
2188 </ul> <em>Applet Known Issues</em>
2190 <li>Core PDB parsing code requires Jmol</li>
2191 <li>Sequence canvas panel goes white when alignment
2192 window is being resized</li>
2198 <td><div align="center">
2199 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2201 <td><em>General</em>
2203 <li>Updated Java code signing certificate donated by
2205 <li>Features and annotation preserved when performing
2206 pairwise alignment</li>
2207 <li>RNA pseudoknot annotation can be
2208 imported/exported/displayed</li>
2209 <li>'colour by annotation' can colour by RNA and
2210 protein secondary structure</li>
2211 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2212 post-hoc with 2.9 release</em>)
2215 </ul> <em>Application</em>
2217 <li>Extract and display secondary structure for sequences
2218 with 3D structures</li>
2219 <li>Support for parsing RNAML</li>
2220 <li>Annotations menu for layout
2222 <li>sort sequence annotation rows by alignment</li>
2223 <li>place sequence annotation above/below alignment
2226 <li>Output in Stockholm format</li>
2227 <li>Internationalisation: improved Spanish (es)
2229 <li>Structure viewer preferences tab</li>
2230 <li>Disorder and Secondary Structure annotation tracks
2231 shared between alignments</li>
2232 <li>UCSF Chimera launch and linked highlighting from
2234 <li>Show/hide all sequence associated annotation rows for
2235 all or current selection</li>
2236 <li>disorder and secondary structure predictions
2237 available as dataset annotation</li>
2238 <li>Per-sequence rna helices colouring</li>
2241 <li>Sequence database accessions imported when fetching
2242 alignments from Rfam</li>
2243 <li>update VARNA version to 3.91</li>
2245 <li>New groovy scripts for exporting aligned positions,
2246 conservation values, and calculating sum of pairs scores.</li>
2247 <li>Command line argument to set default JABAWS server</li>
2248 <li>include installation type in build properties and
2249 console log output</li>
2250 <li>Updated Jalview project format to preserve dataset
2254 <!-- issues resolved --> <em>Application</em>
2256 <li>Distinguish alignment and sequence associated RNA
2257 structure in structure->view->VARNA</li>
2258 <li>Raise dialog box if user deletes all sequences in an
2260 <li>Pressing F1 results in documentation opening twice</li>
2261 <li>Sequence feature tooltip is wrapped</li>
2262 <li>Double click on sequence associated annotation
2263 selects only first column</li>
2264 <li>Redundancy removal doesn't result in unlinked
2265 leaves shown in tree</li>
2266 <li>Undos after several redundancy removals don't undo
2268 <li>Hide sequence doesn't hide associated annotation</li>
2269 <li>User defined colours dialog box too big to fit on
2270 screen and buttons not visible</li>
2271 <li>author list isn't updated if already written to
2272 Jalview properties</li>
2273 <li>Popup menu won't open after retrieving sequence
2275 <li>File open window for associate PDB doesn't open</li>
2276 <li>Left-then-right click on a sequence id opens a
2277 browser search window</li>
2278 <li>Cannot open sequence feature shading/sort popup menu
2279 in feature settings dialog</li>
2280 <li>better tooltip placement for some areas of Jalview
2282 <li>Allow addition of JABAWS Server which doesn't
2283 pass validation</li>
2284 <li>Web services parameters dialog box is too large to
2286 <li>Muscle nucleotide alignment preset obscured by
2288 <li>JABAWS preset submenus don't contain newly
2289 defined user preset</li>
2290 <li>MSA web services warns user if they were launched
2291 with invalid input</li>
2292 <li>Jalview cannot contact DAS Registy when running on
2295 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2296 'Superpose with' submenu not shown when new view
2300 </ul> <!-- <em>Applet</em>
2302 </ul> <em>General</em>
2304 </ul>--> <em>Deployment and Documentation</em>
2306 <li>2G and 1G options in launchApp have no effect on
2307 memory allocation</li>
2308 <li>launchApp service doesn't automatically open
2309 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2311 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2312 InstallAnywhere reports cannot find valid JVM when Java
2313 1.7_055 is available
2315 </ul> <em>Application Known issues</em>
2318 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2319 corrupted or unreadable alignment display when scrolling
2323 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2324 retrieval fails but progress bar continues for DAS retrieval
2325 with large number of ID
2328 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2329 flatfile output of visible region has incorrect sequence
2333 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2334 rna structure consensus doesn't update when secondary
2335 structure tracks are rearranged
2338 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2339 invalid rna structure positional highlighting does not
2340 highlight position of invalid base pairs
2343 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2344 out of memory errors are not raised when saving Jalview
2345 project from alignment window file menu
2348 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2349 Switching to RNA Helices colouring doesn't propagate to
2353 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2354 colour by RNA Helices not enabled when user created
2355 annotation added to alignment
2358 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2359 Jalview icon not shown on dock in Mountain Lion/Webstart
2361 </ul> <em>Applet Known Issues</em>
2364 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2365 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2368 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2369 Jalview and Jmol example not compatible with IE9
2372 <li>Sort by annotation score doesn't reverse order
2378 <td><div align="center">
2379 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2382 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2385 <li>Internationalisation of user interface (usually
2386 called i18n support) and translation for Spanish locale</li>
2387 <li>Define/Undefine group on current selection with
2388 Ctrl-G/Shift Ctrl-G</li>
2389 <li>Improved group creation/removal options in
2390 alignment/sequence Popup menu</li>
2391 <li>Sensible precision for symbol distribution
2392 percentages shown in logo tooltip.</li>
2393 <li>Annotation panel height set according to amount of
2394 annotation when alignment first opened</li>
2395 </ul> <em>Application</em>
2397 <li>Interactive consensus RNA secondary structure
2398 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2399 <li>Select columns containing particular features from
2400 Feature Settings dialog</li>
2401 <li>View all 'representative' PDB structures for selected
2403 <li>Update Jalview project format:
2405 <li>New file extension for Jalview projects '.jvp'</li>
2406 <li>Preserve sequence and annotation dataset (to
2407 store secondary structure annotation,etc)</li>
2408 <li>Per group and alignment annotation and RNA helix
2412 <li>New similarity measures for PCA and Tree calculation
2414 <li>Experimental support for retrieval and viewing of
2415 flanking regions for an alignment</li>
2419 <!-- issues resolved --> <em>Application</em>
2421 <li>logo keeps spinning and status remains at queued or
2422 running after job is cancelled</li>
2423 <li>cannot export features from alignments imported from
2424 Jalview/VAMSAS projects</li>
2425 <li>Buggy slider for web service parameters that take
2427 <li>Newly created RNA secondary structure line doesn't
2428 have 'display all symbols' flag set</li>
2429 <li>T-COFFEE alignment score shading scheme and other
2430 annotation shading not saved in Jalview project</li>
2431 <li>Local file cannot be loaded in freshly downloaded
2433 <li>Jalview icon not shown on dock in Mountain
2435 <li>Load file from desktop file browser fails</li>
2436 <li>Occasional NPE thrown when calculating large trees</li>
2437 <li>Cannot reorder or slide sequences after dragging an
2438 alignment onto desktop</li>
2439 <li>Colour by annotation dialog throws NPE after using
2440 'extract scores' function</li>
2441 <li>Loading/cut'n'pasting an empty file leads to a grey
2442 alignment window</li>
2443 <li>Disorder thresholds rendered incorrectly after
2444 performing IUPred disorder prediction</li>
2445 <li>Multiple group annotated consensus rows shown when
2446 changing 'normalise logo' display setting</li>
2447 <li>Find shows blank dialog after 'finished searching' if
2448 nothing matches query</li>
2449 <li>Null Pointer Exceptions raised when sorting by
2450 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2452 <li>Errors in Jmol console when structures in alignment
2453 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2455 <li>Not all working JABAWS services are shown in
2457 <li>JAVAWS version of Jalview fails to launch with
2458 'invalid literal/length code'</li>
2459 <li>Annotation/RNA Helix colourschemes cannot be applied
2460 to alignment with groups (actually fixed in 2.8.0b1)</li>
2461 <li>RNA Helices and T-Coffee Scores available as default
2464 </ul> <em>Applet</em>
2466 <li>Remove group option is shown even when selection is
2468 <li>Apply to all groups ticked but colourscheme changes
2469 don't affect groups</li>
2470 <li>Documented RNA Helices and T-Coffee Scores as valid
2471 colourscheme name</li>
2472 <li>Annotation labels drawn on sequence IDs when
2473 Annotation panel is not displayed</li>
2474 <li>Increased font size for dropdown menus on OSX and
2475 embedded windows</li>
2476 </ul> <em>Other</em>
2478 <li>Consensus sequence for alignments/groups with a
2479 single sequence were not calculated</li>
2480 <li>annotation files that contain only groups imported as
2481 annotation and junk sequences</li>
2482 <li>Fasta files with sequences containing '*' incorrectly
2483 recognised as PFAM or BLC</li>
2484 <li>conservation/PID slider apply all groups option
2485 doesn't affect background (2.8.0b1)
2487 <li>redundancy highlighting is erratic at 0% and 100%</li>
2488 <li>Remove gapped columns fails for sequences with ragged
2490 <li>AMSA annotation row with leading spaces is not
2491 registered correctly on import</li>
2492 <li>Jalview crashes when selecting PCA analysis for
2493 certain alignments</li>
2494 <li>Opening the colour by annotation dialog for an
2495 existing annotation based 'use original colours'
2496 colourscheme loses original colours setting</li>
2501 <td><div align="center">
2502 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2503 <em>30/1/2014</em></strong>
2507 <li>Trusted certificates for JalviewLite applet and
2508 Jalview Desktop application<br />Certificate was donated by
2509 <a href="https://www.certum.eu">Certum</a> to the Jalview
2510 open source project).
2512 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2513 <li>Output in Stockholm format</li>
2514 <li>Allow import of data from gzipped files</li>
2515 <li>Export/import group and sequence associated line
2516 graph thresholds</li>
2517 <li>Nucleotide substitution matrix that supports RNA and
2518 ambiguity codes</li>
2519 <li>Allow disorder predictions to be made on the current
2520 selection (or visible selection) in the same way that JPred
2522 <li>Groovy scripting for headless Jalview operation</li>
2523 </ul> <em>Other improvements</em>
2525 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2526 <li>COMBINE statement uses current SEQUENCE_REF and
2527 GROUP_REF scope to group annotation rows</li>
2528 <li>Support '' style escaping of quotes in Newick
2530 <li>Group options for JABAWS service by command line name</li>
2531 <li>Empty tooltip shown for JABA service options with a
2532 link but no description</li>
2533 <li>Select primary source when selecting authority in
2534 database fetcher GUI</li>
2535 <li>Add .mfa to FASTA file extensions recognised by
2537 <li>Annotation label tooltip text wrap</li>
2542 <li>Slow scrolling when lots of annotation rows are
2544 <li>Lots of NPE (and slowness) after creating RNA
2545 secondary structure annotation line</li>
2546 <li>Sequence database accessions not imported when
2547 fetching alignments from Rfam</li>
2548 <li>Incorrect SHMR submission for sequences with
2550 <li>View all structures does not always superpose
2552 <li>Option widgets in service parameters not updated to
2553 reflect user or preset settings</li>
2554 <li>Null pointer exceptions for some services without
2555 presets or adjustable parameters</li>
2556 <li>Discover PDB IDs entry in structure menu doesn't
2557 discover PDB xRefs</li>
2558 <li>Exception encountered while trying to retrieve
2559 features with DAS</li>
2560 <li>Lowest value in annotation row isn't coloured
2561 when colour by annotation (per sequence) is coloured</li>
2562 <li>Keyboard mode P jumps to start of gapped region when
2563 residue follows a gap</li>
2564 <li>Jalview appears to hang importing an alignment with
2565 Wrap as default or after enabling Wrap</li>
2566 <li>'Right click to add annotations' message
2567 shown in wrap mode when no annotations present</li>
2568 <li>Disorder predictions fail with NPE if no automatic
2569 annotation already exists on alignment</li>
2570 <li>oninit javascript function should be called after
2571 initialisation completes</li>
2572 <li>Remove redundancy after disorder prediction corrupts
2573 alignment window display</li>
2574 <li>Example annotation file in documentation is invalid</li>
2575 <li>Grouped line graph annotation rows are not exported
2576 to annotation file</li>
2577 <li>Multi-harmony analysis cannot be run when only two
2579 <li>Cannot create multiple groups of line graphs with
2580 several 'combine' statements in annotation file</li>
2581 <li>Pressing return several times causes Number Format
2582 exceptions in keyboard mode</li>
2583 <li>Multi-harmony (SHMMR) method doesn't submit
2584 correct partitions for input data</li>
2585 <li>Translation from DNA to Amino Acids fails</li>
2586 <li>Jalview fail to load newick tree with quoted label</li>
2587 <li>--headless flag isn't understood</li>
2588 <li>ClassCastException when generating EPS in headless
2590 <li>Adjusting sequence-associated shading threshold only
2591 changes one row's threshold</li>
2592 <li>Preferences and Feature settings panel panel
2593 doesn't open</li>
2594 <li>hide consensus histogram also hides conservation and
2595 quality histograms</li>
2600 <td><div align="center">
2601 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2603 <td><em>Application</em>
2605 <li>Support for JABAWS 2.0 Services (AACon alignment
2606 conservation, protein disorder and Clustal Omega)</li>
2607 <li>JABAWS server status indicator in Web Services
2609 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2610 in Jalview alignment window</li>
2611 <li>Updated Jalview build and deploy framework for OSX
2612 mountain lion, windows 7, and 8</li>
2613 <li>Nucleotide substitution matrix for PCA that supports
2614 RNA and ambiguity codes</li>
2616 <li>Improved sequence database retrieval GUI</li>
2617 <li>Support fetching and database reference look up
2618 against multiple DAS sources (Fetch all from in 'fetch db
2620 <li>Jalview project improvements
2622 <li>Store and retrieve the 'belowAlignment'
2623 flag for annotation</li>
2624 <li>calcId attribute to group annotation rows on the
2626 <li>Store AACon calculation settings for a view in
2627 Jalview project</li>
2631 <li>horizontal scrolling gesture support</li>
2632 <li>Visual progress indicator when PCA calculation is
2634 <li>Simpler JABA web services menus</li>
2635 <li>visual indication that web service results are still
2636 being retrieved from server</li>
2637 <li>Serialise the dialogs that are shown when Jalview
2638 starts up for first time</li>
2639 <li>Jalview user agent string for interacting with HTTP
2641 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2643 <li>Examples directory and Groovy library included in
2644 InstallAnywhere distribution</li>
2645 </ul> <em>Applet</em>
2647 <li>RNA alignment and secondary structure annotation
2648 visualization applet example</li>
2649 </ul> <em>General</em>
2651 <li>Normalise option for consensus sequence logo</li>
2652 <li>Reset button in PCA window to return dimensions to
2654 <li>Allow seqspace or Jalview variant of alignment PCA
2656 <li>PCA with either nucleic acid and protein substitution
2658 <li>Allow windows containing HTML reports to be exported
2660 <li>Interactive display and editing of RNA secondary
2661 structure contacts</li>
2662 <li>RNA Helix Alignment Colouring</li>
2663 <li>RNA base pair logo consensus</li>
2664 <li>Parse sequence associated secondary structure
2665 information in Stockholm files</li>
2666 <li>HTML Export database accessions and annotation
2667 information presented in tooltip for sequences</li>
2668 <li>Import secondary structure from LOCARNA clustalw
2669 style RNA alignment files</li>
2670 <li>import and visualise T-COFFEE quality scores for an
2672 <li>'colour by annotation' per sequence option to
2673 shade each sequence according to its associated alignment
2675 <li>New Jalview Logo</li>
2676 </ul> <em>Documentation and Development</em>
2678 <li>documentation for score matrices used in Jalview</li>
2679 <li>New Website!</li>
2681 <td><em>Application</em>
2683 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2684 wsdbfetch REST service</li>
2685 <li>Stop windows being moved outside desktop on OSX</li>
2686 <li>Filetype associations not installed for webstart
2688 <li>Jalview does not always retrieve progress of a JABAWS
2689 job execution in full once it is complete</li>
2690 <li>revise SHMR RSBS definition to ensure alignment is
2691 uploaded via ali_file parameter</li>
2692 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2693 <li>View all structures superposed fails with exception</li>
2694 <li>Jnet job queues forever if a very short sequence is
2695 submitted for prediction</li>
2696 <li>Cut and paste menu not opened when mouse clicked on
2698 <li>Putting fractional value into integer text box in
2699 alignment parameter dialog causes Jalview to hang</li>
2700 <li>Structure view highlighting doesn't work on
2702 <li>View all structures fails with exception shown in
2704 <li>Characters in filename associated with PDBEntry not
2705 escaped in a platform independent way</li>
2706 <li>Jalview desktop fails to launch with exception when
2708 <li>Tree calculation reports 'you must have 2 or more
2709 sequences selected' when selection is empty</li>
2710 <li>Jalview desktop fails to launch with jar signature
2711 failure when java web start temporary file caching is
2713 <li>DAS Sequence retrieval with range qualification
2714 results in sequence xref which includes range qualification</li>
2715 <li>Errors during processing of command line arguments
2716 cause progress bar (JAL-898) to be removed</li>
2717 <li>Replace comma for semi-colon option not disabled for
2718 DAS sources in sequence fetcher</li>
2719 <li>Cannot close news reader when JABAWS server warning
2720 dialog is shown</li>
2721 <li>Option widgets not updated to reflect user settings</li>
2722 <li>Edited sequence not submitted to web service</li>
2723 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2724 <li>InstallAnywhere installer doesn't unpack and run
2725 on OSX Mountain Lion</li>
2726 <li>Annotation panel not given a scroll bar when
2727 sequences with alignment annotation are pasted into the
2729 <li>Sequence associated annotation rows not associated
2730 when loaded from Jalview project</li>
2731 <li>Browser launch fails with NPE on java 1.7</li>
2732 <li>JABAWS alignment marked as finished when job was
2733 cancelled or job failed due to invalid input</li>
2734 <li>NPE with v2.7 example when clicking on Tree
2735 associated with all views</li>
2736 <li>Exceptions when copy/paste sequences with grouped
2737 annotation rows to new window</li>
2738 </ul> <em>Applet</em>
2740 <li>Sequence features are momentarily displayed before
2741 they are hidden using hidefeaturegroups applet parameter</li>
2742 <li>loading features via javascript API automatically
2743 enables feature display</li>
2744 <li>scrollToColumnIn javascript API method doesn't
2746 </ul> <em>General</em>
2748 <li>Redundancy removal fails for rna alignment</li>
2749 <li>PCA calculation fails when sequence has been selected
2750 and then deselected</li>
2751 <li>PCA window shows grey box when first opened on OSX</li>
2752 <li>Letters coloured pink in sequence logo when alignment
2753 coloured with clustalx</li>
2754 <li>Choosing fonts without letter symbols defined causes
2755 exceptions and redraw errors</li>
2756 <li>Initial PCA plot view is not same as manually
2757 reconfigured view</li>
2758 <li>Grouped annotation graph label has incorrect line
2760 <li>Grouped annotation graph label display is corrupted
2761 for lots of labels</li>
2766 <div align="center">
2767 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2770 <td><em>Application</em>
2772 <li>Jalview Desktop News Reader</li>
2773 <li>Tweaked default layout of web services menu</li>
2774 <li>View/alignment association menu to enable user to
2775 easily specify which alignment a multi-structure view takes
2776 its colours/correspondences from</li>
2777 <li>Allow properties file location to be specified as URL</li>
2778 <li>Extend Jalview project to preserve associations
2779 between many alignment views and a single Jmol display</li>
2780 <li>Store annotation row height in Jalview project file</li>
2781 <li>Annotation row column label formatting attributes
2782 stored in project file</li>
2783 <li>Annotation row order for auto-calculated annotation
2784 rows preserved in Jalview project file</li>
2785 <li>Visual progress indication when Jalview state is
2786 saved using Desktop window menu</li>
2787 <li>Visual indication that command line arguments are
2788 still being processed</li>
2789 <li>Groovy script execution from URL</li>
2790 <li>Colour by annotation default min and max colours in
2792 <li>Automatically associate PDB files dragged onto an
2793 alignment with sequences that have high similarity and
2795 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2796 <li>'view structures' option to open many
2797 structures in same window</li>
2798 <li>Sort associated views menu option for tree panel</li>
2799 <li>Group all JABA and non-JABA services for a particular
2800 analysis function in its own submenu</li>
2801 </ul> <em>Applet</em>
2803 <li>Userdefined and autogenerated annotation rows for
2805 <li>Adjustment of alignment annotation pane height</li>
2806 <li>Annotation scrollbar for annotation panel</li>
2807 <li>Drag to reorder annotation rows in annotation panel</li>
2808 <li>'automaticScrolling' parameter</li>
2809 <li>Allow sequences with partial ID string matches to be
2810 annotated from GFF/Jalview features files</li>
2811 <li>Sequence logo annotation row in applet</li>
2812 <li>Absolute paths relative to host server in applet
2813 parameters are treated as such</li>
2814 <li>New in the JalviewLite javascript API:
2816 <li>JalviewLite.js javascript library</li>
2817 <li>Javascript callbacks for
2819 <li>Applet initialisation</li>
2820 <li>Sequence/alignment mouse-overs and selections</li>
2823 <li>scrollTo row and column alignment scrolling
2825 <li>Select sequence/alignment regions from javascript</li>
2826 <li>javascript structure viewer harness to pass
2827 messages between Jmol and Jalview when running as
2828 distinct applets</li>
2829 <li>sortBy method</li>
2830 <li>Set of applet and application examples shipped
2831 with documentation</li>
2832 <li>New example to demonstrate JalviewLite and Jmol
2833 javascript message exchange</li>
2835 </ul> <em>General</em>
2837 <li>Enable Jmol displays to be associated with multiple
2838 multiple alignments</li>
2839 <li>Option to automatically sort alignment with new tree</li>
2840 <li>User configurable link to enable redirects to a
2841 www.Jalview.org mirror</li>
2842 <li>Jmol colours option for Jmol displays</li>
2843 <li>Configurable newline string when writing alignment
2844 and other flat files</li>
2845 <li>Allow alignment annotation description lines to
2846 contain html tags</li>
2847 </ul> <em>Documentation and Development</em>
2849 <li>Add groovy test harness for bulk load testing to
2851 <li>Groovy script to load and align a set of sequences
2852 using a web service before displaying the result in the
2853 Jalview desktop</li>
2854 <li>Restructured javascript and applet api documentation</li>
2855 <li>Ant target to publish example html files with applet
2857 <li>Netbeans project for building Jalview from source</li>
2858 <li>ant task to create online javadoc for Jalview source</li>
2860 <td><em>Application</em>
2862 <li>User defined colourscheme throws exception when
2863 current built in colourscheme is saved as new scheme</li>
2864 <li>AlignFrame->Save in application pops up save
2865 dialog for valid filename/format</li>
2866 <li>Cannot view associated structure for UniProt sequence</li>
2867 <li>PDB file association breaks for UniProt sequence
2869 <li>Associate PDB from file dialog does not tell you
2870 which sequence is to be associated with the file</li>
2871 <li>Find All raises null pointer exception when query
2872 only matches sequence IDs</li>
2873 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2874 <li>Jalview project with Jmol views created with Jalview
2875 2.4 cannot be loaded</li>
2876 <li>Filetype associations not installed for webstart
2878 <li>Two or more chains in a single PDB file associated
2879 with sequences in different alignments do not get coloured
2880 by their associated sequence</li>
2881 <li>Visibility status of autocalculated annotation row
2882 not preserved when project is loaded</li>
2883 <li>Annotation row height and visibility attributes not
2884 stored in Jalview project</li>
2885 <li>Tree bootstraps are not preserved when saved as a
2886 Jalview project</li>
2887 <li>Envision2 workflow tooltips are corrupted</li>
2888 <li>Enabling show group conservation also enables colour
2889 by conservation</li>
2890 <li>Duplicate group associated conservation or consensus
2891 created on new view</li>
2892 <li>Annotation scrollbar not displayed after 'show
2893 all hidden annotation rows' option selected</li>
2894 <li>Alignment quality not updated after alignment
2895 annotation row is hidden then shown</li>
2896 <li>Preserve colouring of structures coloured by
2897 sequences in pre Jalview 2.7 projects</li>
2898 <li>Web service job parameter dialog is not laid out
2900 <li>Web services menu not refreshed after 'reset
2901 services' button is pressed in preferences</li>
2902 <li>Annotation off by one in Jalview v2_3 example project</li>
2903 <li>Structures imported from file and saved in project
2904 get name like jalview_pdb1234.txt when reloaded</li>
2905 <li>Jalview does not always retrieve progress of a JABAWS
2906 job execution in full once it is complete</li>
2907 </ul> <em>Applet</em>
2909 <li>Alignment height set incorrectly when lots of
2910 annotation rows are displayed</li>
2911 <li>Relative URLs in feature HTML text not resolved to
2913 <li>View follows highlighting does not work for positions
2915 <li><= shown as = in tooltip</li>
2916 <li>Export features raises exception when no features
2918 <li>Separator string used for serialising lists of IDs
2919 for javascript api is modified when separator string
2920 provided as parameter</li>
2921 <li>Null pointer exception when selecting tree leaves for
2922 alignment with no existing selection</li>
2923 <li>Relative URLs for datasources assumed to be relative
2924 to applet's codebase</li>
2925 <li>Status bar not updated after finished searching and
2926 search wraps around to first result</li>
2927 <li>StructureSelectionManager instance shared between
2928 several Jalview applets causes race conditions and memory
2930 <li>Hover tooltip and mouseover of position on structure
2931 not sent from Jmol in applet</li>
2932 <li>Certain sequences of javascript method calls to
2933 applet API fatally hang browser</li>
2934 </ul> <em>General</em>
2936 <li>View follows structure mouseover scrolls beyond
2937 position with wrapped view and hidden regions</li>
2938 <li>Find sequence position moves to wrong residue
2939 with/without hidden columns</li>
2940 <li>Sequence length given in alignment properties window
2942 <li>InvalidNumberFormat exceptions thrown when trying to
2943 import PDB like structure files</li>
2944 <li>Positional search results are only highlighted
2945 between user-supplied sequence start/end bounds</li>
2946 <li>End attribute of sequence is not validated</li>
2947 <li>Find dialog only finds first sequence containing a
2948 given sequence position</li>
2949 <li>Sequence numbering not preserved in MSF alignment
2951 <li>Jalview PDB file reader does not extract sequence
2952 from nucleotide chains correctly</li>
2953 <li>Structure colours not updated when tree partition
2954 changed in alignment</li>
2955 <li>Sequence associated secondary structure not correctly
2956 parsed in interleaved stockholm</li>
2957 <li>Colour by annotation dialog does not restore current
2959 <li>Hiding (nearly) all sequences doesn't work
2961 <li>Sequences containing lowercase letters are not
2962 properly associated with their pdb files</li>
2963 </ul> <em>Documentation and Development</em>
2965 <li>schemas/JalviewWsParamSet.xsd corrupted by
2966 ApplyCopyright tool</li>
2971 <div align="center">
2972 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2975 <td><em>Application</em>
2977 <li>New warning dialog when the Jalview Desktop cannot
2978 contact web services</li>
2979 <li>JABA service parameters for a preset are shown in
2980 service job window</li>
2981 <li>JABA Service menu entries reworded</li>
2985 <li>Modeller PIR IO broken - cannot correctly import a
2986 pir file emitted by Jalview</li>
2987 <li>Existing feature settings transferred to new
2988 alignment view created from cut'n'paste</li>
2989 <li>Improved test for mixed amino/nucleotide chains when
2990 parsing PDB files</li>
2991 <li>Consensus and conservation annotation rows
2992 occasionally become blank for all new windows</li>
2993 <li>Exception raised when right clicking above sequences
2994 in wrapped view mode</li>
2995 </ul> <em>Application</em>
2997 <li>multiple multiply aligned structure views cause cpu
2998 usage to hit 100% and computer to hang</li>
2999 <li>Web Service parameter layout breaks for long user
3000 parameter names</li>
3001 <li>Jaba service discovery hangs desktop if Jaba server
3008 <div align="center">
3009 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3012 <td><em>Application</em>
3014 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3015 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3018 <li>Web Services preference tab</li>
3019 <li>Analysis parameters dialog box and user defined
3021 <li>Improved speed and layout of Envision2 service menu</li>
3022 <li>Superpose structures using associated sequence
3024 <li>Export coordinates and projection as CSV from PCA
3026 </ul> <em>Applet</em>
3028 <li>enable javascript: execution by the applet via the
3029 link out mechanism</li>
3030 </ul> <em>Other</em>
3032 <li>Updated the Jmol Jalview interface to work with Jmol
3034 <li>The Jalview Desktop and JalviewLite applet now
3035 require Java 1.5</li>
3036 <li>Allow Jalview feature colour specification for GFF
3037 sequence annotation files</li>
3038 <li>New 'colour by label' keword in Jalview feature file
3039 type colour specification</li>
3040 <li>New Jalview Desktop Groovy API method that allows a
3041 script to check if it being run in an interactive session or
3042 in a batch operation from the Jalview command line</li>
3046 <li>clustalx colourscheme colours Ds preferentially when
3047 both D+E are present in over 50% of the column</li>
3048 </ul> <em>Application</em>
3050 <li>typo in AlignmentFrame->View->Hide->all but
3051 selected Regions menu item</li>
3052 <li>sequence fetcher replaces ',' for ';' when the ',' is
3053 part of a valid accession ID</li>
3054 <li>fatal OOM if object retrieved by sequence fetcher
3055 runs out of memory</li>
3056 <li>unhandled Out of Memory Error when viewing pca
3057 analysis results</li>
3058 <li>InstallAnywhere builds fail to launch on OS X java
3059 10.5 update 4 (due to apple Java 1.6 update)</li>
3060 <li>Installanywhere Jalview silently fails to launch</li>
3061 </ul> <em>Applet</em>
3063 <li>Jalview.getFeatureGroups() raises an
3064 ArrayIndexOutOfBoundsException if no feature groups are
3071 <div align="center">
3072 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3078 <li>Alignment prettyprinter doesn't cope with long
3080 <li>clustalx colourscheme colours Ds preferentially when
3081 both D+E are present in over 50% of the column</li>
3082 <li>nucleic acid structures retrieved from PDB do not
3083 import correctly</li>
3084 <li>More columns get selected than were clicked on when a
3085 number of columns are hidden</li>
3086 <li>annotation label popup menu not providing correct
3087 add/hide/show options when rows are hidden or none are
3089 <li>Stockholm format shown in list of readable formats,
3090 and parser copes better with alignments from RFAM.</li>
3091 <li>CSV output of consensus only includes the percentage
3092 of all symbols if sequence logo display is enabled</li>
3094 </ul> <em>Applet</em>
3096 <li>annotation panel disappears when annotation is
3098 </ul> <em>Application</em>
3100 <li>Alignment view not redrawn properly when new
3101 alignment opened where annotation panel is visible but no
3102 annotations are present on alignment</li>
3103 <li>pasted region containing hidden columns is
3104 incorrectly displayed in new alignment window</li>
3105 <li>Jalview slow to complete operations when stdout is
3106 flooded (fix is to close the Jalview console)</li>
3107 <li>typo in AlignmentFrame->View->Hide->all but
3108 selected Rregions menu item.</li>
3109 <li>inconsistent group submenu and Format submenu entry
3110 'Un' or 'Non'conserved</li>
3111 <li>Sequence feature settings are being shared by
3112 multiple distinct alignments</li>
3113 <li>group annotation not recreated when tree partition is
3115 <li>double click on group annotation to select sequences
3116 does not propagate to associated trees</li>
3117 <li>Mac OSX specific issues:
3119 <li>exception raised when mouse clicked on desktop
3120 window background</li>
3121 <li>Desktop menu placed on menu bar and application
3122 name set correctly</li>
3123 <li>sequence feature settings not wide enough for the
3124 save feature colourscheme button</li>
3133 <div align="center">
3134 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3137 <td><em>New Capabilities</em>
3139 <li>URL links generated from description line for
3140 regular-expression based URL links (applet and application)
3142 <li>Non-positional feature URL links are shown in link
3144 <li>Linked viewing of nucleic acid sequences and
3146 <li>Automatic Scrolling option in View menu to display
3147 the currently highlighted region of an alignment.</li>
3148 <li>Order an alignment by sequence length, or using the
3149 average score or total feature count for each sequence.</li>
3150 <li>Shading features by score or associated description</li>
3151 <li>Subdivide alignment and groups based on identity of
3152 selected subsequence (Make Groups from Selection).</li>
3153 <li>New hide/show options including Shift+Control+H to
3154 hide everything but the currently selected region.</li>
3155 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3156 </ul> <em>Application</em>
3158 <li>Fetch DB References capabilities and UI expanded to
3159 support retrieval from DAS sequence sources</li>
3160 <li>Local DAS Sequence sources can be added via the
3161 command line or via the Add local source dialog box.</li>
3162 <li>DAS Dbref and DbxRef feature types are parsed as
3163 database references and protein_name is parsed as
3164 description line (BioSapiens terms).</li>
3165 <li>Enable or disable non-positional feature and database
3166 references in sequence ID tooltip from View menu in
3168 <!-- <li>New hidden columns and rows and representatives capabilities
3169 in annotations file (in progress - not yet fully implemented)</li> -->
3170 <li>Group-associated consensus, sequence logos and
3171 conservation plots</li>
3172 <li>Symbol distributions for each column can be exported
3173 and visualized as sequence logos</li>
3174 <li>Optionally scale multi-character column labels to fit
3175 within each column of annotation row<!-- todo for applet -->
3177 <li>Optional automatic sort of associated alignment view
3178 when a new tree is opened.</li>
3179 <li>Jalview Java Console</li>
3180 <li>Better placement of desktop window when moving
3181 between different screens.</li>
3182 <li>New preference items for sequence ID tooltip and
3183 consensus annotation</li>
3184 <li>Client to submit sequences and IDs to Envision2
3186 <li><em>Vamsas Capabilities</em>
3188 <li>Improved VAMSAS synchronization (Jalview archive
3189 used to preserve views, structures, and tree display
3191 <li>Import of vamsas documents from disk or URL via
3193 <li>Sharing of selected regions between views and
3194 with other VAMSAS applications (Experimental feature!)</li>
3195 <li>Updated API to VAMSAS version 0.2</li>
3197 </ul> <em>Applet</em>
3199 <li>Middle button resizes annotation row height</li>
3202 <li>sortByTree (true/false) - automatically sort the
3203 associated alignment view by the tree when a new tree is
3205 <li>showTreeBootstraps (true/false) - show or hide
3206 branch bootstraps (default is to show them if available)</li>
3207 <li>showTreeDistances (true/false) - show or hide
3208 branch lengths (default is to show them if available)</li>
3209 <li>showUnlinkedTreeNodes (true/false) - indicate if
3210 unassociated nodes should be highlighted in the tree
3212 <li>heightScale and widthScale (1.0 or more) -
3213 increase the height or width of a cell in the alignment
3214 grid relative to the current font size.</li>
3217 <li>Non-positional features displayed in sequence ID
3219 </ul> <em>Other</em>
3221 <li>Features format: graduated colour definitions and
3222 specification of feature scores</li>
3223 <li>Alignment Annotations format: new keywords for group
3224 associated annotation (GROUP_REF) and annotation row display
3225 properties (ROW_PROPERTIES)</li>
3226 <li>XML formats extended to support graduated feature
3227 colourschemes, group associated annotation, and profile
3228 visualization settings.</li></td>
3231 <li>Source field in GFF files parsed as feature source
3232 rather than description</li>
3233 <li>Non-positional features are now included in sequence
3234 feature and gff files (controlled via non-positional feature
3235 visibility in tooltip).</li>
3236 <li>URL links generated for all feature links (bugfix)</li>
3237 <li>Added URL embedding instructions to features file
3239 <li>Codons containing ambiguous nucleotides translated as
3240 'X' in peptide product</li>
3241 <li>Match case switch in find dialog box works for both
3242 sequence ID and sequence string and query strings do not
3243 have to be in upper case to match case-insensitively.</li>
3244 <li>AMSA files only contain first column of
3245 multi-character column annotation labels</li>
3246 <li>Jalview Annotation File generation/parsing consistent
3247 with documentation (e.g. Stockholm annotation can be
3248 exported and re-imported)</li>
3249 <li>PDB files without embedded PDB IDs given a friendly
3251 <li>Find incrementally searches ID string matches as well
3252 as subsequence matches, and correctly reports total number
3256 <li>Better handling of exceptions during sequence
3258 <li>Dasobert generated non-positional feature URL
3259 link text excludes the start_end suffix</li>
3260 <li>DAS feature and source retrieval buttons disabled
3261 when fetch or registry operations in progress.</li>
3262 <li>PDB files retrieved from URLs are cached properly</li>
3263 <li>Sequence description lines properly shared via
3265 <li>Sequence fetcher fetches multiple records for all
3267 <li>Ensured that command line das feature retrieval
3268 completes before alignment figures are generated.</li>
3269 <li>Reduced time taken when opening file browser for
3271 <li>isAligned check prior to calculating tree, PCA or
3272 submitting an MSA to JNet now excludes hidden sequences.</li>
3273 <li>User defined group colours properly recovered
3274 from Jalview projects.</li>
3283 <div align="center">
3284 <strong>2.4.0.b2</strong><br> 28/10/2009
3289 <li>Experimental support for google analytics usage
3291 <li>Jalview privacy settings (user preferences and docs).</li>
3296 <li>Race condition in applet preventing startup in
3298 <li>Exception when feature created from selection beyond
3299 length of sequence.</li>
3300 <li>Allow synthetic PDB files to be imported gracefully</li>
3301 <li>Sequence associated annotation rows associate with
3302 all sequences with a given id</li>
3303 <li>Find function matches case-insensitively for sequence
3304 ID string searches</li>
3305 <li>Non-standard characters do not cause pairwise
3306 alignment to fail with exception</li>
3307 </ul> <em>Application Issues</em>
3309 <li>Sequences are now validated against EMBL database</li>
3310 <li>Sequence fetcher fetches multiple records for all
3312 </ul> <em>InstallAnywhere Issues</em>
3314 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3315 issue with installAnywhere mechanism)</li>
3316 <li>Command line launching of JARs from InstallAnywhere
3317 version (java class versioning error fixed)</li>
3324 <div align="center">
3325 <strong>2.4</strong><br> 27/8/2008
3328 <td><em>User Interface</em>
3330 <li>Linked highlighting of codon and amino acid from
3331 translation and protein products</li>
3332 <li>Linked highlighting of structure associated with
3333 residue mapping to codon position</li>
3334 <li>Sequence Fetcher provides example accession numbers
3335 and 'clear' button</li>
3336 <li>MemoryMonitor added as an option under Desktop's
3338 <li>Extract score function to parse whitespace separated
3339 numeric data in description line</li>
3340 <li>Column labels in alignment annotation can be centred.</li>
3341 <li>Tooltip for sequence associated annotation give name
3343 </ul> <em>Web Services and URL fetching</em>
3345 <li>JPred3 web service</li>
3346 <li>Prototype sequence search client (no public services
3348 <li>Fetch either seed alignment or full alignment from
3350 <li>URL Links created for matching database cross
3351 references as well as sequence ID</li>
3352 <li>URL Links can be created using regular-expressions</li>
3353 </ul> <em>Sequence Database Connectivity</em>
3355 <li>Retrieval of cross-referenced sequences from other
3357 <li>Generalised database reference retrieval and
3358 validation to all fetchable databases</li>
3359 <li>Fetch sequences from DAS sources supporting the
3360 sequence command</li>
3361 </ul> <em>Import and Export</em>
3362 <li>export annotation rows as CSV for spreadsheet import</li>
3363 <li>Jalview projects record alignment dataset associations,
3364 EMBL products, and cDNA sequence mappings</li>
3365 <li>Sequence Group colour can be specified in Annotation
3367 <li>Ad-hoc colouring of group in Annotation File using RGB
3368 triplet as name of colourscheme</li>
3369 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3371 <li>treenode binding for VAMSAS tree exchange</li>
3372 <li>local editing and update of sequences in VAMSAS
3373 alignments (experimental)</li>
3374 <li>Create new or select existing session to join</li>
3375 <li>load and save of vamsas documents</li>
3376 </ul> <em>Application command line</em>
3378 <li>-tree parameter to open trees (introduced for passing
3380 <li>-fetchfrom command line argument to specify nicknames
3381 of DAS servers to query for alignment features</li>
3382 <li>-dasserver command line argument to add new servers
3383 that are also automatically queried for features</li>
3384 <li>-groovy command line argument executes a given groovy
3385 script after all input data has been loaded and parsed</li>
3386 </ul> <em>Applet-Application data exchange</em>
3388 <li>Trees passed as applet parameters can be passed to
3389 application (when using "View in full
3390 application")</li>
3391 </ul> <em>Applet Parameters</em>
3393 <li>feature group display control parameter</li>
3394 <li>debug parameter</li>
3395 <li>showbutton parameter</li>
3396 </ul> <em>Applet API methods</em>
3398 <li>newView public method</li>
3399 <li>Window (current view) specific get/set public methods</li>
3400 <li>Feature display control methods</li>
3401 <li>get list of currently selected sequences</li>
3402 </ul> <em>New Jalview distribution features</em>
3404 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3405 <li>RELEASE file gives build properties for the latest
3406 Jalview release.</li>
3407 <li>Java 1.1 Applet build made easier and donotobfuscate
3408 property controls execution of obfuscator</li>
3409 <li>Build target for generating source distribution</li>
3410 <li>Debug flag for javacc</li>
3411 <li>.jalview_properties file is documented (slightly) in
3412 jalview.bin.Cache</li>
3413 <li>Continuous Build Integration for stable and
3414 development version of Application, Applet and source
3419 <li>selected region output includes visible annotations
3420 (for certain formats)</li>
3421 <li>edit label/displaychar contains existing label/char
3423 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3424 <li>shorter peptide product names from EMBL records</li>
3425 <li>Newick string generator makes compact representations</li>
3426 <li>bootstrap values parsed correctly for tree files with
3428 <li>pathological filechooser bug avoided by not allowing
3429 filenames containing a ':'</li>
3430 <li>Fixed exception when parsing GFF files containing
3431 global sequence features</li>
3432 <li>Alignment datasets are finalized only when number of
3433 references from alignment sequences goes to zero</li>
3434 <li>Close of tree branch colour box without colour
3435 selection causes cascading exceptions</li>
3436 <li>occasional negative imgwidth exceptions</li>
3437 <li>better reporting of non-fatal warnings to user when
3438 file parsing fails.</li>
3439 <li>Save works when Jalview project is default format</li>
3440 <li>Save as dialog opened if current alignment format is
3441 not a valid output format</li>
3442 <li>UniProt canonical names introduced for both das and
3444 <li>Histidine should be midblue (not pink!) in Zappo</li>
3445 <li>error messages passed up and output when data read
3447 <li>edit undo recovers previous dataset sequence when
3448 sequence is edited</li>
3449 <li>allow PDB files without pdb ID HEADER lines (like
3450 those generated by MODELLER) to be read in properly</li>
3451 <li>allow reading of JPred concise files as a normal
3453 <li>Stockholm annotation parsing and alignment properties
3454 import fixed for PFAM records</li>
3455 <li>Structure view windows have correct name in Desktop
3457 <li>annotation consisting of sequence associated scores
3458 can be read and written correctly to annotation file</li>
3459 <li>Aligned cDNA translation to aligned peptide works
3461 <li>Fixed display of hidden sequence markers and
3462 non-italic font for representatives in Applet</li>
3463 <li>Applet Menus are always embedded in applet window on
3465 <li>Newly shown features appear at top of stack (in
3467 <li>Annotations added via parameter not drawn properly
3468 due to null pointer exceptions</li>
3469 <li>Secondary structure lines are drawn starting from
3470 first column of alignment</li>
3471 <li>UniProt XML import updated for new schema release in
3473 <li>Sequence feature to sequence ID match for Features
3474 file is case-insensitive</li>
3475 <li>Sequence features read from Features file appended to
3476 all sequences with matching IDs</li>
3477 <li>PDB structure coloured correctly for associated views
3478 containing a sub-sequence</li>
3479 <li>PDB files can be retrieved by applet from Jar files</li>
3480 <li>feature and annotation file applet parameters
3481 referring to different directories are retrieved correctly</li>
3482 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3483 <li>Fixed application hang whilst waiting for
3484 splash-screen version check to complete</li>
3485 <li>Applet properly URLencodes input parameter values
3486 when passing them to the launchApp service</li>
3487 <li>display name and local features preserved in results
3488 retrieved from web service</li>
3489 <li>Visual delay indication for sequence retrieval and
3490 sequence fetcher initialisation</li>
3491 <li>updated Application to use DAS 1.53e version of
3492 dasobert DAS client</li>
3493 <li>Re-instated Full AMSA support and .amsa file
3495 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3503 <div align="center">
3504 <strong>2.3</strong><br> 9/5/07
3509 <li>Jmol 11.0.2 integration</li>
3510 <li>PDB views stored in Jalview XML files</li>
3511 <li>Slide sequences</li>
3512 <li>Edit sequence in place</li>
3513 <li>EMBL CDS features</li>
3514 <li>DAS Feature mapping</li>
3515 <li>Feature ordering</li>
3516 <li>Alignment Properties</li>
3517 <li>Annotation Scores</li>
3518 <li>Sort by scores</li>
3519 <li>Feature/annotation editing in applet</li>
3524 <li>Headless state operation in 2.2.1</li>
3525 <li>Incorrect and unstable DNA pairwise alignment</li>
3526 <li>Cut and paste of sequences with annotation</li>
3527 <li>Feature group display state in XML</li>
3528 <li>Feature ordering in XML</li>
3529 <li>blc file iteration selection using filename # suffix</li>
3530 <li>Stockholm alignment properties</li>
3531 <li>Stockhom alignment secondary structure annotation</li>
3532 <li>2.2.1 applet had no feature transparency</li>
3533 <li>Number pad keys can be used in cursor mode</li>
3534 <li>Structure Viewer mirror image resolved</li>
3541 <div align="center">
3542 <strong>2.2.1</strong><br> 12/2/07
3547 <li>Non standard characters can be read and displayed
3548 <li>Annotations/Features can be imported/exported to the
3550 <li>Applet allows editing of sequence/annotation/group
3551 name & description
3552 <li>Preference setting to display sequence name in
3554 <li>Annotation file format extended to allow
3555 Sequence_groups to be defined
3556 <li>Default opening of alignment overview panel can be
3557 specified in preferences
3558 <li>PDB residue numbering annotation added to associated
3564 <li>Applet crash under certain Linux OS with Java 1.6
3566 <li>Annotation file export / import bugs fixed
3567 <li>PNG / EPS image output bugs fixed
3573 <div align="center">
3574 <strong>2.2</strong><br> 27/11/06
3579 <li>Multiple views on alignment
3580 <li>Sequence feature editing
3581 <li>"Reload" alignment
3582 <li>"Save" to current filename
3583 <li>Background dependent text colour
3584 <li>Right align sequence ids
3585 <li>User-defined lower case residue colours
3588 <li>Menu item accelerator keys
3589 <li>Control-V pastes to current alignment
3590 <li>Cancel button for DAS Feature Fetching
3591 <li>PCA and PDB Viewers zoom via mouse roller
3592 <li>User-defined sub-tree colours and sub-tree selection
3594 <li>'New Window' button on the 'Output to Text box'
3599 <li>New memory efficient Undo/Redo System
3600 <li>Optimised symbol lookups and conservation/consensus
3602 <li>Region Conservation/Consensus recalculated after
3604 <li>Fixed Remove Empty Columns Bug (empty columns at end
3606 <li>Slowed DAS Feature Fetching for increased robustness.
3608 <li>Made angle brackets in ASCII feature descriptions
3610 <li>Re-instated Zoom function for PCA
3611 <li>Sequence descriptions conserved in web service
3613 <li>UniProt ID discoverer uses any word separated by
3615 <li>WsDbFetch query/result association resolved
3616 <li>Tree leaf to sequence mapping improved
3617 <li>Smooth fonts switch moved to FontChooser dialog box.
3624 <div align="center">
3625 <strong>2.1.1</strong><br> 12/9/06
3630 <li>Copy consensus sequence to clipboard</li>
3635 <li>Image output - rightmost residues are rendered if
3636 sequence id panel has been resized</li>
3637 <li>Image output - all offscreen group boundaries are
3639 <li>Annotation files with sequence references - all
3640 elements in file are relative to sequence position</li>
3641 <li>Mac Applet users can use Alt key for group editing</li>
3647 <div align="center">
3648 <strong>2.1</strong><br> 22/8/06
3653 <li>MAFFT Multiple Alignment in default Web Service list</li>
3654 <li>DAS Feature fetching</li>
3655 <li>Hide sequences and columns</li>
3656 <li>Export Annotations and Features</li>
3657 <li>GFF file reading / writing</li>
3658 <li>Associate structures with sequences from local PDB
3660 <li>Add sequences to exisiting alignment</li>
3661 <li>Recently opened files / URL lists</li>
3662 <li>Applet can launch the full application</li>
3663 <li>Applet has transparency for features (Java 1.2
3665 <li>Applet has user defined colours parameter</li>
3666 <li>Applet can load sequences from parameter
3667 "sequence<em>x</em>"
3673 <li>Redundancy Panel reinstalled in the Applet</li>
3674 <li>Monospaced font - EPS / rescaling bug fixed</li>
3675 <li>Annotation files with sequence references bug fixed</li>
3681 <div align="center">
3682 <strong>2.08.1</strong><br> 2/5/06
3687 <li>Change case of selected region from Popup menu</li>
3688 <li>Choose to match case when searching</li>
3689 <li>Middle mouse button and mouse movement can compress /
3690 expand the visible width and height of the alignment</li>
3695 <li>Annotation Panel displays complete JNet results</li>
3701 <div align="center">
3702 <strong>2.08b</strong><br> 18/4/06
3708 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3709 <li>Righthand label on wrapped alignments shows correct
3716 <div align="center">
3717 <strong>2.08</strong><br> 10/4/06
3722 <li>Editing can be locked to the selection area</li>
3723 <li>Keyboard editing</li>
3724 <li>Create sequence features from searches</li>
3725 <li>Precalculated annotations can be loaded onto
3727 <li>Features file allows grouping of features</li>
3728 <li>Annotation Colouring scheme added</li>
3729 <li>Smooth fonts off by default - Faster rendering</li>
3730 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3735 <li>Drag & Drop fixed on Linux</li>
3736 <li>Jalview Archive file faster to load/save, sequence
3737 descriptions saved.</li>
3743 <div align="center">
3744 <strong>2.07</strong><br> 12/12/05
3749 <li>PDB Structure Viewer enhanced</li>
3750 <li>Sequence Feature retrieval and display enhanced</li>
3751 <li>Choose to output sequence start-end after sequence
3752 name for file output</li>
3753 <li>Sequence Fetcher WSDBFetch@EBI</li>
3754 <li>Applet can read feature files, PDB files and can be
3755 used for HTML form input</li>
3760 <li>HTML output writes groups and features</li>
3761 <li>Group editing is Control and mouse click</li>
3762 <li>File IO bugs</li>
3768 <div align="center">
3769 <strong>2.06</strong><br> 28/9/05
3774 <li>View annotations in wrapped mode</li>
3775 <li>More options for PCA viewer</li>
3780 <li>GUI bugs resolved</li>
3781 <li>Runs with -nodisplay from command line</li>
3787 <div align="center">
3788 <strong>2.05b</strong><br> 15/9/05
3793 <li>Choose EPS export as lineart or text</li>
3794 <li>Jar files are executable</li>
3795 <li>Can read in Uracil - maps to unknown residue</li>
3800 <li>Known OutOfMemory errors give warning message</li>
3801 <li>Overview window calculated more efficiently</li>
3802 <li>Several GUI bugs resolved</li>
3808 <div align="center">
3809 <strong>2.05</strong><br> 30/8/05
3814 <li>Edit and annotate in "Wrapped" view</li>
3819 <li>Several GUI bugs resolved</li>
3825 <div align="center">
3826 <strong>2.04</strong><br> 24/8/05
3831 <li>Hold down mouse wheel & scroll to change font
3837 <li>Improved JPred client reliability</li>
3838 <li>Improved loading of Jalview files</li>
3844 <div align="center">
3845 <strong>2.03</strong><br> 18/8/05
3850 <li>Set Proxy server name and port in preferences</li>
3851 <li>Multiple URL links from sequence ids</li>
3852 <li>User Defined Colours can have a scheme name and added
3854 <li>Choose to ignore gaps in consensus calculation</li>
3855 <li>Unix users can set default web browser</li>
3856 <li>Runs without GUI for batch processing</li>
3857 <li>Dynamically generated Web Service Menus</li>
3862 <li>InstallAnywhere download for Sparc Solaris</li>
3868 <div align="center">
3869 <strong>2.02</strong><br> 18/7/05
3875 <li>Copy & Paste order of sequences maintains
3876 alignment order.</li>
3882 <div align="center">
3883 <strong>2.01</strong><br> 12/7/05
3888 <li>Use delete key for deleting selection.</li>
3889 <li>Use Mouse wheel to scroll sequences.</li>
3890 <li>Help file updated to describe how to add alignment
3892 <li>Version and build date written to build properties
3894 <li>InstallAnywhere installation will check for updates
3895 at launch of Jalview.</li>
3900 <li>Delete gaps bug fixed.</li>
3901 <li>FileChooser sorts columns.</li>
3902 <li>Can remove groups one by one.</li>
3903 <li>Filechooser icons installed.</li>
3904 <li>Finder ignores return character when searching.
3905 Return key will initiate a search.<br>
3912 <div align="center">
3913 <strong>2.0</strong><br> 20/6/05
3918 <li>New codebase</li>