3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
74 <em>27/05/2018</em></strong>
77 <td><div align="left">
81 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
82 onto the Jalview Desktop
86 <td><div align="left">
90 <!-- JAL-2997 -->Clustal files with sequence positions in
91 right-hand column parsed correctly
94 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
95 window has input focus
98 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
99 not alignment area in exported graphic
102 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
103 Jalview desktop on Windows doesn't open file<br />
104 <em>Dragging the currently open URL and links from a page viewed in Firefox or Chrome on
105 Windows is now fully supported. If you are using Edge, only
106 links in the page can be dragged, and with Internet Explorer, only
107 the currently open URL in the browser can be dropped onto
117 <td width="60" nowrap>
119 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
122 <td><div align="left">
126 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
127 for disabling automatic superposition of multiple
128 structures and open structures in existing views
131 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
132 ID and annotation area margins can be click-dragged to
136 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
140 <!-- JAL-2759 -->Improved performance for large alignments
141 and lots of hidden columns
144 <!-- JAL-2593 -->Improved performance when rendering lots
145 of features (particularly when transparency is disabled)
150 <td><div align="left">
153 <!-- JAL-2899 -->Structure and Overview aren't updated
154 when Colour By Annotation threshold slider is adjusted
157 <!-- JAL-2778 -->Slow redraw when Overview panel shown
158 overlapping alignment panel
161 <!-- JAL-2929 -->Overview doesn't show end of unpadded
165 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
166 improved: CDS not handled correctly if transcript has no
170 <!-- JAL-2321 -->Secondary structure and temperature
171 factor annotation not added to sequence when local PDB
172 file associated with it by drag'n'drop or structure
176 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
177 dialog doesn't import PDB files dropped on an alignment
180 <!-- JAL-2666 -->Linked scrolling via protein horizontal
181 scroll bar doesn't work for some CDS/Protein views
184 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
185 Java 1.8u153 onwards and Java 1.9u4+.
188 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
189 columns in annotation row
192 <!-- JAL-2913 -->Preferences panel's ID Width control is not
193 honored in batch mode
196 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
197 for structures added to existing Jmol view
200 <!-- JAL-2223 -->'View Mappings' includes duplicate
201 entries after importing project with multiple views
204 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
205 protein sequences via SIFTS from associated PDB entries
206 with negative residue numbers or missing residues fails
209 <!-- JAL-2952 -->Exception when shading sequence with negative
210 Temperature Factor values from annotated PDB files (e.g.
211 as generated by CONSURF)
214 <!-- JAL-2920 -->Uniprot 'sequence variant' features
215 tooltip doesn't include a text description of mutation
218 <!-- JAL-2922 -->Invert displayed features very slow when
219 structure and/or overview windows are also shown
222 <!-- JAL-2954 -->Selecting columns from highlighted regions
223 very slow for alignments with large numbers of sequences
226 <!-- JAL-2925 -->Copy Consensus fails for group consensus
227 with 'StringIndexOutOfBounds'
230 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
231 platforms running Java 10
234 <!-- JAL-2960 -->Adding a structure to existing structure
235 view appears to do nothing because the view is hidden behind the alignment view
241 <!-- JAL-2926 -->Copy consensus sequence option in applet
242 should copy the group consensus when popup is opened on it
248 <!-- JAL-2913 -->Fixed ID width preference is not respected
251 <em>New Known Defects</em>
254 <!-- JAL-2973 --> Exceptions occasionally raised when
255 editing a large alignment and overview is displayed
258 <!-- JAL-2974 -->'Overview updating' progress bar is shown
259 repeatedly after a series of edits even when the overview
260 is no longer reflecting updates
263 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
264 structures for protein subsequence (if 'Trim Retrieved
265 Sequences' enabled) or Ensembl isoforms (Workaround in
266 2.10.4 is to fail back to N&W mapping)
273 <td width="60" nowrap>
275 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
278 <td><div align="left">
279 <ul><li>Updated Certum Codesigning Certificate
280 (Valid till 30th November 2018)</li></ul></div></td>
281 <td><div align="left">
284 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
285 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
286 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
287 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
288 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
289 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
290 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
296 <td width="60" nowrap>
298 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
301 <td><div align="left">
305 <!-- JAL-2446 -->Faster and more efficient management and
306 rendering of sequence features
309 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
310 429 rate limit request hander
313 <!-- JAL-2773 -->Structure views don't get updated unless
314 their colours have changed
317 <!-- JAL-2495 -->All linked sequences are highlighted for
318 a structure mousover (Jmol) or selection (Chimera)
321 <!-- JAL-2790 -->'Cancel' button in progress bar for
322 JABAWS AACon, RNAAliFold and Disorder prediction jobs
325 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
326 view from Ensembl locus cross-references
329 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
333 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
334 feature can be disabled
337 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
338 PDB easier retrieval of sequences for lists of IDs
341 <!-- JAL-2758 -->Short names for sequences retrieved from
347 <li>Groovy interpreter updated to 2.4.12</li>
348 <li>Example groovy script for generating a matrix of
349 percent identity scores for current alignment.</li>
351 <em>Testing and Deployment</em>
354 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
358 <td><div align="left">
362 <!-- JAL-2643 -->Pressing tab after updating the colour
363 threshold text field doesn't trigger an update to the
367 <!-- JAL-2682 -->Race condition when parsing sequence ID
371 <!-- JAL-2608 -->Overview windows are also closed when
372 alignment window is closed
375 <!-- JAL-2548 -->Export of features doesn't always respect
379 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
380 takes a long time in Cursor mode
386 <!-- JAL-2777 -->Structures with whitespace chainCode
387 cannot be viewed in Chimera
390 <!-- JAL-2728 -->Protein annotation panel too high in
394 <!-- JAL-2757 -->Can't edit the query after the server
395 error warning icon is shown in Uniprot and PDB Free Text
399 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
402 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
405 <!-- JAL-2739 -->Hidden column marker in last column not
406 rendered when switching back from Wrapped to normal view
409 <!-- JAL-2768 -->Annotation display corrupted when
410 scrolling right in unwapped alignment view
413 <!-- JAL-2542 -->Existing features on subsequence
414 incorrectly relocated when full sequence retrieved from
418 <!-- JAL-2733 -->Last reported memory still shown when
419 Desktop->Show Memory is unticked (OSX only)
422 <!-- JAL-2658 -->Amend Features dialog doesn't allow
423 features of same type and group to be selected for
427 <!-- JAL-2524 -->Jalview becomes sluggish in wide
428 alignments when hidden columns are present
431 <!-- JAL-2392 -->Jalview freezes when loading and
432 displaying several structures
435 <!-- JAL-2732 -->Black outlines left after resizing or
439 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
440 within the Jalview desktop on OSX
443 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
444 when in wrapped alignment mode
447 <!-- JAL-2636 -->Scale mark not shown when close to right
448 hand end of alignment
451 <!-- JAL-2684 -->Pairwise alignment of selected regions of
452 each selected sequence do not have correct start/end
456 <!-- JAL-2793 -->Alignment ruler height set incorrectly
457 after canceling the Alignment Window's Font dialog
460 <!-- JAL-2036 -->Show cross-references not enabled after
461 restoring project until a new view is created
464 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
465 URL links appears when only default EMBL-EBI link is
466 configured (since 2.10.2b2)
469 <!-- JAL-2775 -->Overview redraws whole window when box
473 <!-- JAL-2225 -->Structure viewer doesn't map all chains
474 in a multi-chain structure when viewing alignment
475 involving more than one chain (since 2.10)
478 <!-- JAL-2811 -->Double residue highlights in cursor mode
479 if new selection moves alignment window
482 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
483 arrow key in cursor mode to pass hidden column marker
486 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
487 that produces correctly annotated transcripts and products
490 <!-- JAL-2776 -->Toggling a feature group after first time
491 doesn't update associated structure view
494 <em>Applet</em><br />
497 <!-- JAL-2687 -->Concurrent modification exception when
498 closing alignment panel
501 <em>BioJSON</em><br />
504 <!-- JAL-2546 -->BioJSON export does not preserve
505 non-positional features
508 <em>New Known Issues</em>
511 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
512 sequence features correctly (for many previous versions of
516 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
517 using cursor in wrapped panel other than top
520 <!-- JAL-2791 -->Select columns containing feature ignores
521 graduated colour threshold
524 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
525 always preserve numbering and sequence features
528 <em>Known Java 9 Issues</em>
531 <!-- JAL-2902 -->Groovy Console very slow to open and is
532 not responsive when entering characters (Webstart, Java
539 <td width="60" nowrap>
541 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
542 <em>2/10/2017</em></strong>
545 <td><div align="left">
546 <em>New features in Jalview Desktop</em>
549 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
551 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
555 <td><div align="left">
559 <td width="60" nowrap>
561 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
562 <em>7/9/2017</em></strong>
565 <td><div align="left">
569 <!-- JAL-2588 -->Show gaps in overview window by colouring
570 in grey (sequences used to be coloured grey, and gaps were
574 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
578 <!-- JAL-2587 -->Overview updates immediately on increase
579 in size and progress bar shown as higher resolution
580 overview is recalculated
585 <td><div align="left">
589 <!-- JAL-2664 -->Overview window redraws every hidden
590 column region row by row
593 <!-- JAL-2681 -->duplicate protein sequences shown after
594 retrieving Ensembl crossrefs for sequences from Uniprot
597 <!-- JAL-2603 -->Overview window throws NPE if show boxes
598 format setting is unticked
601 <!-- JAL-2610 -->Groups are coloured wrongly in overview
602 if group has show boxes format setting unticked
605 <!-- JAL-2672,JAL-2665 -->Redraw problems when
606 autoscrolling whilst dragging current selection group to
607 include sequences and columns not currently displayed
610 <!-- JAL-2691 -->Not all chains are mapped when multimeric
611 assemblies are imported via CIF file
614 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
615 displayed when threshold or conservation colouring is also
619 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
623 <!-- JAL-2673 -->Jalview continues to scroll after
624 dragging a selected region off the visible region of the
628 <!-- JAL-2724 -->Cannot apply annotation based
629 colourscheme to all groups in a view
632 <!-- JAL-2511 -->IDs don't line up with sequences
633 initially after font size change using the Font chooser or
640 <td width="60" nowrap>
642 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
645 <td><div align="left">
646 <em>Calculations</em>
650 <!-- JAL-1933 -->Occupancy annotation row shows number of
651 ungapped positions in each column of the alignment.
654 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
655 a calculation dialog box
658 <!-- JAL-2379 -->Revised implementation of PCA for speed
659 and memory efficiency (~30x faster)
662 <!-- JAL-2403 -->Revised implementation of sequence
663 similarity scores as used by Tree, PCA, Shading Consensus
664 and other calculations
667 <!-- JAL-2416 -->Score matrices are stored as resource
668 files within the Jalview codebase
671 <!-- JAL-2500 -->Trees computed on Sequence Feature
672 Similarity may have different topology due to increased
679 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
680 model for alignments and groups
683 <!-- JAL-384 -->Custom shading schemes created via groovy
690 <!-- JAL-2526 -->Efficiency improvements for interacting
691 with alignment and overview windows
694 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
698 <!-- JAL-2388 -->Hidden columns and sequences can be
702 <!-- JAL-2611 -->Click-drag in visible area allows fine
703 adjustment of visible position
707 <em>Data import/export</em>
710 <!-- JAL-2535 -->Posterior probability annotation from
711 Stockholm files imported as sequence associated annotation
714 <!-- JAL-2507 -->More robust per-sequence positional
715 annotation input/output via stockholm flatfile
718 <!-- JAL-2533 -->Sequence names don't include file
719 extension when importing structure files without embedded
720 names or PDB accessions
723 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
724 format sequence substitution matrices
727 <em>User Interface</em>
730 <!-- JAL-2447 --> Experimental Features Checkbox in
731 Desktop's Tools menu to hide or show untested features in
735 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
736 via Overview or sequence motif search operations
739 <!-- JAL-2547 -->Amend sequence features dialog box can be
740 opened by double clicking gaps within sequence feature
744 <!-- JAL-1476 -->Status bar message shown when not enough
745 aligned positions were available to create a 3D structure
749 <em>3D Structure</em>
752 <!-- JAL-2430 -->Hidden regions in alignment views are not
753 coloured in linked structure views
756 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
757 file-based command exchange
760 <!-- JAL-2375 -->Structure chooser automatically shows
761 Cached Structures rather than querying the PDBe if
762 structures are already available for sequences
765 <!-- JAL-2520 -->Structures imported via URL are cached in
766 the Jalview project rather than downloaded again when the
770 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
771 to transfer Chimera's structure attributes as Jalview
772 features, and vice-versa (<strong>Experimental
776 <em>Web Services</em>
779 <!-- JAL-2549 -->Updated JABAWS client to v2.2
782 <!-- JAL-2335 -->Filter non-standard amino acids and
783 nucleotides when submitting to AACon and other MSA
787 <!-- JAL-2316, -->URLs for viewing database
788 cross-references provided by identifiers.org and the
796 <!-- JAL-2344 -->FileFormatI interface for describing and
797 identifying file formats (instead of String constants)
800 <!-- JAL-2228 -->FeatureCounter script refactored for
801 efficiency when counting all displayed features (not
802 backwards compatible with 2.10.1)
805 <em>Example files</em>
808 <!-- JAL-2631 -->Graduated feature colour style example
809 included in the example feature file
812 <em>Documentation</em>
815 <!-- JAL-2339 -->Release notes reformatted for readability
816 with the built-in Java help viewer
819 <!-- JAL-1644 -->Find documentation updated with 'search
820 sequence description' option
826 <!-- JAL-2485, -->External service integration tests for
827 Uniprot REST Free Text Search Client
830 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
833 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
838 <td><div align="left">
839 <em>Calculations</em>
842 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
843 matrix - C->R should be '-3'<br />Old matrix restored
844 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
846 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
847 Jalview's treatment of gaps in PCA and substitution matrix
848 based Tree calculations.<br /> <br />In earlier versions
849 of Jalview, gaps matching gaps were penalised, and gaps
850 matching non-gaps penalised even more. In the PCA
851 calculation, gaps were actually treated as non-gaps - so
852 different costs were applied, which meant Jalview's PCAs
853 were different to those produced by SeqSpace.<br />Jalview
854 now treats gaps in the same way as SeqSpace (ie it scores
855 them as 0). <br /> <br />Enter the following in the
856 Groovy console to restore pre-2.10.2 behaviour:<br />
857 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
858 // for 2.10.1 mode <br />
859 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
860 // to restore 2.10.2 mode <br /> <br /> <em>Note:
861 these settings will affect all subsequent tree and PCA
862 calculations (not recommended)</em></li>
864 <!-- JAL-2424 -->Fixed off-by-one bug that affected
865 scaling of branch lengths for trees computed using
866 Sequence Feature Similarity.
869 <!-- JAL-2377 -->PCA calculation could hang when
870 generating output report when working with highly
874 <!-- JAL-2544 --> Sort by features includes features to
875 right of selected region when gaps present on right-hand
879 <em>User Interface</em>
882 <!-- JAL-2346 -->Reopening Colour by annotation dialog
883 doesn't reselect a specific sequence's associated
884 annotation after it was used for colouring a view
887 <!-- JAL-2419 -->Current selection lost if popup menu
888 opened on a region of alignment without groups
891 <!-- JAL-2374 -->Popup menu not always shown for regions
892 of an alignment with overlapping groups
895 <!-- JAL-2310 -->Finder double counts if both a sequence's
896 name and description match
899 <!-- JAL-2370 -->Hiding column selection containing two
900 hidden regions results in incorrect hidden regions
903 <!-- JAL-2386 -->'Apply to all groups' setting when
904 changing colour does not apply Conservation slider value
908 <!-- JAL-2373 -->Percentage identity and conservation menu
909 items do not show a tick or allow shading to be disabled
912 <!-- JAL-2385 -->Conservation shading or PID threshold
913 lost when base colourscheme changed if slider not visible
916 <!-- JAL-2547 -->Sequence features shown in tooltip for
917 gaps before start of features
920 <!-- JAL-2623 -->Graduated feature colour threshold not
921 restored to UI when feature colour is edited
924 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
925 a time when scrolling vertically in wrapped mode.
928 <!-- JAL-2630 -->Structure and alignment overview update
929 as graduate feature colour settings are modified via the
933 <!-- JAL-2034 -->Overview window doesn't always update
934 when a group defined on the alignment is resized
937 <!-- JAL-2605 -->Mouseovers on left/right scale region in
938 wrapped view result in positional status updates
942 <!-- JAL-2563 -->Status bar doesn't show position for
943 ambiguous amino acid and nucleotide symbols
946 <!-- JAL-2602 -->Copy consensus sequence failed if
947 alignment included gapped columns
950 <!-- JAL-2473 -->Minimum size set for Jalview windows so
951 widgets don't permanently disappear
954 <!-- JAL-2503 -->Cannot select or filter quantitative
955 annotation that are shown only as column labels (e.g.
956 T-Coffee column reliability scores)
959 <!-- JAL-2594 -->Exception thrown if trying to create a
960 sequence feature on gaps only
963 <!-- JAL-2504 -->Features created with 'New feature'
964 button from a Find inherit previously defined feature type
965 rather than the Find query string
968 <!-- JAL-2423 -->incorrect title in output window when
969 exporting tree calculated in Jalview
972 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
973 and then revealing them reorders sequences on the
977 <!-- JAL-964 -->Group panel in sequence feature settings
978 doesn't update to reflect available set of groups after
979 interactively adding or modifying features
982 <!-- JAL-2225 -->Sequence Database chooser unusable on
986 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
987 only excluded gaps in current sequence and ignored
994 <!-- JAL-2421 -->Overview window visible region moves
995 erratically when hidden rows or columns are present
998 <!-- JAL-2362 -->Per-residue colourschemes applied via the
999 Structure Viewer's colour menu don't correspond to
1003 <!-- JAL-2405 -->Protein specific colours only offered in
1004 colour and group colour menu for protein alignments
1007 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1008 reflect currently selected view or group's shading
1012 <!-- JAL-2624 -->Feature colour thresholds not respected
1013 when rendered on overview and structures when opacity at
1017 <!-- JAL-2589 -->User defined gap colour not shown in
1018 overview when features overlaid on alignment
1021 <em>Data import/export</em>
1024 <!-- JAL-2576 -->Very large alignments take a long time to
1028 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1029 added after a sequence was imported are not written to
1033 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1034 when importing RNA secondary structure via Stockholm
1037 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1038 not shown in correct direction for simple pseudoknots
1041 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1042 with lightGray or darkGray via features file (but can
1046 <!-- JAL-2383 -->Above PID colour threshold not recovered
1047 when alignment view imported from project
1050 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1051 structure and sequences extracted from structure files
1052 imported via URL and viewed in Jmol
1055 <!-- JAL-2520 -->Structures loaded via URL are saved in
1056 Jalview Projects rather than fetched via URL again when
1057 the project is loaded and the structure viewed
1060 <em>Web Services</em>
1063 <!-- JAL-2519 -->EnsemblGenomes example failing after
1064 release of Ensembl v.88
1067 <!-- JAL-2366 -->Proxy server address and port always
1068 appear enabled in Preferences->Connections
1071 <!-- JAL-2461 -->DAS registry not found exceptions
1072 removed from console output
1075 <!-- JAL-2582 -->Cannot retrieve protein products from
1076 Ensembl by Peptide ID
1079 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1080 created from SIFTs, and spurious 'Couldn't open structure
1081 in Chimera' errors raised after April 2017 update (problem
1082 due to 'null' string rather than empty string used for
1083 residues with no corresponding PDB mapping).
1086 <em>Application UI</em>
1089 <!-- JAL-2361 -->User Defined Colours not added to Colour
1093 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1094 case' residues (button in colourscheme editor debugged and
1095 new documentation and tooltips added)
1098 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1099 doesn't restore group-specific text colour thresholds
1102 <!-- JAL-2243 -->Feature settings panel does not update as
1103 new features are added to alignment
1106 <!-- JAL-2532 -->Cancel in feature settings reverts
1107 changes to feature colours via the Amend features dialog
1110 <!-- JAL-2506 -->Null pointer exception when attempting to
1111 edit graduated feature colour via amend features dialog
1115 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1116 selection menu changes colours of alignment views
1119 <!-- JAL-2426 -->Spurious exceptions in console raised
1120 from alignment calculation workers after alignment has
1124 <!-- JAL-1608 -->Typo in selection popup menu - Create
1125 groups now 'Create Group'
1128 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1129 Create/Undefine group doesn't always work
1132 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1133 shown again after pressing 'Cancel'
1136 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1137 adjusts start position in wrap mode
1140 <!-- JAL-2563 -->Status bar doesn't show positions for
1141 ambiguous amino acids
1144 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1145 CDS/Protein view after CDS sequences added for aligned
1149 <!-- JAL-2592 -->User defined colourschemes called 'User
1150 Defined' don't appear in Colours menu
1156 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1157 score models doesn't always result in an updated PCA plot
1160 <!-- JAL-2442 -->Features not rendered as transparent on
1161 overview or linked structure view
1164 <!-- JAL-2372 -->Colour group by conservation doesn't
1168 <!-- JAL-2517 -->Hitting Cancel after applying
1169 user-defined colourscheme doesn't restore original
1176 <!-- JAL-2314 -->Unit test failure:
1177 jalview.ws.jabaws.RNAStructExportImport setup fails
1180 <!-- JAL-2307 -->Unit test failure:
1181 jalview.ws.sifts.SiftsClientTest due to compatibility
1182 problems with deep array comparison equality asserts in
1183 successive versions of TestNG
1186 <!-- JAL-2479 -->Relocated StructureChooserTest and
1187 ParameterUtilsTest Unit tests to Network suite
1190 <em>New Known Issues</em>
1193 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1194 phase after a sequence motif find operation
1197 <!-- JAL-2550 -->Importing annotation file with rows
1198 containing just upper and lower case letters are
1199 interpreted as WUSS RNA secondary structure symbols
1202 <!-- JAL-2590 -->Cannot load and display Newick trees
1203 reliably from eggnog Ortholog database
1206 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1207 containing features of type Highlight' when 'B' is pressed
1208 to mark columns containing highlighted regions.
1211 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1212 doesn't always add secondary structure annotation.
1217 <td width="60" nowrap>
1218 <div align="center">
1219 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1222 <td><div align="left">
1226 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1227 for all consensus calculations
1230 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1233 <li>Updated Jalview's Certum code signing certificate
1236 <em>Application</em>
1239 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1240 set of database cross-references, sorted alphabetically
1243 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1244 from database cross references. Users with custom links
1245 will receive a <a href="webServices/urllinks.html#warning">warning
1246 dialog</a> asking them to update their preferences.
1249 <!-- JAL-2287-->Cancel button and escape listener on
1250 dialog warning user about disconnecting Jalview from a
1254 <!-- JAL-2320-->Jalview's Chimera control window closes if
1255 the Chimera it is connected to is shut down
1258 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1259 columns menu item to mark columns containing highlighted
1260 regions (e.g. from structure selections or results of a
1264 <!-- JAL-2284-->Command line option for batch-generation
1265 of HTML pages rendering alignment data with the BioJS
1275 <!-- JAL-2286 -->Columns with more than one modal residue
1276 are not coloured or thresholded according to percent
1277 identity (first observed in Jalview 2.8.2)
1280 <!-- JAL-2301 -->Threonine incorrectly reported as not
1284 <!-- JAL-2318 -->Updates to documentation pages (above PID
1285 threshold, amino acid properties)
1288 <!-- JAL-2292 -->Lower case residues in sequences are not
1289 reported as mapped to residues in a structure file in the
1293 <!--JAL-2324 -->Identical features with non-numeric scores
1294 could be added multiple times to a sequence
1297 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1298 bond features shown as two highlighted residues rather
1299 than a range in linked structure views, and treated
1300 correctly when selecting and computing trees from features
1303 <!-- JAL-2281-->Custom URL links for database
1304 cross-references are matched to database name regardless
1309 <em>Application</em>
1312 <!-- JAL-2282-->Custom URL links for specific database
1313 names without regular expressions also offer links from
1317 <!-- JAL-2315-->Removing a single configured link in the
1318 URL links pane in Connections preferences doesn't actually
1319 update Jalview configuration
1322 <!-- JAL-2272-->CTRL-Click on a selected region to open
1323 the alignment area popup menu doesn't work on El-Capitan
1326 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1327 files with similarly named sequences if dropped onto the
1331 <!-- JAL-2312 -->Additional mappings are shown for PDB
1332 entries where more chains exist in the PDB accession than
1333 are reported in the SIFTS file
1336 <!-- JAL-2317-->Certain structures do not get mapped to
1337 the structure view when displayed with Chimera
1340 <!-- JAL-2317-->No chains shown in the Chimera view
1341 panel's View->Show Chains submenu
1344 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1345 work for wrapped alignment views
1348 <!--JAL-2197 -->Rename UI components for running JPred
1349 predictions from 'JNet' to 'JPred'
1352 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1353 corrupted when annotation panel vertical scroll is not at
1354 first annotation row
1357 <!--JAL-2332 -->Attempting to view structure for Hen
1358 lysozyme results in a PDB Client error dialog box
1361 <!-- JAL-2319 -->Structure View's mapping report switched
1362 ranges for PDB and sequence for SIFTS
1365 SIFTS 'Not_Observed' residues mapped to non-existant
1369 <!-- <em>New Known Issues</em>
1376 <td width="60" nowrap>
1377 <div align="center">
1378 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1379 <em>25/10/2016</em></strong>
1382 <td><em>Application</em>
1384 <li>3D Structure chooser opens with 'Cached structures'
1385 view if structures already loaded</li>
1386 <li>Progress bar reports models as they are loaded to
1387 structure views</li>
1393 <li>Colour by conservation always enabled and no tick
1394 shown in menu when BLOSUM or PID shading applied</li>
1395 <li>FER1_ARATH and FER2_ARATH labels were switched in
1396 example sequences/projects/trees</li>
1398 <em>Application</em>
1400 <li>Jalview projects with views of local PDB structure
1401 files saved on Windows cannot be opened on OSX</li>
1402 <li>Multiple structure views can be opened and superposed
1403 without timeout for structures with multiple models or
1404 multiple sequences in alignment</li>
1405 <li>Cannot import or associated local PDB files without a
1406 PDB ID HEADER line</li>
1407 <li>RMSD is not output in Jmol console when superposition
1409 <li>Drag and drop of URL from Browser fails for Linux and
1410 OSX versions earlier than El Capitan</li>
1411 <li>ENA client ignores invalid content from ENA server</li>
1412 <li>Exceptions are not raised in console when ENA client
1413 attempts to fetch non-existent IDs via Fetch DB Refs UI
1415 <li>Exceptions are not raised in console when a new view
1416 is created on the alignment</li>
1417 <li>OSX right-click fixed for group selections: CMD-click
1418 to insert/remove gaps in groups and CTRL-click to open group
1421 <em>Build and deployment</em>
1423 <li>URL link checker now copes with multi-line anchor
1426 <em>New Known Issues</em>
1428 <li>Drag and drop from URL links in browsers do not work
1435 <td width="60" nowrap>
1436 <div align="center">
1437 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1440 <td><em>General</em>
1443 <!-- JAL-2124 -->Updated Spanish translations.
1446 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1447 for importing structure data to Jalview. Enables mmCIF and
1451 <!-- JAL-192 --->Alignment ruler shows positions relative to
1455 <!-- JAL-2202 -->Position/residue shown in status bar when
1456 mousing over sequence associated annotation
1459 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1463 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1464 '()', canonical '[]' and invalid '{}' base pair populations
1468 <!-- JAL-2092 -->Feature settings popup menu options for
1469 showing or hiding columns containing a feature
1472 <!-- JAL-1557 -->Edit selected group by double clicking on
1473 group and sequence associated annotation labels
1476 <!-- JAL-2236 -->Sequence name added to annotation label in
1477 select/hide columns by annotation and colour by annotation
1481 </ul> <em>Application</em>
1484 <!-- JAL-2050-->Automatically hide introns when opening a
1485 gene/transcript view
1488 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1492 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1493 structure mappings with the EMBL-EBI PDBe SIFTS database
1496 <!-- JAL-2079 -->Updated download sites used for Rfam and
1497 Pfam sources to xfam.org
1500 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1503 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1504 over sequences in Jalview
1507 <!-- JAL-2027-->Support for reverse-complement coding
1508 regions in ENA and EMBL
1511 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1512 for record retrieval via ENA rest API
1515 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1519 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1520 groovy script execution
1523 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1524 alignment window's Calculate menu
1527 <!-- JAL-1812 -->Allow groovy scripts that call
1528 Jalview.getAlignFrames() to run in headless mode
1531 <!-- JAL-2068 -->Support for creating new alignment
1532 calculation workers from groovy scripts
1535 <!-- JAL-1369 --->Store/restore reference sequence in
1539 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1540 associations are now saved/restored from project
1543 <!-- JAL-1993 -->Database selection dialog always shown
1544 before sequence fetcher is opened
1547 <!-- JAL-2183 -->Double click on an entry in Jalview's
1548 database chooser opens a sequence fetcher
1551 <!-- JAL-1563 -->Free-text search client for UniProt using
1552 the UniProt REST API
1555 <!-- JAL-2168 -->-nonews command line parameter to prevent
1556 the news reader opening
1559 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1560 querying stored in preferences
1563 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1567 <!-- JAL-1977-->Tooltips shown on database chooser
1570 <!-- JAL-391 -->Reverse complement function in calculate
1571 menu for nucleotide sequences
1574 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1575 and feature counts preserves alignment ordering (and
1576 debugged for complex feature sets).
1579 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1580 viewing structures with Jalview 2.10
1583 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1584 genome, transcript CCDS and gene ids via the Ensembl and
1585 Ensembl Genomes REST API
1588 <!-- JAL-2049 -->Protein sequence variant annotation
1589 computed for 'sequence_variant' annotation on CDS regions
1593 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1597 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1598 Ref Fetcher fails to match, or otherwise updates sequence
1599 data from external database records.
1602 <!-- JAL-2154 -->Revised Jalview Project format for
1603 efficient recovery of sequence coding and alignment
1604 annotation relationships.
1606 </ul> <!-- <em>Applet</em>
1617 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1621 <!-- JAL-2018-->Export features in Jalview format (again)
1622 includes graduated colourschemes
1625 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1626 working with big alignments and lots of hidden columns
1629 <!-- JAL-2053-->Hidden column markers not always rendered
1630 at right of alignment window
1633 <!-- JAL-2067 -->Tidied up links in help file table of
1637 <!-- JAL-2072 -->Feature based tree calculation not shown
1641 <!-- JAL-2075 -->Hidden columns ignored during feature
1642 based tree calculation
1645 <!-- JAL-2065 -->Alignment view stops updating when show
1646 unconserved enabled for group on alignment
1649 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1653 <!-- JAL-2146 -->Alignment column in status incorrectly
1654 shown as "Sequence position" when mousing over
1658 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1659 hidden columns present
1662 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1663 user created annotation added to alignment
1666 <!-- JAL-1841 -->RNA Structure consensus only computed for
1667 '()' base pair annotation
1670 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1671 in zero scores for all base pairs in RNA Structure
1675 <!-- JAL-2174-->Extend selection with columns containing
1679 <!-- JAL-2275 -->Pfam format writer puts extra space at
1680 beginning of sequence
1683 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1687 <!-- JAL-2238 -->Cannot create groups on an alignment from
1688 from a tree when t-coffee scores are shown
1691 <!-- JAL-1836,1967 -->Cannot import and view PDB
1692 structures with chains containing negative resnums (4q4h)
1695 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1699 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1700 to Clustal, PIR and PileUp output
1703 <!-- JAL-2008 -->Reordering sequence features that are
1704 not visible causes alignment window to repaint
1707 <!-- JAL-2006 -->Threshold sliders don't work in
1708 graduated colour and colour by annotation row for e-value
1709 scores associated with features and annotation rows
1712 <!-- JAL-1797 -->amino acid physicochemical conservation
1713 calculation should be case independent
1716 <!-- JAL-2173 -->Remove annotation also updates hidden
1720 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1721 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1722 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1725 <!-- JAL-2065 -->Null pointer exceptions and redraw
1726 problems when reference sequence defined and 'show
1727 non-conserved' enabled
1730 <!-- JAL-1306 -->Quality and Conservation are now shown on
1731 load even when Consensus calculation is disabled
1734 <!-- JAL-1932 -->Remove right on penultimate column of
1735 alignment does nothing
1738 <em>Application</em>
1741 <!-- JAL-1552-->URLs and links can't be imported by
1742 drag'n'drop on OSX when launched via webstart (note - not
1743 yet fixed for El Capitan)
1746 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1747 output when running on non-gb/us i18n platforms
1750 <!-- JAL-1944 -->Error thrown when exporting a view with
1751 hidden sequences as flat-file alignment
1754 <!-- JAL-2030-->InstallAnywhere distribution fails when
1758 <!-- JAL-2080-->Jalview very slow to launch via webstart
1759 (also hotfix for 2.9.0b2)
1762 <!-- JAL-2085 -->Cannot save project when view has a
1763 reference sequence defined
1766 <!-- JAL-1011 -->Columns are suddenly selected in other
1767 alignments and views when revealing hidden columns
1770 <!-- JAL-1989 -->Hide columns not mirrored in complement
1771 view in a cDNA/Protein splitframe
1774 <!-- JAL-1369 -->Cannot save/restore representative
1775 sequence from project when only one sequence is
1779 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1780 in Structure Chooser
1783 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1784 structure consensus didn't refresh annotation panel
1787 <!-- JAL-1962 -->View mapping in structure view shows
1788 mappings between sequence and all chains in a PDB file
1791 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1792 dialogs format columns correctly, don't display array
1793 data, sort columns according to type
1796 <!-- JAL-1975 -->Export complete shown after destination
1797 file chooser is cancelled during an image export
1800 <!-- JAL-2025 -->Error when querying PDB Service with
1801 sequence name containing special characters
1804 <!-- JAL-2024 -->Manual PDB structure querying should be
1808 <!-- JAL-2104 -->Large tooltips with broken HTML
1809 formatting don't wrap
1812 <!-- JAL-1128 -->Figures exported from wrapped view are
1813 truncated so L looks like I in consensus annotation
1816 <!-- JAL-2003 -->Export features should only export the
1817 currently displayed features for the current selection or
1821 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1822 after fetching cross-references, and restoring from
1826 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1827 followed in the structure viewer
1830 <!-- JAL-2163 -->Titles for individual alignments in
1831 splitframe not restored from project
1834 <!-- JAL-2145 -->missing autocalculated annotation at
1835 trailing end of protein alignment in transcript/product
1836 splitview when pad-gaps not enabled by default
1839 <!-- JAL-1797 -->amino acid physicochemical conservation
1843 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1844 article has been read (reopened issue due to
1845 internationalisation problems)
1848 <!-- JAL-1960 -->Only offer PDB structures in structure
1849 viewer based on sequence name, PDB and UniProt
1854 <!-- JAL-1976 -->No progress bar shown during export of
1858 <!-- JAL-2213 -->Structures not always superimposed after
1859 multiple structures are shown for one or more sequences.
1862 <!-- JAL-1370 -->Reference sequence characters should not
1863 be replaced with '.' when 'Show unconserved' format option
1867 <!-- JAL-1823 -->Cannot specify chain code when entering
1868 specific PDB id for sequence
1871 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1872 'Export hidden sequences' is enabled, but 'export hidden
1873 columns' is disabled.
1876 <!--JAL-2026-->Best Quality option in structure chooser
1877 selects lowest rather than highest resolution structures
1881 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1882 to sequence mapping in 'View Mappings' report
1885 <!-- JAL-2284 -->Unable to read old Jalview projects that
1886 contain non-XML data added after Jalvew wrote project.
1889 <!-- JAL-2118 -->Newly created annotation row reorders
1890 after clicking on it to create new annotation for a
1894 <!-- JAL-1980 -->Null Pointer Exception raised when
1895 pressing Add on an orphaned cut'n'paste window.
1897 <!-- may exclude, this is an external service stability issue JAL-1941
1898 -- > RNA 3D structure not added via DSSR service</li> -->
1903 <!-- JAL-2151 -->Incorrect columns are selected when
1904 hidden columns present before start of sequence
1907 <!-- JAL-1986 -->Missing dependencies on applet pages
1911 <!-- JAL-1947 -->Overview pixel size changes when
1912 sequences are hidden in applet
1915 <!-- JAL-1996 -->Updated instructions for applet
1916 deployment on examples pages.
1923 <td width="60" nowrap>
1924 <div align="center">
1925 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1926 <em>16/10/2015</em></strong>
1929 <td><em>General</em>
1931 <li>Time stamps for signed Jalview application and applet
1936 <em>Application</em>
1938 <li>Duplicate group consensus and conservation rows
1939 shown when tree is partitioned</li>
1940 <li>Erratic behaviour when tree partitions made with
1941 multiple cDNA/Protein split views</li>
1947 <td width="60" nowrap>
1948 <div align="center">
1949 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1950 <em>8/10/2015</em></strong>
1953 <td><em>General</em>
1955 <li>Updated Spanish translations of localized text for
1957 </ul> <em>Application</em>
1959 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1960 <li>Signed OSX InstallAnywhere installer<br></li>
1961 <li>Support for per-sequence based annotations in BioJSON</li>
1962 </ul> <em>Applet</em>
1964 <li>Split frame example added to applet examples page</li>
1965 </ul> <em>Build and Deployment</em>
1968 <!-- JAL-1888 -->New ant target for running Jalview's test
1976 <li>Mapping of cDNA to protein in split frames
1977 incorrect when sequence start > 1</li>
1978 <li>Broken images in filter column by annotation dialog
1980 <li>Feature colours not parsed from features file</li>
1981 <li>Exceptions and incomplete link URLs recovered when
1982 loading a features file containing HTML tags in feature
1986 <em>Application</em>
1988 <li>Annotations corrupted after BioJS export and
1990 <li>Incorrect sequence limits after Fetch DB References
1991 with 'trim retrieved sequences'</li>
1992 <li>Incorrect warning about deleting all data when
1993 deleting selected columns</li>
1994 <li>Patch to build system for shipping properly signed
1995 JNLP templates for webstart launch</li>
1996 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1997 unreleased structures for download or viewing</li>
1998 <li>Tab/space/return keystroke operation of EMBL-PDBe
1999 fetcher/viewer dialogs works correctly</li>
2000 <li>Disabled 'minimise' button on Jalview windows
2001 running on OSX to workaround redraw hang bug</li>
2002 <li>Split cDNA/Protein view position and geometry not
2003 recovered from jalview project</li>
2004 <li>Initial enabled/disabled state of annotation menu
2005 sorter 'show autocalculated first/last' corresponds to
2007 <li>Restoring of Clustal, RNA Helices and T-Coffee
2008 color schemes from BioJSON</li>
2012 <li>Reorder sequences mirrored in cDNA/Protein split
2014 <li>Applet with Jmol examples not loading correctly</li>
2020 <td><div align="center">
2021 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2023 <td><em>General</em>
2025 <li>Linked visualisation and analysis of DNA and Protein
2028 <li>Translated cDNA alignments shown as split protein
2029 and DNA alignment views</li>
2030 <li>Codon consensus annotation for linked protein and
2031 cDNA alignment views</li>
2032 <li>Link cDNA or Protein product sequences by loading
2033 them onto Protein or cDNA alignments</li>
2034 <li>Reconstruct linked cDNA alignment from aligned
2035 protein sequences</li>
2038 <li>Jmol integration updated to Jmol v14.2.14</li>
2039 <li>Import and export of Jalview alignment views as <a
2040 href="features/bioJsonFormat.html">BioJSON</a></li>
2041 <li>New alignment annotation file statements for
2042 reference sequences and marking hidden columns</li>
2043 <li>Reference sequence based alignment shading to
2044 highlight variation</li>
2045 <li>Select or hide columns according to alignment
2047 <li>Find option for locating sequences by description</li>
2048 <li>Conserved physicochemical properties shown in amino
2049 acid conservation row</li>
2050 <li>Alignments can be sorted by number of RNA helices</li>
2051 </ul> <em>Application</em>
2053 <li>New cDNA/Protein analysis capabilities
2055 <li>Get Cross-References should open a Split Frame
2056 view with cDNA/Protein</li>
2057 <li>Detect when nucleotide sequences and protein
2058 sequences are placed in the same alignment</li>
2059 <li>Split cDNA/Protein views are saved in Jalview
2064 <li>Use REST API to talk to Chimera</li>
2065 <li>Selected regions in Chimera are highlighted in linked
2066 Jalview windows</li>
2068 <li>VARNA RNA viewer updated to v3.93</li>
2069 <li>VARNA views are saved in Jalview Projects</li>
2070 <li>Pseudoknots displayed as Jalview RNA annotation can
2071 be shown in VARNA</li>
2073 <li>Make groups for selection uses marked columns as well
2074 as the active selected region</li>
2076 <li>Calculate UPGMA and NJ trees using sequence feature
2078 <li>New Export options
2080 <li>New Export Settings dialog to control hidden
2081 region export in flat file generation</li>
2083 <li>Export alignment views for display with the <a
2084 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2086 <li>Export scrollable SVG in HTML page</li>
2087 <li>Optional embedding of BioJSON data when exporting
2088 alignment figures to HTML</li>
2090 <li>3D structure retrieval and display
2092 <li>Free text and structured queries with the PDBe
2094 <li>PDBe Search API based discovery and selection of
2095 PDB structures for a sequence set</li>
2099 <li>JPred4 employed for protein secondary structure
2101 <li>Hide Insertions menu option to hide unaligned columns
2102 for one or a group of sequences</li>
2103 <li>Automatically hide insertions in alignments imported
2104 from the JPred4 web server</li>
2105 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2106 system on OSX<br />LGPL libraries courtesy of <a
2107 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2109 <li>changed 'View nucleotide structure' submenu to 'View
2110 VARNA 2D Structure'</li>
2111 <li>change "View protein structure" menu option to "3D
2114 </ul> <em>Applet</em>
2116 <li>New layout for applet example pages</li>
2117 <li>New parameters to enable SplitFrame view
2118 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2119 <li>New example demonstrating linked viewing of cDNA and
2120 Protein alignments</li>
2121 </ul> <em>Development and deployment</em>
2123 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2124 <li>Include installation type and git revision in build
2125 properties and console log output</li>
2126 <li>Jalview Github organisation, and new github site for
2127 storing BioJsMSA Templates</li>
2128 <li>Jalview's unit tests now managed with TestNG</li>
2131 <!-- <em>General</em>
2133 </ul> --> <!-- issues resolved --> <em>Application</em>
2135 <li>Escape should close any open find dialogs</li>
2136 <li>Typo in select-by-features status report</li>
2137 <li>Consensus RNA secondary secondary structure
2138 predictions are not highlighted in amber</li>
2139 <li>Missing gap character in v2.7 example file means
2140 alignment appears unaligned when pad-gaps is not enabled</li>
2141 <li>First switch to RNA Helices colouring doesn't colour
2142 associated structure views</li>
2143 <li>ID width preference option is greyed out when auto
2144 width checkbox not enabled</li>
2145 <li>Stopped a warning dialog from being shown when
2146 creating user defined colours</li>
2147 <li>'View Mapping' in structure viewer shows sequence
2148 mappings for just that viewer's sequences</li>
2149 <li>Workaround for superposing PDB files containing
2150 multiple models in Chimera</li>
2151 <li>Report sequence position in status bar when hovering
2152 over Jmol structure</li>
2153 <li>Cannot output gaps as '.' symbols with Selection ->
2154 output to text box</li>
2155 <li>Flat file exports of alignments with hidden columns
2156 have incorrect sequence start/end</li>
2157 <li>'Aligning' a second chain to a Chimera structure from
2159 <li>Colour schemes applied to structure viewers don't
2160 work for nucleotide</li>
2161 <li>Loading/cut'n'pasting an empty or invalid file leads
2162 to a grey/invisible alignment window</li>
2163 <li>Exported Jpred annotation from a sequence region
2164 imports to different position</li>
2165 <li>Space at beginning of sequence feature tooltips shown
2166 on some platforms</li>
2167 <li>Chimera viewer 'View | Show Chain' menu is not
2169 <li>'New View' fails with a Null Pointer Exception in
2170 console if Chimera has been opened</li>
2171 <li>Mouseover to Chimera not working</li>
2172 <li>Miscellaneous ENA XML feature qualifiers not
2174 <li>NPE in annotation renderer after 'Extract Scores'</li>
2175 <li>If two structures in one Chimera window, mouseover of
2176 either sequence shows on first structure</li>
2177 <li>'Show annotations' options should not make
2178 non-positional annotations visible</li>
2179 <li>Subsequence secondary structure annotation not shown
2180 in right place after 'view flanking regions'</li>
2181 <li>File Save As type unset when current file format is
2183 <li>Save as '.jar' option removed for saving Jalview
2185 <li>Colour by Sequence colouring in Chimera more
2187 <li>Cannot 'add reference annotation' for a sequence in
2188 several views on same alignment</li>
2189 <li>Cannot show linked products for EMBL / ENA records</li>
2190 <li>Jalview's tooltip wraps long texts containing no
2192 </ul> <em>Applet</em>
2194 <li>Jmol to JalviewLite mouseover/link not working</li>
2195 <li>JalviewLite can't import sequences with ID
2196 descriptions containing angle brackets</li>
2197 </ul> <em>General</em>
2199 <li>Cannot export and reimport RNA secondary structure
2200 via jalview annotation file</li>
2201 <li>Random helix colour palette for colour by annotation
2202 with RNA secondary structure</li>
2203 <li>Mouseover to cDNA from STOP residue in protein
2204 translation doesn't work.</li>
2205 <li>hints when using the select by annotation dialog box</li>
2206 <li>Jmol alignment incorrect if PDB file has alternate CA
2208 <li>FontChooser message dialog appears to hang after
2209 choosing 1pt font</li>
2210 <li>Peptide secondary structure incorrectly imported from
2211 annotation file when annotation display text includes 'e' or
2213 <li>Cannot set colour of new feature type whilst creating
2215 <li>cDNA translation alignment should not be sequence
2216 order dependent</li>
2217 <li>'Show unconserved' doesn't work for lower case
2219 <li>Nucleotide ambiguity codes involving R not recognised</li>
2220 </ul> <em>Deployment and Documentation</em>
2222 <li>Applet example pages appear different to the rest of
2223 www.jalview.org</li>
2224 </ul> <em>Application Known issues</em>
2226 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2227 <li>Misleading message appears after trying to delete
2229 <li>Jalview icon not shown in dock after InstallAnywhere
2230 version launches</li>
2231 <li>Fetching EMBL reference for an RNA sequence results
2232 fails with a sequence mismatch</li>
2233 <li>Corrupted or unreadable alignment display when
2234 scrolling alignment to right</li>
2235 <li>ArrayIndexOutOfBoundsException thrown when remove
2236 empty columns called on alignment with ragged gapped ends</li>
2237 <li>auto calculated alignment annotation rows do not get
2238 placed above or below non-autocalculated rows</li>
2239 <li>Jalview dekstop becomes sluggish at full screen in
2240 ultra-high resolution</li>
2241 <li>Cannot disable consensus calculation independently of
2242 quality and conservation</li>
2243 <li>Mouseover highlighting between cDNA and protein can
2244 become sluggish with more than one splitframe shown</li>
2245 </ul> <em>Applet Known Issues</em>
2247 <li>Core PDB parsing code requires Jmol</li>
2248 <li>Sequence canvas panel goes white when alignment
2249 window is being resized</li>
2255 <td><div align="center">
2256 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2258 <td><em>General</em>
2260 <li>Updated Java code signing certificate donated by
2262 <li>Features and annotation preserved when performing
2263 pairwise alignment</li>
2264 <li>RNA pseudoknot annotation can be
2265 imported/exported/displayed</li>
2266 <li>'colour by annotation' can colour by RNA and
2267 protein secondary structure</li>
2268 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2269 post-hoc with 2.9 release</em>)
2272 </ul> <em>Application</em>
2274 <li>Extract and display secondary structure for sequences
2275 with 3D structures</li>
2276 <li>Support for parsing RNAML</li>
2277 <li>Annotations menu for layout
2279 <li>sort sequence annotation rows by alignment</li>
2280 <li>place sequence annotation above/below alignment
2283 <li>Output in Stockholm format</li>
2284 <li>Internationalisation: improved Spanish (es)
2286 <li>Structure viewer preferences tab</li>
2287 <li>Disorder and Secondary Structure annotation tracks
2288 shared between alignments</li>
2289 <li>UCSF Chimera launch and linked highlighting from
2291 <li>Show/hide all sequence associated annotation rows for
2292 all or current selection</li>
2293 <li>disorder and secondary structure predictions
2294 available as dataset annotation</li>
2295 <li>Per-sequence rna helices colouring</li>
2298 <li>Sequence database accessions imported when fetching
2299 alignments from Rfam</li>
2300 <li>update VARNA version to 3.91</li>
2302 <li>New groovy scripts for exporting aligned positions,
2303 conservation values, and calculating sum of pairs scores.</li>
2304 <li>Command line argument to set default JABAWS server</li>
2305 <li>include installation type in build properties and
2306 console log output</li>
2307 <li>Updated Jalview project format to preserve dataset
2311 <!-- issues resolved --> <em>Application</em>
2313 <li>Distinguish alignment and sequence associated RNA
2314 structure in structure->view->VARNA</li>
2315 <li>Raise dialog box if user deletes all sequences in an
2317 <li>Pressing F1 results in documentation opening twice</li>
2318 <li>Sequence feature tooltip is wrapped</li>
2319 <li>Double click on sequence associated annotation
2320 selects only first column</li>
2321 <li>Redundancy removal doesn't result in unlinked
2322 leaves shown in tree</li>
2323 <li>Undos after several redundancy removals don't undo
2325 <li>Hide sequence doesn't hide associated annotation</li>
2326 <li>User defined colours dialog box too big to fit on
2327 screen and buttons not visible</li>
2328 <li>author list isn't updated if already written to
2329 Jalview properties</li>
2330 <li>Popup menu won't open after retrieving sequence
2332 <li>File open window for associate PDB doesn't open</li>
2333 <li>Left-then-right click on a sequence id opens a
2334 browser search window</li>
2335 <li>Cannot open sequence feature shading/sort popup menu
2336 in feature settings dialog</li>
2337 <li>better tooltip placement for some areas of Jalview
2339 <li>Allow addition of JABAWS Server which doesn't
2340 pass validation</li>
2341 <li>Web services parameters dialog box is too large to
2343 <li>Muscle nucleotide alignment preset obscured by
2345 <li>JABAWS preset submenus don't contain newly
2346 defined user preset</li>
2347 <li>MSA web services warns user if they were launched
2348 with invalid input</li>
2349 <li>Jalview cannot contact DAS Registy when running on
2352 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2353 'Superpose with' submenu not shown when new view
2357 </ul> <!-- <em>Applet</em>
2359 </ul> <em>General</em>
2361 </ul>--> <em>Deployment and Documentation</em>
2363 <li>2G and 1G options in launchApp have no effect on
2364 memory allocation</li>
2365 <li>launchApp service doesn't automatically open
2366 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2368 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2369 InstallAnywhere reports cannot find valid JVM when Java
2370 1.7_055 is available
2372 </ul> <em>Application Known issues</em>
2375 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2376 corrupted or unreadable alignment display when scrolling
2380 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2381 retrieval fails but progress bar continues for DAS retrieval
2382 with large number of ID
2385 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2386 flatfile output of visible region has incorrect sequence
2390 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2391 rna structure consensus doesn't update when secondary
2392 structure tracks are rearranged
2395 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2396 invalid rna structure positional highlighting does not
2397 highlight position of invalid base pairs
2400 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2401 out of memory errors are not raised when saving Jalview
2402 project from alignment window file menu
2405 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2406 Switching to RNA Helices colouring doesn't propagate to
2410 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2411 colour by RNA Helices not enabled when user created
2412 annotation added to alignment
2415 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2416 Jalview icon not shown on dock in Mountain Lion/Webstart
2418 </ul> <em>Applet Known Issues</em>
2421 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2422 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2425 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2426 Jalview and Jmol example not compatible with IE9
2429 <li>Sort by annotation score doesn't reverse order
2435 <td><div align="center">
2436 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2439 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2442 <li>Internationalisation of user interface (usually
2443 called i18n support) and translation for Spanish locale</li>
2444 <li>Define/Undefine group on current selection with
2445 Ctrl-G/Shift Ctrl-G</li>
2446 <li>Improved group creation/removal options in
2447 alignment/sequence Popup menu</li>
2448 <li>Sensible precision for symbol distribution
2449 percentages shown in logo tooltip.</li>
2450 <li>Annotation panel height set according to amount of
2451 annotation when alignment first opened</li>
2452 </ul> <em>Application</em>
2454 <li>Interactive consensus RNA secondary structure
2455 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2456 <li>Select columns containing particular features from
2457 Feature Settings dialog</li>
2458 <li>View all 'representative' PDB structures for selected
2460 <li>Update Jalview project format:
2462 <li>New file extension for Jalview projects '.jvp'</li>
2463 <li>Preserve sequence and annotation dataset (to
2464 store secondary structure annotation,etc)</li>
2465 <li>Per group and alignment annotation and RNA helix
2469 <li>New similarity measures for PCA and Tree calculation
2471 <li>Experimental support for retrieval and viewing of
2472 flanking regions for an alignment</li>
2476 <!-- issues resolved --> <em>Application</em>
2478 <li>logo keeps spinning and status remains at queued or
2479 running after job is cancelled</li>
2480 <li>cannot export features from alignments imported from
2481 Jalview/VAMSAS projects</li>
2482 <li>Buggy slider for web service parameters that take
2484 <li>Newly created RNA secondary structure line doesn't
2485 have 'display all symbols' flag set</li>
2486 <li>T-COFFEE alignment score shading scheme and other
2487 annotation shading not saved in Jalview project</li>
2488 <li>Local file cannot be loaded in freshly downloaded
2490 <li>Jalview icon not shown on dock in Mountain
2492 <li>Load file from desktop file browser fails</li>
2493 <li>Occasional NPE thrown when calculating large trees</li>
2494 <li>Cannot reorder or slide sequences after dragging an
2495 alignment onto desktop</li>
2496 <li>Colour by annotation dialog throws NPE after using
2497 'extract scores' function</li>
2498 <li>Loading/cut'n'pasting an empty file leads to a grey
2499 alignment window</li>
2500 <li>Disorder thresholds rendered incorrectly after
2501 performing IUPred disorder prediction</li>
2502 <li>Multiple group annotated consensus rows shown when
2503 changing 'normalise logo' display setting</li>
2504 <li>Find shows blank dialog after 'finished searching' if
2505 nothing matches query</li>
2506 <li>Null Pointer Exceptions raised when sorting by
2507 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2509 <li>Errors in Jmol console when structures in alignment
2510 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2512 <li>Not all working JABAWS services are shown in
2514 <li>JAVAWS version of Jalview fails to launch with
2515 'invalid literal/length code'</li>
2516 <li>Annotation/RNA Helix colourschemes cannot be applied
2517 to alignment with groups (actually fixed in 2.8.0b1)</li>
2518 <li>RNA Helices and T-Coffee Scores available as default
2521 </ul> <em>Applet</em>
2523 <li>Remove group option is shown even when selection is
2525 <li>Apply to all groups ticked but colourscheme changes
2526 don't affect groups</li>
2527 <li>Documented RNA Helices and T-Coffee Scores as valid
2528 colourscheme name</li>
2529 <li>Annotation labels drawn on sequence IDs when
2530 Annotation panel is not displayed</li>
2531 <li>Increased font size for dropdown menus on OSX and
2532 embedded windows</li>
2533 </ul> <em>Other</em>
2535 <li>Consensus sequence for alignments/groups with a
2536 single sequence were not calculated</li>
2537 <li>annotation files that contain only groups imported as
2538 annotation and junk sequences</li>
2539 <li>Fasta files with sequences containing '*' incorrectly
2540 recognised as PFAM or BLC</li>
2541 <li>conservation/PID slider apply all groups option
2542 doesn't affect background (2.8.0b1)
2544 <li>redundancy highlighting is erratic at 0% and 100%</li>
2545 <li>Remove gapped columns fails for sequences with ragged
2547 <li>AMSA annotation row with leading spaces is not
2548 registered correctly on import</li>
2549 <li>Jalview crashes when selecting PCA analysis for
2550 certain alignments</li>
2551 <li>Opening the colour by annotation dialog for an
2552 existing annotation based 'use original colours'
2553 colourscheme loses original colours setting</li>
2558 <td><div align="center">
2559 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2560 <em>30/1/2014</em></strong>
2564 <li>Trusted certificates for JalviewLite applet and
2565 Jalview Desktop application<br />Certificate was donated by
2566 <a href="https://www.certum.eu">Certum</a> to the Jalview
2567 open source project).
2569 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2570 <li>Output in Stockholm format</li>
2571 <li>Allow import of data from gzipped files</li>
2572 <li>Export/import group and sequence associated line
2573 graph thresholds</li>
2574 <li>Nucleotide substitution matrix that supports RNA and
2575 ambiguity codes</li>
2576 <li>Allow disorder predictions to be made on the current
2577 selection (or visible selection) in the same way that JPred
2579 <li>Groovy scripting for headless Jalview operation</li>
2580 </ul> <em>Other improvements</em>
2582 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2583 <li>COMBINE statement uses current SEQUENCE_REF and
2584 GROUP_REF scope to group annotation rows</li>
2585 <li>Support '' style escaping of quotes in Newick
2587 <li>Group options for JABAWS service by command line name</li>
2588 <li>Empty tooltip shown for JABA service options with a
2589 link but no description</li>
2590 <li>Select primary source when selecting authority in
2591 database fetcher GUI</li>
2592 <li>Add .mfa to FASTA file extensions recognised by
2594 <li>Annotation label tooltip text wrap</li>
2599 <li>Slow scrolling when lots of annotation rows are
2601 <li>Lots of NPE (and slowness) after creating RNA
2602 secondary structure annotation line</li>
2603 <li>Sequence database accessions not imported when
2604 fetching alignments from Rfam</li>
2605 <li>Incorrect SHMR submission for sequences with
2607 <li>View all structures does not always superpose
2609 <li>Option widgets in service parameters not updated to
2610 reflect user or preset settings</li>
2611 <li>Null pointer exceptions for some services without
2612 presets or adjustable parameters</li>
2613 <li>Discover PDB IDs entry in structure menu doesn't
2614 discover PDB xRefs</li>
2615 <li>Exception encountered while trying to retrieve
2616 features with DAS</li>
2617 <li>Lowest value in annotation row isn't coloured
2618 when colour by annotation (per sequence) is coloured</li>
2619 <li>Keyboard mode P jumps to start of gapped region when
2620 residue follows a gap</li>
2621 <li>Jalview appears to hang importing an alignment with
2622 Wrap as default or after enabling Wrap</li>
2623 <li>'Right click to add annotations' message
2624 shown in wrap mode when no annotations present</li>
2625 <li>Disorder predictions fail with NPE if no automatic
2626 annotation already exists on alignment</li>
2627 <li>oninit javascript function should be called after
2628 initialisation completes</li>
2629 <li>Remove redundancy after disorder prediction corrupts
2630 alignment window display</li>
2631 <li>Example annotation file in documentation is invalid</li>
2632 <li>Grouped line graph annotation rows are not exported
2633 to annotation file</li>
2634 <li>Multi-harmony analysis cannot be run when only two
2636 <li>Cannot create multiple groups of line graphs with
2637 several 'combine' statements in annotation file</li>
2638 <li>Pressing return several times causes Number Format
2639 exceptions in keyboard mode</li>
2640 <li>Multi-harmony (SHMMR) method doesn't submit
2641 correct partitions for input data</li>
2642 <li>Translation from DNA to Amino Acids fails</li>
2643 <li>Jalview fail to load newick tree with quoted label</li>
2644 <li>--headless flag isn't understood</li>
2645 <li>ClassCastException when generating EPS in headless
2647 <li>Adjusting sequence-associated shading threshold only
2648 changes one row's threshold</li>
2649 <li>Preferences and Feature settings panel panel
2650 doesn't open</li>
2651 <li>hide consensus histogram also hides conservation and
2652 quality histograms</li>
2657 <td><div align="center">
2658 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2660 <td><em>Application</em>
2662 <li>Support for JABAWS 2.0 Services (AACon alignment
2663 conservation, protein disorder and Clustal Omega)</li>
2664 <li>JABAWS server status indicator in Web Services
2666 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2667 in Jalview alignment window</li>
2668 <li>Updated Jalview build and deploy framework for OSX
2669 mountain lion, windows 7, and 8</li>
2670 <li>Nucleotide substitution matrix for PCA that supports
2671 RNA and ambiguity codes</li>
2673 <li>Improved sequence database retrieval GUI</li>
2674 <li>Support fetching and database reference look up
2675 against multiple DAS sources (Fetch all from in 'fetch db
2677 <li>Jalview project improvements
2679 <li>Store and retrieve the 'belowAlignment'
2680 flag for annotation</li>
2681 <li>calcId attribute to group annotation rows on the
2683 <li>Store AACon calculation settings for a view in
2684 Jalview project</li>
2688 <li>horizontal scrolling gesture support</li>
2689 <li>Visual progress indicator when PCA calculation is
2691 <li>Simpler JABA web services menus</li>
2692 <li>visual indication that web service results are still
2693 being retrieved from server</li>
2694 <li>Serialise the dialogs that are shown when Jalview
2695 starts up for first time</li>
2696 <li>Jalview user agent string for interacting with HTTP
2698 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2700 <li>Examples directory and Groovy library included in
2701 InstallAnywhere distribution</li>
2702 </ul> <em>Applet</em>
2704 <li>RNA alignment and secondary structure annotation
2705 visualization applet example</li>
2706 </ul> <em>General</em>
2708 <li>Normalise option for consensus sequence logo</li>
2709 <li>Reset button in PCA window to return dimensions to
2711 <li>Allow seqspace or Jalview variant of alignment PCA
2713 <li>PCA with either nucleic acid and protein substitution
2715 <li>Allow windows containing HTML reports to be exported
2717 <li>Interactive display and editing of RNA secondary
2718 structure contacts</li>
2719 <li>RNA Helix Alignment Colouring</li>
2720 <li>RNA base pair logo consensus</li>
2721 <li>Parse sequence associated secondary structure
2722 information in Stockholm files</li>
2723 <li>HTML Export database accessions and annotation
2724 information presented in tooltip for sequences</li>
2725 <li>Import secondary structure from LOCARNA clustalw
2726 style RNA alignment files</li>
2727 <li>import and visualise T-COFFEE quality scores for an
2729 <li>'colour by annotation' per sequence option to
2730 shade each sequence according to its associated alignment
2732 <li>New Jalview Logo</li>
2733 </ul> <em>Documentation and Development</em>
2735 <li>documentation for score matrices used in Jalview</li>
2736 <li>New Website!</li>
2738 <td><em>Application</em>
2740 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2741 wsdbfetch REST service</li>
2742 <li>Stop windows being moved outside desktop on OSX</li>
2743 <li>Filetype associations not installed for webstart
2745 <li>Jalview does not always retrieve progress of a JABAWS
2746 job execution in full once it is complete</li>
2747 <li>revise SHMR RSBS definition to ensure alignment is
2748 uploaded via ali_file parameter</li>
2749 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2750 <li>View all structures superposed fails with exception</li>
2751 <li>Jnet job queues forever if a very short sequence is
2752 submitted for prediction</li>
2753 <li>Cut and paste menu not opened when mouse clicked on
2755 <li>Putting fractional value into integer text box in
2756 alignment parameter dialog causes Jalview to hang</li>
2757 <li>Structure view highlighting doesn't work on
2759 <li>View all structures fails with exception shown in
2761 <li>Characters in filename associated with PDBEntry not
2762 escaped in a platform independent way</li>
2763 <li>Jalview desktop fails to launch with exception when
2765 <li>Tree calculation reports 'you must have 2 or more
2766 sequences selected' when selection is empty</li>
2767 <li>Jalview desktop fails to launch with jar signature
2768 failure when java web start temporary file caching is
2770 <li>DAS Sequence retrieval with range qualification
2771 results in sequence xref which includes range qualification</li>
2772 <li>Errors during processing of command line arguments
2773 cause progress bar (JAL-898) to be removed</li>
2774 <li>Replace comma for semi-colon option not disabled for
2775 DAS sources in sequence fetcher</li>
2776 <li>Cannot close news reader when JABAWS server warning
2777 dialog is shown</li>
2778 <li>Option widgets not updated to reflect user settings</li>
2779 <li>Edited sequence not submitted to web service</li>
2780 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2781 <li>InstallAnywhere installer doesn't unpack and run
2782 on OSX Mountain Lion</li>
2783 <li>Annotation panel not given a scroll bar when
2784 sequences with alignment annotation are pasted into the
2786 <li>Sequence associated annotation rows not associated
2787 when loaded from Jalview project</li>
2788 <li>Browser launch fails with NPE on java 1.7</li>
2789 <li>JABAWS alignment marked as finished when job was
2790 cancelled or job failed due to invalid input</li>
2791 <li>NPE with v2.7 example when clicking on Tree
2792 associated with all views</li>
2793 <li>Exceptions when copy/paste sequences with grouped
2794 annotation rows to new window</li>
2795 </ul> <em>Applet</em>
2797 <li>Sequence features are momentarily displayed before
2798 they are hidden using hidefeaturegroups applet parameter</li>
2799 <li>loading features via javascript API automatically
2800 enables feature display</li>
2801 <li>scrollToColumnIn javascript API method doesn't
2803 </ul> <em>General</em>
2805 <li>Redundancy removal fails for rna alignment</li>
2806 <li>PCA calculation fails when sequence has been selected
2807 and then deselected</li>
2808 <li>PCA window shows grey box when first opened on OSX</li>
2809 <li>Letters coloured pink in sequence logo when alignment
2810 coloured with clustalx</li>
2811 <li>Choosing fonts without letter symbols defined causes
2812 exceptions and redraw errors</li>
2813 <li>Initial PCA plot view is not same as manually
2814 reconfigured view</li>
2815 <li>Grouped annotation graph label has incorrect line
2817 <li>Grouped annotation graph label display is corrupted
2818 for lots of labels</li>
2823 <div align="center">
2824 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2827 <td><em>Application</em>
2829 <li>Jalview Desktop News Reader</li>
2830 <li>Tweaked default layout of web services menu</li>
2831 <li>View/alignment association menu to enable user to
2832 easily specify which alignment a multi-structure view takes
2833 its colours/correspondences from</li>
2834 <li>Allow properties file location to be specified as URL</li>
2835 <li>Extend Jalview project to preserve associations
2836 between many alignment views and a single Jmol display</li>
2837 <li>Store annotation row height in Jalview project file</li>
2838 <li>Annotation row column label formatting attributes
2839 stored in project file</li>
2840 <li>Annotation row order for auto-calculated annotation
2841 rows preserved in Jalview project file</li>
2842 <li>Visual progress indication when Jalview state is
2843 saved using Desktop window menu</li>
2844 <li>Visual indication that command line arguments are
2845 still being processed</li>
2846 <li>Groovy script execution from URL</li>
2847 <li>Colour by annotation default min and max colours in
2849 <li>Automatically associate PDB files dragged onto an
2850 alignment with sequences that have high similarity and
2852 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2853 <li>'view structures' option to open many
2854 structures in same window</li>
2855 <li>Sort associated views menu option for tree panel</li>
2856 <li>Group all JABA and non-JABA services for a particular
2857 analysis function in its own submenu</li>
2858 </ul> <em>Applet</em>
2860 <li>Userdefined and autogenerated annotation rows for
2862 <li>Adjustment of alignment annotation pane height</li>
2863 <li>Annotation scrollbar for annotation panel</li>
2864 <li>Drag to reorder annotation rows in annotation panel</li>
2865 <li>'automaticScrolling' parameter</li>
2866 <li>Allow sequences with partial ID string matches to be
2867 annotated from GFF/Jalview features files</li>
2868 <li>Sequence logo annotation row in applet</li>
2869 <li>Absolute paths relative to host server in applet
2870 parameters are treated as such</li>
2871 <li>New in the JalviewLite javascript API:
2873 <li>JalviewLite.js javascript library</li>
2874 <li>Javascript callbacks for
2876 <li>Applet initialisation</li>
2877 <li>Sequence/alignment mouse-overs and selections</li>
2880 <li>scrollTo row and column alignment scrolling
2882 <li>Select sequence/alignment regions from javascript</li>
2883 <li>javascript structure viewer harness to pass
2884 messages between Jmol and Jalview when running as
2885 distinct applets</li>
2886 <li>sortBy method</li>
2887 <li>Set of applet and application examples shipped
2888 with documentation</li>
2889 <li>New example to demonstrate JalviewLite and Jmol
2890 javascript message exchange</li>
2892 </ul> <em>General</em>
2894 <li>Enable Jmol displays to be associated with multiple
2895 multiple alignments</li>
2896 <li>Option to automatically sort alignment with new tree</li>
2897 <li>User configurable link to enable redirects to a
2898 www.Jalview.org mirror</li>
2899 <li>Jmol colours option for Jmol displays</li>
2900 <li>Configurable newline string when writing alignment
2901 and other flat files</li>
2902 <li>Allow alignment annotation description lines to
2903 contain html tags</li>
2904 </ul> <em>Documentation and Development</em>
2906 <li>Add groovy test harness for bulk load testing to
2908 <li>Groovy script to load and align a set of sequences
2909 using a web service before displaying the result in the
2910 Jalview desktop</li>
2911 <li>Restructured javascript and applet api documentation</li>
2912 <li>Ant target to publish example html files with applet
2914 <li>Netbeans project for building Jalview from source</li>
2915 <li>ant task to create online javadoc for Jalview source</li>
2917 <td><em>Application</em>
2919 <li>User defined colourscheme throws exception when
2920 current built in colourscheme is saved as new scheme</li>
2921 <li>AlignFrame->Save in application pops up save
2922 dialog for valid filename/format</li>
2923 <li>Cannot view associated structure for UniProt sequence</li>
2924 <li>PDB file association breaks for UniProt sequence
2926 <li>Associate PDB from file dialog does not tell you
2927 which sequence is to be associated with the file</li>
2928 <li>Find All raises null pointer exception when query
2929 only matches sequence IDs</li>
2930 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2931 <li>Jalview project with Jmol views created with Jalview
2932 2.4 cannot be loaded</li>
2933 <li>Filetype associations not installed for webstart
2935 <li>Two or more chains in a single PDB file associated
2936 with sequences in different alignments do not get coloured
2937 by their associated sequence</li>
2938 <li>Visibility status of autocalculated annotation row
2939 not preserved when project is loaded</li>
2940 <li>Annotation row height and visibility attributes not
2941 stored in Jalview project</li>
2942 <li>Tree bootstraps are not preserved when saved as a
2943 Jalview project</li>
2944 <li>Envision2 workflow tooltips are corrupted</li>
2945 <li>Enabling show group conservation also enables colour
2946 by conservation</li>
2947 <li>Duplicate group associated conservation or consensus
2948 created on new view</li>
2949 <li>Annotation scrollbar not displayed after 'show
2950 all hidden annotation rows' option selected</li>
2951 <li>Alignment quality not updated after alignment
2952 annotation row is hidden then shown</li>
2953 <li>Preserve colouring of structures coloured by
2954 sequences in pre Jalview 2.7 projects</li>
2955 <li>Web service job parameter dialog is not laid out
2957 <li>Web services menu not refreshed after 'reset
2958 services' button is pressed in preferences</li>
2959 <li>Annotation off by one in Jalview v2_3 example project</li>
2960 <li>Structures imported from file and saved in project
2961 get name like jalview_pdb1234.txt when reloaded</li>
2962 <li>Jalview does not always retrieve progress of a JABAWS
2963 job execution in full once it is complete</li>
2964 </ul> <em>Applet</em>
2966 <li>Alignment height set incorrectly when lots of
2967 annotation rows are displayed</li>
2968 <li>Relative URLs in feature HTML text not resolved to
2970 <li>View follows highlighting does not work for positions
2972 <li><= shown as = in tooltip</li>
2973 <li>Export features raises exception when no features
2975 <li>Separator string used for serialising lists of IDs
2976 for javascript api is modified when separator string
2977 provided as parameter</li>
2978 <li>Null pointer exception when selecting tree leaves for
2979 alignment with no existing selection</li>
2980 <li>Relative URLs for datasources assumed to be relative
2981 to applet's codebase</li>
2982 <li>Status bar not updated after finished searching and
2983 search wraps around to first result</li>
2984 <li>StructureSelectionManager instance shared between
2985 several Jalview applets causes race conditions and memory
2987 <li>Hover tooltip and mouseover of position on structure
2988 not sent from Jmol in applet</li>
2989 <li>Certain sequences of javascript method calls to
2990 applet API fatally hang browser</li>
2991 </ul> <em>General</em>
2993 <li>View follows structure mouseover scrolls beyond
2994 position with wrapped view and hidden regions</li>
2995 <li>Find sequence position moves to wrong residue
2996 with/without hidden columns</li>
2997 <li>Sequence length given in alignment properties window
2999 <li>InvalidNumberFormat exceptions thrown when trying to
3000 import PDB like structure files</li>
3001 <li>Positional search results are only highlighted
3002 between user-supplied sequence start/end bounds</li>
3003 <li>End attribute of sequence is not validated</li>
3004 <li>Find dialog only finds first sequence containing a
3005 given sequence position</li>
3006 <li>Sequence numbering not preserved in MSF alignment
3008 <li>Jalview PDB file reader does not extract sequence
3009 from nucleotide chains correctly</li>
3010 <li>Structure colours not updated when tree partition
3011 changed in alignment</li>
3012 <li>Sequence associated secondary structure not correctly
3013 parsed in interleaved stockholm</li>
3014 <li>Colour by annotation dialog does not restore current
3016 <li>Hiding (nearly) all sequences doesn't work
3018 <li>Sequences containing lowercase letters are not
3019 properly associated with their pdb files</li>
3020 </ul> <em>Documentation and Development</em>
3022 <li>schemas/JalviewWsParamSet.xsd corrupted by
3023 ApplyCopyright tool</li>
3028 <div align="center">
3029 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3032 <td><em>Application</em>
3034 <li>New warning dialog when the Jalview Desktop cannot
3035 contact web services</li>
3036 <li>JABA service parameters for a preset are shown in
3037 service job window</li>
3038 <li>JABA Service menu entries reworded</li>
3042 <li>Modeller PIR IO broken - cannot correctly import a
3043 pir file emitted by Jalview</li>
3044 <li>Existing feature settings transferred to new
3045 alignment view created from cut'n'paste</li>
3046 <li>Improved test for mixed amino/nucleotide chains when
3047 parsing PDB files</li>
3048 <li>Consensus and conservation annotation rows
3049 occasionally become blank for all new windows</li>
3050 <li>Exception raised when right clicking above sequences
3051 in wrapped view mode</li>
3052 </ul> <em>Application</em>
3054 <li>multiple multiply aligned structure views cause cpu
3055 usage to hit 100% and computer to hang</li>
3056 <li>Web Service parameter layout breaks for long user
3057 parameter names</li>
3058 <li>Jaba service discovery hangs desktop if Jaba server
3065 <div align="center">
3066 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3069 <td><em>Application</em>
3071 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3072 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3075 <li>Web Services preference tab</li>
3076 <li>Analysis parameters dialog box and user defined
3078 <li>Improved speed and layout of Envision2 service menu</li>
3079 <li>Superpose structures using associated sequence
3081 <li>Export coordinates and projection as CSV from PCA
3083 </ul> <em>Applet</em>
3085 <li>enable javascript: execution by the applet via the
3086 link out mechanism</li>
3087 </ul> <em>Other</em>
3089 <li>Updated the Jmol Jalview interface to work with Jmol
3091 <li>The Jalview Desktop and JalviewLite applet now
3092 require Java 1.5</li>
3093 <li>Allow Jalview feature colour specification for GFF
3094 sequence annotation files</li>
3095 <li>New 'colour by label' keword in Jalview feature file
3096 type colour specification</li>
3097 <li>New Jalview Desktop Groovy API method that allows a
3098 script to check if it being run in an interactive session or
3099 in a batch operation from the Jalview command line</li>
3103 <li>clustalx colourscheme colours Ds preferentially when
3104 both D+E are present in over 50% of the column</li>
3105 </ul> <em>Application</em>
3107 <li>typo in AlignmentFrame->View->Hide->all but
3108 selected Regions menu item</li>
3109 <li>sequence fetcher replaces ',' for ';' when the ',' is
3110 part of a valid accession ID</li>
3111 <li>fatal OOM if object retrieved by sequence fetcher
3112 runs out of memory</li>
3113 <li>unhandled Out of Memory Error when viewing pca
3114 analysis results</li>
3115 <li>InstallAnywhere builds fail to launch on OS X java
3116 10.5 update 4 (due to apple Java 1.6 update)</li>
3117 <li>Installanywhere Jalview silently fails to launch</li>
3118 </ul> <em>Applet</em>
3120 <li>Jalview.getFeatureGroups() raises an
3121 ArrayIndexOutOfBoundsException if no feature groups are
3128 <div align="center">
3129 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3135 <li>Alignment prettyprinter doesn't cope with long
3137 <li>clustalx colourscheme colours Ds preferentially when
3138 both D+E are present in over 50% of the column</li>
3139 <li>nucleic acid structures retrieved from PDB do not
3140 import correctly</li>
3141 <li>More columns get selected than were clicked on when a
3142 number of columns are hidden</li>
3143 <li>annotation label popup menu not providing correct
3144 add/hide/show options when rows are hidden or none are
3146 <li>Stockholm format shown in list of readable formats,
3147 and parser copes better with alignments from RFAM.</li>
3148 <li>CSV output of consensus only includes the percentage
3149 of all symbols if sequence logo display is enabled</li>
3151 </ul> <em>Applet</em>
3153 <li>annotation panel disappears when annotation is
3155 </ul> <em>Application</em>
3157 <li>Alignment view not redrawn properly when new
3158 alignment opened where annotation panel is visible but no
3159 annotations are present on alignment</li>
3160 <li>pasted region containing hidden columns is
3161 incorrectly displayed in new alignment window</li>
3162 <li>Jalview slow to complete operations when stdout is
3163 flooded (fix is to close the Jalview console)</li>
3164 <li>typo in AlignmentFrame->View->Hide->all but
3165 selected Rregions menu item.</li>
3166 <li>inconsistent group submenu and Format submenu entry
3167 'Un' or 'Non'conserved</li>
3168 <li>Sequence feature settings are being shared by
3169 multiple distinct alignments</li>
3170 <li>group annotation not recreated when tree partition is
3172 <li>double click on group annotation to select sequences
3173 does not propagate to associated trees</li>
3174 <li>Mac OSX specific issues:
3176 <li>exception raised when mouse clicked on desktop
3177 window background</li>
3178 <li>Desktop menu placed on menu bar and application
3179 name set correctly</li>
3180 <li>sequence feature settings not wide enough for the
3181 save feature colourscheme button</li>
3190 <div align="center">
3191 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3194 <td><em>New Capabilities</em>
3196 <li>URL links generated from description line for
3197 regular-expression based URL links (applet and application)
3199 <li>Non-positional feature URL links are shown in link
3201 <li>Linked viewing of nucleic acid sequences and
3203 <li>Automatic Scrolling option in View menu to display
3204 the currently highlighted region of an alignment.</li>
3205 <li>Order an alignment by sequence length, or using the
3206 average score or total feature count for each sequence.</li>
3207 <li>Shading features by score or associated description</li>
3208 <li>Subdivide alignment and groups based on identity of
3209 selected subsequence (Make Groups from Selection).</li>
3210 <li>New hide/show options including Shift+Control+H to
3211 hide everything but the currently selected region.</li>
3212 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3213 </ul> <em>Application</em>
3215 <li>Fetch DB References capabilities and UI expanded to
3216 support retrieval from DAS sequence sources</li>
3217 <li>Local DAS Sequence sources can be added via the
3218 command line or via the Add local source dialog box.</li>
3219 <li>DAS Dbref and DbxRef feature types are parsed as
3220 database references and protein_name is parsed as
3221 description line (BioSapiens terms).</li>
3222 <li>Enable or disable non-positional feature and database
3223 references in sequence ID tooltip from View menu in
3225 <!-- <li>New hidden columns and rows and representatives capabilities
3226 in annotations file (in progress - not yet fully implemented)</li> -->
3227 <li>Group-associated consensus, sequence logos and
3228 conservation plots</li>
3229 <li>Symbol distributions for each column can be exported
3230 and visualized as sequence logos</li>
3231 <li>Optionally scale multi-character column labels to fit
3232 within each column of annotation row<!-- todo for applet -->
3234 <li>Optional automatic sort of associated alignment view
3235 when a new tree is opened.</li>
3236 <li>Jalview Java Console</li>
3237 <li>Better placement of desktop window when moving
3238 between different screens.</li>
3239 <li>New preference items for sequence ID tooltip and
3240 consensus annotation</li>
3241 <li>Client to submit sequences and IDs to Envision2
3243 <li><em>Vamsas Capabilities</em>
3245 <li>Improved VAMSAS synchronization (Jalview archive
3246 used to preserve views, structures, and tree display
3248 <li>Import of vamsas documents from disk or URL via
3250 <li>Sharing of selected regions between views and
3251 with other VAMSAS applications (Experimental feature!)</li>
3252 <li>Updated API to VAMSAS version 0.2</li>
3254 </ul> <em>Applet</em>
3256 <li>Middle button resizes annotation row height</li>
3259 <li>sortByTree (true/false) - automatically sort the
3260 associated alignment view by the tree when a new tree is
3262 <li>showTreeBootstraps (true/false) - show or hide
3263 branch bootstraps (default is to show them if available)</li>
3264 <li>showTreeDistances (true/false) - show or hide
3265 branch lengths (default is to show them if available)</li>
3266 <li>showUnlinkedTreeNodes (true/false) - indicate if
3267 unassociated nodes should be highlighted in the tree
3269 <li>heightScale and widthScale (1.0 or more) -
3270 increase the height or width of a cell in the alignment
3271 grid relative to the current font size.</li>
3274 <li>Non-positional features displayed in sequence ID
3276 </ul> <em>Other</em>
3278 <li>Features format: graduated colour definitions and
3279 specification of feature scores</li>
3280 <li>Alignment Annotations format: new keywords for group
3281 associated annotation (GROUP_REF) and annotation row display
3282 properties (ROW_PROPERTIES)</li>
3283 <li>XML formats extended to support graduated feature
3284 colourschemes, group associated annotation, and profile
3285 visualization settings.</li></td>
3288 <li>Source field in GFF files parsed as feature source
3289 rather than description</li>
3290 <li>Non-positional features are now included in sequence
3291 feature and gff files (controlled via non-positional feature
3292 visibility in tooltip).</li>
3293 <li>URL links generated for all feature links (bugfix)</li>
3294 <li>Added URL embedding instructions to features file
3296 <li>Codons containing ambiguous nucleotides translated as
3297 'X' in peptide product</li>
3298 <li>Match case switch in find dialog box works for both
3299 sequence ID and sequence string and query strings do not
3300 have to be in upper case to match case-insensitively.</li>
3301 <li>AMSA files only contain first column of
3302 multi-character column annotation labels</li>
3303 <li>Jalview Annotation File generation/parsing consistent
3304 with documentation (e.g. Stockholm annotation can be
3305 exported and re-imported)</li>
3306 <li>PDB files without embedded PDB IDs given a friendly
3308 <li>Find incrementally searches ID string matches as well
3309 as subsequence matches, and correctly reports total number
3313 <li>Better handling of exceptions during sequence
3315 <li>Dasobert generated non-positional feature URL
3316 link text excludes the start_end suffix</li>
3317 <li>DAS feature and source retrieval buttons disabled
3318 when fetch or registry operations in progress.</li>
3319 <li>PDB files retrieved from URLs are cached properly</li>
3320 <li>Sequence description lines properly shared via
3322 <li>Sequence fetcher fetches multiple records for all
3324 <li>Ensured that command line das feature retrieval
3325 completes before alignment figures are generated.</li>
3326 <li>Reduced time taken when opening file browser for
3328 <li>isAligned check prior to calculating tree, PCA or
3329 submitting an MSA to JNet now excludes hidden sequences.</li>
3330 <li>User defined group colours properly recovered
3331 from Jalview projects.</li>
3340 <div align="center">
3341 <strong>2.4.0.b2</strong><br> 28/10/2009
3346 <li>Experimental support for google analytics usage
3348 <li>Jalview privacy settings (user preferences and docs).</li>
3353 <li>Race condition in applet preventing startup in
3355 <li>Exception when feature created from selection beyond
3356 length of sequence.</li>
3357 <li>Allow synthetic PDB files to be imported gracefully</li>
3358 <li>Sequence associated annotation rows associate with
3359 all sequences with a given id</li>
3360 <li>Find function matches case-insensitively for sequence
3361 ID string searches</li>
3362 <li>Non-standard characters do not cause pairwise
3363 alignment to fail with exception</li>
3364 </ul> <em>Application Issues</em>
3366 <li>Sequences are now validated against EMBL database</li>
3367 <li>Sequence fetcher fetches multiple records for all
3369 </ul> <em>InstallAnywhere Issues</em>
3371 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3372 issue with installAnywhere mechanism)</li>
3373 <li>Command line launching of JARs from InstallAnywhere
3374 version (java class versioning error fixed)</li>
3381 <div align="center">
3382 <strong>2.4</strong><br> 27/8/2008
3385 <td><em>User Interface</em>
3387 <li>Linked highlighting of codon and amino acid from
3388 translation and protein products</li>
3389 <li>Linked highlighting of structure associated with
3390 residue mapping to codon position</li>
3391 <li>Sequence Fetcher provides example accession numbers
3392 and 'clear' button</li>
3393 <li>MemoryMonitor added as an option under Desktop's
3395 <li>Extract score function to parse whitespace separated
3396 numeric data in description line</li>
3397 <li>Column labels in alignment annotation can be centred.</li>
3398 <li>Tooltip for sequence associated annotation give name
3400 </ul> <em>Web Services and URL fetching</em>
3402 <li>JPred3 web service</li>
3403 <li>Prototype sequence search client (no public services
3405 <li>Fetch either seed alignment or full alignment from
3407 <li>URL Links created for matching database cross
3408 references as well as sequence ID</li>
3409 <li>URL Links can be created using regular-expressions</li>
3410 </ul> <em>Sequence Database Connectivity</em>
3412 <li>Retrieval of cross-referenced sequences from other
3414 <li>Generalised database reference retrieval and
3415 validation to all fetchable databases</li>
3416 <li>Fetch sequences from DAS sources supporting the
3417 sequence command</li>
3418 </ul> <em>Import and Export</em>
3419 <li>export annotation rows as CSV for spreadsheet import</li>
3420 <li>Jalview projects record alignment dataset associations,
3421 EMBL products, and cDNA sequence mappings</li>
3422 <li>Sequence Group colour can be specified in Annotation
3424 <li>Ad-hoc colouring of group in Annotation File using RGB
3425 triplet as name of colourscheme</li>
3426 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3428 <li>treenode binding for VAMSAS tree exchange</li>
3429 <li>local editing and update of sequences in VAMSAS
3430 alignments (experimental)</li>
3431 <li>Create new or select existing session to join</li>
3432 <li>load and save of vamsas documents</li>
3433 </ul> <em>Application command line</em>
3435 <li>-tree parameter to open trees (introduced for passing
3437 <li>-fetchfrom command line argument to specify nicknames
3438 of DAS servers to query for alignment features</li>
3439 <li>-dasserver command line argument to add new servers
3440 that are also automatically queried for features</li>
3441 <li>-groovy command line argument executes a given groovy
3442 script after all input data has been loaded and parsed</li>
3443 </ul> <em>Applet-Application data exchange</em>
3445 <li>Trees passed as applet parameters can be passed to
3446 application (when using "View in full
3447 application")</li>
3448 </ul> <em>Applet Parameters</em>
3450 <li>feature group display control parameter</li>
3451 <li>debug parameter</li>
3452 <li>showbutton parameter</li>
3453 </ul> <em>Applet API methods</em>
3455 <li>newView public method</li>
3456 <li>Window (current view) specific get/set public methods</li>
3457 <li>Feature display control methods</li>
3458 <li>get list of currently selected sequences</li>
3459 </ul> <em>New Jalview distribution features</em>
3461 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3462 <li>RELEASE file gives build properties for the latest
3463 Jalview release.</li>
3464 <li>Java 1.1 Applet build made easier and donotobfuscate
3465 property controls execution of obfuscator</li>
3466 <li>Build target for generating source distribution</li>
3467 <li>Debug flag for javacc</li>
3468 <li>.jalview_properties file is documented (slightly) in
3469 jalview.bin.Cache</li>
3470 <li>Continuous Build Integration for stable and
3471 development version of Application, Applet and source
3476 <li>selected region output includes visible annotations
3477 (for certain formats)</li>
3478 <li>edit label/displaychar contains existing label/char
3480 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3481 <li>shorter peptide product names from EMBL records</li>
3482 <li>Newick string generator makes compact representations</li>
3483 <li>bootstrap values parsed correctly for tree files with
3485 <li>pathological filechooser bug avoided by not allowing
3486 filenames containing a ':'</li>
3487 <li>Fixed exception when parsing GFF files containing
3488 global sequence features</li>
3489 <li>Alignment datasets are finalized only when number of
3490 references from alignment sequences goes to zero</li>
3491 <li>Close of tree branch colour box without colour
3492 selection causes cascading exceptions</li>
3493 <li>occasional negative imgwidth exceptions</li>
3494 <li>better reporting of non-fatal warnings to user when
3495 file parsing fails.</li>
3496 <li>Save works when Jalview project is default format</li>
3497 <li>Save as dialog opened if current alignment format is
3498 not a valid output format</li>
3499 <li>UniProt canonical names introduced for both das and
3501 <li>Histidine should be midblue (not pink!) in Zappo</li>
3502 <li>error messages passed up and output when data read
3504 <li>edit undo recovers previous dataset sequence when
3505 sequence is edited</li>
3506 <li>allow PDB files without pdb ID HEADER lines (like
3507 those generated by MODELLER) to be read in properly</li>
3508 <li>allow reading of JPred concise files as a normal
3510 <li>Stockholm annotation parsing and alignment properties
3511 import fixed for PFAM records</li>
3512 <li>Structure view windows have correct name in Desktop
3514 <li>annotation consisting of sequence associated scores
3515 can be read and written correctly to annotation file</li>
3516 <li>Aligned cDNA translation to aligned peptide works
3518 <li>Fixed display of hidden sequence markers and
3519 non-italic font for representatives in Applet</li>
3520 <li>Applet Menus are always embedded in applet window on
3522 <li>Newly shown features appear at top of stack (in
3524 <li>Annotations added via parameter not drawn properly
3525 due to null pointer exceptions</li>
3526 <li>Secondary structure lines are drawn starting from
3527 first column of alignment</li>
3528 <li>UniProt XML import updated for new schema release in
3530 <li>Sequence feature to sequence ID match for Features
3531 file is case-insensitive</li>
3532 <li>Sequence features read from Features file appended to
3533 all sequences with matching IDs</li>
3534 <li>PDB structure coloured correctly for associated views
3535 containing a sub-sequence</li>
3536 <li>PDB files can be retrieved by applet from Jar files</li>
3537 <li>feature and annotation file applet parameters
3538 referring to different directories are retrieved correctly</li>
3539 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3540 <li>Fixed application hang whilst waiting for
3541 splash-screen version check to complete</li>
3542 <li>Applet properly URLencodes input parameter values
3543 when passing them to the launchApp service</li>
3544 <li>display name and local features preserved in results
3545 retrieved from web service</li>
3546 <li>Visual delay indication for sequence retrieval and
3547 sequence fetcher initialisation</li>
3548 <li>updated Application to use DAS 1.53e version of
3549 dasobert DAS client</li>
3550 <li>Re-instated Full AMSA support and .amsa file
3552 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3560 <div align="center">
3561 <strong>2.3</strong><br> 9/5/07
3566 <li>Jmol 11.0.2 integration</li>
3567 <li>PDB views stored in Jalview XML files</li>
3568 <li>Slide sequences</li>
3569 <li>Edit sequence in place</li>
3570 <li>EMBL CDS features</li>
3571 <li>DAS Feature mapping</li>
3572 <li>Feature ordering</li>
3573 <li>Alignment Properties</li>
3574 <li>Annotation Scores</li>
3575 <li>Sort by scores</li>
3576 <li>Feature/annotation editing in applet</li>
3581 <li>Headless state operation in 2.2.1</li>
3582 <li>Incorrect and unstable DNA pairwise alignment</li>
3583 <li>Cut and paste of sequences with annotation</li>
3584 <li>Feature group display state in XML</li>
3585 <li>Feature ordering in XML</li>
3586 <li>blc file iteration selection using filename # suffix</li>
3587 <li>Stockholm alignment properties</li>
3588 <li>Stockhom alignment secondary structure annotation</li>
3589 <li>2.2.1 applet had no feature transparency</li>
3590 <li>Number pad keys can be used in cursor mode</li>
3591 <li>Structure Viewer mirror image resolved</li>
3598 <div align="center">
3599 <strong>2.2.1</strong><br> 12/2/07
3604 <li>Non standard characters can be read and displayed
3605 <li>Annotations/Features can be imported/exported to the
3607 <li>Applet allows editing of sequence/annotation/group
3608 name & description
3609 <li>Preference setting to display sequence name in
3611 <li>Annotation file format extended to allow
3612 Sequence_groups to be defined
3613 <li>Default opening of alignment overview panel can be
3614 specified in preferences
3615 <li>PDB residue numbering annotation added to associated
3621 <li>Applet crash under certain Linux OS with Java 1.6
3623 <li>Annotation file export / import bugs fixed
3624 <li>PNG / EPS image output bugs fixed
3630 <div align="center">
3631 <strong>2.2</strong><br> 27/11/06
3636 <li>Multiple views on alignment
3637 <li>Sequence feature editing
3638 <li>"Reload" alignment
3639 <li>"Save" to current filename
3640 <li>Background dependent text colour
3641 <li>Right align sequence ids
3642 <li>User-defined lower case residue colours
3645 <li>Menu item accelerator keys
3646 <li>Control-V pastes to current alignment
3647 <li>Cancel button for DAS Feature Fetching
3648 <li>PCA and PDB Viewers zoom via mouse roller
3649 <li>User-defined sub-tree colours and sub-tree selection
3651 <li>'New Window' button on the 'Output to Text box'
3656 <li>New memory efficient Undo/Redo System
3657 <li>Optimised symbol lookups and conservation/consensus
3659 <li>Region Conservation/Consensus recalculated after
3661 <li>Fixed Remove Empty Columns Bug (empty columns at end
3663 <li>Slowed DAS Feature Fetching for increased robustness.
3665 <li>Made angle brackets in ASCII feature descriptions
3667 <li>Re-instated Zoom function for PCA
3668 <li>Sequence descriptions conserved in web service
3670 <li>UniProt ID discoverer uses any word separated by
3672 <li>WsDbFetch query/result association resolved
3673 <li>Tree leaf to sequence mapping improved
3674 <li>Smooth fonts switch moved to FontChooser dialog box.
3681 <div align="center">
3682 <strong>2.1.1</strong><br> 12/9/06
3687 <li>Copy consensus sequence to clipboard</li>
3692 <li>Image output - rightmost residues are rendered if
3693 sequence id panel has been resized</li>
3694 <li>Image output - all offscreen group boundaries are
3696 <li>Annotation files with sequence references - all
3697 elements in file are relative to sequence position</li>
3698 <li>Mac Applet users can use Alt key for group editing</li>
3704 <div align="center">
3705 <strong>2.1</strong><br> 22/8/06
3710 <li>MAFFT Multiple Alignment in default Web Service list</li>
3711 <li>DAS Feature fetching</li>
3712 <li>Hide sequences and columns</li>
3713 <li>Export Annotations and Features</li>
3714 <li>GFF file reading / writing</li>
3715 <li>Associate structures with sequences from local PDB
3717 <li>Add sequences to exisiting alignment</li>
3718 <li>Recently opened files / URL lists</li>
3719 <li>Applet can launch the full application</li>
3720 <li>Applet has transparency for features (Java 1.2
3722 <li>Applet has user defined colours parameter</li>
3723 <li>Applet can load sequences from parameter
3724 "sequence<em>x</em>"
3730 <li>Redundancy Panel reinstalled in the Applet</li>
3731 <li>Monospaced font - EPS / rescaling bug fixed</li>
3732 <li>Annotation files with sequence references bug fixed</li>
3738 <div align="center">
3739 <strong>2.08.1</strong><br> 2/5/06
3744 <li>Change case of selected region from Popup menu</li>
3745 <li>Choose to match case when searching</li>
3746 <li>Middle mouse button and mouse movement can compress /
3747 expand the visible width and height of the alignment</li>
3752 <li>Annotation Panel displays complete JNet results</li>
3758 <div align="center">
3759 <strong>2.08b</strong><br> 18/4/06
3765 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3766 <li>Righthand label on wrapped alignments shows correct
3773 <div align="center">
3774 <strong>2.08</strong><br> 10/4/06
3779 <li>Editing can be locked to the selection area</li>
3780 <li>Keyboard editing</li>
3781 <li>Create sequence features from searches</li>
3782 <li>Precalculated annotations can be loaded onto
3784 <li>Features file allows grouping of features</li>
3785 <li>Annotation Colouring scheme added</li>
3786 <li>Smooth fonts off by default - Faster rendering</li>
3787 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3792 <li>Drag & Drop fixed on Linux</li>
3793 <li>Jalview Archive file faster to load/save, sequence
3794 descriptions saved.</li>
3800 <div align="center">
3801 <strong>2.07</strong><br> 12/12/05
3806 <li>PDB Structure Viewer enhanced</li>
3807 <li>Sequence Feature retrieval and display enhanced</li>
3808 <li>Choose to output sequence start-end after sequence
3809 name for file output</li>
3810 <li>Sequence Fetcher WSDBFetch@EBI</li>
3811 <li>Applet can read feature files, PDB files and can be
3812 used for HTML form input</li>
3817 <li>HTML output writes groups and features</li>
3818 <li>Group editing is Control and mouse click</li>
3819 <li>File IO bugs</li>
3825 <div align="center">
3826 <strong>2.06</strong><br> 28/9/05
3831 <li>View annotations in wrapped mode</li>
3832 <li>More options for PCA viewer</li>
3837 <li>GUI bugs resolved</li>
3838 <li>Runs with -nodisplay from command line</li>
3844 <div align="center">
3845 <strong>2.05b</strong><br> 15/9/05
3850 <li>Choose EPS export as lineart or text</li>
3851 <li>Jar files are executable</li>
3852 <li>Can read in Uracil - maps to unknown residue</li>
3857 <li>Known OutOfMemory errors give warning message</li>
3858 <li>Overview window calculated more efficiently</li>
3859 <li>Several GUI bugs resolved</li>
3865 <div align="center">
3866 <strong>2.05</strong><br> 30/8/05
3871 <li>Edit and annotate in "Wrapped" view</li>
3876 <li>Several GUI bugs resolved</li>
3882 <div align="center">
3883 <strong>2.04</strong><br> 24/8/05
3888 <li>Hold down mouse wheel & scroll to change font
3894 <li>Improved JPred client reliability</li>
3895 <li>Improved loading of Jalview files</li>
3901 <div align="center">
3902 <strong>2.03</strong><br> 18/8/05
3907 <li>Set Proxy server name and port in preferences</li>
3908 <li>Multiple URL links from sequence ids</li>
3909 <li>User Defined Colours can have a scheme name and added
3911 <li>Choose to ignore gaps in consensus calculation</li>
3912 <li>Unix users can set default web browser</li>
3913 <li>Runs without GUI for batch processing</li>
3914 <li>Dynamically generated Web Service Menus</li>
3919 <li>InstallAnywhere download for Sparc Solaris</li>
3925 <div align="center">
3926 <strong>2.02</strong><br> 18/7/05
3932 <li>Copy & Paste order of sequences maintains
3933 alignment order.</li>
3939 <div align="center">
3940 <strong>2.01</strong><br> 12/7/05
3945 <li>Use delete key for deleting selection.</li>
3946 <li>Use Mouse wheel to scroll sequences.</li>
3947 <li>Help file updated to describe how to add alignment
3949 <li>Version and build date written to build properties
3951 <li>InstallAnywhere installation will check for updates
3952 at launch of Jalview.</li>
3957 <li>Delete gaps bug fixed.</li>
3958 <li>FileChooser sorts columns.</li>
3959 <li>Can remove groups one by one.</li>
3960 <li>Filechooser icons installed.</li>
3961 <li>Finder ignores return character when searching.
3962 Return key will initiate a search.<br>
3969 <div align="center">
3970 <strong>2.0</strong><br> 20/6/05
3975 <li>New codebase</li>