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.2.10.5">2.10.5</a><br /> <em>6/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-3101 -->Default memory for Jalview webstart and
81 InstallAnywhere increased to 1G.
84 <!-- JAL-247 -->Hidden sequence markers and representative
85 sequence bolding included when exporting alignment as EPS,
86 SVG, PNG or HTML. <em>Display is configured via the
87 Format menu, or for command-line use via a jalview
91 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
92 API and sequence data now imported as JSON.
95 <!-- JAL-3065 -->Change in recommended way of starting
96 Jalview via a Java command line: add jars in lib directory
97 to CLASSPATH, rather than via the deprecated java.ext.dirs
104 <!-- JAL-3047 -->Support added to execute test suite
105 instrumented with <a href="http://openclover.org/">Open
110 <td><div align="left">
114 <!-- JAL-3087 -->Corrupted display when switching to
115 wrapped mode when sequence panel's vertical scrollbar is
119 <!-- JAL-3003 -->Alignment is black in exported EPS file
120 when sequences are selected in exported view.</em>
123 <!-- JAL-3059 -->Groups with different coloured borders
124 aren't rendered with correct colour.
127 <!-- JAL-3092 -->Jalview could hang when importing certain
128 types of knotted RNA secondary structure.
131 <!-- JAL-3095 -->Sequence highlight and selection in
132 trimmed VARNA 2D structure is incorrect for sequences that
136 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
137 annotation when columns are inserted into an alignment,
138 and when exporting as Stockholm flatfile.
141 <!-- JAL-3053 -->Jalview annotation rows containing upper
142 and lower-case 'E' and 'H' do not automatically get
143 treated as RNA secondary structure.
146 <em>Java 10 Issues</em>
149 <!-- JAL-2988 -->OSX - Can't save new files via the File
150 or export menus by typing in a name into the Save dialog
158 <td width="60" nowrap>
160 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
161 <em>7/06/2018</em></strong>
164 <td><div align="left">
168 <!-- JAL-2920 -->Use HGVS nomenclature for variant
169 annotation retrieved from Uniprot
172 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
173 onto the Jalview Desktop
177 <td><div align="left">
181 <!-- JAL-3017 -->Cannot import features with multiple
182 variant elements (blocks import of some Uniprot records)
185 <!-- JAL-2997 -->Clustal files with sequence positions in
186 right-hand column parsed correctly
189 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
190 not alignment area in exported graphic
193 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
194 window has input focus
197 <!-- JAL-2992 -->Annotation panel set too high when
198 annotation added to view (Windows)
201 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
202 network connectivity is poor
205 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
206 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
207 the currently open URL and links from a page viewed in
208 Firefox or Chrome on Windows is now fully supported. If
209 you are using Edge, only links in the page can be
210 dragged, and with Internet Explorer, only the currently
211 open URL in the browser can be dropped onto Jalview.</em>
217 <td width="60" nowrap>
219 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
222 <td><div align="left">
226 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
227 for disabling automatic superposition of multiple
228 structures and open structures in existing views
231 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
232 ID and annotation area margins can be click-dragged to
236 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
240 <!-- JAL-2759 -->Improved performance for large alignments
241 and lots of hidden columns
244 <!-- JAL-2593 -->Improved performance when rendering lots
245 of features (particularly when transparency is disabled)
250 <td><div align="left">
253 <!-- JAL-2899 -->Structure and Overview aren't updated
254 when Colour By Annotation threshold slider is adjusted
257 <!-- JAL-2778 -->Slow redraw when Overview panel shown
258 overlapping alignment panel
261 <!-- JAL-2929 -->Overview doesn't show end of unpadded
265 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
266 improved: CDS not handled correctly if transcript has no
270 <!-- JAL-2321 -->Secondary structure and temperature
271 factor annotation not added to sequence when local PDB
272 file associated with it by drag'n'drop or structure
276 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
277 dialog doesn't import PDB files dropped on an alignment
280 <!-- JAL-2666 -->Linked scrolling via protein horizontal
281 scroll bar doesn't work for some CDS/Protein views
284 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
285 Java 1.8u153 onwards and Java 1.9u4+.
288 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
289 columns in annotation row
292 <!-- JAL-2913 -->Preferences panel's ID Width control is not
293 honored in batch mode
296 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
297 for structures added to existing Jmol view
300 <!-- JAL-2223 -->'View Mappings' includes duplicate
301 entries after importing project with multiple views
304 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
305 protein sequences via SIFTS from associated PDB entries
306 with negative residue numbers or missing residues fails
309 <!-- JAL-2952 -->Exception when shading sequence with negative
310 Temperature Factor values from annotated PDB files (e.g.
311 as generated by CONSURF)
314 <!-- JAL-2920 -->Uniprot 'sequence variant' features
315 tooltip doesn't include a text description of mutation
318 <!-- JAL-2922 -->Invert displayed features very slow when
319 structure and/or overview windows are also shown
322 <!-- JAL-2954 -->Selecting columns from highlighted regions
323 very slow for alignments with large numbers of sequences
326 <!-- JAL-2925 -->Copy Consensus fails for group consensus
327 with 'StringIndexOutOfBounds'
330 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
331 platforms running Java 10
334 <!-- JAL-2960 -->Adding a structure to existing structure
335 view appears to do nothing because the view is hidden behind the alignment view
341 <!-- JAL-2926 -->Copy consensus sequence option in applet
342 should copy the group consensus when popup is opened on it
348 <!-- JAL-2913 -->Fixed ID width preference is not respected
351 <em>New Known Defects</em>
354 <!-- JAL-2973 --> Exceptions occasionally raised when
355 editing a large alignment and overview is displayed
358 <!-- JAL-2974 -->'Overview updating' progress bar is shown
359 repeatedly after a series of edits even when the overview
360 is no longer reflecting updates
363 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
364 structures for protein subsequence (if 'Trim Retrieved
365 Sequences' enabled) or Ensembl isoforms (Workaround in
366 2.10.4 is to fail back to N&W mapping)
373 <td width="60" nowrap>
375 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
378 <td><div align="left">
379 <ul><li>Updated Certum Codesigning Certificate
380 (Valid till 30th November 2018)</li></ul></div></td>
381 <td><div align="left">
384 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
385 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
386 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
387 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
388 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
389 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
390 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
396 <td width="60" nowrap>
398 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
401 <td><div align="left">
405 <!-- JAL-2446 -->Faster and more efficient management and
406 rendering of sequence features
409 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
410 429 rate limit request hander
413 <!-- JAL-2773 -->Structure views don't get updated unless
414 their colours have changed
417 <!-- JAL-2495 -->All linked sequences are highlighted for
418 a structure mousover (Jmol) or selection (Chimera)
421 <!-- JAL-2790 -->'Cancel' button in progress bar for
422 JABAWS AACon, RNAAliFold and Disorder prediction jobs
425 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
426 view from Ensembl locus cross-references
429 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
433 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
434 feature can be disabled
437 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
438 PDB easier retrieval of sequences for lists of IDs
441 <!-- JAL-2758 -->Short names for sequences retrieved from
447 <li>Groovy interpreter updated to 2.4.12</li>
448 <li>Example groovy script for generating a matrix of
449 percent identity scores for current alignment.</li>
451 <em>Testing and Deployment</em>
454 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
458 <td><div align="left">
462 <!-- JAL-2643 -->Pressing tab after updating the colour
463 threshold text field doesn't trigger an update to the
467 <!-- JAL-2682 -->Race condition when parsing sequence ID
471 <!-- JAL-2608 -->Overview windows are also closed when
472 alignment window is closed
475 <!-- JAL-2548 -->Export of features doesn't always respect
479 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
480 takes a long time in Cursor mode
486 <!-- JAL-2777 -->Structures with whitespace chainCode
487 cannot be viewed in Chimera
490 <!-- JAL-2728 -->Protein annotation panel too high in
494 <!-- JAL-2757 -->Can't edit the query after the server
495 error warning icon is shown in Uniprot and PDB Free Text
499 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
502 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
505 <!-- JAL-2739 -->Hidden column marker in last column not
506 rendered when switching back from Wrapped to normal view
509 <!-- JAL-2768 -->Annotation display corrupted when
510 scrolling right in unwapped alignment view
513 <!-- JAL-2542 -->Existing features on subsequence
514 incorrectly relocated when full sequence retrieved from
518 <!-- JAL-2733 -->Last reported memory still shown when
519 Desktop->Show Memory is unticked (OSX only)
522 <!-- JAL-2658 -->Amend Features dialog doesn't allow
523 features of same type and group to be selected for
527 <!-- JAL-2524 -->Jalview becomes sluggish in wide
528 alignments when hidden columns are present
531 <!-- JAL-2392 -->Jalview freezes when loading and
532 displaying several structures
535 <!-- JAL-2732 -->Black outlines left after resizing or
539 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
540 within the Jalview desktop on OSX
543 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
544 when in wrapped alignment mode
547 <!-- JAL-2636 -->Scale mark not shown when close to right
548 hand end of alignment
551 <!-- JAL-2684 -->Pairwise alignment of selected regions of
552 each selected sequence do not have correct start/end
556 <!-- JAL-2793 -->Alignment ruler height set incorrectly
557 after canceling the Alignment Window's Font dialog
560 <!-- JAL-2036 -->Show cross-references not enabled after
561 restoring project until a new view is created
564 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
565 URL links appears when only default EMBL-EBI link is
566 configured (since 2.10.2b2)
569 <!-- JAL-2775 -->Overview redraws whole window when box
573 <!-- JAL-2225 -->Structure viewer doesn't map all chains
574 in a multi-chain structure when viewing alignment
575 involving more than one chain (since 2.10)
578 <!-- JAL-2811 -->Double residue highlights in cursor mode
579 if new selection moves alignment window
582 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
583 arrow key in cursor mode to pass hidden column marker
586 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
587 that produces correctly annotated transcripts and products
590 <!-- JAL-2776 -->Toggling a feature group after first time
591 doesn't update associated structure view
594 <em>Applet</em><br />
597 <!-- JAL-2687 -->Concurrent modification exception when
598 closing alignment panel
601 <em>BioJSON</em><br />
604 <!-- JAL-2546 -->BioJSON export does not preserve
605 non-positional features
608 <em>New Known Issues</em>
611 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
612 sequence features correctly (for many previous versions of
616 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
617 using cursor in wrapped panel other than top
620 <!-- JAL-2791 -->Select columns containing feature ignores
621 graduated colour threshold
624 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
625 always preserve numbering and sequence features
628 <em>Known Java 9 Issues</em>
631 <!-- JAL-2902 -->Groovy Console very slow to open and is
632 not responsive when entering characters (Webstart, Java
639 <td width="60" nowrap>
641 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
642 <em>2/10/2017</em></strong>
645 <td><div align="left">
646 <em>New features in Jalview Desktop</em>
649 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
651 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
655 <td><div align="left">
659 <td width="60" nowrap>
661 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
662 <em>7/9/2017</em></strong>
665 <td><div align="left">
669 <!-- JAL-2588 -->Show gaps in overview window by colouring
670 in grey (sequences used to be coloured grey, and gaps were
674 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
678 <!-- JAL-2587 -->Overview updates immediately on increase
679 in size and progress bar shown as higher resolution
680 overview is recalculated
685 <td><div align="left">
689 <!-- JAL-2664 -->Overview window redraws every hidden
690 column region row by row
693 <!-- JAL-2681 -->duplicate protein sequences shown after
694 retrieving Ensembl crossrefs for sequences from Uniprot
697 <!-- JAL-2603 -->Overview window throws NPE if show boxes
698 format setting is unticked
701 <!-- JAL-2610 -->Groups are coloured wrongly in overview
702 if group has show boxes format setting unticked
705 <!-- JAL-2672,JAL-2665 -->Redraw problems when
706 autoscrolling whilst dragging current selection group to
707 include sequences and columns not currently displayed
710 <!-- JAL-2691 -->Not all chains are mapped when multimeric
711 assemblies are imported via CIF file
714 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
715 displayed when threshold or conservation colouring is also
719 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
723 <!-- JAL-2673 -->Jalview continues to scroll after
724 dragging a selected region off the visible region of the
728 <!-- JAL-2724 -->Cannot apply annotation based
729 colourscheme to all groups in a view
732 <!-- JAL-2511 -->IDs don't line up with sequences
733 initially after font size change using the Font chooser or
740 <td width="60" nowrap>
742 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
745 <td><div align="left">
746 <em>Calculations</em>
750 <!-- JAL-1933 -->Occupancy annotation row shows number of
751 ungapped positions in each column of the alignment.
754 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
755 a calculation dialog box
758 <!-- JAL-2379 -->Revised implementation of PCA for speed
759 and memory efficiency (~30x faster)
762 <!-- JAL-2403 -->Revised implementation of sequence
763 similarity scores as used by Tree, PCA, Shading Consensus
764 and other calculations
767 <!-- JAL-2416 -->Score matrices are stored as resource
768 files within the Jalview codebase
771 <!-- JAL-2500 -->Trees computed on Sequence Feature
772 Similarity may have different topology due to increased
779 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
780 model for alignments and groups
783 <!-- JAL-384 -->Custom shading schemes created via groovy
790 <!-- JAL-2526 -->Efficiency improvements for interacting
791 with alignment and overview windows
794 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
798 <!-- JAL-2388 -->Hidden columns and sequences can be
802 <!-- JAL-2611 -->Click-drag in visible area allows fine
803 adjustment of visible position
807 <em>Data import/export</em>
810 <!-- JAL-2535 -->Posterior probability annotation from
811 Stockholm files imported as sequence associated annotation
814 <!-- JAL-2507 -->More robust per-sequence positional
815 annotation input/output via stockholm flatfile
818 <!-- JAL-2533 -->Sequence names don't include file
819 extension when importing structure files without embedded
820 names or PDB accessions
823 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
824 format sequence substitution matrices
827 <em>User Interface</em>
830 <!-- JAL-2447 --> Experimental Features Checkbox in
831 Desktop's Tools menu to hide or show untested features in
835 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
836 via Overview or sequence motif search operations
839 <!-- JAL-2547 -->Amend sequence features dialog box can be
840 opened by double clicking gaps within sequence feature
844 <!-- JAL-1476 -->Status bar message shown when not enough
845 aligned positions were available to create a 3D structure
849 <em>3D Structure</em>
852 <!-- JAL-2430 -->Hidden regions in alignment views are not
853 coloured in linked structure views
856 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
857 file-based command exchange
860 <!-- JAL-2375 -->Structure chooser automatically shows
861 Cached Structures rather than querying the PDBe if
862 structures are already available for sequences
865 <!-- JAL-2520 -->Structures imported via URL are cached in
866 the Jalview project rather than downloaded again when the
870 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
871 to transfer Chimera's structure attributes as Jalview
872 features, and vice-versa (<strong>Experimental
876 <em>Web Services</em>
879 <!-- JAL-2549 -->Updated JABAWS client to v2.2
882 <!-- JAL-2335 -->Filter non-standard amino acids and
883 nucleotides when submitting to AACon and other MSA
887 <!-- JAL-2316, -->URLs for viewing database
888 cross-references provided by identifiers.org and the
896 <!-- JAL-2344 -->FileFormatI interface for describing and
897 identifying file formats (instead of String constants)
900 <!-- JAL-2228 -->FeatureCounter script refactored for
901 efficiency when counting all displayed features (not
902 backwards compatible with 2.10.1)
905 <em>Example files</em>
908 <!-- JAL-2631 -->Graduated feature colour style example
909 included in the example feature file
912 <em>Documentation</em>
915 <!-- JAL-2339 -->Release notes reformatted for readability
916 with the built-in Java help viewer
919 <!-- JAL-1644 -->Find documentation updated with 'search
920 sequence description' option
926 <!-- JAL-2485, -->External service integration tests for
927 Uniprot REST Free Text Search Client
930 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
933 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
938 <td><div align="left">
939 <em>Calculations</em>
942 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
943 matrix - C->R should be '-3'<br />Old matrix restored
944 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
946 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
947 Jalview's treatment of gaps in PCA and substitution matrix
948 based Tree calculations.<br /> <br />In earlier versions
949 of Jalview, gaps matching gaps were penalised, and gaps
950 matching non-gaps penalised even more. In the PCA
951 calculation, gaps were actually treated as non-gaps - so
952 different costs were applied, which meant Jalview's PCAs
953 were different to those produced by SeqSpace.<br />Jalview
954 now treats gaps in the same way as SeqSpace (ie it scores
955 them as 0). <br /> <br />Enter the following in the
956 Groovy console to restore pre-2.10.2 behaviour:<br />
957 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
958 // for 2.10.1 mode <br />
959 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
960 // to restore 2.10.2 mode <br /> <br /> <em>Note:
961 these settings will affect all subsequent tree and PCA
962 calculations (not recommended)</em></li>
964 <!-- JAL-2424 -->Fixed off-by-one bug that affected
965 scaling of branch lengths for trees computed using
966 Sequence Feature Similarity.
969 <!-- JAL-2377 -->PCA calculation could hang when
970 generating output report when working with highly
974 <!-- JAL-2544 --> Sort by features includes features to
975 right of selected region when gaps present on right-hand
979 <em>User Interface</em>
982 <!-- JAL-2346 -->Reopening Colour by annotation dialog
983 doesn't reselect a specific sequence's associated
984 annotation after it was used for colouring a view
987 <!-- JAL-2419 -->Current selection lost if popup menu
988 opened on a region of alignment without groups
991 <!-- JAL-2374 -->Popup menu not always shown for regions
992 of an alignment with overlapping groups
995 <!-- JAL-2310 -->Finder double counts if both a sequence's
996 name and description match
999 <!-- JAL-2370 -->Hiding column selection containing two
1000 hidden regions results in incorrect hidden regions
1003 <!-- JAL-2386 -->'Apply to all groups' setting when
1004 changing colour does not apply Conservation slider value
1008 <!-- JAL-2373 -->Percentage identity and conservation menu
1009 items do not show a tick or allow shading to be disabled
1012 <!-- JAL-2385 -->Conservation shading or PID threshold
1013 lost when base colourscheme changed if slider not visible
1016 <!-- JAL-2547 -->Sequence features shown in tooltip for
1017 gaps before start of features
1020 <!-- JAL-2623 -->Graduated feature colour threshold not
1021 restored to UI when feature colour is edited
1024 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1025 a time when scrolling vertically in wrapped mode.
1028 <!-- JAL-2630 -->Structure and alignment overview update
1029 as graduate feature colour settings are modified via the
1033 <!-- JAL-2034 -->Overview window doesn't always update
1034 when a group defined on the alignment is resized
1037 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1038 wrapped view result in positional status updates
1042 <!-- JAL-2563 -->Status bar doesn't show position for
1043 ambiguous amino acid and nucleotide symbols
1046 <!-- JAL-2602 -->Copy consensus sequence failed if
1047 alignment included gapped columns
1050 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1051 widgets don't permanently disappear
1054 <!-- JAL-2503 -->Cannot select or filter quantitative
1055 annotation that are shown only as column labels (e.g.
1056 T-Coffee column reliability scores)
1059 <!-- JAL-2594 -->Exception thrown if trying to create a
1060 sequence feature on gaps only
1063 <!-- JAL-2504 -->Features created with 'New feature'
1064 button from a Find inherit previously defined feature type
1065 rather than the Find query string
1068 <!-- JAL-2423 -->incorrect title in output window when
1069 exporting tree calculated in Jalview
1072 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1073 and then revealing them reorders sequences on the
1077 <!-- JAL-964 -->Group panel in sequence feature settings
1078 doesn't update to reflect available set of groups after
1079 interactively adding or modifying features
1082 <!-- JAL-2225 -->Sequence Database chooser unusable on
1086 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1087 only excluded gaps in current sequence and ignored
1094 <!-- JAL-2421 -->Overview window visible region moves
1095 erratically when hidden rows or columns are present
1098 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1099 Structure Viewer's colour menu don't correspond to
1103 <!-- JAL-2405 -->Protein specific colours only offered in
1104 colour and group colour menu for protein alignments
1107 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1108 reflect currently selected view or group's shading
1112 <!-- JAL-2624 -->Feature colour thresholds not respected
1113 when rendered on overview and structures when opacity at
1117 <!-- JAL-2589 -->User defined gap colour not shown in
1118 overview when features overlaid on alignment
1121 <em>Data import/export</em>
1124 <!-- JAL-2576 -->Very large alignments take a long time to
1128 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1129 added after a sequence was imported are not written to
1133 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1134 when importing RNA secondary structure via Stockholm
1137 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1138 not shown in correct direction for simple pseudoknots
1141 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1142 with lightGray or darkGray via features file (but can
1146 <!-- JAL-2383 -->Above PID colour threshold not recovered
1147 when alignment view imported from project
1150 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1151 structure and sequences extracted from structure files
1152 imported via URL and viewed in Jmol
1155 <!-- JAL-2520 -->Structures loaded via URL are saved in
1156 Jalview Projects rather than fetched via URL again when
1157 the project is loaded and the structure viewed
1160 <em>Web Services</em>
1163 <!-- JAL-2519 -->EnsemblGenomes example failing after
1164 release of Ensembl v.88
1167 <!-- JAL-2366 -->Proxy server address and port always
1168 appear enabled in Preferences->Connections
1171 <!-- JAL-2461 -->DAS registry not found exceptions
1172 removed from console output
1175 <!-- JAL-2582 -->Cannot retrieve protein products from
1176 Ensembl by Peptide ID
1179 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1180 created from SIFTs, and spurious 'Couldn't open structure
1181 in Chimera' errors raised after April 2017 update (problem
1182 due to 'null' string rather than empty string used for
1183 residues with no corresponding PDB mapping).
1186 <em>Application UI</em>
1189 <!-- JAL-2361 -->User Defined Colours not added to Colour
1193 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1194 case' residues (button in colourscheme editor debugged and
1195 new documentation and tooltips added)
1198 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1199 doesn't restore group-specific text colour thresholds
1202 <!-- JAL-2243 -->Feature settings panel does not update as
1203 new features are added to alignment
1206 <!-- JAL-2532 -->Cancel in feature settings reverts
1207 changes to feature colours via the Amend features dialog
1210 <!-- JAL-2506 -->Null pointer exception when attempting to
1211 edit graduated feature colour via amend features dialog
1215 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1216 selection menu changes colours of alignment views
1219 <!-- JAL-2426 -->Spurious exceptions in console raised
1220 from alignment calculation workers after alignment has
1224 <!-- JAL-1608 -->Typo in selection popup menu - Create
1225 groups now 'Create Group'
1228 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1229 Create/Undefine group doesn't always work
1232 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1233 shown again after pressing 'Cancel'
1236 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1237 adjusts start position in wrap mode
1240 <!-- JAL-2563 -->Status bar doesn't show positions for
1241 ambiguous amino acids
1244 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1245 CDS/Protein view after CDS sequences added for aligned
1249 <!-- JAL-2592 -->User defined colourschemes called 'User
1250 Defined' don't appear in Colours menu
1256 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1257 score models doesn't always result in an updated PCA plot
1260 <!-- JAL-2442 -->Features not rendered as transparent on
1261 overview or linked structure view
1264 <!-- JAL-2372 -->Colour group by conservation doesn't
1268 <!-- JAL-2517 -->Hitting Cancel after applying
1269 user-defined colourscheme doesn't restore original
1276 <!-- JAL-2314 -->Unit test failure:
1277 jalview.ws.jabaws.RNAStructExportImport setup fails
1280 <!-- JAL-2307 -->Unit test failure:
1281 jalview.ws.sifts.SiftsClientTest due to compatibility
1282 problems with deep array comparison equality asserts in
1283 successive versions of TestNG
1286 <!-- JAL-2479 -->Relocated StructureChooserTest and
1287 ParameterUtilsTest Unit tests to Network suite
1290 <em>New Known Issues</em>
1293 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1294 phase after a sequence motif find operation
1297 <!-- JAL-2550 -->Importing annotation file with rows
1298 containing just upper and lower case letters are
1299 interpreted as WUSS RNA secondary structure symbols
1302 <!-- JAL-2590 -->Cannot load and display Newick trees
1303 reliably from eggnog Ortholog database
1306 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1307 containing features of type Highlight' when 'B' is pressed
1308 to mark columns containing highlighted regions.
1311 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1312 doesn't always add secondary structure annotation.
1317 <td width="60" nowrap>
1318 <div align="center">
1319 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1322 <td><div align="left">
1326 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1327 for all consensus calculations
1330 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1333 <li>Updated Jalview's Certum code signing certificate
1336 <em>Application</em>
1339 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1340 set of database cross-references, sorted alphabetically
1343 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1344 from database cross references. Users with custom links
1345 will receive a <a href="webServices/urllinks.html#warning">warning
1346 dialog</a> asking them to update their preferences.
1349 <!-- JAL-2287-->Cancel button and escape listener on
1350 dialog warning user about disconnecting Jalview from a
1354 <!-- JAL-2320-->Jalview's Chimera control window closes if
1355 the Chimera it is connected to is shut down
1358 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1359 columns menu item to mark columns containing highlighted
1360 regions (e.g. from structure selections or results of a
1364 <!-- JAL-2284-->Command line option for batch-generation
1365 of HTML pages rendering alignment data with the BioJS
1375 <!-- JAL-2286 -->Columns with more than one modal residue
1376 are not coloured or thresholded according to percent
1377 identity (first observed in Jalview 2.8.2)
1380 <!-- JAL-2301 -->Threonine incorrectly reported as not
1384 <!-- JAL-2318 -->Updates to documentation pages (above PID
1385 threshold, amino acid properties)
1388 <!-- JAL-2292 -->Lower case residues in sequences are not
1389 reported as mapped to residues in a structure file in the
1393 <!--JAL-2324 -->Identical features with non-numeric scores
1394 could be added multiple times to a sequence
1397 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1398 bond features shown as two highlighted residues rather
1399 than a range in linked structure views, and treated
1400 correctly when selecting and computing trees from features
1403 <!-- JAL-2281-->Custom URL links for database
1404 cross-references are matched to database name regardless
1409 <em>Application</em>
1412 <!-- JAL-2282-->Custom URL links for specific database
1413 names without regular expressions also offer links from
1417 <!-- JAL-2315-->Removing a single configured link in the
1418 URL links pane in Connections preferences doesn't actually
1419 update Jalview configuration
1422 <!-- JAL-2272-->CTRL-Click on a selected region to open
1423 the alignment area popup menu doesn't work on El-Capitan
1426 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1427 files with similarly named sequences if dropped onto the
1431 <!-- JAL-2312 -->Additional mappings are shown for PDB
1432 entries where more chains exist in the PDB accession than
1433 are reported in the SIFTS file
1436 <!-- JAL-2317-->Certain structures do not get mapped to
1437 the structure view when displayed with Chimera
1440 <!-- JAL-2317-->No chains shown in the Chimera view
1441 panel's View->Show Chains submenu
1444 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1445 work for wrapped alignment views
1448 <!--JAL-2197 -->Rename UI components for running JPred
1449 predictions from 'JNet' to 'JPred'
1452 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1453 corrupted when annotation panel vertical scroll is not at
1454 first annotation row
1457 <!--JAL-2332 -->Attempting to view structure for Hen
1458 lysozyme results in a PDB Client error dialog box
1461 <!-- JAL-2319 -->Structure View's mapping report switched
1462 ranges for PDB and sequence for SIFTS
1465 SIFTS 'Not_Observed' residues mapped to non-existant
1469 <!-- <em>New Known Issues</em>
1476 <td width="60" nowrap>
1477 <div align="center">
1478 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1479 <em>25/10/2016</em></strong>
1482 <td><em>Application</em>
1484 <li>3D Structure chooser opens with 'Cached structures'
1485 view if structures already loaded</li>
1486 <li>Progress bar reports models as they are loaded to
1487 structure views</li>
1493 <li>Colour by conservation always enabled and no tick
1494 shown in menu when BLOSUM or PID shading applied</li>
1495 <li>FER1_ARATH and FER2_ARATH labels were switched in
1496 example sequences/projects/trees</li>
1498 <em>Application</em>
1500 <li>Jalview projects with views of local PDB structure
1501 files saved on Windows cannot be opened on OSX</li>
1502 <li>Multiple structure views can be opened and superposed
1503 without timeout for structures with multiple models or
1504 multiple sequences in alignment</li>
1505 <li>Cannot import or associated local PDB files without a
1506 PDB ID HEADER line</li>
1507 <li>RMSD is not output in Jmol console when superposition
1509 <li>Drag and drop of URL from Browser fails for Linux and
1510 OSX versions earlier than El Capitan</li>
1511 <li>ENA client ignores invalid content from ENA server</li>
1512 <li>Exceptions are not raised in console when ENA client
1513 attempts to fetch non-existent IDs via Fetch DB Refs UI
1515 <li>Exceptions are not raised in console when a new view
1516 is created on the alignment</li>
1517 <li>OSX right-click fixed for group selections: CMD-click
1518 to insert/remove gaps in groups and CTRL-click to open group
1521 <em>Build and deployment</em>
1523 <li>URL link checker now copes with multi-line anchor
1526 <em>New Known Issues</em>
1528 <li>Drag and drop from URL links in browsers do not work
1535 <td width="60" nowrap>
1536 <div align="center">
1537 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1540 <td><em>General</em>
1543 <!-- JAL-2124 -->Updated Spanish translations.
1546 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1547 for importing structure data to Jalview. Enables mmCIF and
1551 <!-- JAL-192 --->Alignment ruler shows positions relative to
1555 <!-- JAL-2202 -->Position/residue shown in status bar when
1556 mousing over sequence associated annotation
1559 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1563 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1564 '()', canonical '[]' and invalid '{}' base pair populations
1568 <!-- JAL-2092 -->Feature settings popup menu options for
1569 showing or hiding columns containing a feature
1572 <!-- JAL-1557 -->Edit selected group by double clicking on
1573 group and sequence associated annotation labels
1576 <!-- JAL-2236 -->Sequence name added to annotation label in
1577 select/hide columns by annotation and colour by annotation
1581 </ul> <em>Application</em>
1584 <!-- JAL-2050-->Automatically hide introns when opening a
1585 gene/transcript view
1588 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1592 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1593 structure mappings with the EMBL-EBI PDBe SIFTS database
1596 <!-- JAL-2079 -->Updated download sites used for Rfam and
1597 Pfam sources to xfam.org
1600 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1603 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1604 over sequences in Jalview
1607 <!-- JAL-2027-->Support for reverse-complement coding
1608 regions in ENA and EMBL
1611 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1612 for record retrieval via ENA rest API
1615 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1619 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1620 groovy script execution
1623 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1624 alignment window's Calculate menu
1627 <!-- JAL-1812 -->Allow groovy scripts that call
1628 Jalview.getAlignFrames() to run in headless mode
1631 <!-- JAL-2068 -->Support for creating new alignment
1632 calculation workers from groovy scripts
1635 <!-- JAL-1369 --->Store/restore reference sequence in
1639 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1640 associations are now saved/restored from project
1643 <!-- JAL-1993 -->Database selection dialog always shown
1644 before sequence fetcher is opened
1647 <!-- JAL-2183 -->Double click on an entry in Jalview's
1648 database chooser opens a sequence fetcher
1651 <!-- JAL-1563 -->Free-text search client for UniProt using
1652 the UniProt REST API
1655 <!-- JAL-2168 -->-nonews command line parameter to prevent
1656 the news reader opening
1659 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1660 querying stored in preferences
1663 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1667 <!-- JAL-1977-->Tooltips shown on database chooser
1670 <!-- JAL-391 -->Reverse complement function in calculate
1671 menu for nucleotide sequences
1674 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1675 and feature counts preserves alignment ordering (and
1676 debugged for complex feature sets).
1679 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1680 viewing structures with Jalview 2.10
1683 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1684 genome, transcript CCDS and gene ids via the Ensembl and
1685 Ensembl Genomes REST API
1688 <!-- JAL-2049 -->Protein sequence variant annotation
1689 computed for 'sequence_variant' annotation on CDS regions
1693 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1697 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1698 Ref Fetcher fails to match, or otherwise updates sequence
1699 data from external database records.
1702 <!-- JAL-2154 -->Revised Jalview Project format for
1703 efficient recovery of sequence coding and alignment
1704 annotation relationships.
1706 </ul> <!-- <em>Applet</em>
1717 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1721 <!-- JAL-2018-->Export features in Jalview format (again)
1722 includes graduated colourschemes
1725 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1726 working with big alignments and lots of hidden columns
1729 <!-- JAL-2053-->Hidden column markers not always rendered
1730 at right of alignment window
1733 <!-- JAL-2067 -->Tidied up links in help file table of
1737 <!-- JAL-2072 -->Feature based tree calculation not shown
1741 <!-- JAL-2075 -->Hidden columns ignored during feature
1742 based tree calculation
1745 <!-- JAL-2065 -->Alignment view stops updating when show
1746 unconserved enabled for group on alignment
1749 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1753 <!-- JAL-2146 -->Alignment column in status incorrectly
1754 shown as "Sequence position" when mousing over
1758 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1759 hidden columns present
1762 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1763 user created annotation added to alignment
1766 <!-- JAL-1841 -->RNA Structure consensus only computed for
1767 '()' base pair annotation
1770 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1771 in zero scores for all base pairs in RNA Structure
1775 <!-- JAL-2174-->Extend selection with columns containing
1779 <!-- JAL-2275 -->Pfam format writer puts extra space at
1780 beginning of sequence
1783 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1787 <!-- JAL-2238 -->Cannot create groups on an alignment from
1788 from a tree when t-coffee scores are shown
1791 <!-- JAL-1836,1967 -->Cannot import and view PDB
1792 structures with chains containing negative resnums (4q4h)
1795 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1799 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1800 to Clustal, PIR and PileUp output
1803 <!-- JAL-2008 -->Reordering sequence features that are
1804 not visible causes alignment window to repaint
1807 <!-- JAL-2006 -->Threshold sliders don't work in
1808 graduated colour and colour by annotation row for e-value
1809 scores associated with features and annotation rows
1812 <!-- JAL-1797 -->amino acid physicochemical conservation
1813 calculation should be case independent
1816 <!-- JAL-2173 -->Remove annotation also updates hidden
1820 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1821 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1822 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1825 <!-- JAL-2065 -->Null pointer exceptions and redraw
1826 problems when reference sequence defined and 'show
1827 non-conserved' enabled
1830 <!-- JAL-1306 -->Quality and Conservation are now shown on
1831 load even when Consensus calculation is disabled
1834 <!-- JAL-1932 -->Remove right on penultimate column of
1835 alignment does nothing
1838 <em>Application</em>
1841 <!-- JAL-1552-->URLs and links can't be imported by
1842 drag'n'drop on OSX when launched via webstart (note - not
1843 yet fixed for El Capitan)
1846 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1847 output when running on non-gb/us i18n platforms
1850 <!-- JAL-1944 -->Error thrown when exporting a view with
1851 hidden sequences as flat-file alignment
1854 <!-- JAL-2030-->InstallAnywhere distribution fails when
1858 <!-- JAL-2080-->Jalview very slow to launch via webstart
1859 (also hotfix for 2.9.0b2)
1862 <!-- JAL-2085 -->Cannot save project when view has a
1863 reference sequence defined
1866 <!-- JAL-1011 -->Columns are suddenly selected in other
1867 alignments and views when revealing hidden columns
1870 <!-- JAL-1989 -->Hide columns not mirrored in complement
1871 view in a cDNA/Protein splitframe
1874 <!-- JAL-1369 -->Cannot save/restore representative
1875 sequence from project when only one sequence is
1879 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1880 in Structure Chooser
1883 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1884 structure consensus didn't refresh annotation panel
1887 <!-- JAL-1962 -->View mapping in structure view shows
1888 mappings between sequence and all chains in a PDB file
1891 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1892 dialogs format columns correctly, don't display array
1893 data, sort columns according to type
1896 <!-- JAL-1975 -->Export complete shown after destination
1897 file chooser is cancelled during an image export
1900 <!-- JAL-2025 -->Error when querying PDB Service with
1901 sequence name containing special characters
1904 <!-- JAL-2024 -->Manual PDB structure querying should be
1908 <!-- JAL-2104 -->Large tooltips with broken HTML
1909 formatting don't wrap
1912 <!-- JAL-1128 -->Figures exported from wrapped view are
1913 truncated so L looks like I in consensus annotation
1916 <!-- JAL-2003 -->Export features should only export the
1917 currently displayed features for the current selection or
1921 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1922 after fetching cross-references, and restoring from
1926 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1927 followed in the structure viewer
1930 <!-- JAL-2163 -->Titles for individual alignments in
1931 splitframe not restored from project
1934 <!-- JAL-2145 -->missing autocalculated annotation at
1935 trailing end of protein alignment in transcript/product
1936 splitview when pad-gaps not enabled by default
1939 <!-- JAL-1797 -->amino acid physicochemical conservation
1943 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1944 article has been read (reopened issue due to
1945 internationalisation problems)
1948 <!-- JAL-1960 -->Only offer PDB structures in structure
1949 viewer based on sequence name, PDB and UniProt
1954 <!-- JAL-1976 -->No progress bar shown during export of
1958 <!-- JAL-2213 -->Structures not always superimposed after
1959 multiple structures are shown for one or more sequences.
1962 <!-- JAL-1370 -->Reference sequence characters should not
1963 be replaced with '.' when 'Show unconserved' format option
1967 <!-- JAL-1823 -->Cannot specify chain code when entering
1968 specific PDB id for sequence
1971 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1972 'Export hidden sequences' is enabled, but 'export hidden
1973 columns' is disabled.
1976 <!--JAL-2026-->Best Quality option in structure chooser
1977 selects lowest rather than highest resolution structures
1981 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1982 to sequence mapping in 'View Mappings' report
1985 <!-- JAL-2284 -->Unable to read old Jalview projects that
1986 contain non-XML data added after Jalvew wrote project.
1989 <!-- JAL-2118 -->Newly created annotation row reorders
1990 after clicking on it to create new annotation for a
1994 <!-- JAL-1980 -->Null Pointer Exception raised when
1995 pressing Add on an orphaned cut'n'paste window.
1997 <!-- may exclude, this is an external service stability issue JAL-1941
1998 -- > RNA 3D structure not added via DSSR service</li> -->
2003 <!-- JAL-2151 -->Incorrect columns are selected when
2004 hidden columns present before start of sequence
2007 <!-- JAL-1986 -->Missing dependencies on applet pages
2011 <!-- JAL-1947 -->Overview pixel size changes when
2012 sequences are hidden in applet
2015 <!-- JAL-1996 -->Updated instructions for applet
2016 deployment on examples pages.
2023 <td width="60" nowrap>
2024 <div align="center">
2025 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2026 <em>16/10/2015</em></strong>
2029 <td><em>General</em>
2031 <li>Time stamps for signed Jalview application and applet
2036 <em>Application</em>
2038 <li>Duplicate group consensus and conservation rows
2039 shown when tree is partitioned</li>
2040 <li>Erratic behaviour when tree partitions made with
2041 multiple cDNA/Protein split views</li>
2047 <td width="60" nowrap>
2048 <div align="center">
2049 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2050 <em>8/10/2015</em></strong>
2053 <td><em>General</em>
2055 <li>Updated Spanish translations of localized text for
2057 </ul> <em>Application</em>
2059 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2060 <li>Signed OSX InstallAnywhere installer<br></li>
2061 <li>Support for per-sequence based annotations in BioJSON</li>
2062 </ul> <em>Applet</em>
2064 <li>Split frame example added to applet examples page</li>
2065 </ul> <em>Build and Deployment</em>
2068 <!-- JAL-1888 -->New ant target for running Jalview's test
2076 <li>Mapping of cDNA to protein in split frames
2077 incorrect when sequence start > 1</li>
2078 <li>Broken images in filter column by annotation dialog
2080 <li>Feature colours not parsed from features file</li>
2081 <li>Exceptions and incomplete link URLs recovered when
2082 loading a features file containing HTML tags in feature
2086 <em>Application</em>
2088 <li>Annotations corrupted after BioJS export and
2090 <li>Incorrect sequence limits after Fetch DB References
2091 with 'trim retrieved sequences'</li>
2092 <li>Incorrect warning about deleting all data when
2093 deleting selected columns</li>
2094 <li>Patch to build system for shipping properly signed
2095 JNLP templates for webstart launch</li>
2096 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2097 unreleased structures for download or viewing</li>
2098 <li>Tab/space/return keystroke operation of EMBL-PDBe
2099 fetcher/viewer dialogs works correctly</li>
2100 <li>Disabled 'minimise' button on Jalview windows
2101 running on OSX to workaround redraw hang bug</li>
2102 <li>Split cDNA/Protein view position and geometry not
2103 recovered from jalview project</li>
2104 <li>Initial enabled/disabled state of annotation menu
2105 sorter 'show autocalculated first/last' corresponds to
2107 <li>Restoring of Clustal, RNA Helices and T-Coffee
2108 color schemes from BioJSON</li>
2112 <li>Reorder sequences mirrored in cDNA/Protein split
2114 <li>Applet with Jmol examples not loading correctly</li>
2120 <td><div align="center">
2121 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2123 <td><em>General</em>
2125 <li>Linked visualisation and analysis of DNA and Protein
2128 <li>Translated cDNA alignments shown as split protein
2129 and DNA alignment views</li>
2130 <li>Codon consensus annotation for linked protein and
2131 cDNA alignment views</li>
2132 <li>Link cDNA or Protein product sequences by loading
2133 them onto Protein or cDNA alignments</li>
2134 <li>Reconstruct linked cDNA alignment from aligned
2135 protein sequences</li>
2138 <li>Jmol integration updated to Jmol v14.2.14</li>
2139 <li>Import and export of Jalview alignment views as <a
2140 href="features/bioJsonFormat.html">BioJSON</a></li>
2141 <li>New alignment annotation file statements for
2142 reference sequences and marking hidden columns</li>
2143 <li>Reference sequence based alignment shading to
2144 highlight variation</li>
2145 <li>Select or hide columns according to alignment
2147 <li>Find option for locating sequences by description</li>
2148 <li>Conserved physicochemical properties shown in amino
2149 acid conservation row</li>
2150 <li>Alignments can be sorted by number of RNA helices</li>
2151 </ul> <em>Application</em>
2153 <li>New cDNA/Protein analysis capabilities
2155 <li>Get Cross-References should open a Split Frame
2156 view with cDNA/Protein</li>
2157 <li>Detect when nucleotide sequences and protein
2158 sequences are placed in the same alignment</li>
2159 <li>Split cDNA/Protein views are saved in Jalview
2164 <li>Use REST API to talk to Chimera</li>
2165 <li>Selected regions in Chimera are highlighted in linked
2166 Jalview windows</li>
2168 <li>VARNA RNA viewer updated to v3.93</li>
2169 <li>VARNA views are saved in Jalview Projects</li>
2170 <li>Pseudoknots displayed as Jalview RNA annotation can
2171 be shown in VARNA</li>
2173 <li>Make groups for selection uses marked columns as well
2174 as the active selected region</li>
2176 <li>Calculate UPGMA and NJ trees using sequence feature
2178 <li>New Export options
2180 <li>New Export Settings dialog to control hidden
2181 region export in flat file generation</li>
2183 <li>Export alignment views for display with the <a
2184 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2186 <li>Export scrollable SVG in HTML page</li>
2187 <li>Optional embedding of BioJSON data when exporting
2188 alignment figures to HTML</li>
2190 <li>3D structure retrieval and display
2192 <li>Free text and structured queries with the PDBe
2194 <li>PDBe Search API based discovery and selection of
2195 PDB structures for a sequence set</li>
2199 <li>JPred4 employed for protein secondary structure
2201 <li>Hide Insertions menu option to hide unaligned columns
2202 for one or a group of sequences</li>
2203 <li>Automatically hide insertions in alignments imported
2204 from the JPred4 web server</li>
2205 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2206 system on OSX<br />LGPL libraries courtesy of <a
2207 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2209 <li>changed 'View nucleotide structure' submenu to 'View
2210 VARNA 2D Structure'</li>
2211 <li>change "View protein structure" menu option to "3D
2214 </ul> <em>Applet</em>
2216 <li>New layout for applet example pages</li>
2217 <li>New parameters to enable SplitFrame view
2218 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2219 <li>New example demonstrating linked viewing of cDNA and
2220 Protein alignments</li>
2221 </ul> <em>Development and deployment</em>
2223 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2224 <li>Include installation type and git revision in build
2225 properties and console log output</li>
2226 <li>Jalview Github organisation, and new github site for
2227 storing BioJsMSA Templates</li>
2228 <li>Jalview's unit tests now managed with TestNG</li>
2231 <!-- <em>General</em>
2233 </ul> --> <!-- issues resolved --> <em>Application</em>
2235 <li>Escape should close any open find dialogs</li>
2236 <li>Typo in select-by-features status report</li>
2237 <li>Consensus RNA secondary secondary structure
2238 predictions are not highlighted in amber</li>
2239 <li>Missing gap character in v2.7 example file means
2240 alignment appears unaligned when pad-gaps is not enabled</li>
2241 <li>First switch to RNA Helices colouring doesn't colour
2242 associated structure views</li>
2243 <li>ID width preference option is greyed out when auto
2244 width checkbox not enabled</li>
2245 <li>Stopped a warning dialog from being shown when
2246 creating user defined colours</li>
2247 <li>'View Mapping' in structure viewer shows sequence
2248 mappings for just that viewer's sequences</li>
2249 <li>Workaround for superposing PDB files containing
2250 multiple models in Chimera</li>
2251 <li>Report sequence position in status bar when hovering
2252 over Jmol structure</li>
2253 <li>Cannot output gaps as '.' symbols with Selection ->
2254 output to text box</li>
2255 <li>Flat file exports of alignments with hidden columns
2256 have incorrect sequence start/end</li>
2257 <li>'Aligning' a second chain to a Chimera structure from
2259 <li>Colour schemes applied to structure viewers don't
2260 work for nucleotide</li>
2261 <li>Loading/cut'n'pasting an empty or invalid file leads
2262 to a grey/invisible alignment window</li>
2263 <li>Exported Jpred annotation from a sequence region
2264 imports to different position</li>
2265 <li>Space at beginning of sequence feature tooltips shown
2266 on some platforms</li>
2267 <li>Chimera viewer 'View | Show Chain' menu is not
2269 <li>'New View' fails with a Null Pointer Exception in
2270 console if Chimera has been opened</li>
2271 <li>Mouseover to Chimera not working</li>
2272 <li>Miscellaneous ENA XML feature qualifiers not
2274 <li>NPE in annotation renderer after 'Extract Scores'</li>
2275 <li>If two structures in one Chimera window, mouseover of
2276 either sequence shows on first structure</li>
2277 <li>'Show annotations' options should not make
2278 non-positional annotations visible</li>
2279 <li>Subsequence secondary structure annotation not shown
2280 in right place after 'view flanking regions'</li>
2281 <li>File Save As type unset when current file format is
2283 <li>Save as '.jar' option removed for saving Jalview
2285 <li>Colour by Sequence colouring in Chimera more
2287 <li>Cannot 'add reference annotation' for a sequence in
2288 several views on same alignment</li>
2289 <li>Cannot show linked products for EMBL / ENA records</li>
2290 <li>Jalview's tooltip wraps long texts containing no
2292 </ul> <em>Applet</em>
2294 <li>Jmol to JalviewLite mouseover/link not working</li>
2295 <li>JalviewLite can't import sequences with ID
2296 descriptions containing angle brackets</li>
2297 </ul> <em>General</em>
2299 <li>Cannot export and reimport RNA secondary structure
2300 via jalview annotation file</li>
2301 <li>Random helix colour palette for colour by annotation
2302 with RNA secondary structure</li>
2303 <li>Mouseover to cDNA from STOP residue in protein
2304 translation doesn't work.</li>
2305 <li>hints when using the select by annotation dialog box</li>
2306 <li>Jmol alignment incorrect if PDB file has alternate CA
2308 <li>FontChooser message dialog appears to hang after
2309 choosing 1pt font</li>
2310 <li>Peptide secondary structure incorrectly imported from
2311 annotation file when annotation display text includes 'e' or
2313 <li>Cannot set colour of new feature type whilst creating
2315 <li>cDNA translation alignment should not be sequence
2316 order dependent</li>
2317 <li>'Show unconserved' doesn't work for lower case
2319 <li>Nucleotide ambiguity codes involving R not recognised</li>
2320 </ul> <em>Deployment and Documentation</em>
2322 <li>Applet example pages appear different to the rest of
2323 www.jalview.org</li>
2324 </ul> <em>Application Known issues</em>
2326 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2327 <li>Misleading message appears after trying to delete
2329 <li>Jalview icon not shown in dock after InstallAnywhere
2330 version launches</li>
2331 <li>Fetching EMBL reference for an RNA sequence results
2332 fails with a sequence mismatch</li>
2333 <li>Corrupted or unreadable alignment display when
2334 scrolling alignment to right</li>
2335 <li>ArrayIndexOutOfBoundsException thrown when remove
2336 empty columns called on alignment with ragged gapped ends</li>
2337 <li>auto calculated alignment annotation rows do not get
2338 placed above or below non-autocalculated rows</li>
2339 <li>Jalview dekstop becomes sluggish at full screen in
2340 ultra-high resolution</li>
2341 <li>Cannot disable consensus calculation independently of
2342 quality and conservation</li>
2343 <li>Mouseover highlighting between cDNA and protein can
2344 become sluggish with more than one splitframe shown</li>
2345 </ul> <em>Applet Known Issues</em>
2347 <li>Core PDB parsing code requires Jmol</li>
2348 <li>Sequence canvas panel goes white when alignment
2349 window is being resized</li>
2355 <td><div align="center">
2356 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2358 <td><em>General</em>
2360 <li>Updated Java code signing certificate donated by
2362 <li>Features and annotation preserved when performing
2363 pairwise alignment</li>
2364 <li>RNA pseudoknot annotation can be
2365 imported/exported/displayed</li>
2366 <li>'colour by annotation' can colour by RNA and
2367 protein secondary structure</li>
2368 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2369 post-hoc with 2.9 release</em>)
2372 </ul> <em>Application</em>
2374 <li>Extract and display secondary structure for sequences
2375 with 3D structures</li>
2376 <li>Support for parsing RNAML</li>
2377 <li>Annotations menu for layout
2379 <li>sort sequence annotation rows by alignment</li>
2380 <li>place sequence annotation above/below alignment
2383 <li>Output in Stockholm format</li>
2384 <li>Internationalisation: improved Spanish (es)
2386 <li>Structure viewer preferences tab</li>
2387 <li>Disorder and Secondary Structure annotation tracks
2388 shared between alignments</li>
2389 <li>UCSF Chimera launch and linked highlighting from
2391 <li>Show/hide all sequence associated annotation rows for
2392 all or current selection</li>
2393 <li>disorder and secondary structure predictions
2394 available as dataset annotation</li>
2395 <li>Per-sequence rna helices colouring</li>
2398 <li>Sequence database accessions imported when fetching
2399 alignments from Rfam</li>
2400 <li>update VARNA version to 3.91</li>
2402 <li>New groovy scripts for exporting aligned positions,
2403 conservation values, and calculating sum of pairs scores.</li>
2404 <li>Command line argument to set default JABAWS server</li>
2405 <li>include installation type in build properties and
2406 console log output</li>
2407 <li>Updated Jalview project format to preserve dataset
2411 <!-- issues resolved --> <em>Application</em>
2413 <li>Distinguish alignment and sequence associated RNA
2414 structure in structure->view->VARNA</li>
2415 <li>Raise dialog box if user deletes all sequences in an
2417 <li>Pressing F1 results in documentation opening twice</li>
2418 <li>Sequence feature tooltip is wrapped</li>
2419 <li>Double click on sequence associated annotation
2420 selects only first column</li>
2421 <li>Redundancy removal doesn't result in unlinked
2422 leaves shown in tree</li>
2423 <li>Undos after several redundancy removals don't undo
2425 <li>Hide sequence doesn't hide associated annotation</li>
2426 <li>User defined colours dialog box too big to fit on
2427 screen and buttons not visible</li>
2428 <li>author list isn't updated if already written to
2429 Jalview properties</li>
2430 <li>Popup menu won't open after retrieving sequence
2432 <li>File open window for associate PDB doesn't open</li>
2433 <li>Left-then-right click on a sequence id opens a
2434 browser search window</li>
2435 <li>Cannot open sequence feature shading/sort popup menu
2436 in feature settings dialog</li>
2437 <li>better tooltip placement for some areas of Jalview
2439 <li>Allow addition of JABAWS Server which doesn't
2440 pass validation</li>
2441 <li>Web services parameters dialog box is too large to
2443 <li>Muscle nucleotide alignment preset obscured by
2445 <li>JABAWS preset submenus don't contain newly
2446 defined user preset</li>
2447 <li>MSA web services warns user if they were launched
2448 with invalid input</li>
2449 <li>Jalview cannot contact DAS Registy when running on
2452 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2453 'Superpose with' submenu not shown when new view
2457 </ul> <!-- <em>Applet</em>
2459 </ul> <em>General</em>
2461 </ul>--> <em>Deployment and Documentation</em>
2463 <li>2G and 1G options in launchApp have no effect on
2464 memory allocation</li>
2465 <li>launchApp service doesn't automatically open
2466 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2468 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2469 InstallAnywhere reports cannot find valid JVM when Java
2470 1.7_055 is available
2472 </ul> <em>Application Known issues</em>
2475 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2476 corrupted or unreadable alignment display when scrolling
2480 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2481 retrieval fails but progress bar continues for DAS retrieval
2482 with large number of ID
2485 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2486 flatfile output of visible region has incorrect sequence
2490 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2491 rna structure consensus doesn't update when secondary
2492 structure tracks are rearranged
2495 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2496 invalid rna structure positional highlighting does not
2497 highlight position of invalid base pairs
2500 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2501 out of memory errors are not raised when saving Jalview
2502 project from alignment window file menu
2505 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2506 Switching to RNA Helices colouring doesn't propagate to
2510 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2511 colour by RNA Helices not enabled when user created
2512 annotation added to alignment
2515 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2516 Jalview icon not shown on dock in Mountain Lion/Webstart
2518 </ul> <em>Applet Known Issues</em>
2521 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2522 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2525 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2526 Jalview and Jmol example not compatible with IE9
2529 <li>Sort by annotation score doesn't reverse order
2535 <td><div align="center">
2536 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2539 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2542 <li>Internationalisation of user interface (usually
2543 called i18n support) and translation for Spanish locale</li>
2544 <li>Define/Undefine group on current selection with
2545 Ctrl-G/Shift Ctrl-G</li>
2546 <li>Improved group creation/removal options in
2547 alignment/sequence Popup menu</li>
2548 <li>Sensible precision for symbol distribution
2549 percentages shown in logo tooltip.</li>
2550 <li>Annotation panel height set according to amount of
2551 annotation when alignment first opened</li>
2552 </ul> <em>Application</em>
2554 <li>Interactive consensus RNA secondary structure
2555 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2556 <li>Select columns containing particular features from
2557 Feature Settings dialog</li>
2558 <li>View all 'representative' PDB structures for selected
2560 <li>Update Jalview project format:
2562 <li>New file extension for Jalview projects '.jvp'</li>
2563 <li>Preserve sequence and annotation dataset (to
2564 store secondary structure annotation,etc)</li>
2565 <li>Per group and alignment annotation and RNA helix
2569 <li>New similarity measures for PCA and Tree calculation
2571 <li>Experimental support for retrieval and viewing of
2572 flanking regions for an alignment</li>
2576 <!-- issues resolved --> <em>Application</em>
2578 <li>logo keeps spinning and status remains at queued or
2579 running after job is cancelled</li>
2580 <li>cannot export features from alignments imported from
2581 Jalview/VAMSAS projects</li>
2582 <li>Buggy slider for web service parameters that take
2584 <li>Newly created RNA secondary structure line doesn't
2585 have 'display all symbols' flag set</li>
2586 <li>T-COFFEE alignment score shading scheme and other
2587 annotation shading not saved in Jalview project</li>
2588 <li>Local file cannot be loaded in freshly downloaded
2590 <li>Jalview icon not shown on dock in Mountain
2592 <li>Load file from desktop file browser fails</li>
2593 <li>Occasional NPE thrown when calculating large trees</li>
2594 <li>Cannot reorder or slide sequences after dragging an
2595 alignment onto desktop</li>
2596 <li>Colour by annotation dialog throws NPE after using
2597 'extract scores' function</li>
2598 <li>Loading/cut'n'pasting an empty file leads to a grey
2599 alignment window</li>
2600 <li>Disorder thresholds rendered incorrectly after
2601 performing IUPred disorder prediction</li>
2602 <li>Multiple group annotated consensus rows shown when
2603 changing 'normalise logo' display setting</li>
2604 <li>Find shows blank dialog after 'finished searching' if
2605 nothing matches query</li>
2606 <li>Null Pointer Exceptions raised when sorting by
2607 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2609 <li>Errors in Jmol console when structures in alignment
2610 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2612 <li>Not all working JABAWS services are shown in
2614 <li>JAVAWS version of Jalview fails to launch with
2615 'invalid literal/length code'</li>
2616 <li>Annotation/RNA Helix colourschemes cannot be applied
2617 to alignment with groups (actually fixed in 2.8.0b1)</li>
2618 <li>RNA Helices and T-Coffee Scores available as default
2621 </ul> <em>Applet</em>
2623 <li>Remove group option is shown even when selection is
2625 <li>Apply to all groups ticked but colourscheme changes
2626 don't affect groups</li>
2627 <li>Documented RNA Helices and T-Coffee Scores as valid
2628 colourscheme name</li>
2629 <li>Annotation labels drawn on sequence IDs when
2630 Annotation panel is not displayed</li>
2631 <li>Increased font size for dropdown menus on OSX and
2632 embedded windows</li>
2633 </ul> <em>Other</em>
2635 <li>Consensus sequence for alignments/groups with a
2636 single sequence were not calculated</li>
2637 <li>annotation files that contain only groups imported as
2638 annotation and junk sequences</li>
2639 <li>Fasta files with sequences containing '*' incorrectly
2640 recognised as PFAM or BLC</li>
2641 <li>conservation/PID slider apply all groups option
2642 doesn't affect background (2.8.0b1)
2644 <li>redundancy highlighting is erratic at 0% and 100%</li>
2645 <li>Remove gapped columns fails for sequences with ragged
2647 <li>AMSA annotation row with leading spaces is not
2648 registered correctly on import</li>
2649 <li>Jalview crashes when selecting PCA analysis for
2650 certain alignments</li>
2651 <li>Opening the colour by annotation dialog for an
2652 existing annotation based 'use original colours'
2653 colourscheme loses original colours setting</li>
2658 <td><div align="center">
2659 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2660 <em>30/1/2014</em></strong>
2664 <li>Trusted certificates for JalviewLite applet and
2665 Jalview Desktop application<br />Certificate was donated by
2666 <a href="https://www.certum.eu">Certum</a> to the Jalview
2667 open source project).
2669 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2670 <li>Output in Stockholm format</li>
2671 <li>Allow import of data from gzipped files</li>
2672 <li>Export/import group and sequence associated line
2673 graph thresholds</li>
2674 <li>Nucleotide substitution matrix that supports RNA and
2675 ambiguity codes</li>
2676 <li>Allow disorder predictions to be made on the current
2677 selection (or visible selection) in the same way that JPred
2679 <li>Groovy scripting for headless Jalview operation</li>
2680 </ul> <em>Other improvements</em>
2682 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2683 <li>COMBINE statement uses current SEQUENCE_REF and
2684 GROUP_REF scope to group annotation rows</li>
2685 <li>Support '' style escaping of quotes in Newick
2687 <li>Group options for JABAWS service by command line name</li>
2688 <li>Empty tooltip shown for JABA service options with a
2689 link but no description</li>
2690 <li>Select primary source when selecting authority in
2691 database fetcher GUI</li>
2692 <li>Add .mfa to FASTA file extensions recognised by
2694 <li>Annotation label tooltip text wrap</li>
2699 <li>Slow scrolling when lots of annotation rows are
2701 <li>Lots of NPE (and slowness) after creating RNA
2702 secondary structure annotation line</li>
2703 <li>Sequence database accessions not imported when
2704 fetching alignments from Rfam</li>
2705 <li>Incorrect SHMR submission for sequences with
2707 <li>View all structures does not always superpose
2709 <li>Option widgets in service parameters not updated to
2710 reflect user or preset settings</li>
2711 <li>Null pointer exceptions for some services without
2712 presets or adjustable parameters</li>
2713 <li>Discover PDB IDs entry in structure menu doesn't
2714 discover PDB xRefs</li>
2715 <li>Exception encountered while trying to retrieve
2716 features with DAS</li>
2717 <li>Lowest value in annotation row isn't coloured
2718 when colour by annotation (per sequence) is coloured</li>
2719 <li>Keyboard mode P jumps to start of gapped region when
2720 residue follows a gap</li>
2721 <li>Jalview appears to hang importing an alignment with
2722 Wrap as default or after enabling Wrap</li>
2723 <li>'Right click to add annotations' message
2724 shown in wrap mode when no annotations present</li>
2725 <li>Disorder predictions fail with NPE if no automatic
2726 annotation already exists on alignment</li>
2727 <li>oninit javascript function should be called after
2728 initialisation completes</li>
2729 <li>Remove redundancy after disorder prediction corrupts
2730 alignment window display</li>
2731 <li>Example annotation file in documentation is invalid</li>
2732 <li>Grouped line graph annotation rows are not exported
2733 to annotation file</li>
2734 <li>Multi-harmony analysis cannot be run when only two
2736 <li>Cannot create multiple groups of line graphs with
2737 several 'combine' statements in annotation file</li>
2738 <li>Pressing return several times causes Number Format
2739 exceptions in keyboard mode</li>
2740 <li>Multi-harmony (SHMMR) method doesn't submit
2741 correct partitions for input data</li>
2742 <li>Translation from DNA to Amino Acids fails</li>
2743 <li>Jalview fail to load newick tree with quoted label</li>
2744 <li>--headless flag isn't understood</li>
2745 <li>ClassCastException when generating EPS in headless
2747 <li>Adjusting sequence-associated shading threshold only
2748 changes one row's threshold</li>
2749 <li>Preferences and Feature settings panel panel
2750 doesn't open</li>
2751 <li>hide consensus histogram also hides conservation and
2752 quality histograms</li>
2757 <td><div align="center">
2758 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2760 <td><em>Application</em>
2762 <li>Support for JABAWS 2.0 Services (AACon alignment
2763 conservation, protein disorder and Clustal Omega)</li>
2764 <li>JABAWS server status indicator in Web Services
2766 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2767 in Jalview alignment window</li>
2768 <li>Updated Jalview build and deploy framework for OSX
2769 mountain lion, windows 7, and 8</li>
2770 <li>Nucleotide substitution matrix for PCA that supports
2771 RNA and ambiguity codes</li>
2773 <li>Improved sequence database retrieval GUI</li>
2774 <li>Support fetching and database reference look up
2775 against multiple DAS sources (Fetch all from in 'fetch db
2777 <li>Jalview project improvements
2779 <li>Store and retrieve the 'belowAlignment'
2780 flag for annotation</li>
2781 <li>calcId attribute to group annotation rows on the
2783 <li>Store AACon calculation settings for a view in
2784 Jalview project</li>
2788 <li>horizontal scrolling gesture support</li>
2789 <li>Visual progress indicator when PCA calculation is
2791 <li>Simpler JABA web services menus</li>
2792 <li>visual indication that web service results are still
2793 being retrieved from server</li>
2794 <li>Serialise the dialogs that are shown when Jalview
2795 starts up for first time</li>
2796 <li>Jalview user agent string for interacting with HTTP
2798 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2800 <li>Examples directory and Groovy library included in
2801 InstallAnywhere distribution</li>
2802 </ul> <em>Applet</em>
2804 <li>RNA alignment and secondary structure annotation
2805 visualization applet example</li>
2806 </ul> <em>General</em>
2808 <li>Normalise option for consensus sequence logo</li>
2809 <li>Reset button in PCA window to return dimensions to
2811 <li>Allow seqspace or Jalview variant of alignment PCA
2813 <li>PCA with either nucleic acid and protein substitution
2815 <li>Allow windows containing HTML reports to be exported
2817 <li>Interactive display and editing of RNA secondary
2818 structure contacts</li>
2819 <li>RNA Helix Alignment Colouring</li>
2820 <li>RNA base pair logo consensus</li>
2821 <li>Parse sequence associated secondary structure
2822 information in Stockholm files</li>
2823 <li>HTML Export database accessions and annotation
2824 information presented in tooltip for sequences</li>
2825 <li>Import secondary structure from LOCARNA clustalw
2826 style RNA alignment files</li>
2827 <li>import and visualise T-COFFEE quality scores for an
2829 <li>'colour by annotation' per sequence option to
2830 shade each sequence according to its associated alignment
2832 <li>New Jalview Logo</li>
2833 </ul> <em>Documentation and Development</em>
2835 <li>documentation for score matrices used in Jalview</li>
2836 <li>New Website!</li>
2838 <td><em>Application</em>
2840 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2841 wsdbfetch REST service</li>
2842 <li>Stop windows being moved outside desktop on OSX</li>
2843 <li>Filetype associations not installed for webstart
2845 <li>Jalview does not always retrieve progress of a JABAWS
2846 job execution in full once it is complete</li>
2847 <li>revise SHMR RSBS definition to ensure alignment is
2848 uploaded via ali_file parameter</li>
2849 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2850 <li>View all structures superposed fails with exception</li>
2851 <li>Jnet job queues forever if a very short sequence is
2852 submitted for prediction</li>
2853 <li>Cut and paste menu not opened when mouse clicked on
2855 <li>Putting fractional value into integer text box in
2856 alignment parameter dialog causes Jalview to hang</li>
2857 <li>Structure view highlighting doesn't work on
2859 <li>View all structures fails with exception shown in
2861 <li>Characters in filename associated with PDBEntry not
2862 escaped in a platform independent way</li>
2863 <li>Jalview desktop fails to launch with exception when
2865 <li>Tree calculation reports 'you must have 2 or more
2866 sequences selected' when selection is empty</li>
2867 <li>Jalview desktop fails to launch with jar signature
2868 failure when java web start temporary file caching is
2870 <li>DAS Sequence retrieval with range qualification
2871 results in sequence xref which includes range qualification</li>
2872 <li>Errors during processing of command line arguments
2873 cause progress bar (JAL-898) to be removed</li>
2874 <li>Replace comma for semi-colon option not disabled for
2875 DAS sources in sequence fetcher</li>
2876 <li>Cannot close news reader when JABAWS server warning
2877 dialog is shown</li>
2878 <li>Option widgets not updated to reflect user settings</li>
2879 <li>Edited sequence not submitted to web service</li>
2880 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2881 <li>InstallAnywhere installer doesn't unpack and run
2882 on OSX Mountain Lion</li>
2883 <li>Annotation panel not given a scroll bar when
2884 sequences with alignment annotation are pasted into the
2886 <li>Sequence associated annotation rows not associated
2887 when loaded from Jalview project</li>
2888 <li>Browser launch fails with NPE on java 1.7</li>
2889 <li>JABAWS alignment marked as finished when job was
2890 cancelled or job failed due to invalid input</li>
2891 <li>NPE with v2.7 example when clicking on Tree
2892 associated with all views</li>
2893 <li>Exceptions when copy/paste sequences with grouped
2894 annotation rows to new window</li>
2895 </ul> <em>Applet</em>
2897 <li>Sequence features are momentarily displayed before
2898 they are hidden using hidefeaturegroups applet parameter</li>
2899 <li>loading features via javascript API automatically
2900 enables feature display</li>
2901 <li>scrollToColumnIn javascript API method doesn't
2903 </ul> <em>General</em>
2905 <li>Redundancy removal fails for rna alignment</li>
2906 <li>PCA calculation fails when sequence has been selected
2907 and then deselected</li>
2908 <li>PCA window shows grey box when first opened on OSX</li>
2909 <li>Letters coloured pink in sequence logo when alignment
2910 coloured with clustalx</li>
2911 <li>Choosing fonts without letter symbols defined causes
2912 exceptions and redraw errors</li>
2913 <li>Initial PCA plot view is not same as manually
2914 reconfigured view</li>
2915 <li>Grouped annotation graph label has incorrect line
2917 <li>Grouped annotation graph label display is corrupted
2918 for lots of labels</li>
2923 <div align="center">
2924 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2927 <td><em>Application</em>
2929 <li>Jalview Desktop News Reader</li>
2930 <li>Tweaked default layout of web services menu</li>
2931 <li>View/alignment association menu to enable user to
2932 easily specify which alignment a multi-structure view takes
2933 its colours/correspondences from</li>
2934 <li>Allow properties file location to be specified as URL</li>
2935 <li>Extend Jalview project to preserve associations
2936 between many alignment views and a single Jmol display</li>
2937 <li>Store annotation row height in Jalview project file</li>
2938 <li>Annotation row column label formatting attributes
2939 stored in project file</li>
2940 <li>Annotation row order for auto-calculated annotation
2941 rows preserved in Jalview project file</li>
2942 <li>Visual progress indication when Jalview state is
2943 saved using Desktop window menu</li>
2944 <li>Visual indication that command line arguments are
2945 still being processed</li>
2946 <li>Groovy script execution from URL</li>
2947 <li>Colour by annotation default min and max colours in
2949 <li>Automatically associate PDB files dragged onto an
2950 alignment with sequences that have high similarity and
2952 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2953 <li>'view structures' option to open many
2954 structures in same window</li>
2955 <li>Sort associated views menu option for tree panel</li>
2956 <li>Group all JABA and non-JABA services for a particular
2957 analysis function in its own submenu</li>
2958 </ul> <em>Applet</em>
2960 <li>Userdefined and autogenerated annotation rows for
2962 <li>Adjustment of alignment annotation pane height</li>
2963 <li>Annotation scrollbar for annotation panel</li>
2964 <li>Drag to reorder annotation rows in annotation panel</li>
2965 <li>'automaticScrolling' parameter</li>
2966 <li>Allow sequences with partial ID string matches to be
2967 annotated from GFF/Jalview features files</li>
2968 <li>Sequence logo annotation row in applet</li>
2969 <li>Absolute paths relative to host server in applet
2970 parameters are treated as such</li>
2971 <li>New in the JalviewLite javascript API:
2973 <li>JalviewLite.js javascript library</li>
2974 <li>Javascript callbacks for
2976 <li>Applet initialisation</li>
2977 <li>Sequence/alignment mouse-overs and selections</li>
2980 <li>scrollTo row and column alignment scrolling
2982 <li>Select sequence/alignment regions from javascript</li>
2983 <li>javascript structure viewer harness to pass
2984 messages between Jmol and Jalview when running as
2985 distinct applets</li>
2986 <li>sortBy method</li>
2987 <li>Set of applet and application examples shipped
2988 with documentation</li>
2989 <li>New example to demonstrate JalviewLite and Jmol
2990 javascript message exchange</li>
2992 </ul> <em>General</em>
2994 <li>Enable Jmol displays to be associated with multiple
2995 multiple alignments</li>
2996 <li>Option to automatically sort alignment with new tree</li>
2997 <li>User configurable link to enable redirects to a
2998 www.Jalview.org mirror</li>
2999 <li>Jmol colours option for Jmol displays</li>
3000 <li>Configurable newline string when writing alignment
3001 and other flat files</li>
3002 <li>Allow alignment annotation description lines to
3003 contain html tags</li>
3004 </ul> <em>Documentation and Development</em>
3006 <li>Add groovy test harness for bulk load testing to
3008 <li>Groovy script to load and align a set of sequences
3009 using a web service before displaying the result in the
3010 Jalview desktop</li>
3011 <li>Restructured javascript and applet api documentation</li>
3012 <li>Ant target to publish example html files with applet
3014 <li>Netbeans project for building Jalview from source</li>
3015 <li>ant task to create online javadoc for Jalview source</li>
3017 <td><em>Application</em>
3019 <li>User defined colourscheme throws exception when
3020 current built in colourscheme is saved as new scheme</li>
3021 <li>AlignFrame->Save in application pops up save
3022 dialog for valid filename/format</li>
3023 <li>Cannot view associated structure for UniProt sequence</li>
3024 <li>PDB file association breaks for UniProt sequence
3026 <li>Associate PDB from file dialog does not tell you
3027 which sequence is to be associated with the file</li>
3028 <li>Find All raises null pointer exception when query
3029 only matches sequence IDs</li>
3030 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3031 <li>Jalview project with Jmol views created with Jalview
3032 2.4 cannot be loaded</li>
3033 <li>Filetype associations not installed for webstart
3035 <li>Two or more chains in a single PDB file associated
3036 with sequences in different alignments do not get coloured
3037 by their associated sequence</li>
3038 <li>Visibility status of autocalculated annotation row
3039 not preserved when project is loaded</li>
3040 <li>Annotation row height and visibility attributes not
3041 stored in Jalview project</li>
3042 <li>Tree bootstraps are not preserved when saved as a
3043 Jalview project</li>
3044 <li>Envision2 workflow tooltips are corrupted</li>
3045 <li>Enabling show group conservation also enables colour
3046 by conservation</li>
3047 <li>Duplicate group associated conservation or consensus
3048 created on new view</li>
3049 <li>Annotation scrollbar not displayed after 'show
3050 all hidden annotation rows' option selected</li>
3051 <li>Alignment quality not updated after alignment
3052 annotation row is hidden then shown</li>
3053 <li>Preserve colouring of structures coloured by
3054 sequences in pre Jalview 2.7 projects</li>
3055 <li>Web service job parameter dialog is not laid out
3057 <li>Web services menu not refreshed after 'reset
3058 services' button is pressed in preferences</li>
3059 <li>Annotation off by one in Jalview v2_3 example project</li>
3060 <li>Structures imported from file and saved in project
3061 get name like jalview_pdb1234.txt when reloaded</li>
3062 <li>Jalview does not always retrieve progress of a JABAWS
3063 job execution in full once it is complete</li>
3064 </ul> <em>Applet</em>
3066 <li>Alignment height set incorrectly when lots of
3067 annotation rows are displayed</li>
3068 <li>Relative URLs in feature HTML text not resolved to
3070 <li>View follows highlighting does not work for positions
3072 <li><= shown as = in tooltip</li>
3073 <li>Export features raises exception when no features
3075 <li>Separator string used for serialising lists of IDs
3076 for javascript api is modified when separator string
3077 provided as parameter</li>
3078 <li>Null pointer exception when selecting tree leaves for
3079 alignment with no existing selection</li>
3080 <li>Relative URLs for datasources assumed to be relative
3081 to applet's codebase</li>
3082 <li>Status bar not updated after finished searching and
3083 search wraps around to first result</li>
3084 <li>StructureSelectionManager instance shared between
3085 several Jalview applets causes race conditions and memory
3087 <li>Hover tooltip and mouseover of position on structure
3088 not sent from Jmol in applet</li>
3089 <li>Certain sequences of javascript method calls to
3090 applet API fatally hang browser</li>
3091 </ul> <em>General</em>
3093 <li>View follows structure mouseover scrolls beyond
3094 position with wrapped view and hidden regions</li>
3095 <li>Find sequence position moves to wrong residue
3096 with/without hidden columns</li>
3097 <li>Sequence length given in alignment properties window
3099 <li>InvalidNumberFormat exceptions thrown when trying to
3100 import PDB like structure files</li>
3101 <li>Positional search results are only highlighted
3102 between user-supplied sequence start/end bounds</li>
3103 <li>End attribute of sequence is not validated</li>
3104 <li>Find dialog only finds first sequence containing a
3105 given sequence position</li>
3106 <li>Sequence numbering not preserved in MSF alignment
3108 <li>Jalview PDB file reader does not extract sequence
3109 from nucleotide chains correctly</li>
3110 <li>Structure colours not updated when tree partition
3111 changed in alignment</li>
3112 <li>Sequence associated secondary structure not correctly
3113 parsed in interleaved stockholm</li>
3114 <li>Colour by annotation dialog does not restore current
3116 <li>Hiding (nearly) all sequences doesn't work
3118 <li>Sequences containing lowercase letters are not
3119 properly associated with their pdb files</li>
3120 </ul> <em>Documentation and Development</em>
3122 <li>schemas/JalviewWsParamSet.xsd corrupted by
3123 ApplyCopyright tool</li>
3128 <div align="center">
3129 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3132 <td><em>Application</em>
3134 <li>New warning dialog when the Jalview Desktop cannot
3135 contact web services</li>
3136 <li>JABA service parameters for a preset are shown in
3137 service job window</li>
3138 <li>JABA Service menu entries reworded</li>
3142 <li>Modeller PIR IO broken - cannot correctly import a
3143 pir file emitted by Jalview</li>
3144 <li>Existing feature settings transferred to new
3145 alignment view created from cut'n'paste</li>
3146 <li>Improved test for mixed amino/nucleotide chains when
3147 parsing PDB files</li>
3148 <li>Consensus and conservation annotation rows
3149 occasionally become blank for all new windows</li>
3150 <li>Exception raised when right clicking above sequences
3151 in wrapped view mode</li>
3152 </ul> <em>Application</em>
3154 <li>multiple multiply aligned structure views cause cpu
3155 usage to hit 100% and computer to hang</li>
3156 <li>Web Service parameter layout breaks for long user
3157 parameter names</li>
3158 <li>Jaba service discovery hangs desktop if Jaba server
3165 <div align="center">
3166 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3169 <td><em>Application</em>
3171 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3172 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3175 <li>Web Services preference tab</li>
3176 <li>Analysis parameters dialog box and user defined
3178 <li>Improved speed and layout of Envision2 service menu</li>
3179 <li>Superpose structures using associated sequence
3181 <li>Export coordinates and projection as CSV from PCA
3183 </ul> <em>Applet</em>
3185 <li>enable javascript: execution by the applet via the
3186 link out mechanism</li>
3187 </ul> <em>Other</em>
3189 <li>Updated the Jmol Jalview interface to work with Jmol
3191 <li>The Jalview Desktop and JalviewLite applet now
3192 require Java 1.5</li>
3193 <li>Allow Jalview feature colour specification for GFF
3194 sequence annotation files</li>
3195 <li>New 'colour by label' keword in Jalview feature file
3196 type colour specification</li>
3197 <li>New Jalview Desktop Groovy API method that allows a
3198 script to check if it being run in an interactive session or
3199 in a batch operation from the Jalview command line</li>
3203 <li>clustalx colourscheme colours Ds preferentially when
3204 both D+E are present in over 50% of the column</li>
3205 </ul> <em>Application</em>
3207 <li>typo in AlignmentFrame->View->Hide->all but
3208 selected Regions menu item</li>
3209 <li>sequence fetcher replaces ',' for ';' when the ',' is
3210 part of a valid accession ID</li>
3211 <li>fatal OOM if object retrieved by sequence fetcher
3212 runs out of memory</li>
3213 <li>unhandled Out of Memory Error when viewing pca
3214 analysis results</li>
3215 <li>InstallAnywhere builds fail to launch on OS X java
3216 10.5 update 4 (due to apple Java 1.6 update)</li>
3217 <li>Installanywhere Jalview silently fails to launch</li>
3218 </ul> <em>Applet</em>
3220 <li>Jalview.getFeatureGroups() raises an
3221 ArrayIndexOutOfBoundsException if no feature groups are
3228 <div align="center">
3229 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3235 <li>Alignment prettyprinter doesn't cope with long
3237 <li>clustalx colourscheme colours Ds preferentially when
3238 both D+E are present in over 50% of the column</li>
3239 <li>nucleic acid structures retrieved from PDB do not
3240 import correctly</li>
3241 <li>More columns get selected than were clicked on when a
3242 number of columns are hidden</li>
3243 <li>annotation label popup menu not providing correct
3244 add/hide/show options when rows are hidden or none are
3246 <li>Stockholm format shown in list of readable formats,
3247 and parser copes better with alignments from RFAM.</li>
3248 <li>CSV output of consensus only includes the percentage
3249 of all symbols if sequence logo display is enabled</li>
3251 </ul> <em>Applet</em>
3253 <li>annotation panel disappears when annotation is
3255 </ul> <em>Application</em>
3257 <li>Alignment view not redrawn properly when new
3258 alignment opened where annotation panel is visible but no
3259 annotations are present on alignment</li>
3260 <li>pasted region containing hidden columns is
3261 incorrectly displayed in new alignment window</li>
3262 <li>Jalview slow to complete operations when stdout is
3263 flooded (fix is to close the Jalview console)</li>
3264 <li>typo in AlignmentFrame->View->Hide->all but
3265 selected Rregions menu item.</li>
3266 <li>inconsistent group submenu and Format submenu entry
3267 'Un' or 'Non'conserved</li>
3268 <li>Sequence feature settings are being shared by
3269 multiple distinct alignments</li>
3270 <li>group annotation not recreated when tree partition is
3272 <li>double click on group annotation to select sequences
3273 does not propagate to associated trees</li>
3274 <li>Mac OSX specific issues:
3276 <li>exception raised when mouse clicked on desktop
3277 window background</li>
3278 <li>Desktop menu placed on menu bar and application
3279 name set correctly</li>
3280 <li>sequence feature settings not wide enough for the
3281 save feature colourscheme button</li>
3290 <div align="center">
3291 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3294 <td><em>New Capabilities</em>
3296 <li>URL links generated from description line for
3297 regular-expression based URL links (applet and application)
3299 <li>Non-positional feature URL links are shown in link
3301 <li>Linked viewing of nucleic acid sequences and
3303 <li>Automatic Scrolling option in View menu to display
3304 the currently highlighted region of an alignment.</li>
3305 <li>Order an alignment by sequence length, or using the
3306 average score or total feature count for each sequence.</li>
3307 <li>Shading features by score or associated description</li>
3308 <li>Subdivide alignment and groups based on identity of
3309 selected subsequence (Make Groups from Selection).</li>
3310 <li>New hide/show options including Shift+Control+H to
3311 hide everything but the currently selected region.</li>
3312 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3313 </ul> <em>Application</em>
3315 <li>Fetch DB References capabilities and UI expanded to
3316 support retrieval from DAS sequence sources</li>
3317 <li>Local DAS Sequence sources can be added via the
3318 command line or via the Add local source dialog box.</li>
3319 <li>DAS Dbref and DbxRef feature types are parsed as
3320 database references and protein_name is parsed as
3321 description line (BioSapiens terms).</li>
3322 <li>Enable or disable non-positional feature and database
3323 references in sequence ID tooltip from View menu in
3325 <!-- <li>New hidden columns and rows and representatives capabilities
3326 in annotations file (in progress - not yet fully implemented)</li> -->
3327 <li>Group-associated consensus, sequence logos and
3328 conservation plots</li>
3329 <li>Symbol distributions for each column can be exported
3330 and visualized as sequence logos</li>
3331 <li>Optionally scale multi-character column labels to fit
3332 within each column of annotation row<!-- todo for applet -->
3334 <li>Optional automatic sort of associated alignment view
3335 when a new tree is opened.</li>
3336 <li>Jalview Java Console</li>
3337 <li>Better placement of desktop window when moving
3338 between different screens.</li>
3339 <li>New preference items for sequence ID tooltip and
3340 consensus annotation</li>
3341 <li>Client to submit sequences and IDs to Envision2
3343 <li><em>Vamsas Capabilities</em>
3345 <li>Improved VAMSAS synchronization (Jalview archive
3346 used to preserve views, structures, and tree display
3348 <li>Import of vamsas documents from disk or URL via
3350 <li>Sharing of selected regions between views and
3351 with other VAMSAS applications (Experimental feature!)</li>
3352 <li>Updated API to VAMSAS version 0.2</li>
3354 </ul> <em>Applet</em>
3356 <li>Middle button resizes annotation row height</li>
3359 <li>sortByTree (true/false) - automatically sort the
3360 associated alignment view by the tree when a new tree is
3362 <li>showTreeBootstraps (true/false) - show or hide
3363 branch bootstraps (default is to show them if available)</li>
3364 <li>showTreeDistances (true/false) - show or hide
3365 branch lengths (default is to show them if available)</li>
3366 <li>showUnlinkedTreeNodes (true/false) - indicate if
3367 unassociated nodes should be highlighted in the tree
3369 <li>heightScale and widthScale (1.0 or more) -
3370 increase the height or width of a cell in the alignment
3371 grid relative to the current font size.</li>
3374 <li>Non-positional features displayed in sequence ID
3376 </ul> <em>Other</em>
3378 <li>Features format: graduated colour definitions and
3379 specification of feature scores</li>
3380 <li>Alignment Annotations format: new keywords for group
3381 associated annotation (GROUP_REF) and annotation row display
3382 properties (ROW_PROPERTIES)</li>
3383 <li>XML formats extended to support graduated feature
3384 colourschemes, group associated annotation, and profile
3385 visualization settings.</li></td>
3388 <li>Source field in GFF files parsed as feature source
3389 rather than description</li>
3390 <li>Non-positional features are now included in sequence
3391 feature and gff files (controlled via non-positional feature
3392 visibility in tooltip).</li>
3393 <li>URL links generated for all feature links (bugfix)</li>
3394 <li>Added URL embedding instructions to features file
3396 <li>Codons containing ambiguous nucleotides translated as
3397 'X' in peptide product</li>
3398 <li>Match case switch in find dialog box works for both
3399 sequence ID and sequence string and query strings do not
3400 have to be in upper case to match case-insensitively.</li>
3401 <li>AMSA files only contain first column of
3402 multi-character column annotation labels</li>
3403 <li>Jalview Annotation File generation/parsing consistent
3404 with documentation (e.g. Stockholm annotation can be
3405 exported and re-imported)</li>
3406 <li>PDB files without embedded PDB IDs given a friendly
3408 <li>Find incrementally searches ID string matches as well
3409 as subsequence matches, and correctly reports total number
3413 <li>Better handling of exceptions during sequence
3415 <li>Dasobert generated non-positional feature URL
3416 link text excludes the start_end suffix</li>
3417 <li>DAS feature and source retrieval buttons disabled
3418 when fetch or registry operations in progress.</li>
3419 <li>PDB files retrieved from URLs are cached properly</li>
3420 <li>Sequence description lines properly shared via
3422 <li>Sequence fetcher fetches multiple records for all
3424 <li>Ensured that command line das feature retrieval
3425 completes before alignment figures are generated.</li>
3426 <li>Reduced time taken when opening file browser for
3428 <li>isAligned check prior to calculating tree, PCA or
3429 submitting an MSA to JNet now excludes hidden sequences.</li>
3430 <li>User defined group colours properly recovered
3431 from Jalview projects.</li>
3440 <div align="center">
3441 <strong>2.4.0.b2</strong><br> 28/10/2009
3446 <li>Experimental support for google analytics usage
3448 <li>Jalview privacy settings (user preferences and docs).</li>
3453 <li>Race condition in applet preventing startup in
3455 <li>Exception when feature created from selection beyond
3456 length of sequence.</li>
3457 <li>Allow synthetic PDB files to be imported gracefully</li>
3458 <li>Sequence associated annotation rows associate with
3459 all sequences with a given id</li>
3460 <li>Find function matches case-insensitively for sequence
3461 ID string searches</li>
3462 <li>Non-standard characters do not cause pairwise
3463 alignment to fail with exception</li>
3464 </ul> <em>Application Issues</em>
3466 <li>Sequences are now validated against EMBL database</li>
3467 <li>Sequence fetcher fetches multiple records for all
3469 </ul> <em>InstallAnywhere Issues</em>
3471 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3472 issue with installAnywhere mechanism)</li>
3473 <li>Command line launching of JARs from InstallAnywhere
3474 version (java class versioning error fixed)</li>
3481 <div align="center">
3482 <strong>2.4</strong><br> 27/8/2008
3485 <td><em>User Interface</em>
3487 <li>Linked highlighting of codon and amino acid from
3488 translation and protein products</li>
3489 <li>Linked highlighting of structure associated with
3490 residue mapping to codon position</li>
3491 <li>Sequence Fetcher provides example accession numbers
3492 and 'clear' button</li>
3493 <li>MemoryMonitor added as an option under Desktop's
3495 <li>Extract score function to parse whitespace separated
3496 numeric data in description line</li>
3497 <li>Column labels in alignment annotation can be centred.</li>
3498 <li>Tooltip for sequence associated annotation give name
3500 </ul> <em>Web Services and URL fetching</em>
3502 <li>JPred3 web service</li>
3503 <li>Prototype sequence search client (no public services
3505 <li>Fetch either seed alignment or full alignment from
3507 <li>URL Links created for matching database cross
3508 references as well as sequence ID</li>
3509 <li>URL Links can be created using regular-expressions</li>
3510 </ul> <em>Sequence Database Connectivity</em>
3512 <li>Retrieval of cross-referenced sequences from other
3514 <li>Generalised database reference retrieval and
3515 validation to all fetchable databases</li>
3516 <li>Fetch sequences from DAS sources supporting the
3517 sequence command</li>
3518 </ul> <em>Import and Export</em>
3519 <li>export annotation rows as CSV for spreadsheet import</li>
3520 <li>Jalview projects record alignment dataset associations,
3521 EMBL products, and cDNA sequence mappings</li>
3522 <li>Sequence Group colour can be specified in Annotation
3524 <li>Ad-hoc colouring of group in Annotation File using RGB
3525 triplet as name of colourscheme</li>
3526 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3528 <li>treenode binding for VAMSAS tree exchange</li>
3529 <li>local editing and update of sequences in VAMSAS
3530 alignments (experimental)</li>
3531 <li>Create new or select existing session to join</li>
3532 <li>load and save of vamsas documents</li>
3533 </ul> <em>Application command line</em>
3535 <li>-tree parameter to open trees (introduced for passing
3537 <li>-fetchfrom command line argument to specify nicknames
3538 of DAS servers to query for alignment features</li>
3539 <li>-dasserver command line argument to add new servers
3540 that are also automatically queried for features</li>
3541 <li>-groovy command line argument executes a given groovy
3542 script after all input data has been loaded and parsed</li>
3543 </ul> <em>Applet-Application data exchange</em>
3545 <li>Trees passed as applet parameters can be passed to
3546 application (when using "View in full
3547 application")</li>
3548 </ul> <em>Applet Parameters</em>
3550 <li>feature group display control parameter</li>
3551 <li>debug parameter</li>
3552 <li>showbutton parameter</li>
3553 </ul> <em>Applet API methods</em>
3555 <li>newView public method</li>
3556 <li>Window (current view) specific get/set public methods</li>
3557 <li>Feature display control methods</li>
3558 <li>get list of currently selected sequences</li>
3559 </ul> <em>New Jalview distribution features</em>
3561 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3562 <li>RELEASE file gives build properties for the latest
3563 Jalview release.</li>
3564 <li>Java 1.1 Applet build made easier and donotobfuscate
3565 property controls execution of obfuscator</li>
3566 <li>Build target for generating source distribution</li>
3567 <li>Debug flag for javacc</li>
3568 <li>.jalview_properties file is documented (slightly) in
3569 jalview.bin.Cache</li>
3570 <li>Continuous Build Integration for stable and
3571 development version of Application, Applet and source
3576 <li>selected region output includes visible annotations
3577 (for certain formats)</li>
3578 <li>edit label/displaychar contains existing label/char
3580 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3581 <li>shorter peptide product names from EMBL records</li>
3582 <li>Newick string generator makes compact representations</li>
3583 <li>bootstrap values parsed correctly for tree files with
3585 <li>pathological filechooser bug avoided by not allowing
3586 filenames containing a ':'</li>
3587 <li>Fixed exception when parsing GFF files containing
3588 global sequence features</li>
3589 <li>Alignment datasets are finalized only when number of
3590 references from alignment sequences goes to zero</li>
3591 <li>Close of tree branch colour box without colour
3592 selection causes cascading exceptions</li>
3593 <li>occasional negative imgwidth exceptions</li>
3594 <li>better reporting of non-fatal warnings to user when
3595 file parsing fails.</li>
3596 <li>Save works when Jalview project is default format</li>
3597 <li>Save as dialog opened if current alignment format is
3598 not a valid output format</li>
3599 <li>UniProt canonical names introduced for both das and
3601 <li>Histidine should be midblue (not pink!) in Zappo</li>
3602 <li>error messages passed up and output when data read
3604 <li>edit undo recovers previous dataset sequence when
3605 sequence is edited</li>
3606 <li>allow PDB files without pdb ID HEADER lines (like
3607 those generated by MODELLER) to be read in properly</li>
3608 <li>allow reading of JPred concise files as a normal
3610 <li>Stockholm annotation parsing and alignment properties
3611 import fixed for PFAM records</li>
3612 <li>Structure view windows have correct name in Desktop
3614 <li>annotation consisting of sequence associated scores
3615 can be read and written correctly to annotation file</li>
3616 <li>Aligned cDNA translation to aligned peptide works
3618 <li>Fixed display of hidden sequence markers and
3619 non-italic font for representatives in Applet</li>
3620 <li>Applet Menus are always embedded in applet window on
3622 <li>Newly shown features appear at top of stack (in
3624 <li>Annotations added via parameter not drawn properly
3625 due to null pointer exceptions</li>
3626 <li>Secondary structure lines are drawn starting from
3627 first column of alignment</li>
3628 <li>UniProt XML import updated for new schema release in
3630 <li>Sequence feature to sequence ID match for Features
3631 file is case-insensitive</li>
3632 <li>Sequence features read from Features file appended to
3633 all sequences with matching IDs</li>
3634 <li>PDB structure coloured correctly for associated views
3635 containing a sub-sequence</li>
3636 <li>PDB files can be retrieved by applet from Jar files</li>
3637 <li>feature and annotation file applet parameters
3638 referring to different directories are retrieved correctly</li>
3639 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3640 <li>Fixed application hang whilst waiting for
3641 splash-screen version check to complete</li>
3642 <li>Applet properly URLencodes input parameter values
3643 when passing them to the launchApp service</li>
3644 <li>display name and local features preserved in results
3645 retrieved from web service</li>
3646 <li>Visual delay indication for sequence retrieval and
3647 sequence fetcher initialisation</li>
3648 <li>updated Application to use DAS 1.53e version of
3649 dasobert DAS client</li>
3650 <li>Re-instated Full AMSA support and .amsa file
3652 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3660 <div align="center">
3661 <strong>2.3</strong><br> 9/5/07
3666 <li>Jmol 11.0.2 integration</li>
3667 <li>PDB views stored in Jalview XML files</li>
3668 <li>Slide sequences</li>
3669 <li>Edit sequence in place</li>
3670 <li>EMBL CDS features</li>
3671 <li>DAS Feature mapping</li>
3672 <li>Feature ordering</li>
3673 <li>Alignment Properties</li>
3674 <li>Annotation Scores</li>
3675 <li>Sort by scores</li>
3676 <li>Feature/annotation editing in applet</li>
3681 <li>Headless state operation in 2.2.1</li>
3682 <li>Incorrect and unstable DNA pairwise alignment</li>
3683 <li>Cut and paste of sequences with annotation</li>
3684 <li>Feature group display state in XML</li>
3685 <li>Feature ordering in XML</li>
3686 <li>blc file iteration selection using filename # suffix</li>
3687 <li>Stockholm alignment properties</li>
3688 <li>Stockhom alignment secondary structure annotation</li>
3689 <li>2.2.1 applet had no feature transparency</li>
3690 <li>Number pad keys can be used in cursor mode</li>
3691 <li>Structure Viewer mirror image resolved</li>
3698 <div align="center">
3699 <strong>2.2.1</strong><br> 12/2/07
3704 <li>Non standard characters can be read and displayed
3705 <li>Annotations/Features can be imported/exported to the
3707 <li>Applet allows editing of sequence/annotation/group
3708 name & description
3709 <li>Preference setting to display sequence name in
3711 <li>Annotation file format extended to allow
3712 Sequence_groups to be defined
3713 <li>Default opening of alignment overview panel can be
3714 specified in preferences
3715 <li>PDB residue numbering annotation added to associated
3721 <li>Applet crash under certain Linux OS with Java 1.6
3723 <li>Annotation file export / import bugs fixed
3724 <li>PNG / EPS image output bugs fixed
3730 <div align="center">
3731 <strong>2.2</strong><br> 27/11/06
3736 <li>Multiple views on alignment
3737 <li>Sequence feature editing
3738 <li>"Reload" alignment
3739 <li>"Save" to current filename
3740 <li>Background dependent text colour
3741 <li>Right align sequence ids
3742 <li>User-defined lower case residue colours
3745 <li>Menu item accelerator keys
3746 <li>Control-V pastes to current alignment
3747 <li>Cancel button for DAS Feature Fetching
3748 <li>PCA and PDB Viewers zoom via mouse roller
3749 <li>User-defined sub-tree colours and sub-tree selection
3751 <li>'New Window' button on the 'Output to Text box'
3756 <li>New memory efficient Undo/Redo System
3757 <li>Optimised symbol lookups and conservation/consensus
3759 <li>Region Conservation/Consensus recalculated after
3761 <li>Fixed Remove Empty Columns Bug (empty columns at end
3763 <li>Slowed DAS Feature Fetching for increased robustness.
3765 <li>Made angle brackets in ASCII feature descriptions
3767 <li>Re-instated Zoom function for PCA
3768 <li>Sequence descriptions conserved in web service
3770 <li>UniProt ID discoverer uses any word separated by
3772 <li>WsDbFetch query/result association resolved
3773 <li>Tree leaf to sequence mapping improved
3774 <li>Smooth fonts switch moved to FontChooser dialog box.
3781 <div align="center">
3782 <strong>2.1.1</strong><br> 12/9/06
3787 <li>Copy consensus sequence to clipboard</li>
3792 <li>Image output - rightmost residues are rendered if
3793 sequence id panel has been resized</li>
3794 <li>Image output - all offscreen group boundaries are
3796 <li>Annotation files with sequence references - all
3797 elements in file are relative to sequence position</li>
3798 <li>Mac Applet users can use Alt key for group editing</li>
3804 <div align="center">
3805 <strong>2.1</strong><br> 22/8/06
3810 <li>MAFFT Multiple Alignment in default Web Service list</li>
3811 <li>DAS Feature fetching</li>
3812 <li>Hide sequences and columns</li>
3813 <li>Export Annotations and Features</li>
3814 <li>GFF file reading / writing</li>
3815 <li>Associate structures with sequences from local PDB
3817 <li>Add sequences to exisiting alignment</li>
3818 <li>Recently opened files / URL lists</li>
3819 <li>Applet can launch the full application</li>
3820 <li>Applet has transparency for features (Java 1.2
3822 <li>Applet has user defined colours parameter</li>
3823 <li>Applet can load sequences from parameter
3824 "sequence<em>x</em>"
3830 <li>Redundancy Panel reinstalled in the Applet</li>
3831 <li>Monospaced font - EPS / rescaling bug fixed</li>
3832 <li>Annotation files with sequence references bug fixed</li>
3838 <div align="center">
3839 <strong>2.08.1</strong><br> 2/5/06
3844 <li>Change case of selected region from Popup menu</li>
3845 <li>Choose to match case when searching</li>
3846 <li>Middle mouse button and mouse movement can compress /
3847 expand the visible width and height of the alignment</li>
3852 <li>Annotation Panel displays complete JNet results</li>
3858 <div align="center">
3859 <strong>2.08b</strong><br> 18/4/06
3865 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3866 <li>Righthand label on wrapped alignments shows correct
3873 <div align="center">
3874 <strong>2.08</strong><br> 10/4/06
3879 <li>Editing can be locked to the selection area</li>
3880 <li>Keyboard editing</li>
3881 <li>Create sequence features from searches</li>
3882 <li>Precalculated annotations can be loaded onto
3884 <li>Features file allows grouping of features</li>
3885 <li>Annotation Colouring scheme added</li>
3886 <li>Smooth fonts off by default - Faster rendering</li>
3887 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3892 <li>Drag & Drop fixed on Linux</li>
3893 <li>Jalview Archive file faster to load/save, sequence
3894 descriptions saved.</li>
3900 <div align="center">
3901 <strong>2.07</strong><br> 12/12/05
3906 <li>PDB Structure Viewer enhanced</li>
3907 <li>Sequence Feature retrieval and display enhanced</li>
3908 <li>Choose to output sequence start-end after sequence
3909 name for file output</li>
3910 <li>Sequence Fetcher WSDBFetch@EBI</li>
3911 <li>Applet can read feature files, PDB files and can be
3912 used for HTML form input</li>
3917 <li>HTML output writes groups and features</li>
3918 <li>Group editing is Control and mouse click</li>
3919 <li>File IO bugs</li>
3925 <div align="center">
3926 <strong>2.06</strong><br> 28/9/05
3931 <li>View annotations in wrapped mode</li>
3932 <li>More options for PCA viewer</li>
3937 <li>GUI bugs resolved</li>
3938 <li>Runs with -nodisplay from command line</li>
3944 <div align="center">
3945 <strong>2.05b</strong><br> 15/9/05
3950 <li>Choose EPS export as lineart or text</li>
3951 <li>Jar files are executable</li>
3952 <li>Can read in Uracil - maps to unknown residue</li>
3957 <li>Known OutOfMemory errors give warning message</li>
3958 <li>Overview window calculated more efficiently</li>
3959 <li>Several GUI bugs resolved</li>
3965 <div align="center">
3966 <strong>2.05</strong><br> 30/8/05
3971 <li>Edit and annotate in "Wrapped" view</li>
3976 <li>Several GUI bugs resolved</li>
3982 <div align="center">
3983 <strong>2.04</strong><br> 24/8/05
3988 <li>Hold down mouse wheel & scroll to change font
3994 <li>Improved JPred client reliability</li>
3995 <li>Improved loading of Jalview files</li>
4001 <div align="center">
4002 <strong>2.03</strong><br> 18/8/05
4007 <li>Set Proxy server name and port in preferences</li>
4008 <li>Multiple URL links from sequence ids</li>
4009 <li>User Defined Colours can have a scheme name and added
4011 <li>Choose to ignore gaps in consensus calculation</li>
4012 <li>Unix users can set default web browser</li>
4013 <li>Runs without GUI for batch processing</li>
4014 <li>Dynamically generated Web Service Menus</li>
4019 <li>InstallAnywhere download for Sparc Solaris</li>
4025 <div align="center">
4026 <strong>2.02</strong><br> 18/7/05
4032 <li>Copy & Paste order of sequences maintains
4033 alignment order.</li>
4039 <div align="center">
4040 <strong>2.01</strong><br> 12/7/05
4045 <li>Use delete key for deleting selection.</li>
4046 <li>Use Mouse wheel to scroll sequences.</li>
4047 <li>Help file updated to describe how to add alignment
4049 <li>Version and build date written to build properties
4051 <li>InstallAnywhere installation will check for updates
4052 at launch of Jalview.</li>
4057 <li>Delete gaps bug fixed.</li>
4058 <li>FileChooser sorts columns.</li>
4059 <li>Can remove groups one by one.</li>
4060 <li>Filechooser icons installed.</li>
4061 <li>Finder ignores return character when searching.
4062 Return key will initiate a search.<br>
4069 <div align="center">
4070 <strong>2.0</strong><br> 20/6/05
4075 <li>New codebase</li>