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>4/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-247 -->Hidden sequence markers and representative
81 sequence bolding included when exporting alignment as EPS,
82 SVG, PNG or HTML. <em>Display is configured via the
83 Format menu, or for command-line use via a jalview
87 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
88 API and sequence data now imported as JSON
91 <!-- JAL-3065 -->Change in recommended way of starting
92 Jalview via a Java command line: add jars in lib directory
93 to CLASSPATH, rather than via the deprecated java.ext.dirs
100 <!-- JAL-3047 -->Support added to execute test suite
101 instrumented with <a href="http://openclover.org/">Open
106 <td><div align="left">
110 <!-- JAL-3087 -->Corrupted display when switching to
111 wrapped mode when sequence panel's vertical scrollbar is
115 <!-- JAL-3003 -->Alignment is black in exported EPS file
116 when sequences are selected in exported view.</em>
119 <!-- JAL-3059 -->Groups with different coloured borders
120 aren't rendered with correct colour.
123 <!-- JAL-3092 -->Jalview could hang when importing certain
124 types of knotted RNA secondary structure
127 <!-- JAL-3095 -->Sequence highlight and selection in
128 trimmed VARNA 2D structure is incorrect for sequences that
132 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
133 annotation when columns are inserted into an alignment,
134 and when exporting as Stockolm flatfile.
137 <!-- JAL-3053 -->Jalview annotation rows containing upper
138 and lower-case 'E' and 'H' do not automatically get
139 treated as RNA secondary structure
146 <td width="60" nowrap>
148 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
149 <em>7/06/2018</em></strong>
152 <td><div align="left">
156 <!-- JAL-2920 -->Use HGVS nomenclature for variant
157 annotation retrieved from Uniprot
160 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
161 onto the Jalview Desktop
165 <td><div align="left">
169 <!-- JAL-3017 -->Cannot import features with multiple
170 variant elements (blocks import of some Uniprot records)
173 <!-- JAL-2997 -->Clustal files with sequence positions in
174 right-hand column parsed correctly
177 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
178 not alignment area in exported graphic
181 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
182 window has input focus
185 <!-- JAL-2992 -->Annotation panel set too high when
186 annotation added to view (Windows)
189 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
190 network connectivity is poor
193 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
194 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
195 the currently open URL and links from a page viewed in
196 Firefox or Chrome on Windows is now fully supported. If
197 you are using Edge, only links in the page can be
198 dragged, and with Internet Explorer, only the currently
199 open URL in the browser can be dropped onto Jalview.</em>
205 <td width="60" nowrap>
207 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
210 <td><div align="left">
214 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
215 for disabling automatic superposition of multiple
216 structures and open structures in existing views
219 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
220 ID and annotation area margins can be click-dragged to
224 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
228 <!-- JAL-2759 -->Improved performance for large alignments
229 and lots of hidden columns
232 <!-- JAL-2593 -->Improved performance when rendering lots
233 of features (particularly when transparency is disabled)
238 <td><div align="left">
241 <!-- JAL-2899 -->Structure and Overview aren't updated
242 when Colour By Annotation threshold slider is adjusted
245 <!-- JAL-2778 -->Slow redraw when Overview panel shown
246 overlapping alignment panel
249 <!-- JAL-2929 -->Overview doesn't show end of unpadded
253 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
254 improved: CDS not handled correctly if transcript has no
258 <!-- JAL-2321 -->Secondary structure and temperature
259 factor annotation not added to sequence when local PDB
260 file associated with it by drag'n'drop or structure
264 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
265 dialog doesn't import PDB files dropped on an alignment
268 <!-- JAL-2666 -->Linked scrolling via protein horizontal
269 scroll bar doesn't work for some CDS/Protein views
272 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
273 Java 1.8u153 onwards and Java 1.9u4+.
276 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
277 columns in annotation row
280 <!-- JAL-2913 -->Preferences panel's ID Width control is not
281 honored in batch mode
284 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
285 for structures added to existing Jmol view
288 <!-- JAL-2223 -->'View Mappings' includes duplicate
289 entries after importing project with multiple views
292 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
293 protein sequences via SIFTS from associated PDB entries
294 with negative residue numbers or missing residues fails
297 <!-- JAL-2952 -->Exception when shading sequence with negative
298 Temperature Factor values from annotated PDB files (e.g.
299 as generated by CONSURF)
302 <!-- JAL-2920 -->Uniprot 'sequence variant' features
303 tooltip doesn't include a text description of mutation
306 <!-- JAL-2922 -->Invert displayed features very slow when
307 structure and/or overview windows are also shown
310 <!-- JAL-2954 -->Selecting columns from highlighted regions
311 very slow for alignments with large numbers of sequences
314 <!-- JAL-2925 -->Copy Consensus fails for group consensus
315 with 'StringIndexOutOfBounds'
318 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
319 platforms running Java 10
322 <!-- JAL-2960 -->Adding a structure to existing structure
323 view appears to do nothing because the view is hidden behind the alignment view
329 <!-- JAL-2926 -->Copy consensus sequence option in applet
330 should copy the group consensus when popup is opened on it
336 <!-- JAL-2913 -->Fixed ID width preference is not respected
339 <em>New Known Defects</em>
342 <!-- JAL-2973 --> Exceptions occasionally raised when
343 editing a large alignment and overview is displayed
346 <!-- JAL-2974 -->'Overview updating' progress bar is shown
347 repeatedly after a series of edits even when the overview
348 is no longer reflecting updates
351 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
352 structures for protein subsequence (if 'Trim Retrieved
353 Sequences' enabled) or Ensembl isoforms (Workaround in
354 2.10.4 is to fail back to N&W mapping)
361 <td width="60" nowrap>
363 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
366 <td><div align="left">
367 <ul><li>Updated Certum Codesigning Certificate
368 (Valid till 30th November 2018)</li></ul></div></td>
369 <td><div align="left">
372 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
373 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
374 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
375 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
376 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
377 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
378 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
384 <td width="60" nowrap>
386 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
389 <td><div align="left">
393 <!-- JAL-2446 -->Faster and more efficient management and
394 rendering of sequence features
397 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
398 429 rate limit request hander
401 <!-- JAL-2773 -->Structure views don't get updated unless
402 their colours have changed
405 <!-- JAL-2495 -->All linked sequences are highlighted for
406 a structure mousover (Jmol) or selection (Chimera)
409 <!-- JAL-2790 -->'Cancel' button in progress bar for
410 JABAWS AACon, RNAAliFold and Disorder prediction jobs
413 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
414 view from Ensembl locus cross-references
417 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
421 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
422 feature can be disabled
425 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
426 PDB easier retrieval of sequences for lists of IDs
429 <!-- JAL-2758 -->Short names for sequences retrieved from
435 <li>Groovy interpreter updated to 2.4.12</li>
436 <li>Example groovy script for generating a matrix of
437 percent identity scores for current alignment.</li>
439 <em>Testing and Deployment</em>
442 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
446 <td><div align="left">
450 <!-- JAL-2643 -->Pressing tab after updating the colour
451 threshold text field doesn't trigger an update to the
455 <!-- JAL-2682 -->Race condition when parsing sequence ID
459 <!-- JAL-2608 -->Overview windows are also closed when
460 alignment window is closed
463 <!-- JAL-2548 -->Export of features doesn't always respect
467 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
468 takes a long time in Cursor mode
474 <!-- JAL-2777 -->Structures with whitespace chainCode
475 cannot be viewed in Chimera
478 <!-- JAL-2728 -->Protein annotation panel too high in
482 <!-- JAL-2757 -->Can't edit the query after the server
483 error warning icon is shown in Uniprot and PDB Free Text
487 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
490 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
493 <!-- JAL-2739 -->Hidden column marker in last column not
494 rendered when switching back from Wrapped to normal view
497 <!-- JAL-2768 -->Annotation display corrupted when
498 scrolling right in unwapped alignment view
501 <!-- JAL-2542 -->Existing features on subsequence
502 incorrectly relocated when full sequence retrieved from
506 <!-- JAL-2733 -->Last reported memory still shown when
507 Desktop->Show Memory is unticked (OSX only)
510 <!-- JAL-2658 -->Amend Features dialog doesn't allow
511 features of same type and group to be selected for
515 <!-- JAL-2524 -->Jalview becomes sluggish in wide
516 alignments when hidden columns are present
519 <!-- JAL-2392 -->Jalview freezes when loading and
520 displaying several structures
523 <!-- JAL-2732 -->Black outlines left after resizing or
527 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
528 within the Jalview desktop on OSX
531 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
532 when in wrapped alignment mode
535 <!-- JAL-2636 -->Scale mark not shown when close to right
536 hand end of alignment
539 <!-- JAL-2684 -->Pairwise alignment of selected regions of
540 each selected sequence do not have correct start/end
544 <!-- JAL-2793 -->Alignment ruler height set incorrectly
545 after canceling the Alignment Window's Font dialog
548 <!-- JAL-2036 -->Show cross-references not enabled after
549 restoring project until a new view is created
552 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
553 URL links appears when only default EMBL-EBI link is
554 configured (since 2.10.2b2)
557 <!-- JAL-2775 -->Overview redraws whole window when box
561 <!-- JAL-2225 -->Structure viewer doesn't map all chains
562 in a multi-chain structure when viewing alignment
563 involving more than one chain (since 2.10)
566 <!-- JAL-2811 -->Double residue highlights in cursor mode
567 if new selection moves alignment window
570 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
571 arrow key in cursor mode to pass hidden column marker
574 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
575 that produces correctly annotated transcripts and products
578 <!-- JAL-2776 -->Toggling a feature group after first time
579 doesn't update associated structure view
582 <em>Applet</em><br />
585 <!-- JAL-2687 -->Concurrent modification exception when
586 closing alignment panel
589 <em>BioJSON</em><br />
592 <!-- JAL-2546 -->BioJSON export does not preserve
593 non-positional features
596 <em>New Known Issues</em>
599 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
600 sequence features correctly (for many previous versions of
604 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
605 using cursor in wrapped panel other than top
608 <!-- JAL-2791 -->Select columns containing feature ignores
609 graduated colour threshold
612 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
613 always preserve numbering and sequence features
616 <em>Known Java 9 Issues</em>
619 <!-- JAL-2902 -->Groovy Console very slow to open and is
620 not responsive when entering characters (Webstart, Java
627 <td width="60" nowrap>
629 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
630 <em>2/10/2017</em></strong>
633 <td><div align="left">
634 <em>New features in Jalview Desktop</em>
637 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
639 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
643 <td><div align="left">
647 <td width="60" nowrap>
649 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
650 <em>7/9/2017</em></strong>
653 <td><div align="left">
657 <!-- JAL-2588 -->Show gaps in overview window by colouring
658 in grey (sequences used to be coloured grey, and gaps were
662 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
666 <!-- JAL-2587 -->Overview updates immediately on increase
667 in size and progress bar shown as higher resolution
668 overview is recalculated
673 <td><div align="left">
677 <!-- JAL-2664 -->Overview window redraws every hidden
678 column region row by row
681 <!-- JAL-2681 -->duplicate protein sequences shown after
682 retrieving Ensembl crossrefs for sequences from Uniprot
685 <!-- JAL-2603 -->Overview window throws NPE if show boxes
686 format setting is unticked
689 <!-- JAL-2610 -->Groups are coloured wrongly in overview
690 if group has show boxes format setting unticked
693 <!-- JAL-2672,JAL-2665 -->Redraw problems when
694 autoscrolling whilst dragging current selection group to
695 include sequences and columns not currently displayed
698 <!-- JAL-2691 -->Not all chains are mapped when multimeric
699 assemblies are imported via CIF file
702 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
703 displayed when threshold or conservation colouring is also
707 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
711 <!-- JAL-2673 -->Jalview continues to scroll after
712 dragging a selected region off the visible region of the
716 <!-- JAL-2724 -->Cannot apply annotation based
717 colourscheme to all groups in a view
720 <!-- JAL-2511 -->IDs don't line up with sequences
721 initially after font size change using the Font chooser or
728 <td width="60" nowrap>
730 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
733 <td><div align="left">
734 <em>Calculations</em>
738 <!-- JAL-1933 -->Occupancy annotation row shows number of
739 ungapped positions in each column of the alignment.
742 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
743 a calculation dialog box
746 <!-- JAL-2379 -->Revised implementation of PCA for speed
747 and memory efficiency (~30x faster)
750 <!-- JAL-2403 -->Revised implementation of sequence
751 similarity scores as used by Tree, PCA, Shading Consensus
752 and other calculations
755 <!-- JAL-2416 -->Score matrices are stored as resource
756 files within the Jalview codebase
759 <!-- JAL-2500 -->Trees computed on Sequence Feature
760 Similarity may have different topology due to increased
767 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
768 model for alignments and groups
771 <!-- JAL-384 -->Custom shading schemes created via groovy
778 <!-- JAL-2526 -->Efficiency improvements for interacting
779 with alignment and overview windows
782 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
786 <!-- JAL-2388 -->Hidden columns and sequences can be
790 <!-- JAL-2611 -->Click-drag in visible area allows fine
791 adjustment of visible position
795 <em>Data import/export</em>
798 <!-- JAL-2535 -->Posterior probability annotation from
799 Stockholm files imported as sequence associated annotation
802 <!-- JAL-2507 -->More robust per-sequence positional
803 annotation input/output via stockholm flatfile
806 <!-- JAL-2533 -->Sequence names don't include file
807 extension when importing structure files without embedded
808 names or PDB accessions
811 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
812 format sequence substitution matrices
815 <em>User Interface</em>
818 <!-- JAL-2447 --> Experimental Features Checkbox in
819 Desktop's Tools menu to hide or show untested features in
823 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
824 via Overview or sequence motif search operations
827 <!-- JAL-2547 -->Amend sequence features dialog box can be
828 opened by double clicking gaps within sequence feature
832 <!-- JAL-1476 -->Status bar message shown when not enough
833 aligned positions were available to create a 3D structure
837 <em>3D Structure</em>
840 <!-- JAL-2430 -->Hidden regions in alignment views are not
841 coloured in linked structure views
844 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
845 file-based command exchange
848 <!-- JAL-2375 -->Structure chooser automatically shows
849 Cached Structures rather than querying the PDBe if
850 structures are already available for sequences
853 <!-- JAL-2520 -->Structures imported via URL are cached in
854 the Jalview project rather than downloaded again when the
858 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
859 to transfer Chimera's structure attributes as Jalview
860 features, and vice-versa (<strong>Experimental
864 <em>Web Services</em>
867 <!-- JAL-2549 -->Updated JABAWS client to v2.2
870 <!-- JAL-2335 -->Filter non-standard amino acids and
871 nucleotides when submitting to AACon and other MSA
875 <!-- JAL-2316, -->URLs for viewing database
876 cross-references provided by identifiers.org and the
884 <!-- JAL-2344 -->FileFormatI interface for describing and
885 identifying file formats (instead of String constants)
888 <!-- JAL-2228 -->FeatureCounter script refactored for
889 efficiency when counting all displayed features (not
890 backwards compatible with 2.10.1)
893 <em>Example files</em>
896 <!-- JAL-2631 -->Graduated feature colour style example
897 included in the example feature file
900 <em>Documentation</em>
903 <!-- JAL-2339 -->Release notes reformatted for readability
904 with the built-in Java help viewer
907 <!-- JAL-1644 -->Find documentation updated with 'search
908 sequence description' option
914 <!-- JAL-2485, -->External service integration tests for
915 Uniprot REST Free Text Search Client
918 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
921 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
926 <td><div align="left">
927 <em>Calculations</em>
930 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
931 matrix - C->R should be '-3'<br />Old matrix restored
932 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
934 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
935 Jalview's treatment of gaps in PCA and substitution matrix
936 based Tree calculations.<br /> <br />In earlier versions
937 of Jalview, gaps matching gaps were penalised, and gaps
938 matching non-gaps penalised even more. In the PCA
939 calculation, gaps were actually treated as non-gaps - so
940 different costs were applied, which meant Jalview's PCAs
941 were different to those produced by SeqSpace.<br />Jalview
942 now treats gaps in the same way as SeqSpace (ie it scores
943 them as 0). <br /> <br />Enter the following in the
944 Groovy console to restore pre-2.10.2 behaviour:<br />
945 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
946 // for 2.10.1 mode <br />
947 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
948 // to restore 2.10.2 mode <br /> <br /> <em>Note:
949 these settings will affect all subsequent tree and PCA
950 calculations (not recommended)</em></li>
952 <!-- JAL-2424 -->Fixed off-by-one bug that affected
953 scaling of branch lengths for trees computed using
954 Sequence Feature Similarity.
957 <!-- JAL-2377 -->PCA calculation could hang when
958 generating output report when working with highly
962 <!-- JAL-2544 --> Sort by features includes features to
963 right of selected region when gaps present on right-hand
967 <em>User Interface</em>
970 <!-- JAL-2346 -->Reopening Colour by annotation dialog
971 doesn't reselect a specific sequence's associated
972 annotation after it was used for colouring a view
975 <!-- JAL-2419 -->Current selection lost if popup menu
976 opened on a region of alignment without groups
979 <!-- JAL-2374 -->Popup menu not always shown for regions
980 of an alignment with overlapping groups
983 <!-- JAL-2310 -->Finder double counts if both a sequence's
984 name and description match
987 <!-- JAL-2370 -->Hiding column selection containing two
988 hidden regions results in incorrect hidden regions
991 <!-- JAL-2386 -->'Apply to all groups' setting when
992 changing colour does not apply Conservation slider value
996 <!-- JAL-2373 -->Percentage identity and conservation menu
997 items do not show a tick or allow shading to be disabled
1000 <!-- JAL-2385 -->Conservation shading or PID threshold
1001 lost when base colourscheme changed if slider not visible
1004 <!-- JAL-2547 -->Sequence features shown in tooltip for
1005 gaps before start of features
1008 <!-- JAL-2623 -->Graduated feature colour threshold not
1009 restored to UI when feature colour is edited
1012 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1013 a time when scrolling vertically in wrapped mode.
1016 <!-- JAL-2630 -->Structure and alignment overview update
1017 as graduate feature colour settings are modified via the
1021 <!-- JAL-2034 -->Overview window doesn't always update
1022 when a group defined on the alignment is resized
1025 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1026 wrapped view result in positional status updates
1030 <!-- JAL-2563 -->Status bar doesn't show position for
1031 ambiguous amino acid and nucleotide symbols
1034 <!-- JAL-2602 -->Copy consensus sequence failed if
1035 alignment included gapped columns
1038 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1039 widgets don't permanently disappear
1042 <!-- JAL-2503 -->Cannot select or filter quantitative
1043 annotation that are shown only as column labels (e.g.
1044 T-Coffee column reliability scores)
1047 <!-- JAL-2594 -->Exception thrown if trying to create a
1048 sequence feature on gaps only
1051 <!-- JAL-2504 -->Features created with 'New feature'
1052 button from a Find inherit previously defined feature type
1053 rather than the Find query string
1056 <!-- JAL-2423 -->incorrect title in output window when
1057 exporting tree calculated in Jalview
1060 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1061 and then revealing them reorders sequences on the
1065 <!-- JAL-964 -->Group panel in sequence feature settings
1066 doesn't update to reflect available set of groups after
1067 interactively adding or modifying features
1070 <!-- JAL-2225 -->Sequence Database chooser unusable on
1074 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1075 only excluded gaps in current sequence and ignored
1082 <!-- JAL-2421 -->Overview window visible region moves
1083 erratically when hidden rows or columns are present
1086 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1087 Structure Viewer's colour menu don't correspond to
1091 <!-- JAL-2405 -->Protein specific colours only offered in
1092 colour and group colour menu for protein alignments
1095 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1096 reflect currently selected view or group's shading
1100 <!-- JAL-2624 -->Feature colour thresholds not respected
1101 when rendered on overview and structures when opacity at
1105 <!-- JAL-2589 -->User defined gap colour not shown in
1106 overview when features overlaid on alignment
1109 <em>Data import/export</em>
1112 <!-- JAL-2576 -->Very large alignments take a long time to
1116 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1117 added after a sequence was imported are not written to
1121 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1122 when importing RNA secondary structure via Stockholm
1125 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1126 not shown in correct direction for simple pseudoknots
1129 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1130 with lightGray or darkGray via features file (but can
1134 <!-- JAL-2383 -->Above PID colour threshold not recovered
1135 when alignment view imported from project
1138 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1139 structure and sequences extracted from structure files
1140 imported via URL and viewed in Jmol
1143 <!-- JAL-2520 -->Structures loaded via URL are saved in
1144 Jalview Projects rather than fetched via URL again when
1145 the project is loaded and the structure viewed
1148 <em>Web Services</em>
1151 <!-- JAL-2519 -->EnsemblGenomes example failing after
1152 release of Ensembl v.88
1155 <!-- JAL-2366 -->Proxy server address and port always
1156 appear enabled in Preferences->Connections
1159 <!-- JAL-2461 -->DAS registry not found exceptions
1160 removed from console output
1163 <!-- JAL-2582 -->Cannot retrieve protein products from
1164 Ensembl by Peptide ID
1167 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1168 created from SIFTs, and spurious 'Couldn't open structure
1169 in Chimera' errors raised after April 2017 update (problem
1170 due to 'null' string rather than empty string used for
1171 residues with no corresponding PDB mapping).
1174 <em>Application UI</em>
1177 <!-- JAL-2361 -->User Defined Colours not added to Colour
1181 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1182 case' residues (button in colourscheme editor debugged and
1183 new documentation and tooltips added)
1186 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1187 doesn't restore group-specific text colour thresholds
1190 <!-- JAL-2243 -->Feature settings panel does not update as
1191 new features are added to alignment
1194 <!-- JAL-2532 -->Cancel in feature settings reverts
1195 changes to feature colours via the Amend features dialog
1198 <!-- JAL-2506 -->Null pointer exception when attempting to
1199 edit graduated feature colour via amend features dialog
1203 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1204 selection menu changes colours of alignment views
1207 <!-- JAL-2426 -->Spurious exceptions in console raised
1208 from alignment calculation workers after alignment has
1212 <!-- JAL-1608 -->Typo in selection popup menu - Create
1213 groups now 'Create Group'
1216 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1217 Create/Undefine group doesn't always work
1220 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1221 shown again after pressing 'Cancel'
1224 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1225 adjusts start position in wrap mode
1228 <!-- JAL-2563 -->Status bar doesn't show positions for
1229 ambiguous amino acids
1232 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1233 CDS/Protein view after CDS sequences added for aligned
1237 <!-- JAL-2592 -->User defined colourschemes called 'User
1238 Defined' don't appear in Colours menu
1244 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1245 score models doesn't always result in an updated PCA plot
1248 <!-- JAL-2442 -->Features not rendered as transparent on
1249 overview or linked structure view
1252 <!-- JAL-2372 -->Colour group by conservation doesn't
1256 <!-- JAL-2517 -->Hitting Cancel after applying
1257 user-defined colourscheme doesn't restore original
1264 <!-- JAL-2314 -->Unit test failure:
1265 jalview.ws.jabaws.RNAStructExportImport setup fails
1268 <!-- JAL-2307 -->Unit test failure:
1269 jalview.ws.sifts.SiftsClientTest due to compatibility
1270 problems with deep array comparison equality asserts in
1271 successive versions of TestNG
1274 <!-- JAL-2479 -->Relocated StructureChooserTest and
1275 ParameterUtilsTest Unit tests to Network suite
1278 <em>New Known Issues</em>
1281 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1282 phase after a sequence motif find operation
1285 <!-- JAL-2550 -->Importing annotation file with rows
1286 containing just upper and lower case letters are
1287 interpreted as WUSS RNA secondary structure symbols
1290 <!-- JAL-2590 -->Cannot load and display Newick trees
1291 reliably from eggnog Ortholog database
1294 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1295 containing features of type Highlight' when 'B' is pressed
1296 to mark columns containing highlighted regions.
1299 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1300 doesn't always add secondary structure annotation.
1305 <td width="60" nowrap>
1306 <div align="center">
1307 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1310 <td><div align="left">
1314 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1315 for all consensus calculations
1318 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1321 <li>Updated Jalview's Certum code signing certificate
1324 <em>Application</em>
1327 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1328 set of database cross-references, sorted alphabetically
1331 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1332 from database cross references. Users with custom links
1333 will receive a <a href="webServices/urllinks.html#warning">warning
1334 dialog</a> asking them to update their preferences.
1337 <!-- JAL-2287-->Cancel button and escape listener on
1338 dialog warning user about disconnecting Jalview from a
1342 <!-- JAL-2320-->Jalview's Chimera control window closes if
1343 the Chimera it is connected to is shut down
1346 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1347 columns menu item to mark columns containing highlighted
1348 regions (e.g. from structure selections or results of a
1352 <!-- JAL-2284-->Command line option for batch-generation
1353 of HTML pages rendering alignment data with the BioJS
1363 <!-- JAL-2286 -->Columns with more than one modal residue
1364 are not coloured or thresholded according to percent
1365 identity (first observed in Jalview 2.8.2)
1368 <!-- JAL-2301 -->Threonine incorrectly reported as not
1372 <!-- JAL-2318 -->Updates to documentation pages (above PID
1373 threshold, amino acid properties)
1376 <!-- JAL-2292 -->Lower case residues in sequences are not
1377 reported as mapped to residues in a structure file in the
1381 <!--JAL-2324 -->Identical features with non-numeric scores
1382 could be added multiple times to a sequence
1385 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1386 bond features shown as two highlighted residues rather
1387 than a range in linked structure views, and treated
1388 correctly when selecting and computing trees from features
1391 <!-- JAL-2281-->Custom URL links for database
1392 cross-references are matched to database name regardless
1397 <em>Application</em>
1400 <!-- JAL-2282-->Custom URL links for specific database
1401 names without regular expressions also offer links from
1405 <!-- JAL-2315-->Removing a single configured link in the
1406 URL links pane in Connections preferences doesn't actually
1407 update Jalview configuration
1410 <!-- JAL-2272-->CTRL-Click on a selected region to open
1411 the alignment area popup menu doesn't work on El-Capitan
1414 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1415 files with similarly named sequences if dropped onto the
1419 <!-- JAL-2312 -->Additional mappings are shown for PDB
1420 entries where more chains exist in the PDB accession than
1421 are reported in the SIFTS file
1424 <!-- JAL-2317-->Certain structures do not get mapped to
1425 the structure view when displayed with Chimera
1428 <!-- JAL-2317-->No chains shown in the Chimera view
1429 panel's View->Show Chains submenu
1432 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1433 work for wrapped alignment views
1436 <!--JAL-2197 -->Rename UI components for running JPred
1437 predictions from 'JNet' to 'JPred'
1440 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1441 corrupted when annotation panel vertical scroll is not at
1442 first annotation row
1445 <!--JAL-2332 -->Attempting to view structure for Hen
1446 lysozyme results in a PDB Client error dialog box
1449 <!-- JAL-2319 -->Structure View's mapping report switched
1450 ranges for PDB and sequence for SIFTS
1453 SIFTS 'Not_Observed' residues mapped to non-existant
1457 <!-- <em>New Known Issues</em>
1464 <td width="60" nowrap>
1465 <div align="center">
1466 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1467 <em>25/10/2016</em></strong>
1470 <td><em>Application</em>
1472 <li>3D Structure chooser opens with 'Cached structures'
1473 view if structures already loaded</li>
1474 <li>Progress bar reports models as they are loaded to
1475 structure views</li>
1481 <li>Colour by conservation always enabled and no tick
1482 shown in menu when BLOSUM or PID shading applied</li>
1483 <li>FER1_ARATH and FER2_ARATH labels were switched in
1484 example sequences/projects/trees</li>
1486 <em>Application</em>
1488 <li>Jalview projects with views of local PDB structure
1489 files saved on Windows cannot be opened on OSX</li>
1490 <li>Multiple structure views can be opened and superposed
1491 without timeout for structures with multiple models or
1492 multiple sequences in alignment</li>
1493 <li>Cannot import or associated local PDB files without a
1494 PDB ID HEADER line</li>
1495 <li>RMSD is not output in Jmol console when superposition
1497 <li>Drag and drop of URL from Browser fails for Linux and
1498 OSX versions earlier than El Capitan</li>
1499 <li>ENA client ignores invalid content from ENA server</li>
1500 <li>Exceptions are not raised in console when ENA client
1501 attempts to fetch non-existent IDs via Fetch DB Refs UI
1503 <li>Exceptions are not raised in console when a new view
1504 is created on the alignment</li>
1505 <li>OSX right-click fixed for group selections: CMD-click
1506 to insert/remove gaps in groups and CTRL-click to open group
1509 <em>Build and deployment</em>
1511 <li>URL link checker now copes with multi-line anchor
1514 <em>New Known Issues</em>
1516 <li>Drag and drop from URL links in browsers do not work
1523 <td width="60" nowrap>
1524 <div align="center">
1525 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1528 <td><em>General</em>
1531 <!-- JAL-2124 -->Updated Spanish translations.
1534 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1535 for importing structure data to Jalview. Enables mmCIF and
1539 <!-- JAL-192 --->Alignment ruler shows positions relative to
1543 <!-- JAL-2202 -->Position/residue shown in status bar when
1544 mousing over sequence associated annotation
1547 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1551 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1552 '()', canonical '[]' and invalid '{}' base pair populations
1556 <!-- JAL-2092 -->Feature settings popup menu options for
1557 showing or hiding columns containing a feature
1560 <!-- JAL-1557 -->Edit selected group by double clicking on
1561 group and sequence associated annotation labels
1564 <!-- JAL-2236 -->Sequence name added to annotation label in
1565 select/hide columns by annotation and colour by annotation
1569 </ul> <em>Application</em>
1572 <!-- JAL-2050-->Automatically hide introns when opening a
1573 gene/transcript view
1576 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1580 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1581 structure mappings with the EMBL-EBI PDBe SIFTS database
1584 <!-- JAL-2079 -->Updated download sites used for Rfam and
1585 Pfam sources to xfam.org
1588 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1591 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1592 over sequences in Jalview
1595 <!-- JAL-2027-->Support for reverse-complement coding
1596 regions in ENA and EMBL
1599 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1600 for record retrieval via ENA rest API
1603 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1607 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1608 groovy script execution
1611 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1612 alignment window's Calculate menu
1615 <!-- JAL-1812 -->Allow groovy scripts that call
1616 Jalview.getAlignFrames() to run in headless mode
1619 <!-- JAL-2068 -->Support for creating new alignment
1620 calculation workers from groovy scripts
1623 <!-- JAL-1369 --->Store/restore reference sequence in
1627 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1628 associations are now saved/restored from project
1631 <!-- JAL-1993 -->Database selection dialog always shown
1632 before sequence fetcher is opened
1635 <!-- JAL-2183 -->Double click on an entry in Jalview's
1636 database chooser opens a sequence fetcher
1639 <!-- JAL-1563 -->Free-text search client for UniProt using
1640 the UniProt REST API
1643 <!-- JAL-2168 -->-nonews command line parameter to prevent
1644 the news reader opening
1647 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1648 querying stored in preferences
1651 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1655 <!-- JAL-1977-->Tooltips shown on database chooser
1658 <!-- JAL-391 -->Reverse complement function in calculate
1659 menu for nucleotide sequences
1662 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1663 and feature counts preserves alignment ordering (and
1664 debugged for complex feature sets).
1667 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1668 viewing structures with Jalview 2.10
1671 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1672 genome, transcript CCDS and gene ids via the Ensembl and
1673 Ensembl Genomes REST API
1676 <!-- JAL-2049 -->Protein sequence variant annotation
1677 computed for 'sequence_variant' annotation on CDS regions
1681 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1685 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1686 Ref Fetcher fails to match, or otherwise updates sequence
1687 data from external database records.
1690 <!-- JAL-2154 -->Revised Jalview Project format for
1691 efficient recovery of sequence coding and alignment
1692 annotation relationships.
1694 </ul> <!-- <em>Applet</em>
1705 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1709 <!-- JAL-2018-->Export features in Jalview format (again)
1710 includes graduated colourschemes
1713 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1714 working with big alignments and lots of hidden columns
1717 <!-- JAL-2053-->Hidden column markers not always rendered
1718 at right of alignment window
1721 <!-- JAL-2067 -->Tidied up links in help file table of
1725 <!-- JAL-2072 -->Feature based tree calculation not shown
1729 <!-- JAL-2075 -->Hidden columns ignored during feature
1730 based tree calculation
1733 <!-- JAL-2065 -->Alignment view stops updating when show
1734 unconserved enabled for group on alignment
1737 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1741 <!-- JAL-2146 -->Alignment column in status incorrectly
1742 shown as "Sequence position" when mousing over
1746 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1747 hidden columns present
1750 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1751 user created annotation added to alignment
1754 <!-- JAL-1841 -->RNA Structure consensus only computed for
1755 '()' base pair annotation
1758 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1759 in zero scores for all base pairs in RNA Structure
1763 <!-- JAL-2174-->Extend selection with columns containing
1767 <!-- JAL-2275 -->Pfam format writer puts extra space at
1768 beginning of sequence
1771 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1775 <!-- JAL-2238 -->Cannot create groups on an alignment from
1776 from a tree when t-coffee scores are shown
1779 <!-- JAL-1836,1967 -->Cannot import and view PDB
1780 structures with chains containing negative resnums (4q4h)
1783 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1787 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1788 to Clustal, PIR and PileUp output
1791 <!-- JAL-2008 -->Reordering sequence features that are
1792 not visible causes alignment window to repaint
1795 <!-- JAL-2006 -->Threshold sliders don't work in
1796 graduated colour and colour by annotation row for e-value
1797 scores associated with features and annotation rows
1800 <!-- JAL-1797 -->amino acid physicochemical conservation
1801 calculation should be case independent
1804 <!-- JAL-2173 -->Remove annotation also updates hidden
1808 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1809 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1810 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1813 <!-- JAL-2065 -->Null pointer exceptions and redraw
1814 problems when reference sequence defined and 'show
1815 non-conserved' enabled
1818 <!-- JAL-1306 -->Quality and Conservation are now shown on
1819 load even when Consensus calculation is disabled
1822 <!-- JAL-1932 -->Remove right on penultimate column of
1823 alignment does nothing
1826 <em>Application</em>
1829 <!-- JAL-1552-->URLs and links can't be imported by
1830 drag'n'drop on OSX when launched via webstart (note - not
1831 yet fixed for El Capitan)
1834 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1835 output when running on non-gb/us i18n platforms
1838 <!-- JAL-1944 -->Error thrown when exporting a view with
1839 hidden sequences as flat-file alignment
1842 <!-- JAL-2030-->InstallAnywhere distribution fails when
1846 <!-- JAL-2080-->Jalview very slow to launch via webstart
1847 (also hotfix for 2.9.0b2)
1850 <!-- JAL-2085 -->Cannot save project when view has a
1851 reference sequence defined
1854 <!-- JAL-1011 -->Columns are suddenly selected in other
1855 alignments and views when revealing hidden columns
1858 <!-- JAL-1989 -->Hide columns not mirrored in complement
1859 view in a cDNA/Protein splitframe
1862 <!-- JAL-1369 -->Cannot save/restore representative
1863 sequence from project when only one sequence is
1867 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1868 in Structure Chooser
1871 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1872 structure consensus didn't refresh annotation panel
1875 <!-- JAL-1962 -->View mapping in structure view shows
1876 mappings between sequence and all chains in a PDB file
1879 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1880 dialogs format columns correctly, don't display array
1881 data, sort columns according to type
1884 <!-- JAL-1975 -->Export complete shown after destination
1885 file chooser is cancelled during an image export
1888 <!-- JAL-2025 -->Error when querying PDB Service with
1889 sequence name containing special characters
1892 <!-- JAL-2024 -->Manual PDB structure querying should be
1896 <!-- JAL-2104 -->Large tooltips with broken HTML
1897 formatting don't wrap
1900 <!-- JAL-1128 -->Figures exported from wrapped view are
1901 truncated so L looks like I in consensus annotation
1904 <!-- JAL-2003 -->Export features should only export the
1905 currently displayed features for the current selection or
1909 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1910 after fetching cross-references, and restoring from
1914 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1915 followed in the structure viewer
1918 <!-- JAL-2163 -->Titles for individual alignments in
1919 splitframe not restored from project
1922 <!-- JAL-2145 -->missing autocalculated annotation at
1923 trailing end of protein alignment in transcript/product
1924 splitview when pad-gaps not enabled by default
1927 <!-- JAL-1797 -->amino acid physicochemical conservation
1931 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1932 article has been read (reopened issue due to
1933 internationalisation problems)
1936 <!-- JAL-1960 -->Only offer PDB structures in structure
1937 viewer based on sequence name, PDB and UniProt
1942 <!-- JAL-1976 -->No progress bar shown during export of
1946 <!-- JAL-2213 -->Structures not always superimposed after
1947 multiple structures are shown for one or more sequences.
1950 <!-- JAL-1370 -->Reference sequence characters should not
1951 be replaced with '.' when 'Show unconserved' format option
1955 <!-- JAL-1823 -->Cannot specify chain code when entering
1956 specific PDB id for sequence
1959 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1960 'Export hidden sequences' is enabled, but 'export hidden
1961 columns' is disabled.
1964 <!--JAL-2026-->Best Quality option in structure chooser
1965 selects lowest rather than highest resolution structures
1969 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1970 to sequence mapping in 'View Mappings' report
1973 <!-- JAL-2284 -->Unable to read old Jalview projects that
1974 contain non-XML data added after Jalvew wrote project.
1977 <!-- JAL-2118 -->Newly created annotation row reorders
1978 after clicking on it to create new annotation for a
1982 <!-- JAL-1980 -->Null Pointer Exception raised when
1983 pressing Add on an orphaned cut'n'paste window.
1985 <!-- may exclude, this is an external service stability issue JAL-1941
1986 -- > RNA 3D structure not added via DSSR service</li> -->
1991 <!-- JAL-2151 -->Incorrect columns are selected when
1992 hidden columns present before start of sequence
1995 <!-- JAL-1986 -->Missing dependencies on applet pages
1999 <!-- JAL-1947 -->Overview pixel size changes when
2000 sequences are hidden in applet
2003 <!-- JAL-1996 -->Updated instructions for applet
2004 deployment on examples pages.
2011 <td width="60" nowrap>
2012 <div align="center">
2013 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2014 <em>16/10/2015</em></strong>
2017 <td><em>General</em>
2019 <li>Time stamps for signed Jalview application and applet
2024 <em>Application</em>
2026 <li>Duplicate group consensus and conservation rows
2027 shown when tree is partitioned</li>
2028 <li>Erratic behaviour when tree partitions made with
2029 multiple cDNA/Protein split views</li>
2035 <td width="60" nowrap>
2036 <div align="center">
2037 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2038 <em>8/10/2015</em></strong>
2041 <td><em>General</em>
2043 <li>Updated Spanish translations of localized text for
2045 </ul> <em>Application</em>
2047 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2048 <li>Signed OSX InstallAnywhere installer<br></li>
2049 <li>Support for per-sequence based annotations in BioJSON</li>
2050 </ul> <em>Applet</em>
2052 <li>Split frame example added to applet examples page</li>
2053 </ul> <em>Build and Deployment</em>
2056 <!-- JAL-1888 -->New ant target for running Jalview's test
2064 <li>Mapping of cDNA to protein in split frames
2065 incorrect when sequence start > 1</li>
2066 <li>Broken images in filter column by annotation dialog
2068 <li>Feature colours not parsed from features file</li>
2069 <li>Exceptions and incomplete link URLs recovered when
2070 loading a features file containing HTML tags in feature
2074 <em>Application</em>
2076 <li>Annotations corrupted after BioJS export and
2078 <li>Incorrect sequence limits after Fetch DB References
2079 with 'trim retrieved sequences'</li>
2080 <li>Incorrect warning about deleting all data when
2081 deleting selected columns</li>
2082 <li>Patch to build system for shipping properly signed
2083 JNLP templates for webstart launch</li>
2084 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2085 unreleased structures for download or viewing</li>
2086 <li>Tab/space/return keystroke operation of EMBL-PDBe
2087 fetcher/viewer dialogs works correctly</li>
2088 <li>Disabled 'minimise' button on Jalview windows
2089 running on OSX to workaround redraw hang bug</li>
2090 <li>Split cDNA/Protein view position and geometry not
2091 recovered from jalview project</li>
2092 <li>Initial enabled/disabled state of annotation menu
2093 sorter 'show autocalculated first/last' corresponds to
2095 <li>Restoring of Clustal, RNA Helices and T-Coffee
2096 color schemes from BioJSON</li>
2100 <li>Reorder sequences mirrored in cDNA/Protein split
2102 <li>Applet with Jmol examples not loading correctly</li>
2108 <td><div align="center">
2109 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2111 <td><em>General</em>
2113 <li>Linked visualisation and analysis of DNA and Protein
2116 <li>Translated cDNA alignments shown as split protein
2117 and DNA alignment views</li>
2118 <li>Codon consensus annotation for linked protein and
2119 cDNA alignment views</li>
2120 <li>Link cDNA or Protein product sequences by loading
2121 them onto Protein or cDNA alignments</li>
2122 <li>Reconstruct linked cDNA alignment from aligned
2123 protein sequences</li>
2126 <li>Jmol integration updated to Jmol v14.2.14</li>
2127 <li>Import and export of Jalview alignment views as <a
2128 href="features/bioJsonFormat.html">BioJSON</a></li>
2129 <li>New alignment annotation file statements for
2130 reference sequences and marking hidden columns</li>
2131 <li>Reference sequence based alignment shading to
2132 highlight variation</li>
2133 <li>Select or hide columns according to alignment
2135 <li>Find option for locating sequences by description</li>
2136 <li>Conserved physicochemical properties shown in amino
2137 acid conservation row</li>
2138 <li>Alignments can be sorted by number of RNA helices</li>
2139 </ul> <em>Application</em>
2141 <li>New cDNA/Protein analysis capabilities
2143 <li>Get Cross-References should open a Split Frame
2144 view with cDNA/Protein</li>
2145 <li>Detect when nucleotide sequences and protein
2146 sequences are placed in the same alignment</li>
2147 <li>Split cDNA/Protein views are saved in Jalview
2152 <li>Use REST API to talk to Chimera</li>
2153 <li>Selected regions in Chimera are highlighted in linked
2154 Jalview windows</li>
2156 <li>VARNA RNA viewer updated to v3.93</li>
2157 <li>VARNA views are saved in Jalview Projects</li>
2158 <li>Pseudoknots displayed as Jalview RNA annotation can
2159 be shown in VARNA</li>
2161 <li>Make groups for selection uses marked columns as well
2162 as the active selected region</li>
2164 <li>Calculate UPGMA and NJ trees using sequence feature
2166 <li>New Export options
2168 <li>New Export Settings dialog to control hidden
2169 region export in flat file generation</li>
2171 <li>Export alignment views for display with the <a
2172 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2174 <li>Export scrollable SVG in HTML page</li>
2175 <li>Optional embedding of BioJSON data when exporting
2176 alignment figures to HTML</li>
2178 <li>3D structure retrieval and display
2180 <li>Free text and structured queries with the PDBe
2182 <li>PDBe Search API based discovery and selection of
2183 PDB structures for a sequence set</li>
2187 <li>JPred4 employed for protein secondary structure
2189 <li>Hide Insertions menu option to hide unaligned columns
2190 for one or a group of sequences</li>
2191 <li>Automatically hide insertions in alignments imported
2192 from the JPred4 web server</li>
2193 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2194 system on OSX<br />LGPL libraries courtesy of <a
2195 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2197 <li>changed 'View nucleotide structure' submenu to 'View
2198 VARNA 2D Structure'</li>
2199 <li>change "View protein structure" menu option to "3D
2202 </ul> <em>Applet</em>
2204 <li>New layout for applet example pages</li>
2205 <li>New parameters to enable SplitFrame view
2206 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2207 <li>New example demonstrating linked viewing of cDNA and
2208 Protein alignments</li>
2209 </ul> <em>Development and deployment</em>
2211 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2212 <li>Include installation type and git revision in build
2213 properties and console log output</li>
2214 <li>Jalview Github organisation, and new github site for
2215 storing BioJsMSA Templates</li>
2216 <li>Jalview's unit tests now managed with TestNG</li>
2219 <!-- <em>General</em>
2221 </ul> --> <!-- issues resolved --> <em>Application</em>
2223 <li>Escape should close any open find dialogs</li>
2224 <li>Typo in select-by-features status report</li>
2225 <li>Consensus RNA secondary secondary structure
2226 predictions are not highlighted in amber</li>
2227 <li>Missing gap character in v2.7 example file means
2228 alignment appears unaligned when pad-gaps is not enabled</li>
2229 <li>First switch to RNA Helices colouring doesn't colour
2230 associated structure views</li>
2231 <li>ID width preference option is greyed out when auto
2232 width checkbox not enabled</li>
2233 <li>Stopped a warning dialog from being shown when
2234 creating user defined colours</li>
2235 <li>'View Mapping' in structure viewer shows sequence
2236 mappings for just that viewer's sequences</li>
2237 <li>Workaround for superposing PDB files containing
2238 multiple models in Chimera</li>
2239 <li>Report sequence position in status bar when hovering
2240 over Jmol structure</li>
2241 <li>Cannot output gaps as '.' symbols with Selection ->
2242 output to text box</li>
2243 <li>Flat file exports of alignments with hidden columns
2244 have incorrect sequence start/end</li>
2245 <li>'Aligning' a second chain to a Chimera structure from
2247 <li>Colour schemes applied to structure viewers don't
2248 work for nucleotide</li>
2249 <li>Loading/cut'n'pasting an empty or invalid file leads
2250 to a grey/invisible alignment window</li>
2251 <li>Exported Jpred annotation from a sequence region
2252 imports to different position</li>
2253 <li>Space at beginning of sequence feature tooltips shown
2254 on some platforms</li>
2255 <li>Chimera viewer 'View | Show Chain' menu is not
2257 <li>'New View' fails with a Null Pointer Exception in
2258 console if Chimera has been opened</li>
2259 <li>Mouseover to Chimera not working</li>
2260 <li>Miscellaneous ENA XML feature qualifiers not
2262 <li>NPE in annotation renderer after 'Extract Scores'</li>
2263 <li>If two structures in one Chimera window, mouseover of
2264 either sequence shows on first structure</li>
2265 <li>'Show annotations' options should not make
2266 non-positional annotations visible</li>
2267 <li>Subsequence secondary structure annotation not shown
2268 in right place after 'view flanking regions'</li>
2269 <li>File Save As type unset when current file format is
2271 <li>Save as '.jar' option removed for saving Jalview
2273 <li>Colour by Sequence colouring in Chimera more
2275 <li>Cannot 'add reference annotation' for a sequence in
2276 several views on same alignment</li>
2277 <li>Cannot show linked products for EMBL / ENA records</li>
2278 <li>Jalview's tooltip wraps long texts containing no
2280 </ul> <em>Applet</em>
2282 <li>Jmol to JalviewLite mouseover/link not working</li>
2283 <li>JalviewLite can't import sequences with ID
2284 descriptions containing angle brackets</li>
2285 </ul> <em>General</em>
2287 <li>Cannot export and reimport RNA secondary structure
2288 via jalview annotation file</li>
2289 <li>Random helix colour palette for colour by annotation
2290 with RNA secondary structure</li>
2291 <li>Mouseover to cDNA from STOP residue in protein
2292 translation doesn't work.</li>
2293 <li>hints when using the select by annotation dialog box</li>
2294 <li>Jmol alignment incorrect if PDB file has alternate CA
2296 <li>FontChooser message dialog appears to hang after
2297 choosing 1pt font</li>
2298 <li>Peptide secondary structure incorrectly imported from
2299 annotation file when annotation display text includes 'e' or
2301 <li>Cannot set colour of new feature type whilst creating
2303 <li>cDNA translation alignment should not be sequence
2304 order dependent</li>
2305 <li>'Show unconserved' doesn't work for lower case
2307 <li>Nucleotide ambiguity codes involving R not recognised</li>
2308 </ul> <em>Deployment and Documentation</em>
2310 <li>Applet example pages appear different to the rest of
2311 www.jalview.org</li>
2312 </ul> <em>Application Known issues</em>
2314 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2315 <li>Misleading message appears after trying to delete
2317 <li>Jalview icon not shown in dock after InstallAnywhere
2318 version launches</li>
2319 <li>Fetching EMBL reference for an RNA sequence results
2320 fails with a sequence mismatch</li>
2321 <li>Corrupted or unreadable alignment display when
2322 scrolling alignment to right</li>
2323 <li>ArrayIndexOutOfBoundsException thrown when remove
2324 empty columns called on alignment with ragged gapped ends</li>
2325 <li>auto calculated alignment annotation rows do not get
2326 placed above or below non-autocalculated rows</li>
2327 <li>Jalview dekstop becomes sluggish at full screen in
2328 ultra-high resolution</li>
2329 <li>Cannot disable consensus calculation independently of
2330 quality and conservation</li>
2331 <li>Mouseover highlighting between cDNA and protein can
2332 become sluggish with more than one splitframe shown</li>
2333 </ul> <em>Applet Known Issues</em>
2335 <li>Core PDB parsing code requires Jmol</li>
2336 <li>Sequence canvas panel goes white when alignment
2337 window is being resized</li>
2343 <td><div align="center">
2344 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2346 <td><em>General</em>
2348 <li>Updated Java code signing certificate donated by
2350 <li>Features and annotation preserved when performing
2351 pairwise alignment</li>
2352 <li>RNA pseudoknot annotation can be
2353 imported/exported/displayed</li>
2354 <li>'colour by annotation' can colour by RNA and
2355 protein secondary structure</li>
2356 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2357 post-hoc with 2.9 release</em>)
2360 </ul> <em>Application</em>
2362 <li>Extract and display secondary structure for sequences
2363 with 3D structures</li>
2364 <li>Support for parsing RNAML</li>
2365 <li>Annotations menu for layout
2367 <li>sort sequence annotation rows by alignment</li>
2368 <li>place sequence annotation above/below alignment
2371 <li>Output in Stockholm format</li>
2372 <li>Internationalisation: improved Spanish (es)
2374 <li>Structure viewer preferences tab</li>
2375 <li>Disorder and Secondary Structure annotation tracks
2376 shared between alignments</li>
2377 <li>UCSF Chimera launch and linked highlighting from
2379 <li>Show/hide all sequence associated annotation rows for
2380 all or current selection</li>
2381 <li>disorder and secondary structure predictions
2382 available as dataset annotation</li>
2383 <li>Per-sequence rna helices colouring</li>
2386 <li>Sequence database accessions imported when fetching
2387 alignments from Rfam</li>
2388 <li>update VARNA version to 3.91</li>
2390 <li>New groovy scripts for exporting aligned positions,
2391 conservation values, and calculating sum of pairs scores.</li>
2392 <li>Command line argument to set default JABAWS server</li>
2393 <li>include installation type in build properties and
2394 console log output</li>
2395 <li>Updated Jalview project format to preserve dataset
2399 <!-- issues resolved --> <em>Application</em>
2401 <li>Distinguish alignment and sequence associated RNA
2402 structure in structure->view->VARNA</li>
2403 <li>Raise dialog box if user deletes all sequences in an
2405 <li>Pressing F1 results in documentation opening twice</li>
2406 <li>Sequence feature tooltip is wrapped</li>
2407 <li>Double click on sequence associated annotation
2408 selects only first column</li>
2409 <li>Redundancy removal doesn't result in unlinked
2410 leaves shown in tree</li>
2411 <li>Undos after several redundancy removals don't undo
2413 <li>Hide sequence doesn't hide associated annotation</li>
2414 <li>User defined colours dialog box too big to fit on
2415 screen and buttons not visible</li>
2416 <li>author list isn't updated if already written to
2417 Jalview properties</li>
2418 <li>Popup menu won't open after retrieving sequence
2420 <li>File open window for associate PDB doesn't open</li>
2421 <li>Left-then-right click on a sequence id opens a
2422 browser search window</li>
2423 <li>Cannot open sequence feature shading/sort popup menu
2424 in feature settings dialog</li>
2425 <li>better tooltip placement for some areas of Jalview
2427 <li>Allow addition of JABAWS Server which doesn't
2428 pass validation</li>
2429 <li>Web services parameters dialog box is too large to
2431 <li>Muscle nucleotide alignment preset obscured by
2433 <li>JABAWS preset submenus don't contain newly
2434 defined user preset</li>
2435 <li>MSA web services warns user if they were launched
2436 with invalid input</li>
2437 <li>Jalview cannot contact DAS Registy when running on
2440 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2441 'Superpose with' submenu not shown when new view
2445 </ul> <!-- <em>Applet</em>
2447 </ul> <em>General</em>
2449 </ul>--> <em>Deployment and Documentation</em>
2451 <li>2G and 1G options in launchApp have no effect on
2452 memory allocation</li>
2453 <li>launchApp service doesn't automatically open
2454 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2456 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2457 InstallAnywhere reports cannot find valid JVM when Java
2458 1.7_055 is available
2460 </ul> <em>Application Known issues</em>
2463 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2464 corrupted or unreadable alignment display when scrolling
2468 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2469 retrieval fails but progress bar continues for DAS retrieval
2470 with large number of ID
2473 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2474 flatfile output of visible region has incorrect sequence
2478 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2479 rna structure consensus doesn't update when secondary
2480 structure tracks are rearranged
2483 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2484 invalid rna structure positional highlighting does not
2485 highlight position of invalid base pairs
2488 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2489 out of memory errors are not raised when saving Jalview
2490 project from alignment window file menu
2493 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2494 Switching to RNA Helices colouring doesn't propagate to
2498 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2499 colour by RNA Helices not enabled when user created
2500 annotation added to alignment
2503 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2504 Jalview icon not shown on dock in Mountain Lion/Webstart
2506 </ul> <em>Applet Known Issues</em>
2509 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2510 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2513 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2514 Jalview and Jmol example not compatible with IE9
2517 <li>Sort by annotation score doesn't reverse order
2523 <td><div align="center">
2524 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2527 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2530 <li>Internationalisation of user interface (usually
2531 called i18n support) and translation for Spanish locale</li>
2532 <li>Define/Undefine group on current selection with
2533 Ctrl-G/Shift Ctrl-G</li>
2534 <li>Improved group creation/removal options in
2535 alignment/sequence Popup menu</li>
2536 <li>Sensible precision for symbol distribution
2537 percentages shown in logo tooltip.</li>
2538 <li>Annotation panel height set according to amount of
2539 annotation when alignment first opened</li>
2540 </ul> <em>Application</em>
2542 <li>Interactive consensus RNA secondary structure
2543 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2544 <li>Select columns containing particular features from
2545 Feature Settings dialog</li>
2546 <li>View all 'representative' PDB structures for selected
2548 <li>Update Jalview project format:
2550 <li>New file extension for Jalview projects '.jvp'</li>
2551 <li>Preserve sequence and annotation dataset (to
2552 store secondary structure annotation,etc)</li>
2553 <li>Per group and alignment annotation and RNA helix
2557 <li>New similarity measures for PCA and Tree calculation
2559 <li>Experimental support for retrieval and viewing of
2560 flanking regions for an alignment</li>
2564 <!-- issues resolved --> <em>Application</em>
2566 <li>logo keeps spinning and status remains at queued or
2567 running after job is cancelled</li>
2568 <li>cannot export features from alignments imported from
2569 Jalview/VAMSAS projects</li>
2570 <li>Buggy slider for web service parameters that take
2572 <li>Newly created RNA secondary structure line doesn't
2573 have 'display all symbols' flag set</li>
2574 <li>T-COFFEE alignment score shading scheme and other
2575 annotation shading not saved in Jalview project</li>
2576 <li>Local file cannot be loaded in freshly downloaded
2578 <li>Jalview icon not shown on dock in Mountain
2580 <li>Load file from desktop file browser fails</li>
2581 <li>Occasional NPE thrown when calculating large trees</li>
2582 <li>Cannot reorder or slide sequences after dragging an
2583 alignment onto desktop</li>
2584 <li>Colour by annotation dialog throws NPE after using
2585 'extract scores' function</li>
2586 <li>Loading/cut'n'pasting an empty file leads to a grey
2587 alignment window</li>
2588 <li>Disorder thresholds rendered incorrectly after
2589 performing IUPred disorder prediction</li>
2590 <li>Multiple group annotated consensus rows shown when
2591 changing 'normalise logo' display setting</li>
2592 <li>Find shows blank dialog after 'finished searching' if
2593 nothing matches query</li>
2594 <li>Null Pointer Exceptions raised when sorting by
2595 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2597 <li>Errors in Jmol console when structures in alignment
2598 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2600 <li>Not all working JABAWS services are shown in
2602 <li>JAVAWS version of Jalview fails to launch with
2603 'invalid literal/length code'</li>
2604 <li>Annotation/RNA Helix colourschemes cannot be applied
2605 to alignment with groups (actually fixed in 2.8.0b1)</li>
2606 <li>RNA Helices and T-Coffee Scores available as default
2609 </ul> <em>Applet</em>
2611 <li>Remove group option is shown even when selection is
2613 <li>Apply to all groups ticked but colourscheme changes
2614 don't affect groups</li>
2615 <li>Documented RNA Helices and T-Coffee Scores as valid
2616 colourscheme name</li>
2617 <li>Annotation labels drawn on sequence IDs when
2618 Annotation panel is not displayed</li>
2619 <li>Increased font size for dropdown menus on OSX and
2620 embedded windows</li>
2621 </ul> <em>Other</em>
2623 <li>Consensus sequence for alignments/groups with a
2624 single sequence were not calculated</li>
2625 <li>annotation files that contain only groups imported as
2626 annotation and junk sequences</li>
2627 <li>Fasta files with sequences containing '*' incorrectly
2628 recognised as PFAM or BLC</li>
2629 <li>conservation/PID slider apply all groups option
2630 doesn't affect background (2.8.0b1)
2632 <li>redundancy highlighting is erratic at 0% and 100%</li>
2633 <li>Remove gapped columns fails for sequences with ragged
2635 <li>AMSA annotation row with leading spaces is not
2636 registered correctly on import</li>
2637 <li>Jalview crashes when selecting PCA analysis for
2638 certain alignments</li>
2639 <li>Opening the colour by annotation dialog for an
2640 existing annotation based 'use original colours'
2641 colourscheme loses original colours setting</li>
2646 <td><div align="center">
2647 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2648 <em>30/1/2014</em></strong>
2652 <li>Trusted certificates for JalviewLite applet and
2653 Jalview Desktop application<br />Certificate was donated by
2654 <a href="https://www.certum.eu">Certum</a> to the Jalview
2655 open source project).
2657 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2658 <li>Output in Stockholm format</li>
2659 <li>Allow import of data from gzipped files</li>
2660 <li>Export/import group and sequence associated line
2661 graph thresholds</li>
2662 <li>Nucleotide substitution matrix that supports RNA and
2663 ambiguity codes</li>
2664 <li>Allow disorder predictions to be made on the current
2665 selection (or visible selection) in the same way that JPred
2667 <li>Groovy scripting for headless Jalview operation</li>
2668 </ul> <em>Other improvements</em>
2670 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2671 <li>COMBINE statement uses current SEQUENCE_REF and
2672 GROUP_REF scope to group annotation rows</li>
2673 <li>Support '' style escaping of quotes in Newick
2675 <li>Group options for JABAWS service by command line name</li>
2676 <li>Empty tooltip shown for JABA service options with a
2677 link but no description</li>
2678 <li>Select primary source when selecting authority in
2679 database fetcher GUI</li>
2680 <li>Add .mfa to FASTA file extensions recognised by
2682 <li>Annotation label tooltip text wrap</li>
2687 <li>Slow scrolling when lots of annotation rows are
2689 <li>Lots of NPE (and slowness) after creating RNA
2690 secondary structure annotation line</li>
2691 <li>Sequence database accessions not imported when
2692 fetching alignments from Rfam</li>
2693 <li>Incorrect SHMR submission for sequences with
2695 <li>View all structures does not always superpose
2697 <li>Option widgets in service parameters not updated to
2698 reflect user or preset settings</li>
2699 <li>Null pointer exceptions for some services without
2700 presets or adjustable parameters</li>
2701 <li>Discover PDB IDs entry in structure menu doesn't
2702 discover PDB xRefs</li>
2703 <li>Exception encountered while trying to retrieve
2704 features with DAS</li>
2705 <li>Lowest value in annotation row isn't coloured
2706 when colour by annotation (per sequence) is coloured</li>
2707 <li>Keyboard mode P jumps to start of gapped region when
2708 residue follows a gap</li>
2709 <li>Jalview appears to hang importing an alignment with
2710 Wrap as default or after enabling Wrap</li>
2711 <li>'Right click to add annotations' message
2712 shown in wrap mode when no annotations present</li>
2713 <li>Disorder predictions fail with NPE if no automatic
2714 annotation already exists on alignment</li>
2715 <li>oninit javascript function should be called after
2716 initialisation completes</li>
2717 <li>Remove redundancy after disorder prediction corrupts
2718 alignment window display</li>
2719 <li>Example annotation file in documentation is invalid</li>
2720 <li>Grouped line graph annotation rows are not exported
2721 to annotation file</li>
2722 <li>Multi-harmony analysis cannot be run when only two
2724 <li>Cannot create multiple groups of line graphs with
2725 several 'combine' statements in annotation file</li>
2726 <li>Pressing return several times causes Number Format
2727 exceptions in keyboard mode</li>
2728 <li>Multi-harmony (SHMMR) method doesn't submit
2729 correct partitions for input data</li>
2730 <li>Translation from DNA to Amino Acids fails</li>
2731 <li>Jalview fail to load newick tree with quoted label</li>
2732 <li>--headless flag isn't understood</li>
2733 <li>ClassCastException when generating EPS in headless
2735 <li>Adjusting sequence-associated shading threshold only
2736 changes one row's threshold</li>
2737 <li>Preferences and Feature settings panel panel
2738 doesn't open</li>
2739 <li>hide consensus histogram also hides conservation and
2740 quality histograms</li>
2745 <td><div align="center">
2746 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2748 <td><em>Application</em>
2750 <li>Support for JABAWS 2.0 Services (AACon alignment
2751 conservation, protein disorder and Clustal Omega)</li>
2752 <li>JABAWS server status indicator in Web Services
2754 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2755 in Jalview alignment window</li>
2756 <li>Updated Jalview build and deploy framework for OSX
2757 mountain lion, windows 7, and 8</li>
2758 <li>Nucleotide substitution matrix for PCA that supports
2759 RNA and ambiguity codes</li>
2761 <li>Improved sequence database retrieval GUI</li>
2762 <li>Support fetching and database reference look up
2763 against multiple DAS sources (Fetch all from in 'fetch db
2765 <li>Jalview project improvements
2767 <li>Store and retrieve the 'belowAlignment'
2768 flag for annotation</li>
2769 <li>calcId attribute to group annotation rows on the
2771 <li>Store AACon calculation settings for a view in
2772 Jalview project</li>
2776 <li>horizontal scrolling gesture support</li>
2777 <li>Visual progress indicator when PCA calculation is
2779 <li>Simpler JABA web services menus</li>
2780 <li>visual indication that web service results are still
2781 being retrieved from server</li>
2782 <li>Serialise the dialogs that are shown when Jalview
2783 starts up for first time</li>
2784 <li>Jalview user agent string for interacting with HTTP
2786 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2788 <li>Examples directory and Groovy library included in
2789 InstallAnywhere distribution</li>
2790 </ul> <em>Applet</em>
2792 <li>RNA alignment and secondary structure annotation
2793 visualization applet example</li>
2794 </ul> <em>General</em>
2796 <li>Normalise option for consensus sequence logo</li>
2797 <li>Reset button in PCA window to return dimensions to
2799 <li>Allow seqspace or Jalview variant of alignment PCA
2801 <li>PCA with either nucleic acid and protein substitution
2803 <li>Allow windows containing HTML reports to be exported
2805 <li>Interactive display and editing of RNA secondary
2806 structure contacts</li>
2807 <li>RNA Helix Alignment Colouring</li>
2808 <li>RNA base pair logo consensus</li>
2809 <li>Parse sequence associated secondary structure
2810 information in Stockholm files</li>
2811 <li>HTML Export database accessions and annotation
2812 information presented in tooltip for sequences</li>
2813 <li>Import secondary structure from LOCARNA clustalw
2814 style RNA alignment files</li>
2815 <li>import and visualise T-COFFEE quality scores for an
2817 <li>'colour by annotation' per sequence option to
2818 shade each sequence according to its associated alignment
2820 <li>New Jalview Logo</li>
2821 </ul> <em>Documentation and Development</em>
2823 <li>documentation for score matrices used in Jalview</li>
2824 <li>New Website!</li>
2826 <td><em>Application</em>
2828 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2829 wsdbfetch REST service</li>
2830 <li>Stop windows being moved outside desktop on OSX</li>
2831 <li>Filetype associations not installed for webstart
2833 <li>Jalview does not always retrieve progress of a JABAWS
2834 job execution in full once it is complete</li>
2835 <li>revise SHMR RSBS definition to ensure alignment is
2836 uploaded via ali_file parameter</li>
2837 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2838 <li>View all structures superposed fails with exception</li>
2839 <li>Jnet job queues forever if a very short sequence is
2840 submitted for prediction</li>
2841 <li>Cut and paste menu not opened when mouse clicked on
2843 <li>Putting fractional value into integer text box in
2844 alignment parameter dialog causes Jalview to hang</li>
2845 <li>Structure view highlighting doesn't work on
2847 <li>View all structures fails with exception shown in
2849 <li>Characters in filename associated with PDBEntry not
2850 escaped in a platform independent way</li>
2851 <li>Jalview desktop fails to launch with exception when
2853 <li>Tree calculation reports 'you must have 2 or more
2854 sequences selected' when selection is empty</li>
2855 <li>Jalview desktop fails to launch with jar signature
2856 failure when java web start temporary file caching is
2858 <li>DAS Sequence retrieval with range qualification
2859 results in sequence xref which includes range qualification</li>
2860 <li>Errors during processing of command line arguments
2861 cause progress bar (JAL-898) to be removed</li>
2862 <li>Replace comma for semi-colon option not disabled for
2863 DAS sources in sequence fetcher</li>
2864 <li>Cannot close news reader when JABAWS server warning
2865 dialog is shown</li>
2866 <li>Option widgets not updated to reflect user settings</li>
2867 <li>Edited sequence not submitted to web service</li>
2868 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2869 <li>InstallAnywhere installer doesn't unpack and run
2870 on OSX Mountain Lion</li>
2871 <li>Annotation panel not given a scroll bar when
2872 sequences with alignment annotation are pasted into the
2874 <li>Sequence associated annotation rows not associated
2875 when loaded from Jalview project</li>
2876 <li>Browser launch fails with NPE on java 1.7</li>
2877 <li>JABAWS alignment marked as finished when job was
2878 cancelled or job failed due to invalid input</li>
2879 <li>NPE with v2.7 example when clicking on Tree
2880 associated with all views</li>
2881 <li>Exceptions when copy/paste sequences with grouped
2882 annotation rows to new window</li>
2883 </ul> <em>Applet</em>
2885 <li>Sequence features are momentarily displayed before
2886 they are hidden using hidefeaturegroups applet parameter</li>
2887 <li>loading features via javascript API automatically
2888 enables feature display</li>
2889 <li>scrollToColumnIn javascript API method doesn't
2891 </ul> <em>General</em>
2893 <li>Redundancy removal fails for rna alignment</li>
2894 <li>PCA calculation fails when sequence has been selected
2895 and then deselected</li>
2896 <li>PCA window shows grey box when first opened on OSX</li>
2897 <li>Letters coloured pink in sequence logo when alignment
2898 coloured with clustalx</li>
2899 <li>Choosing fonts without letter symbols defined causes
2900 exceptions and redraw errors</li>
2901 <li>Initial PCA plot view is not same as manually
2902 reconfigured view</li>
2903 <li>Grouped annotation graph label has incorrect line
2905 <li>Grouped annotation graph label display is corrupted
2906 for lots of labels</li>
2911 <div align="center">
2912 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2915 <td><em>Application</em>
2917 <li>Jalview Desktop News Reader</li>
2918 <li>Tweaked default layout of web services menu</li>
2919 <li>View/alignment association menu to enable user to
2920 easily specify which alignment a multi-structure view takes
2921 its colours/correspondences from</li>
2922 <li>Allow properties file location to be specified as URL</li>
2923 <li>Extend Jalview project to preserve associations
2924 between many alignment views and a single Jmol display</li>
2925 <li>Store annotation row height in Jalview project file</li>
2926 <li>Annotation row column label formatting attributes
2927 stored in project file</li>
2928 <li>Annotation row order for auto-calculated annotation
2929 rows preserved in Jalview project file</li>
2930 <li>Visual progress indication when Jalview state is
2931 saved using Desktop window menu</li>
2932 <li>Visual indication that command line arguments are
2933 still being processed</li>
2934 <li>Groovy script execution from URL</li>
2935 <li>Colour by annotation default min and max colours in
2937 <li>Automatically associate PDB files dragged onto an
2938 alignment with sequences that have high similarity and
2940 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2941 <li>'view structures' option to open many
2942 structures in same window</li>
2943 <li>Sort associated views menu option for tree panel</li>
2944 <li>Group all JABA and non-JABA services for a particular
2945 analysis function in its own submenu</li>
2946 </ul> <em>Applet</em>
2948 <li>Userdefined and autogenerated annotation rows for
2950 <li>Adjustment of alignment annotation pane height</li>
2951 <li>Annotation scrollbar for annotation panel</li>
2952 <li>Drag to reorder annotation rows in annotation panel</li>
2953 <li>'automaticScrolling' parameter</li>
2954 <li>Allow sequences with partial ID string matches to be
2955 annotated from GFF/Jalview features files</li>
2956 <li>Sequence logo annotation row in applet</li>
2957 <li>Absolute paths relative to host server in applet
2958 parameters are treated as such</li>
2959 <li>New in the JalviewLite javascript API:
2961 <li>JalviewLite.js javascript library</li>
2962 <li>Javascript callbacks for
2964 <li>Applet initialisation</li>
2965 <li>Sequence/alignment mouse-overs and selections</li>
2968 <li>scrollTo row and column alignment scrolling
2970 <li>Select sequence/alignment regions from javascript</li>
2971 <li>javascript structure viewer harness to pass
2972 messages between Jmol and Jalview when running as
2973 distinct applets</li>
2974 <li>sortBy method</li>
2975 <li>Set of applet and application examples shipped
2976 with documentation</li>
2977 <li>New example to demonstrate JalviewLite and Jmol
2978 javascript message exchange</li>
2980 </ul> <em>General</em>
2982 <li>Enable Jmol displays to be associated with multiple
2983 multiple alignments</li>
2984 <li>Option to automatically sort alignment with new tree</li>
2985 <li>User configurable link to enable redirects to a
2986 www.Jalview.org mirror</li>
2987 <li>Jmol colours option for Jmol displays</li>
2988 <li>Configurable newline string when writing alignment
2989 and other flat files</li>
2990 <li>Allow alignment annotation description lines to
2991 contain html tags</li>
2992 </ul> <em>Documentation and Development</em>
2994 <li>Add groovy test harness for bulk load testing to
2996 <li>Groovy script to load and align a set of sequences
2997 using a web service before displaying the result in the
2998 Jalview desktop</li>
2999 <li>Restructured javascript and applet api documentation</li>
3000 <li>Ant target to publish example html files with applet
3002 <li>Netbeans project for building Jalview from source</li>
3003 <li>ant task to create online javadoc for Jalview source</li>
3005 <td><em>Application</em>
3007 <li>User defined colourscheme throws exception when
3008 current built in colourscheme is saved as new scheme</li>
3009 <li>AlignFrame->Save in application pops up save
3010 dialog for valid filename/format</li>
3011 <li>Cannot view associated structure for UniProt sequence</li>
3012 <li>PDB file association breaks for UniProt sequence
3014 <li>Associate PDB from file dialog does not tell you
3015 which sequence is to be associated with the file</li>
3016 <li>Find All raises null pointer exception when query
3017 only matches sequence IDs</li>
3018 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3019 <li>Jalview project with Jmol views created with Jalview
3020 2.4 cannot be loaded</li>
3021 <li>Filetype associations not installed for webstart
3023 <li>Two or more chains in a single PDB file associated
3024 with sequences in different alignments do not get coloured
3025 by their associated sequence</li>
3026 <li>Visibility status of autocalculated annotation row
3027 not preserved when project is loaded</li>
3028 <li>Annotation row height and visibility attributes not
3029 stored in Jalview project</li>
3030 <li>Tree bootstraps are not preserved when saved as a
3031 Jalview project</li>
3032 <li>Envision2 workflow tooltips are corrupted</li>
3033 <li>Enabling show group conservation also enables colour
3034 by conservation</li>
3035 <li>Duplicate group associated conservation or consensus
3036 created on new view</li>
3037 <li>Annotation scrollbar not displayed after 'show
3038 all hidden annotation rows' option selected</li>
3039 <li>Alignment quality not updated after alignment
3040 annotation row is hidden then shown</li>
3041 <li>Preserve colouring of structures coloured by
3042 sequences in pre Jalview 2.7 projects</li>
3043 <li>Web service job parameter dialog is not laid out
3045 <li>Web services menu not refreshed after 'reset
3046 services' button is pressed in preferences</li>
3047 <li>Annotation off by one in Jalview v2_3 example project</li>
3048 <li>Structures imported from file and saved in project
3049 get name like jalview_pdb1234.txt when reloaded</li>
3050 <li>Jalview does not always retrieve progress of a JABAWS
3051 job execution in full once it is complete</li>
3052 </ul> <em>Applet</em>
3054 <li>Alignment height set incorrectly when lots of
3055 annotation rows are displayed</li>
3056 <li>Relative URLs in feature HTML text not resolved to
3058 <li>View follows highlighting does not work for positions
3060 <li><= shown as = in tooltip</li>
3061 <li>Export features raises exception when no features
3063 <li>Separator string used for serialising lists of IDs
3064 for javascript api is modified when separator string
3065 provided as parameter</li>
3066 <li>Null pointer exception when selecting tree leaves for
3067 alignment with no existing selection</li>
3068 <li>Relative URLs for datasources assumed to be relative
3069 to applet's codebase</li>
3070 <li>Status bar not updated after finished searching and
3071 search wraps around to first result</li>
3072 <li>StructureSelectionManager instance shared between
3073 several Jalview applets causes race conditions and memory
3075 <li>Hover tooltip and mouseover of position on structure
3076 not sent from Jmol in applet</li>
3077 <li>Certain sequences of javascript method calls to
3078 applet API fatally hang browser</li>
3079 </ul> <em>General</em>
3081 <li>View follows structure mouseover scrolls beyond
3082 position with wrapped view and hidden regions</li>
3083 <li>Find sequence position moves to wrong residue
3084 with/without hidden columns</li>
3085 <li>Sequence length given in alignment properties window
3087 <li>InvalidNumberFormat exceptions thrown when trying to
3088 import PDB like structure files</li>
3089 <li>Positional search results are only highlighted
3090 between user-supplied sequence start/end bounds</li>
3091 <li>End attribute of sequence is not validated</li>
3092 <li>Find dialog only finds first sequence containing a
3093 given sequence position</li>
3094 <li>Sequence numbering not preserved in MSF alignment
3096 <li>Jalview PDB file reader does not extract sequence
3097 from nucleotide chains correctly</li>
3098 <li>Structure colours not updated when tree partition
3099 changed in alignment</li>
3100 <li>Sequence associated secondary structure not correctly
3101 parsed in interleaved stockholm</li>
3102 <li>Colour by annotation dialog does not restore current
3104 <li>Hiding (nearly) all sequences doesn't work
3106 <li>Sequences containing lowercase letters are not
3107 properly associated with their pdb files</li>
3108 </ul> <em>Documentation and Development</em>
3110 <li>schemas/JalviewWsParamSet.xsd corrupted by
3111 ApplyCopyright tool</li>
3116 <div align="center">
3117 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3120 <td><em>Application</em>
3122 <li>New warning dialog when the Jalview Desktop cannot
3123 contact web services</li>
3124 <li>JABA service parameters for a preset are shown in
3125 service job window</li>
3126 <li>JABA Service menu entries reworded</li>
3130 <li>Modeller PIR IO broken - cannot correctly import a
3131 pir file emitted by Jalview</li>
3132 <li>Existing feature settings transferred to new
3133 alignment view created from cut'n'paste</li>
3134 <li>Improved test for mixed amino/nucleotide chains when
3135 parsing PDB files</li>
3136 <li>Consensus and conservation annotation rows
3137 occasionally become blank for all new windows</li>
3138 <li>Exception raised when right clicking above sequences
3139 in wrapped view mode</li>
3140 </ul> <em>Application</em>
3142 <li>multiple multiply aligned structure views cause cpu
3143 usage to hit 100% and computer to hang</li>
3144 <li>Web Service parameter layout breaks for long user
3145 parameter names</li>
3146 <li>Jaba service discovery hangs desktop if Jaba server
3153 <div align="center">
3154 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3157 <td><em>Application</em>
3159 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3160 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3163 <li>Web Services preference tab</li>
3164 <li>Analysis parameters dialog box and user defined
3166 <li>Improved speed and layout of Envision2 service menu</li>
3167 <li>Superpose structures using associated sequence
3169 <li>Export coordinates and projection as CSV from PCA
3171 </ul> <em>Applet</em>
3173 <li>enable javascript: execution by the applet via the
3174 link out mechanism</li>
3175 </ul> <em>Other</em>
3177 <li>Updated the Jmol Jalview interface to work with Jmol
3179 <li>The Jalview Desktop and JalviewLite applet now
3180 require Java 1.5</li>
3181 <li>Allow Jalview feature colour specification for GFF
3182 sequence annotation files</li>
3183 <li>New 'colour by label' keword in Jalview feature file
3184 type colour specification</li>
3185 <li>New Jalview Desktop Groovy API method that allows a
3186 script to check if it being run in an interactive session or
3187 in a batch operation from the Jalview command line</li>
3191 <li>clustalx colourscheme colours Ds preferentially when
3192 both D+E are present in over 50% of the column</li>
3193 </ul> <em>Application</em>
3195 <li>typo in AlignmentFrame->View->Hide->all but
3196 selected Regions menu item</li>
3197 <li>sequence fetcher replaces ',' for ';' when the ',' is
3198 part of a valid accession ID</li>
3199 <li>fatal OOM if object retrieved by sequence fetcher
3200 runs out of memory</li>
3201 <li>unhandled Out of Memory Error when viewing pca
3202 analysis results</li>
3203 <li>InstallAnywhere builds fail to launch on OS X java
3204 10.5 update 4 (due to apple Java 1.6 update)</li>
3205 <li>Installanywhere Jalview silently fails to launch</li>
3206 </ul> <em>Applet</em>
3208 <li>Jalview.getFeatureGroups() raises an
3209 ArrayIndexOutOfBoundsException if no feature groups are
3216 <div align="center">
3217 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3223 <li>Alignment prettyprinter doesn't cope with long
3225 <li>clustalx colourscheme colours Ds preferentially when
3226 both D+E are present in over 50% of the column</li>
3227 <li>nucleic acid structures retrieved from PDB do not
3228 import correctly</li>
3229 <li>More columns get selected than were clicked on when a
3230 number of columns are hidden</li>
3231 <li>annotation label popup menu not providing correct
3232 add/hide/show options when rows are hidden or none are
3234 <li>Stockholm format shown in list of readable formats,
3235 and parser copes better with alignments from RFAM.</li>
3236 <li>CSV output of consensus only includes the percentage
3237 of all symbols if sequence logo display is enabled</li>
3239 </ul> <em>Applet</em>
3241 <li>annotation panel disappears when annotation is
3243 </ul> <em>Application</em>
3245 <li>Alignment view not redrawn properly when new
3246 alignment opened where annotation panel is visible but no
3247 annotations are present on alignment</li>
3248 <li>pasted region containing hidden columns is
3249 incorrectly displayed in new alignment window</li>
3250 <li>Jalview slow to complete operations when stdout is
3251 flooded (fix is to close the Jalview console)</li>
3252 <li>typo in AlignmentFrame->View->Hide->all but
3253 selected Rregions menu item.</li>
3254 <li>inconsistent group submenu and Format submenu entry
3255 'Un' or 'Non'conserved</li>
3256 <li>Sequence feature settings are being shared by
3257 multiple distinct alignments</li>
3258 <li>group annotation not recreated when tree partition is
3260 <li>double click on group annotation to select sequences
3261 does not propagate to associated trees</li>
3262 <li>Mac OSX specific issues:
3264 <li>exception raised when mouse clicked on desktop
3265 window background</li>
3266 <li>Desktop menu placed on menu bar and application
3267 name set correctly</li>
3268 <li>sequence feature settings not wide enough for the
3269 save feature colourscheme button</li>
3278 <div align="center">
3279 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3282 <td><em>New Capabilities</em>
3284 <li>URL links generated from description line for
3285 regular-expression based URL links (applet and application)
3287 <li>Non-positional feature URL links are shown in link
3289 <li>Linked viewing of nucleic acid sequences and
3291 <li>Automatic Scrolling option in View menu to display
3292 the currently highlighted region of an alignment.</li>
3293 <li>Order an alignment by sequence length, or using the
3294 average score or total feature count for each sequence.</li>
3295 <li>Shading features by score or associated description</li>
3296 <li>Subdivide alignment and groups based on identity of
3297 selected subsequence (Make Groups from Selection).</li>
3298 <li>New hide/show options including Shift+Control+H to
3299 hide everything but the currently selected region.</li>
3300 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3301 </ul> <em>Application</em>
3303 <li>Fetch DB References capabilities and UI expanded to
3304 support retrieval from DAS sequence sources</li>
3305 <li>Local DAS Sequence sources can be added via the
3306 command line or via the Add local source dialog box.</li>
3307 <li>DAS Dbref and DbxRef feature types are parsed as
3308 database references and protein_name is parsed as
3309 description line (BioSapiens terms).</li>
3310 <li>Enable or disable non-positional feature and database
3311 references in sequence ID tooltip from View menu in
3313 <!-- <li>New hidden columns and rows and representatives capabilities
3314 in annotations file (in progress - not yet fully implemented)</li> -->
3315 <li>Group-associated consensus, sequence logos and
3316 conservation plots</li>
3317 <li>Symbol distributions for each column can be exported
3318 and visualized as sequence logos</li>
3319 <li>Optionally scale multi-character column labels to fit
3320 within each column of annotation row<!-- todo for applet -->
3322 <li>Optional automatic sort of associated alignment view
3323 when a new tree is opened.</li>
3324 <li>Jalview Java Console</li>
3325 <li>Better placement of desktop window when moving
3326 between different screens.</li>
3327 <li>New preference items for sequence ID tooltip and
3328 consensus annotation</li>
3329 <li>Client to submit sequences and IDs to Envision2
3331 <li><em>Vamsas Capabilities</em>
3333 <li>Improved VAMSAS synchronization (Jalview archive
3334 used to preserve views, structures, and tree display
3336 <li>Import of vamsas documents from disk or URL via
3338 <li>Sharing of selected regions between views and
3339 with other VAMSAS applications (Experimental feature!)</li>
3340 <li>Updated API to VAMSAS version 0.2</li>
3342 </ul> <em>Applet</em>
3344 <li>Middle button resizes annotation row height</li>
3347 <li>sortByTree (true/false) - automatically sort the
3348 associated alignment view by the tree when a new tree is
3350 <li>showTreeBootstraps (true/false) - show or hide
3351 branch bootstraps (default is to show them if available)</li>
3352 <li>showTreeDistances (true/false) - show or hide
3353 branch lengths (default is to show them if available)</li>
3354 <li>showUnlinkedTreeNodes (true/false) - indicate if
3355 unassociated nodes should be highlighted in the tree
3357 <li>heightScale and widthScale (1.0 or more) -
3358 increase the height or width of a cell in the alignment
3359 grid relative to the current font size.</li>
3362 <li>Non-positional features displayed in sequence ID
3364 </ul> <em>Other</em>
3366 <li>Features format: graduated colour definitions and
3367 specification of feature scores</li>
3368 <li>Alignment Annotations format: new keywords for group
3369 associated annotation (GROUP_REF) and annotation row display
3370 properties (ROW_PROPERTIES)</li>
3371 <li>XML formats extended to support graduated feature
3372 colourschemes, group associated annotation, and profile
3373 visualization settings.</li></td>
3376 <li>Source field in GFF files parsed as feature source
3377 rather than description</li>
3378 <li>Non-positional features are now included in sequence
3379 feature and gff files (controlled via non-positional feature
3380 visibility in tooltip).</li>
3381 <li>URL links generated for all feature links (bugfix)</li>
3382 <li>Added URL embedding instructions to features file
3384 <li>Codons containing ambiguous nucleotides translated as
3385 'X' in peptide product</li>
3386 <li>Match case switch in find dialog box works for both
3387 sequence ID and sequence string and query strings do not
3388 have to be in upper case to match case-insensitively.</li>
3389 <li>AMSA files only contain first column of
3390 multi-character column annotation labels</li>
3391 <li>Jalview Annotation File generation/parsing consistent
3392 with documentation (e.g. Stockholm annotation can be
3393 exported and re-imported)</li>
3394 <li>PDB files without embedded PDB IDs given a friendly
3396 <li>Find incrementally searches ID string matches as well
3397 as subsequence matches, and correctly reports total number
3401 <li>Better handling of exceptions during sequence
3403 <li>Dasobert generated non-positional feature URL
3404 link text excludes the start_end suffix</li>
3405 <li>DAS feature and source retrieval buttons disabled
3406 when fetch or registry operations in progress.</li>
3407 <li>PDB files retrieved from URLs are cached properly</li>
3408 <li>Sequence description lines properly shared via
3410 <li>Sequence fetcher fetches multiple records for all
3412 <li>Ensured that command line das feature retrieval
3413 completes before alignment figures are generated.</li>
3414 <li>Reduced time taken when opening file browser for
3416 <li>isAligned check prior to calculating tree, PCA or
3417 submitting an MSA to JNet now excludes hidden sequences.</li>
3418 <li>User defined group colours properly recovered
3419 from Jalview projects.</li>
3428 <div align="center">
3429 <strong>2.4.0.b2</strong><br> 28/10/2009
3434 <li>Experimental support for google analytics usage
3436 <li>Jalview privacy settings (user preferences and docs).</li>
3441 <li>Race condition in applet preventing startup in
3443 <li>Exception when feature created from selection beyond
3444 length of sequence.</li>
3445 <li>Allow synthetic PDB files to be imported gracefully</li>
3446 <li>Sequence associated annotation rows associate with
3447 all sequences with a given id</li>
3448 <li>Find function matches case-insensitively for sequence
3449 ID string searches</li>
3450 <li>Non-standard characters do not cause pairwise
3451 alignment to fail with exception</li>
3452 </ul> <em>Application Issues</em>
3454 <li>Sequences are now validated against EMBL database</li>
3455 <li>Sequence fetcher fetches multiple records for all
3457 </ul> <em>InstallAnywhere Issues</em>
3459 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3460 issue with installAnywhere mechanism)</li>
3461 <li>Command line launching of JARs from InstallAnywhere
3462 version (java class versioning error fixed)</li>
3469 <div align="center">
3470 <strong>2.4</strong><br> 27/8/2008
3473 <td><em>User Interface</em>
3475 <li>Linked highlighting of codon and amino acid from
3476 translation and protein products</li>
3477 <li>Linked highlighting of structure associated with
3478 residue mapping to codon position</li>
3479 <li>Sequence Fetcher provides example accession numbers
3480 and 'clear' button</li>
3481 <li>MemoryMonitor added as an option under Desktop's
3483 <li>Extract score function to parse whitespace separated
3484 numeric data in description line</li>
3485 <li>Column labels in alignment annotation can be centred.</li>
3486 <li>Tooltip for sequence associated annotation give name
3488 </ul> <em>Web Services and URL fetching</em>
3490 <li>JPred3 web service</li>
3491 <li>Prototype sequence search client (no public services
3493 <li>Fetch either seed alignment or full alignment from
3495 <li>URL Links created for matching database cross
3496 references as well as sequence ID</li>
3497 <li>URL Links can be created using regular-expressions</li>
3498 </ul> <em>Sequence Database Connectivity</em>
3500 <li>Retrieval of cross-referenced sequences from other
3502 <li>Generalised database reference retrieval and
3503 validation to all fetchable databases</li>
3504 <li>Fetch sequences from DAS sources supporting the
3505 sequence command</li>
3506 </ul> <em>Import and Export</em>
3507 <li>export annotation rows as CSV for spreadsheet import</li>
3508 <li>Jalview projects record alignment dataset associations,
3509 EMBL products, and cDNA sequence mappings</li>
3510 <li>Sequence Group colour can be specified in Annotation
3512 <li>Ad-hoc colouring of group in Annotation File using RGB
3513 triplet as name of colourscheme</li>
3514 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3516 <li>treenode binding for VAMSAS tree exchange</li>
3517 <li>local editing and update of sequences in VAMSAS
3518 alignments (experimental)</li>
3519 <li>Create new or select existing session to join</li>
3520 <li>load and save of vamsas documents</li>
3521 </ul> <em>Application command line</em>
3523 <li>-tree parameter to open trees (introduced for passing
3525 <li>-fetchfrom command line argument to specify nicknames
3526 of DAS servers to query for alignment features</li>
3527 <li>-dasserver command line argument to add new servers
3528 that are also automatically queried for features</li>
3529 <li>-groovy command line argument executes a given groovy
3530 script after all input data has been loaded and parsed</li>
3531 </ul> <em>Applet-Application data exchange</em>
3533 <li>Trees passed as applet parameters can be passed to
3534 application (when using "View in full
3535 application")</li>
3536 </ul> <em>Applet Parameters</em>
3538 <li>feature group display control parameter</li>
3539 <li>debug parameter</li>
3540 <li>showbutton parameter</li>
3541 </ul> <em>Applet API methods</em>
3543 <li>newView public method</li>
3544 <li>Window (current view) specific get/set public methods</li>
3545 <li>Feature display control methods</li>
3546 <li>get list of currently selected sequences</li>
3547 </ul> <em>New Jalview distribution features</em>
3549 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3550 <li>RELEASE file gives build properties for the latest
3551 Jalview release.</li>
3552 <li>Java 1.1 Applet build made easier and donotobfuscate
3553 property controls execution of obfuscator</li>
3554 <li>Build target for generating source distribution</li>
3555 <li>Debug flag for javacc</li>
3556 <li>.jalview_properties file is documented (slightly) in
3557 jalview.bin.Cache</li>
3558 <li>Continuous Build Integration for stable and
3559 development version of Application, Applet and source
3564 <li>selected region output includes visible annotations
3565 (for certain formats)</li>
3566 <li>edit label/displaychar contains existing label/char
3568 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3569 <li>shorter peptide product names from EMBL records</li>
3570 <li>Newick string generator makes compact representations</li>
3571 <li>bootstrap values parsed correctly for tree files with
3573 <li>pathological filechooser bug avoided by not allowing
3574 filenames containing a ':'</li>
3575 <li>Fixed exception when parsing GFF files containing
3576 global sequence features</li>
3577 <li>Alignment datasets are finalized only when number of
3578 references from alignment sequences goes to zero</li>
3579 <li>Close of tree branch colour box without colour
3580 selection causes cascading exceptions</li>
3581 <li>occasional negative imgwidth exceptions</li>
3582 <li>better reporting of non-fatal warnings to user when
3583 file parsing fails.</li>
3584 <li>Save works when Jalview project is default format</li>
3585 <li>Save as dialog opened if current alignment format is
3586 not a valid output format</li>
3587 <li>UniProt canonical names introduced for both das and
3589 <li>Histidine should be midblue (not pink!) in Zappo</li>
3590 <li>error messages passed up and output when data read
3592 <li>edit undo recovers previous dataset sequence when
3593 sequence is edited</li>
3594 <li>allow PDB files without pdb ID HEADER lines (like
3595 those generated by MODELLER) to be read in properly</li>
3596 <li>allow reading of JPred concise files as a normal
3598 <li>Stockholm annotation parsing and alignment properties
3599 import fixed for PFAM records</li>
3600 <li>Structure view windows have correct name in Desktop
3602 <li>annotation consisting of sequence associated scores
3603 can be read and written correctly to annotation file</li>
3604 <li>Aligned cDNA translation to aligned peptide works
3606 <li>Fixed display of hidden sequence markers and
3607 non-italic font for representatives in Applet</li>
3608 <li>Applet Menus are always embedded in applet window on
3610 <li>Newly shown features appear at top of stack (in
3612 <li>Annotations added via parameter not drawn properly
3613 due to null pointer exceptions</li>
3614 <li>Secondary structure lines are drawn starting from
3615 first column of alignment</li>
3616 <li>UniProt XML import updated for new schema release in
3618 <li>Sequence feature to sequence ID match for Features
3619 file is case-insensitive</li>
3620 <li>Sequence features read from Features file appended to
3621 all sequences with matching IDs</li>
3622 <li>PDB structure coloured correctly for associated views
3623 containing a sub-sequence</li>
3624 <li>PDB files can be retrieved by applet from Jar files</li>
3625 <li>feature and annotation file applet parameters
3626 referring to different directories are retrieved correctly</li>
3627 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3628 <li>Fixed application hang whilst waiting for
3629 splash-screen version check to complete</li>
3630 <li>Applet properly URLencodes input parameter values
3631 when passing them to the launchApp service</li>
3632 <li>display name and local features preserved in results
3633 retrieved from web service</li>
3634 <li>Visual delay indication for sequence retrieval and
3635 sequence fetcher initialisation</li>
3636 <li>updated Application to use DAS 1.53e version of
3637 dasobert DAS client</li>
3638 <li>Re-instated Full AMSA support and .amsa file
3640 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3648 <div align="center">
3649 <strong>2.3</strong><br> 9/5/07
3654 <li>Jmol 11.0.2 integration</li>
3655 <li>PDB views stored in Jalview XML files</li>
3656 <li>Slide sequences</li>
3657 <li>Edit sequence in place</li>
3658 <li>EMBL CDS features</li>
3659 <li>DAS Feature mapping</li>
3660 <li>Feature ordering</li>
3661 <li>Alignment Properties</li>
3662 <li>Annotation Scores</li>
3663 <li>Sort by scores</li>
3664 <li>Feature/annotation editing in applet</li>
3669 <li>Headless state operation in 2.2.1</li>
3670 <li>Incorrect and unstable DNA pairwise alignment</li>
3671 <li>Cut and paste of sequences with annotation</li>
3672 <li>Feature group display state in XML</li>
3673 <li>Feature ordering in XML</li>
3674 <li>blc file iteration selection using filename # suffix</li>
3675 <li>Stockholm alignment properties</li>
3676 <li>Stockhom alignment secondary structure annotation</li>
3677 <li>2.2.1 applet had no feature transparency</li>
3678 <li>Number pad keys can be used in cursor mode</li>
3679 <li>Structure Viewer mirror image resolved</li>
3686 <div align="center">
3687 <strong>2.2.1</strong><br> 12/2/07
3692 <li>Non standard characters can be read and displayed
3693 <li>Annotations/Features can be imported/exported to the
3695 <li>Applet allows editing of sequence/annotation/group
3696 name & description
3697 <li>Preference setting to display sequence name in
3699 <li>Annotation file format extended to allow
3700 Sequence_groups to be defined
3701 <li>Default opening of alignment overview panel can be
3702 specified in preferences
3703 <li>PDB residue numbering annotation added to associated
3709 <li>Applet crash under certain Linux OS with Java 1.6
3711 <li>Annotation file export / import bugs fixed
3712 <li>PNG / EPS image output bugs fixed
3718 <div align="center">
3719 <strong>2.2</strong><br> 27/11/06
3724 <li>Multiple views on alignment
3725 <li>Sequence feature editing
3726 <li>"Reload" alignment
3727 <li>"Save" to current filename
3728 <li>Background dependent text colour
3729 <li>Right align sequence ids
3730 <li>User-defined lower case residue colours
3733 <li>Menu item accelerator keys
3734 <li>Control-V pastes to current alignment
3735 <li>Cancel button for DAS Feature Fetching
3736 <li>PCA and PDB Viewers zoom via mouse roller
3737 <li>User-defined sub-tree colours and sub-tree selection
3739 <li>'New Window' button on the 'Output to Text box'
3744 <li>New memory efficient Undo/Redo System
3745 <li>Optimised symbol lookups and conservation/consensus
3747 <li>Region Conservation/Consensus recalculated after
3749 <li>Fixed Remove Empty Columns Bug (empty columns at end
3751 <li>Slowed DAS Feature Fetching for increased robustness.
3753 <li>Made angle brackets in ASCII feature descriptions
3755 <li>Re-instated Zoom function for PCA
3756 <li>Sequence descriptions conserved in web service
3758 <li>UniProt ID discoverer uses any word separated by
3760 <li>WsDbFetch query/result association resolved
3761 <li>Tree leaf to sequence mapping improved
3762 <li>Smooth fonts switch moved to FontChooser dialog box.
3769 <div align="center">
3770 <strong>2.1.1</strong><br> 12/9/06
3775 <li>Copy consensus sequence to clipboard</li>
3780 <li>Image output - rightmost residues are rendered if
3781 sequence id panel has been resized</li>
3782 <li>Image output - all offscreen group boundaries are
3784 <li>Annotation files with sequence references - all
3785 elements in file are relative to sequence position</li>
3786 <li>Mac Applet users can use Alt key for group editing</li>
3792 <div align="center">
3793 <strong>2.1</strong><br> 22/8/06
3798 <li>MAFFT Multiple Alignment in default Web Service list</li>
3799 <li>DAS Feature fetching</li>
3800 <li>Hide sequences and columns</li>
3801 <li>Export Annotations and Features</li>
3802 <li>GFF file reading / writing</li>
3803 <li>Associate structures with sequences from local PDB
3805 <li>Add sequences to exisiting alignment</li>
3806 <li>Recently opened files / URL lists</li>
3807 <li>Applet can launch the full application</li>
3808 <li>Applet has transparency for features (Java 1.2
3810 <li>Applet has user defined colours parameter</li>
3811 <li>Applet can load sequences from parameter
3812 "sequence<em>x</em>"
3818 <li>Redundancy Panel reinstalled in the Applet</li>
3819 <li>Monospaced font - EPS / rescaling bug fixed</li>
3820 <li>Annotation files with sequence references bug fixed</li>
3826 <div align="center">
3827 <strong>2.08.1</strong><br> 2/5/06
3832 <li>Change case of selected region from Popup menu</li>
3833 <li>Choose to match case when searching</li>
3834 <li>Middle mouse button and mouse movement can compress /
3835 expand the visible width and height of the alignment</li>
3840 <li>Annotation Panel displays complete JNet results</li>
3846 <div align="center">
3847 <strong>2.08b</strong><br> 18/4/06
3853 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3854 <li>Righthand label on wrapped alignments shows correct
3861 <div align="center">
3862 <strong>2.08</strong><br> 10/4/06
3867 <li>Editing can be locked to the selection area</li>
3868 <li>Keyboard editing</li>
3869 <li>Create sequence features from searches</li>
3870 <li>Precalculated annotations can be loaded onto
3872 <li>Features file allows grouping of features</li>
3873 <li>Annotation Colouring scheme added</li>
3874 <li>Smooth fonts off by default - Faster rendering</li>
3875 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3880 <li>Drag & Drop fixed on Linux</li>
3881 <li>Jalview Archive file faster to load/save, sequence
3882 descriptions saved.</li>
3888 <div align="center">
3889 <strong>2.07</strong><br> 12/12/05
3894 <li>PDB Structure Viewer enhanced</li>
3895 <li>Sequence Feature retrieval and display enhanced</li>
3896 <li>Choose to output sequence start-end after sequence
3897 name for file output</li>
3898 <li>Sequence Fetcher WSDBFetch@EBI</li>
3899 <li>Applet can read feature files, PDB files and can be
3900 used for HTML form input</li>
3905 <li>HTML output writes groups and features</li>
3906 <li>Group editing is Control and mouse click</li>
3907 <li>File IO bugs</li>
3913 <div align="center">
3914 <strong>2.06</strong><br> 28/9/05
3919 <li>View annotations in wrapped mode</li>
3920 <li>More options for PCA viewer</li>
3925 <li>GUI bugs resolved</li>
3926 <li>Runs with -nodisplay from command line</li>
3932 <div align="center">
3933 <strong>2.05b</strong><br> 15/9/05
3938 <li>Choose EPS export as lineart or text</li>
3939 <li>Jar files are executable</li>
3940 <li>Can read in Uracil - maps to unknown residue</li>
3945 <li>Known OutOfMemory errors give warning message</li>
3946 <li>Overview window calculated more efficiently</li>
3947 <li>Several GUI bugs resolved</li>
3953 <div align="center">
3954 <strong>2.05</strong><br> 30/8/05
3959 <li>Edit and annotate in "Wrapped" view</li>
3964 <li>Several GUI bugs resolved</li>
3970 <div align="center">
3971 <strong>2.04</strong><br> 24/8/05
3976 <li>Hold down mouse wheel & scroll to change font
3982 <li>Improved JPred client reliability</li>
3983 <li>Improved loading of Jalview files</li>
3989 <div align="center">
3990 <strong>2.03</strong><br> 18/8/05
3995 <li>Set Proxy server name and port in preferences</li>
3996 <li>Multiple URL links from sequence ids</li>
3997 <li>User Defined Colours can have a scheme name and added
3999 <li>Choose to ignore gaps in consensus calculation</li>
4000 <li>Unix users can set default web browser</li>
4001 <li>Runs without GUI for batch processing</li>
4002 <li>Dynamically generated Web Service Menus</li>
4007 <li>InstallAnywhere download for Sparc Solaris</li>
4013 <div align="center">
4014 <strong>2.02</strong><br> 18/7/05
4020 <li>Copy & Paste order of sequences maintains
4021 alignment order.</li>
4027 <div align="center">
4028 <strong>2.01</strong><br> 12/7/05
4033 <li>Use delete key for deleting selection.</li>
4034 <li>Use Mouse wheel to scroll sequences.</li>
4035 <li>Help file updated to describe how to add alignment
4037 <li>Version and build date written to build properties
4039 <li>InstallAnywhere installation will check for updates
4040 at launch of Jalview.</li>
4045 <li>Delete gaps bug fixed.</li>
4046 <li>FileChooser sorts columns.</li>
4047 <li>Can remove groups one by one.</li>
4048 <li>Filechooser icons installed.</li>
4049 <li>Finder ignores return character when searching.
4050 Return key will initiate a search.<br>
4057 <div align="center">
4058 <strong>2.0</strong><br> 20/6/05
4063 <li>New codebase</li>