3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>6/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-3101 -->Default memory for Jalview webstart and
81 InstallAnywhere increased to 1G.
84 <!-- JAL-247 -->Hidden sequence markers and representative
85 sequence bolding included when exporting alignment as EPS,
86 SVG, PNG or HTML. <em>Display is configured via the
87 Format menu, or for command-line use via a jalview
91 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
92 API and sequence data now imported as JSON.
95 <!-- JAL-3065 -->Change in recommended way of starting
96 Jalview via a Java command line: add jars in lib directory
97 to CLASSPATH, rather than via the deprecated java.ext.dirs
104 <!-- JAL-3047 -->Support added to execute test suite
105 instrumented with <a href="http://openclover.org/">Open
110 <td><div align="left">
114 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
115 row shown in Feredoxin Structure alignment view of example
119 <!-- JAL-2854 -->Annotation obscures sequences if lots of
120 annotation displayed.
123 <!-- JAL-3087 -->Corrupted display when switching to
124 wrapped mode when sequence panel's vertical scrollbar is
128 <!-- JAL-3003 -->Alignment is black in exported EPS file
129 when sequences are selected in exported view.</em>
132 <!-- JAL-3059 -->Groups with different coloured borders
133 aren't rendered with correct colour.
136 <!-- JAL-3092 -->Jalview could hang when importing certain
137 types of knotted RNA secondary structure.
140 <!-- JAL-3095 -->Sequence highlight and selection in
141 trimmed VARNA 2D structure is incorrect for sequences that
145 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
146 annotation when columns are inserted into an alignment,
147 and when exporting as Stockholm flatfile.
150 <!-- JAL-3053 -->Jalview annotation rows containing upper
151 and lower-case 'E' and 'H' do not automatically get
152 treated as RNA secondary structure.
155 <!-- JAL-3105 -->Mac Users: closing a window correctly
156 transfers focus to previous window on OSX
159 <em>Java 10 Issues</em>
162 <!-- JAL-2988 -->OSX - Can't save new files via the File
163 or export menus by typing in a name into the Save dialog
171 <td width="60" nowrap>
173 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
174 <em>7/06/2018</em></strong>
177 <td><div align="left">
181 <!-- JAL-2920 -->Use HGVS nomenclature for variant
182 annotation retrieved from Uniprot
185 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
186 onto the Jalview Desktop
190 <td><div align="left">
194 <!-- JAL-3017 -->Cannot import features with multiple
195 variant elements (blocks import of some Uniprot records)
198 <!-- JAL-2997 -->Clustal files with sequence positions in
199 right-hand column parsed correctly
202 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
203 not alignment area in exported graphic
206 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
207 window has input focus
210 <!-- JAL-2992 -->Annotation panel set too high when
211 annotation added to view (Windows)
214 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
215 network connectivity is poor
218 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
219 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
220 the currently open URL and links from a page viewed in
221 Firefox or Chrome on Windows is now fully supported. If
222 you are using Edge, only links in the page can be
223 dragged, and with Internet Explorer, only the currently
224 open URL in the browser can be dropped onto Jalview.</em>
230 <td width="60" nowrap>
232 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
235 <td><div align="left">
239 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
240 for disabling automatic superposition of multiple
241 structures and open structures in existing views
244 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
245 ID and annotation area margins can be click-dragged to
249 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
253 <!-- JAL-2759 -->Improved performance for large alignments
254 and lots of hidden columns
257 <!-- JAL-2593 -->Improved performance when rendering lots
258 of features (particularly when transparency is disabled)
263 <td><div align="left">
266 <!-- JAL-2899 -->Structure and Overview aren't updated
267 when Colour By Annotation threshold slider is adjusted
270 <!-- JAL-2778 -->Slow redraw when Overview panel shown
271 overlapping alignment panel
274 <!-- JAL-2929 -->Overview doesn't show end of unpadded
278 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
279 improved: CDS not handled correctly if transcript has no
283 <!-- JAL-2321 -->Secondary structure and temperature
284 factor annotation not added to sequence when local PDB
285 file associated with it by drag'n'drop or structure
289 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
290 dialog doesn't import PDB files dropped on an alignment
293 <!-- JAL-2666 -->Linked scrolling via protein horizontal
294 scroll bar doesn't work for some CDS/Protein views
297 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
298 Java 1.8u153 onwards and Java 1.9u4+.
301 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
302 columns in annotation row
305 <!-- JAL-2913 -->Preferences panel's ID Width control is not
306 honored in batch mode
309 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
310 for structures added to existing Jmol view
313 <!-- JAL-2223 -->'View Mappings' includes duplicate
314 entries after importing project with multiple views
317 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
318 protein sequences via SIFTS from associated PDB entries
319 with negative residue numbers or missing residues fails
322 <!-- JAL-2952 -->Exception when shading sequence with negative
323 Temperature Factor values from annotated PDB files (e.g.
324 as generated by CONSURF)
327 <!-- JAL-2920 -->Uniprot 'sequence variant' features
328 tooltip doesn't include a text description of mutation
331 <!-- JAL-2922 -->Invert displayed features very slow when
332 structure and/or overview windows are also shown
335 <!-- JAL-2954 -->Selecting columns from highlighted regions
336 very slow for alignments with large numbers of sequences
339 <!-- JAL-2925 -->Copy Consensus fails for group consensus
340 with 'StringIndexOutOfBounds'
343 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
344 platforms running Java 10
347 <!-- JAL-2960 -->Adding a structure to existing structure
348 view appears to do nothing because the view is hidden behind the alignment view
354 <!-- JAL-2926 -->Copy consensus sequence option in applet
355 should copy the group consensus when popup is opened on it
361 <!-- JAL-2913 -->Fixed ID width preference is not respected
364 <em>New Known Defects</em>
367 <!-- JAL-2973 --> Exceptions occasionally raised when
368 editing a large alignment and overview is displayed
371 <!-- JAL-2974 -->'Overview updating' progress bar is shown
372 repeatedly after a series of edits even when the overview
373 is no longer reflecting updates
376 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
377 structures for protein subsequence (if 'Trim Retrieved
378 Sequences' enabled) or Ensembl isoforms (Workaround in
379 2.10.4 is to fail back to N&W mapping)
386 <td width="60" nowrap>
388 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
391 <td><div align="left">
392 <ul><li>Updated Certum Codesigning Certificate
393 (Valid till 30th November 2018)</li></ul></div></td>
394 <td><div align="left">
397 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
398 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
399 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
400 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
401 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
402 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
403 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
409 <td width="60" nowrap>
411 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
414 <td><div align="left">
418 <!-- JAL-2446 -->Faster and more efficient management and
419 rendering of sequence features
422 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
423 429 rate limit request hander
426 <!-- JAL-2773 -->Structure views don't get updated unless
427 their colours have changed
430 <!-- JAL-2495 -->All linked sequences are highlighted for
431 a structure mousover (Jmol) or selection (Chimera)
434 <!-- JAL-2790 -->'Cancel' button in progress bar for
435 JABAWS AACon, RNAAliFold and Disorder prediction jobs
438 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
439 view from Ensembl locus cross-references
442 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
446 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
447 feature can be disabled
450 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
451 PDB easier retrieval of sequences for lists of IDs
454 <!-- JAL-2758 -->Short names for sequences retrieved from
460 <li>Groovy interpreter updated to 2.4.12</li>
461 <li>Example groovy script for generating a matrix of
462 percent identity scores for current alignment.</li>
464 <em>Testing and Deployment</em>
467 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
471 <td><div align="left">
475 <!-- JAL-2643 -->Pressing tab after updating the colour
476 threshold text field doesn't trigger an update to the
480 <!-- JAL-2682 -->Race condition when parsing sequence ID
484 <!-- JAL-2608 -->Overview windows are also closed when
485 alignment window is closed
488 <!-- JAL-2548 -->Export of features doesn't always respect
492 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
493 takes a long time in Cursor mode
499 <!-- JAL-2777 -->Structures with whitespace chainCode
500 cannot be viewed in Chimera
503 <!-- JAL-2728 -->Protein annotation panel too high in
507 <!-- JAL-2757 -->Can't edit the query after the server
508 error warning icon is shown in Uniprot and PDB Free Text
512 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
515 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
518 <!-- JAL-2739 -->Hidden column marker in last column not
519 rendered when switching back from Wrapped to normal view
522 <!-- JAL-2768 -->Annotation display corrupted when
523 scrolling right in unwapped alignment view
526 <!-- JAL-2542 -->Existing features on subsequence
527 incorrectly relocated when full sequence retrieved from
531 <!-- JAL-2733 -->Last reported memory still shown when
532 Desktop->Show Memory is unticked (OSX only)
535 <!-- JAL-2658 -->Amend Features dialog doesn't allow
536 features of same type and group to be selected for
540 <!-- JAL-2524 -->Jalview becomes sluggish in wide
541 alignments when hidden columns are present
544 <!-- JAL-2392 -->Jalview freezes when loading and
545 displaying several structures
548 <!-- JAL-2732 -->Black outlines left after resizing or
552 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
553 within the Jalview desktop on OSX
556 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
557 when in wrapped alignment mode
560 <!-- JAL-2636 -->Scale mark not shown when close to right
561 hand end of alignment
564 <!-- JAL-2684 -->Pairwise alignment of selected regions of
565 each selected sequence do not have correct start/end
569 <!-- JAL-2793 -->Alignment ruler height set incorrectly
570 after canceling the Alignment Window's Font dialog
573 <!-- JAL-2036 -->Show cross-references not enabled after
574 restoring project until a new view is created
577 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
578 URL links appears when only default EMBL-EBI link is
579 configured (since 2.10.2b2)
582 <!-- JAL-2775 -->Overview redraws whole window when box
586 <!-- JAL-2225 -->Structure viewer doesn't map all chains
587 in a multi-chain structure when viewing alignment
588 involving more than one chain (since 2.10)
591 <!-- JAL-2811 -->Double residue highlights in cursor mode
592 if new selection moves alignment window
595 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
596 arrow key in cursor mode to pass hidden column marker
599 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
600 that produces correctly annotated transcripts and products
603 <!-- JAL-2776 -->Toggling a feature group after first time
604 doesn't update associated structure view
607 <em>Applet</em><br />
610 <!-- JAL-2687 -->Concurrent modification exception when
611 closing alignment panel
614 <em>BioJSON</em><br />
617 <!-- JAL-2546 -->BioJSON export does not preserve
618 non-positional features
621 <em>New Known Issues</em>
624 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
625 sequence features correctly (for many previous versions of
629 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
630 using cursor in wrapped panel other than top
633 <!-- JAL-2791 -->Select columns containing feature ignores
634 graduated colour threshold
637 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
638 always preserve numbering and sequence features
641 <em>Known Java 9 Issues</em>
644 <!-- JAL-2902 -->Groovy Console very slow to open and is
645 not responsive when entering characters (Webstart, Java
652 <td width="60" nowrap>
654 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
655 <em>2/10/2017</em></strong>
658 <td><div align="left">
659 <em>New features in Jalview Desktop</em>
662 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
664 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
668 <td><div align="left">
672 <td width="60" nowrap>
674 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
675 <em>7/9/2017</em></strong>
678 <td><div align="left">
682 <!-- JAL-2588 -->Show gaps in overview window by colouring
683 in grey (sequences used to be coloured grey, and gaps were
687 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
691 <!-- JAL-2587 -->Overview updates immediately on increase
692 in size and progress bar shown as higher resolution
693 overview is recalculated
698 <td><div align="left">
702 <!-- JAL-2664 -->Overview window redraws every hidden
703 column region row by row
706 <!-- JAL-2681 -->duplicate protein sequences shown after
707 retrieving Ensembl crossrefs for sequences from Uniprot
710 <!-- JAL-2603 -->Overview window throws NPE if show boxes
711 format setting is unticked
714 <!-- JAL-2610 -->Groups are coloured wrongly in overview
715 if group has show boxes format setting unticked
718 <!-- JAL-2672,JAL-2665 -->Redraw problems when
719 autoscrolling whilst dragging current selection group to
720 include sequences and columns not currently displayed
723 <!-- JAL-2691 -->Not all chains are mapped when multimeric
724 assemblies are imported via CIF file
727 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
728 displayed when threshold or conservation colouring is also
732 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
736 <!-- JAL-2673 -->Jalview continues to scroll after
737 dragging a selected region off the visible region of the
741 <!-- JAL-2724 -->Cannot apply annotation based
742 colourscheme to all groups in a view
745 <!-- JAL-2511 -->IDs don't line up with sequences
746 initially after font size change using the Font chooser or
753 <td width="60" nowrap>
755 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
758 <td><div align="left">
759 <em>Calculations</em>
763 <!-- JAL-1933 -->Occupancy annotation row shows number of
764 ungapped positions in each column of the alignment.
767 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
768 a calculation dialog box
771 <!-- JAL-2379 -->Revised implementation of PCA for speed
772 and memory efficiency (~30x faster)
775 <!-- JAL-2403 -->Revised implementation of sequence
776 similarity scores as used by Tree, PCA, Shading Consensus
777 and other calculations
780 <!-- JAL-2416 -->Score matrices are stored as resource
781 files within the Jalview codebase
784 <!-- JAL-2500 -->Trees computed on Sequence Feature
785 Similarity may have different topology due to increased
792 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
793 model for alignments and groups
796 <!-- JAL-384 -->Custom shading schemes created via groovy
803 <!-- JAL-2526 -->Efficiency improvements for interacting
804 with alignment and overview windows
807 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
811 <!-- JAL-2388 -->Hidden columns and sequences can be
815 <!-- JAL-2611 -->Click-drag in visible area allows fine
816 adjustment of visible position
820 <em>Data import/export</em>
823 <!-- JAL-2535 -->Posterior probability annotation from
824 Stockholm files imported as sequence associated annotation
827 <!-- JAL-2507 -->More robust per-sequence positional
828 annotation input/output via stockholm flatfile
831 <!-- JAL-2533 -->Sequence names don't include file
832 extension when importing structure files without embedded
833 names or PDB accessions
836 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
837 format sequence substitution matrices
840 <em>User Interface</em>
843 <!-- JAL-2447 --> Experimental Features Checkbox in
844 Desktop's Tools menu to hide or show untested features in
848 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
849 via Overview or sequence motif search operations
852 <!-- JAL-2547 -->Amend sequence features dialog box can be
853 opened by double clicking gaps within sequence feature
857 <!-- JAL-1476 -->Status bar message shown when not enough
858 aligned positions were available to create a 3D structure
862 <em>3D Structure</em>
865 <!-- JAL-2430 -->Hidden regions in alignment views are not
866 coloured in linked structure views
869 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
870 file-based command exchange
873 <!-- JAL-2375 -->Structure chooser automatically shows
874 Cached Structures rather than querying the PDBe if
875 structures are already available for sequences
878 <!-- JAL-2520 -->Structures imported via URL are cached in
879 the Jalview project rather than downloaded again when the
883 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
884 to transfer Chimera's structure attributes as Jalview
885 features, and vice-versa (<strong>Experimental
889 <em>Web Services</em>
892 <!-- JAL-2549 -->Updated JABAWS client to v2.2
895 <!-- JAL-2335 -->Filter non-standard amino acids and
896 nucleotides when submitting to AACon and other MSA
900 <!-- JAL-2316, -->URLs for viewing database
901 cross-references provided by identifiers.org and the
909 <!-- JAL-2344 -->FileFormatI interface for describing and
910 identifying file formats (instead of String constants)
913 <!-- JAL-2228 -->FeatureCounter script refactored for
914 efficiency when counting all displayed features (not
915 backwards compatible with 2.10.1)
918 <em>Example files</em>
921 <!-- JAL-2631 -->Graduated feature colour style example
922 included in the example feature file
925 <em>Documentation</em>
928 <!-- JAL-2339 -->Release notes reformatted for readability
929 with the built-in Java help viewer
932 <!-- JAL-1644 -->Find documentation updated with 'search
933 sequence description' option
939 <!-- JAL-2485, -->External service integration tests for
940 Uniprot REST Free Text Search Client
943 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
946 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
951 <td><div align="left">
952 <em>Calculations</em>
955 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
956 matrix - C->R should be '-3'<br />Old matrix restored
957 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
959 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
960 Jalview's treatment of gaps in PCA and substitution matrix
961 based Tree calculations.<br /> <br />In earlier versions
962 of Jalview, gaps matching gaps were penalised, and gaps
963 matching non-gaps penalised even more. In the PCA
964 calculation, gaps were actually treated as non-gaps - so
965 different costs were applied, which meant Jalview's PCAs
966 were different to those produced by SeqSpace.<br />Jalview
967 now treats gaps in the same way as SeqSpace (ie it scores
968 them as 0). <br /> <br />Enter the following in the
969 Groovy console to restore pre-2.10.2 behaviour:<br />
970 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
971 // for 2.10.1 mode <br />
972 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
973 // to restore 2.10.2 mode <br /> <br /> <em>Note:
974 these settings will affect all subsequent tree and PCA
975 calculations (not recommended)</em></li>
977 <!-- JAL-2424 -->Fixed off-by-one bug that affected
978 scaling of branch lengths for trees computed using
979 Sequence Feature Similarity.
982 <!-- JAL-2377 -->PCA calculation could hang when
983 generating output report when working with highly
987 <!-- JAL-2544 --> Sort by features includes features to
988 right of selected region when gaps present on right-hand
992 <em>User Interface</em>
995 <!-- JAL-2346 -->Reopening Colour by annotation dialog
996 doesn't reselect a specific sequence's associated
997 annotation after it was used for colouring a view
1000 <!-- JAL-2419 -->Current selection lost if popup menu
1001 opened on a region of alignment without groups
1004 <!-- JAL-2374 -->Popup menu not always shown for regions
1005 of an alignment with overlapping groups
1008 <!-- JAL-2310 -->Finder double counts if both a sequence's
1009 name and description match
1012 <!-- JAL-2370 -->Hiding column selection containing two
1013 hidden regions results in incorrect hidden regions
1016 <!-- JAL-2386 -->'Apply to all groups' setting when
1017 changing colour does not apply Conservation slider value
1021 <!-- JAL-2373 -->Percentage identity and conservation menu
1022 items do not show a tick or allow shading to be disabled
1025 <!-- JAL-2385 -->Conservation shading or PID threshold
1026 lost when base colourscheme changed if slider not visible
1029 <!-- JAL-2547 -->Sequence features shown in tooltip for
1030 gaps before start of features
1033 <!-- JAL-2623 -->Graduated feature colour threshold not
1034 restored to UI when feature colour is edited
1037 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1038 a time when scrolling vertically in wrapped mode.
1041 <!-- JAL-2630 -->Structure and alignment overview update
1042 as graduate feature colour settings are modified via the
1046 <!-- JAL-2034 -->Overview window doesn't always update
1047 when a group defined on the alignment is resized
1050 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1051 wrapped view result in positional status updates
1055 <!-- JAL-2563 -->Status bar doesn't show position for
1056 ambiguous amino acid and nucleotide symbols
1059 <!-- JAL-2602 -->Copy consensus sequence failed if
1060 alignment included gapped columns
1063 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1064 widgets don't permanently disappear
1067 <!-- JAL-2503 -->Cannot select or filter quantitative
1068 annotation that are shown only as column labels (e.g.
1069 T-Coffee column reliability scores)
1072 <!-- JAL-2594 -->Exception thrown if trying to create a
1073 sequence feature on gaps only
1076 <!-- JAL-2504 -->Features created with 'New feature'
1077 button from a Find inherit previously defined feature type
1078 rather than the Find query string
1081 <!-- JAL-2423 -->incorrect title in output window when
1082 exporting tree calculated in Jalview
1085 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1086 and then revealing them reorders sequences on the
1090 <!-- JAL-964 -->Group panel in sequence feature settings
1091 doesn't update to reflect available set of groups after
1092 interactively adding or modifying features
1095 <!-- JAL-2225 -->Sequence Database chooser unusable on
1099 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1100 only excluded gaps in current sequence and ignored
1107 <!-- JAL-2421 -->Overview window visible region moves
1108 erratically when hidden rows or columns are present
1111 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1112 Structure Viewer's colour menu don't correspond to
1116 <!-- JAL-2405 -->Protein specific colours only offered in
1117 colour and group colour menu for protein alignments
1120 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1121 reflect currently selected view or group's shading
1125 <!-- JAL-2624 -->Feature colour thresholds not respected
1126 when rendered on overview and structures when opacity at
1130 <!-- JAL-2589 -->User defined gap colour not shown in
1131 overview when features overlaid on alignment
1134 <em>Data import/export</em>
1137 <!-- JAL-2576 -->Very large alignments take a long time to
1141 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1142 added after a sequence was imported are not written to
1146 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1147 when importing RNA secondary structure via Stockholm
1150 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1151 not shown in correct direction for simple pseudoknots
1154 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1155 with lightGray or darkGray via features file (but can
1159 <!-- JAL-2383 -->Above PID colour threshold not recovered
1160 when alignment view imported from project
1163 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1164 structure and sequences extracted from structure files
1165 imported via URL and viewed in Jmol
1168 <!-- JAL-2520 -->Structures loaded via URL are saved in
1169 Jalview Projects rather than fetched via URL again when
1170 the project is loaded and the structure viewed
1173 <em>Web Services</em>
1176 <!-- JAL-2519 -->EnsemblGenomes example failing after
1177 release of Ensembl v.88
1180 <!-- JAL-2366 -->Proxy server address and port always
1181 appear enabled in Preferences->Connections
1184 <!-- JAL-2461 -->DAS registry not found exceptions
1185 removed from console output
1188 <!-- JAL-2582 -->Cannot retrieve protein products from
1189 Ensembl by Peptide ID
1192 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1193 created from SIFTs, and spurious 'Couldn't open structure
1194 in Chimera' errors raised after April 2017 update (problem
1195 due to 'null' string rather than empty string used for
1196 residues with no corresponding PDB mapping).
1199 <em>Application UI</em>
1202 <!-- JAL-2361 -->User Defined Colours not added to Colour
1206 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1207 case' residues (button in colourscheme editor debugged and
1208 new documentation and tooltips added)
1211 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1212 doesn't restore group-specific text colour thresholds
1215 <!-- JAL-2243 -->Feature settings panel does not update as
1216 new features are added to alignment
1219 <!-- JAL-2532 -->Cancel in feature settings reverts
1220 changes to feature colours via the Amend features dialog
1223 <!-- JAL-2506 -->Null pointer exception when attempting to
1224 edit graduated feature colour via amend features dialog
1228 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1229 selection menu changes colours of alignment views
1232 <!-- JAL-2426 -->Spurious exceptions in console raised
1233 from alignment calculation workers after alignment has
1237 <!-- JAL-1608 -->Typo in selection popup menu - Create
1238 groups now 'Create Group'
1241 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1242 Create/Undefine group doesn't always work
1245 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1246 shown again after pressing 'Cancel'
1249 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1250 adjusts start position in wrap mode
1253 <!-- JAL-2563 -->Status bar doesn't show positions for
1254 ambiguous amino acids
1257 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1258 CDS/Protein view after CDS sequences added for aligned
1262 <!-- JAL-2592 -->User defined colourschemes called 'User
1263 Defined' don't appear in Colours menu
1269 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1270 score models doesn't always result in an updated PCA plot
1273 <!-- JAL-2442 -->Features not rendered as transparent on
1274 overview or linked structure view
1277 <!-- JAL-2372 -->Colour group by conservation doesn't
1281 <!-- JAL-2517 -->Hitting Cancel after applying
1282 user-defined colourscheme doesn't restore original
1289 <!-- JAL-2314 -->Unit test failure:
1290 jalview.ws.jabaws.RNAStructExportImport setup fails
1293 <!-- JAL-2307 -->Unit test failure:
1294 jalview.ws.sifts.SiftsClientTest due to compatibility
1295 problems with deep array comparison equality asserts in
1296 successive versions of TestNG
1299 <!-- JAL-2479 -->Relocated StructureChooserTest and
1300 ParameterUtilsTest Unit tests to Network suite
1303 <em>New Known Issues</em>
1306 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1307 phase after a sequence motif find operation
1310 <!-- JAL-2550 -->Importing annotation file with rows
1311 containing just upper and lower case letters are
1312 interpreted as WUSS RNA secondary structure symbols
1315 <!-- JAL-2590 -->Cannot load and display Newick trees
1316 reliably from eggnog Ortholog database
1319 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1320 containing features of type Highlight' when 'B' is pressed
1321 to mark columns containing highlighted regions.
1324 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1325 doesn't always add secondary structure annotation.
1330 <td width="60" nowrap>
1331 <div align="center">
1332 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1335 <td><div align="left">
1339 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1340 for all consensus calculations
1343 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1346 <li>Updated Jalview's Certum code signing certificate
1349 <em>Application</em>
1352 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1353 set of database cross-references, sorted alphabetically
1356 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1357 from database cross references. Users with custom links
1358 will receive a <a href="webServices/urllinks.html#warning">warning
1359 dialog</a> asking them to update their preferences.
1362 <!-- JAL-2287-->Cancel button and escape listener on
1363 dialog warning user about disconnecting Jalview from a
1367 <!-- JAL-2320-->Jalview's Chimera control window closes if
1368 the Chimera it is connected to is shut down
1371 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1372 columns menu item to mark columns containing highlighted
1373 regions (e.g. from structure selections or results of a
1377 <!-- JAL-2284-->Command line option for batch-generation
1378 of HTML pages rendering alignment data with the BioJS
1388 <!-- JAL-2286 -->Columns with more than one modal residue
1389 are not coloured or thresholded according to percent
1390 identity (first observed in Jalview 2.8.2)
1393 <!-- JAL-2301 -->Threonine incorrectly reported as not
1397 <!-- JAL-2318 -->Updates to documentation pages (above PID
1398 threshold, amino acid properties)
1401 <!-- JAL-2292 -->Lower case residues in sequences are not
1402 reported as mapped to residues in a structure file in the
1406 <!--JAL-2324 -->Identical features with non-numeric scores
1407 could be added multiple times to a sequence
1410 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1411 bond features shown as two highlighted residues rather
1412 than a range in linked structure views, and treated
1413 correctly when selecting and computing trees from features
1416 <!-- JAL-2281-->Custom URL links for database
1417 cross-references are matched to database name regardless
1422 <em>Application</em>
1425 <!-- JAL-2282-->Custom URL links for specific database
1426 names without regular expressions also offer links from
1430 <!-- JAL-2315-->Removing a single configured link in the
1431 URL links pane in Connections preferences doesn't actually
1432 update Jalview configuration
1435 <!-- JAL-2272-->CTRL-Click on a selected region to open
1436 the alignment area popup menu doesn't work on El-Capitan
1439 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1440 files with similarly named sequences if dropped onto the
1444 <!-- JAL-2312 -->Additional mappings are shown for PDB
1445 entries where more chains exist in the PDB accession than
1446 are reported in the SIFTS file
1449 <!-- JAL-2317-->Certain structures do not get mapped to
1450 the structure view when displayed with Chimera
1453 <!-- JAL-2317-->No chains shown in the Chimera view
1454 panel's View->Show Chains submenu
1457 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1458 work for wrapped alignment views
1461 <!--JAL-2197 -->Rename UI components for running JPred
1462 predictions from 'JNet' to 'JPred'
1465 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1466 corrupted when annotation panel vertical scroll is not at
1467 first annotation row
1470 <!--JAL-2332 -->Attempting to view structure for Hen
1471 lysozyme results in a PDB Client error dialog box
1474 <!-- JAL-2319 -->Structure View's mapping report switched
1475 ranges for PDB and sequence for SIFTS
1478 SIFTS 'Not_Observed' residues mapped to non-existant
1482 <!-- <em>New Known Issues</em>
1489 <td width="60" nowrap>
1490 <div align="center">
1491 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1492 <em>25/10/2016</em></strong>
1495 <td><em>Application</em>
1497 <li>3D Structure chooser opens with 'Cached structures'
1498 view if structures already loaded</li>
1499 <li>Progress bar reports models as they are loaded to
1500 structure views</li>
1506 <li>Colour by conservation always enabled and no tick
1507 shown in menu when BLOSUM or PID shading applied</li>
1508 <li>FER1_ARATH and FER2_ARATH labels were switched in
1509 example sequences/projects/trees</li>
1511 <em>Application</em>
1513 <li>Jalview projects with views of local PDB structure
1514 files saved on Windows cannot be opened on OSX</li>
1515 <li>Multiple structure views can be opened and superposed
1516 without timeout for structures with multiple models or
1517 multiple sequences in alignment</li>
1518 <li>Cannot import or associated local PDB files without a
1519 PDB ID HEADER line</li>
1520 <li>RMSD is not output in Jmol console when superposition
1522 <li>Drag and drop of URL from Browser fails for Linux and
1523 OSX versions earlier than El Capitan</li>
1524 <li>ENA client ignores invalid content from ENA server</li>
1525 <li>Exceptions are not raised in console when ENA client
1526 attempts to fetch non-existent IDs via Fetch DB Refs UI
1528 <li>Exceptions are not raised in console when a new view
1529 is created on the alignment</li>
1530 <li>OSX right-click fixed for group selections: CMD-click
1531 to insert/remove gaps in groups and CTRL-click to open group
1534 <em>Build and deployment</em>
1536 <li>URL link checker now copes with multi-line anchor
1539 <em>New Known Issues</em>
1541 <li>Drag and drop from URL links in browsers do not work
1548 <td width="60" nowrap>
1549 <div align="center">
1550 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1553 <td><em>General</em>
1556 <!-- JAL-2124 -->Updated Spanish translations.
1559 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1560 for importing structure data to Jalview. Enables mmCIF and
1564 <!-- JAL-192 --->Alignment ruler shows positions relative to
1568 <!-- JAL-2202 -->Position/residue shown in status bar when
1569 mousing over sequence associated annotation
1572 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1576 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1577 '()', canonical '[]' and invalid '{}' base pair populations
1581 <!-- JAL-2092 -->Feature settings popup menu options for
1582 showing or hiding columns containing a feature
1585 <!-- JAL-1557 -->Edit selected group by double clicking on
1586 group and sequence associated annotation labels
1589 <!-- JAL-2236 -->Sequence name added to annotation label in
1590 select/hide columns by annotation and colour by annotation
1594 </ul> <em>Application</em>
1597 <!-- JAL-2050-->Automatically hide introns when opening a
1598 gene/transcript view
1601 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1605 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1606 structure mappings with the EMBL-EBI PDBe SIFTS database
1609 <!-- JAL-2079 -->Updated download sites used for Rfam and
1610 Pfam sources to xfam.org
1613 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1616 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1617 over sequences in Jalview
1620 <!-- JAL-2027-->Support for reverse-complement coding
1621 regions in ENA and EMBL
1624 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1625 for record retrieval via ENA rest API
1628 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1632 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1633 groovy script execution
1636 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1637 alignment window's Calculate menu
1640 <!-- JAL-1812 -->Allow groovy scripts that call
1641 Jalview.getAlignFrames() to run in headless mode
1644 <!-- JAL-2068 -->Support for creating new alignment
1645 calculation workers from groovy scripts
1648 <!-- JAL-1369 --->Store/restore reference sequence in
1652 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1653 associations are now saved/restored from project
1656 <!-- JAL-1993 -->Database selection dialog always shown
1657 before sequence fetcher is opened
1660 <!-- JAL-2183 -->Double click on an entry in Jalview's
1661 database chooser opens a sequence fetcher
1664 <!-- JAL-1563 -->Free-text search client for UniProt using
1665 the UniProt REST API
1668 <!-- JAL-2168 -->-nonews command line parameter to prevent
1669 the news reader opening
1672 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1673 querying stored in preferences
1676 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1680 <!-- JAL-1977-->Tooltips shown on database chooser
1683 <!-- JAL-391 -->Reverse complement function in calculate
1684 menu for nucleotide sequences
1687 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1688 and feature counts preserves alignment ordering (and
1689 debugged for complex feature sets).
1692 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1693 viewing structures with Jalview 2.10
1696 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1697 genome, transcript CCDS and gene ids via the Ensembl and
1698 Ensembl Genomes REST API
1701 <!-- JAL-2049 -->Protein sequence variant annotation
1702 computed for 'sequence_variant' annotation on CDS regions
1706 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1710 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1711 Ref Fetcher fails to match, or otherwise updates sequence
1712 data from external database records.
1715 <!-- JAL-2154 -->Revised Jalview Project format for
1716 efficient recovery of sequence coding and alignment
1717 annotation relationships.
1719 </ul> <!-- <em>Applet</em>
1730 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1734 <!-- JAL-2018-->Export features in Jalview format (again)
1735 includes graduated colourschemes
1738 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1739 working with big alignments and lots of hidden columns
1742 <!-- JAL-2053-->Hidden column markers not always rendered
1743 at right of alignment window
1746 <!-- JAL-2067 -->Tidied up links in help file table of
1750 <!-- JAL-2072 -->Feature based tree calculation not shown
1754 <!-- JAL-2075 -->Hidden columns ignored during feature
1755 based tree calculation
1758 <!-- JAL-2065 -->Alignment view stops updating when show
1759 unconserved enabled for group on alignment
1762 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1766 <!-- JAL-2146 -->Alignment column in status incorrectly
1767 shown as "Sequence position" when mousing over
1771 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1772 hidden columns present
1775 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1776 user created annotation added to alignment
1779 <!-- JAL-1841 -->RNA Structure consensus only computed for
1780 '()' base pair annotation
1783 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1784 in zero scores for all base pairs in RNA Structure
1788 <!-- JAL-2174-->Extend selection with columns containing
1792 <!-- JAL-2275 -->Pfam format writer puts extra space at
1793 beginning of sequence
1796 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1800 <!-- JAL-2238 -->Cannot create groups on an alignment from
1801 from a tree when t-coffee scores are shown
1804 <!-- JAL-1836,1967 -->Cannot import and view PDB
1805 structures with chains containing negative resnums (4q4h)
1808 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1812 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1813 to Clustal, PIR and PileUp output
1816 <!-- JAL-2008 -->Reordering sequence features that are
1817 not visible causes alignment window to repaint
1820 <!-- JAL-2006 -->Threshold sliders don't work in
1821 graduated colour and colour by annotation row for e-value
1822 scores associated with features and annotation rows
1825 <!-- JAL-1797 -->amino acid physicochemical conservation
1826 calculation should be case independent
1829 <!-- JAL-2173 -->Remove annotation also updates hidden
1833 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1834 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1835 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1838 <!-- JAL-2065 -->Null pointer exceptions and redraw
1839 problems when reference sequence defined and 'show
1840 non-conserved' enabled
1843 <!-- JAL-1306 -->Quality and Conservation are now shown on
1844 load even when Consensus calculation is disabled
1847 <!-- JAL-1932 -->Remove right on penultimate column of
1848 alignment does nothing
1851 <em>Application</em>
1854 <!-- JAL-1552-->URLs and links can't be imported by
1855 drag'n'drop on OSX when launched via webstart (note - not
1856 yet fixed for El Capitan)
1859 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1860 output when running on non-gb/us i18n platforms
1863 <!-- JAL-1944 -->Error thrown when exporting a view with
1864 hidden sequences as flat-file alignment
1867 <!-- JAL-2030-->InstallAnywhere distribution fails when
1871 <!-- JAL-2080-->Jalview very slow to launch via webstart
1872 (also hotfix for 2.9.0b2)
1875 <!-- JAL-2085 -->Cannot save project when view has a
1876 reference sequence defined
1879 <!-- JAL-1011 -->Columns are suddenly selected in other
1880 alignments and views when revealing hidden columns
1883 <!-- JAL-1989 -->Hide columns not mirrored in complement
1884 view in a cDNA/Protein splitframe
1887 <!-- JAL-1369 -->Cannot save/restore representative
1888 sequence from project when only one sequence is
1892 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1893 in Structure Chooser
1896 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1897 structure consensus didn't refresh annotation panel
1900 <!-- JAL-1962 -->View mapping in structure view shows
1901 mappings between sequence and all chains in a PDB file
1904 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1905 dialogs format columns correctly, don't display array
1906 data, sort columns according to type
1909 <!-- JAL-1975 -->Export complete shown after destination
1910 file chooser is cancelled during an image export
1913 <!-- JAL-2025 -->Error when querying PDB Service with
1914 sequence name containing special characters
1917 <!-- JAL-2024 -->Manual PDB structure querying should be
1921 <!-- JAL-2104 -->Large tooltips with broken HTML
1922 formatting don't wrap
1925 <!-- JAL-1128 -->Figures exported from wrapped view are
1926 truncated so L looks like I in consensus annotation
1929 <!-- JAL-2003 -->Export features should only export the
1930 currently displayed features for the current selection or
1934 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1935 after fetching cross-references, and restoring from
1939 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1940 followed in the structure viewer
1943 <!-- JAL-2163 -->Titles for individual alignments in
1944 splitframe not restored from project
1947 <!-- JAL-2145 -->missing autocalculated annotation at
1948 trailing end of protein alignment in transcript/product
1949 splitview when pad-gaps not enabled by default
1952 <!-- JAL-1797 -->amino acid physicochemical conservation
1956 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1957 article has been read (reopened issue due to
1958 internationalisation problems)
1961 <!-- JAL-1960 -->Only offer PDB structures in structure
1962 viewer based on sequence name, PDB and UniProt
1967 <!-- JAL-1976 -->No progress bar shown during export of
1971 <!-- JAL-2213 -->Structures not always superimposed after
1972 multiple structures are shown for one or more sequences.
1975 <!-- JAL-1370 -->Reference sequence characters should not
1976 be replaced with '.' when 'Show unconserved' format option
1980 <!-- JAL-1823 -->Cannot specify chain code when entering
1981 specific PDB id for sequence
1984 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1985 'Export hidden sequences' is enabled, but 'export hidden
1986 columns' is disabled.
1989 <!--JAL-2026-->Best Quality option in structure chooser
1990 selects lowest rather than highest resolution structures
1994 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1995 to sequence mapping in 'View Mappings' report
1998 <!-- JAL-2284 -->Unable to read old Jalview projects that
1999 contain non-XML data added after Jalvew wrote project.
2002 <!-- JAL-2118 -->Newly created annotation row reorders
2003 after clicking on it to create new annotation for a
2007 <!-- JAL-1980 -->Null Pointer Exception raised when
2008 pressing Add on an orphaned cut'n'paste window.
2010 <!-- may exclude, this is an external service stability issue JAL-1941
2011 -- > RNA 3D structure not added via DSSR service</li> -->
2016 <!-- JAL-2151 -->Incorrect columns are selected when
2017 hidden columns present before start of sequence
2020 <!-- JAL-1986 -->Missing dependencies on applet pages
2024 <!-- JAL-1947 -->Overview pixel size changes when
2025 sequences are hidden in applet
2028 <!-- JAL-1996 -->Updated instructions for applet
2029 deployment on examples pages.
2036 <td width="60" nowrap>
2037 <div align="center">
2038 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2039 <em>16/10/2015</em></strong>
2042 <td><em>General</em>
2044 <li>Time stamps for signed Jalview application and applet
2049 <em>Application</em>
2051 <li>Duplicate group consensus and conservation rows
2052 shown when tree is partitioned</li>
2053 <li>Erratic behaviour when tree partitions made with
2054 multiple cDNA/Protein split views</li>
2060 <td width="60" nowrap>
2061 <div align="center">
2062 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2063 <em>8/10/2015</em></strong>
2066 <td><em>General</em>
2068 <li>Updated Spanish translations of localized text for
2070 </ul> <em>Application</em>
2072 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2073 <li>Signed OSX InstallAnywhere installer<br></li>
2074 <li>Support for per-sequence based annotations in BioJSON</li>
2075 </ul> <em>Applet</em>
2077 <li>Split frame example added to applet examples page</li>
2078 </ul> <em>Build and Deployment</em>
2081 <!-- JAL-1888 -->New ant target for running Jalview's test
2089 <li>Mapping of cDNA to protein in split frames
2090 incorrect when sequence start > 1</li>
2091 <li>Broken images in filter column by annotation dialog
2093 <li>Feature colours not parsed from features file</li>
2094 <li>Exceptions and incomplete link URLs recovered when
2095 loading a features file containing HTML tags in feature
2099 <em>Application</em>
2101 <li>Annotations corrupted after BioJS export and
2103 <li>Incorrect sequence limits after Fetch DB References
2104 with 'trim retrieved sequences'</li>
2105 <li>Incorrect warning about deleting all data when
2106 deleting selected columns</li>
2107 <li>Patch to build system for shipping properly signed
2108 JNLP templates for webstart launch</li>
2109 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2110 unreleased structures for download or viewing</li>
2111 <li>Tab/space/return keystroke operation of EMBL-PDBe
2112 fetcher/viewer dialogs works correctly</li>
2113 <li>Disabled 'minimise' button on Jalview windows
2114 running on OSX to workaround redraw hang bug</li>
2115 <li>Split cDNA/Protein view position and geometry not
2116 recovered from jalview project</li>
2117 <li>Initial enabled/disabled state of annotation menu
2118 sorter 'show autocalculated first/last' corresponds to
2120 <li>Restoring of Clustal, RNA Helices and T-Coffee
2121 color schemes from BioJSON</li>
2125 <li>Reorder sequences mirrored in cDNA/Protein split
2127 <li>Applet with Jmol examples not loading correctly</li>
2133 <td><div align="center">
2134 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2136 <td><em>General</em>
2138 <li>Linked visualisation and analysis of DNA and Protein
2141 <li>Translated cDNA alignments shown as split protein
2142 and DNA alignment views</li>
2143 <li>Codon consensus annotation for linked protein and
2144 cDNA alignment views</li>
2145 <li>Link cDNA or Protein product sequences by loading
2146 them onto Protein or cDNA alignments</li>
2147 <li>Reconstruct linked cDNA alignment from aligned
2148 protein sequences</li>
2151 <li>Jmol integration updated to Jmol v14.2.14</li>
2152 <li>Import and export of Jalview alignment views as <a
2153 href="features/bioJsonFormat.html">BioJSON</a></li>
2154 <li>New alignment annotation file statements for
2155 reference sequences and marking hidden columns</li>
2156 <li>Reference sequence based alignment shading to
2157 highlight variation</li>
2158 <li>Select or hide columns according to alignment
2160 <li>Find option for locating sequences by description</li>
2161 <li>Conserved physicochemical properties shown in amino
2162 acid conservation row</li>
2163 <li>Alignments can be sorted by number of RNA helices</li>
2164 </ul> <em>Application</em>
2166 <li>New cDNA/Protein analysis capabilities
2168 <li>Get Cross-References should open a Split Frame
2169 view with cDNA/Protein</li>
2170 <li>Detect when nucleotide sequences and protein
2171 sequences are placed in the same alignment</li>
2172 <li>Split cDNA/Protein views are saved in Jalview
2177 <li>Use REST API to talk to Chimera</li>
2178 <li>Selected regions in Chimera are highlighted in linked
2179 Jalview windows</li>
2181 <li>VARNA RNA viewer updated to v3.93</li>
2182 <li>VARNA views are saved in Jalview Projects</li>
2183 <li>Pseudoknots displayed as Jalview RNA annotation can
2184 be shown in VARNA</li>
2186 <li>Make groups for selection uses marked columns as well
2187 as the active selected region</li>
2189 <li>Calculate UPGMA and NJ trees using sequence feature
2191 <li>New Export options
2193 <li>New Export Settings dialog to control hidden
2194 region export in flat file generation</li>
2196 <li>Export alignment views for display with the <a
2197 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2199 <li>Export scrollable SVG in HTML page</li>
2200 <li>Optional embedding of BioJSON data when exporting
2201 alignment figures to HTML</li>
2203 <li>3D structure retrieval and display
2205 <li>Free text and structured queries with the PDBe
2207 <li>PDBe Search API based discovery and selection of
2208 PDB structures for a sequence set</li>
2212 <li>JPred4 employed for protein secondary structure
2214 <li>Hide Insertions menu option to hide unaligned columns
2215 for one or a group of sequences</li>
2216 <li>Automatically hide insertions in alignments imported
2217 from the JPred4 web server</li>
2218 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2219 system on OSX<br />LGPL libraries courtesy of <a
2220 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2222 <li>changed 'View nucleotide structure' submenu to 'View
2223 VARNA 2D Structure'</li>
2224 <li>change "View protein structure" menu option to "3D
2227 </ul> <em>Applet</em>
2229 <li>New layout for applet example pages</li>
2230 <li>New parameters to enable SplitFrame view
2231 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2232 <li>New example demonstrating linked viewing of cDNA and
2233 Protein alignments</li>
2234 </ul> <em>Development and deployment</em>
2236 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2237 <li>Include installation type and git revision in build
2238 properties and console log output</li>
2239 <li>Jalview Github organisation, and new github site for
2240 storing BioJsMSA Templates</li>
2241 <li>Jalview's unit tests now managed with TestNG</li>
2244 <!-- <em>General</em>
2246 </ul> --> <!-- issues resolved --> <em>Application</em>
2248 <li>Escape should close any open find dialogs</li>
2249 <li>Typo in select-by-features status report</li>
2250 <li>Consensus RNA secondary secondary structure
2251 predictions are not highlighted in amber</li>
2252 <li>Missing gap character in v2.7 example file means
2253 alignment appears unaligned when pad-gaps is not enabled</li>
2254 <li>First switch to RNA Helices colouring doesn't colour
2255 associated structure views</li>
2256 <li>ID width preference option is greyed out when auto
2257 width checkbox not enabled</li>
2258 <li>Stopped a warning dialog from being shown when
2259 creating user defined colours</li>
2260 <li>'View Mapping' in structure viewer shows sequence
2261 mappings for just that viewer's sequences</li>
2262 <li>Workaround for superposing PDB files containing
2263 multiple models in Chimera</li>
2264 <li>Report sequence position in status bar when hovering
2265 over Jmol structure</li>
2266 <li>Cannot output gaps as '.' symbols with Selection ->
2267 output to text box</li>
2268 <li>Flat file exports of alignments with hidden columns
2269 have incorrect sequence start/end</li>
2270 <li>'Aligning' a second chain to a Chimera structure from
2272 <li>Colour schemes applied to structure viewers don't
2273 work for nucleotide</li>
2274 <li>Loading/cut'n'pasting an empty or invalid file leads
2275 to a grey/invisible alignment window</li>
2276 <li>Exported Jpred annotation from a sequence region
2277 imports to different position</li>
2278 <li>Space at beginning of sequence feature tooltips shown
2279 on some platforms</li>
2280 <li>Chimera viewer 'View | Show Chain' menu is not
2282 <li>'New View' fails with a Null Pointer Exception in
2283 console if Chimera has been opened</li>
2284 <li>Mouseover to Chimera not working</li>
2285 <li>Miscellaneous ENA XML feature qualifiers not
2287 <li>NPE in annotation renderer after 'Extract Scores'</li>
2288 <li>If two structures in one Chimera window, mouseover of
2289 either sequence shows on first structure</li>
2290 <li>'Show annotations' options should not make
2291 non-positional annotations visible</li>
2292 <li>Subsequence secondary structure annotation not shown
2293 in right place after 'view flanking regions'</li>
2294 <li>File Save As type unset when current file format is
2296 <li>Save as '.jar' option removed for saving Jalview
2298 <li>Colour by Sequence colouring in Chimera more
2300 <li>Cannot 'add reference annotation' for a sequence in
2301 several views on same alignment</li>
2302 <li>Cannot show linked products for EMBL / ENA records</li>
2303 <li>Jalview's tooltip wraps long texts containing no
2305 </ul> <em>Applet</em>
2307 <li>Jmol to JalviewLite mouseover/link not working</li>
2308 <li>JalviewLite can't import sequences with ID
2309 descriptions containing angle brackets</li>
2310 </ul> <em>General</em>
2312 <li>Cannot export and reimport RNA secondary structure
2313 via jalview annotation file</li>
2314 <li>Random helix colour palette for colour by annotation
2315 with RNA secondary structure</li>
2316 <li>Mouseover to cDNA from STOP residue in protein
2317 translation doesn't work.</li>
2318 <li>hints when using the select by annotation dialog box</li>
2319 <li>Jmol alignment incorrect if PDB file has alternate CA
2321 <li>FontChooser message dialog appears to hang after
2322 choosing 1pt font</li>
2323 <li>Peptide secondary structure incorrectly imported from
2324 annotation file when annotation display text includes 'e' or
2326 <li>Cannot set colour of new feature type whilst creating
2328 <li>cDNA translation alignment should not be sequence
2329 order dependent</li>
2330 <li>'Show unconserved' doesn't work for lower case
2332 <li>Nucleotide ambiguity codes involving R not recognised</li>
2333 </ul> <em>Deployment and Documentation</em>
2335 <li>Applet example pages appear different to the rest of
2336 www.jalview.org</li>
2337 </ul> <em>Application Known issues</em>
2339 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2340 <li>Misleading message appears after trying to delete
2342 <li>Jalview icon not shown in dock after InstallAnywhere
2343 version launches</li>
2344 <li>Fetching EMBL reference for an RNA sequence results
2345 fails with a sequence mismatch</li>
2346 <li>Corrupted or unreadable alignment display when
2347 scrolling alignment to right</li>
2348 <li>ArrayIndexOutOfBoundsException thrown when remove
2349 empty columns called on alignment with ragged gapped ends</li>
2350 <li>auto calculated alignment annotation rows do not get
2351 placed above or below non-autocalculated rows</li>
2352 <li>Jalview dekstop becomes sluggish at full screen in
2353 ultra-high resolution</li>
2354 <li>Cannot disable consensus calculation independently of
2355 quality and conservation</li>
2356 <li>Mouseover highlighting between cDNA and protein can
2357 become sluggish with more than one splitframe shown</li>
2358 </ul> <em>Applet Known Issues</em>
2360 <li>Core PDB parsing code requires Jmol</li>
2361 <li>Sequence canvas panel goes white when alignment
2362 window is being resized</li>
2368 <td><div align="center">
2369 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2371 <td><em>General</em>
2373 <li>Updated Java code signing certificate donated by
2375 <li>Features and annotation preserved when performing
2376 pairwise alignment</li>
2377 <li>RNA pseudoknot annotation can be
2378 imported/exported/displayed</li>
2379 <li>'colour by annotation' can colour by RNA and
2380 protein secondary structure</li>
2381 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2382 post-hoc with 2.9 release</em>)
2385 </ul> <em>Application</em>
2387 <li>Extract and display secondary structure for sequences
2388 with 3D structures</li>
2389 <li>Support for parsing RNAML</li>
2390 <li>Annotations menu for layout
2392 <li>sort sequence annotation rows by alignment</li>
2393 <li>place sequence annotation above/below alignment
2396 <li>Output in Stockholm format</li>
2397 <li>Internationalisation: improved Spanish (es)
2399 <li>Structure viewer preferences tab</li>
2400 <li>Disorder and Secondary Structure annotation tracks
2401 shared between alignments</li>
2402 <li>UCSF Chimera launch and linked highlighting from
2404 <li>Show/hide all sequence associated annotation rows for
2405 all or current selection</li>
2406 <li>disorder and secondary structure predictions
2407 available as dataset annotation</li>
2408 <li>Per-sequence rna helices colouring</li>
2411 <li>Sequence database accessions imported when fetching
2412 alignments from Rfam</li>
2413 <li>update VARNA version to 3.91</li>
2415 <li>New groovy scripts for exporting aligned positions,
2416 conservation values, and calculating sum of pairs scores.</li>
2417 <li>Command line argument to set default JABAWS server</li>
2418 <li>include installation type in build properties and
2419 console log output</li>
2420 <li>Updated Jalview project format to preserve dataset
2424 <!-- issues resolved --> <em>Application</em>
2426 <li>Distinguish alignment and sequence associated RNA
2427 structure in structure->view->VARNA</li>
2428 <li>Raise dialog box if user deletes all sequences in an
2430 <li>Pressing F1 results in documentation opening twice</li>
2431 <li>Sequence feature tooltip is wrapped</li>
2432 <li>Double click on sequence associated annotation
2433 selects only first column</li>
2434 <li>Redundancy removal doesn't result in unlinked
2435 leaves shown in tree</li>
2436 <li>Undos after several redundancy removals don't undo
2438 <li>Hide sequence doesn't hide associated annotation</li>
2439 <li>User defined colours dialog box too big to fit on
2440 screen and buttons not visible</li>
2441 <li>author list isn't updated if already written to
2442 Jalview properties</li>
2443 <li>Popup menu won't open after retrieving sequence
2445 <li>File open window for associate PDB doesn't open</li>
2446 <li>Left-then-right click on a sequence id opens a
2447 browser search window</li>
2448 <li>Cannot open sequence feature shading/sort popup menu
2449 in feature settings dialog</li>
2450 <li>better tooltip placement for some areas of Jalview
2452 <li>Allow addition of JABAWS Server which doesn't
2453 pass validation</li>
2454 <li>Web services parameters dialog box is too large to
2456 <li>Muscle nucleotide alignment preset obscured by
2458 <li>JABAWS preset submenus don't contain newly
2459 defined user preset</li>
2460 <li>MSA web services warns user if they were launched
2461 with invalid input</li>
2462 <li>Jalview cannot contact DAS Registy when running on
2465 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2466 'Superpose with' submenu not shown when new view
2470 </ul> <!-- <em>Applet</em>
2472 </ul> <em>General</em>
2474 </ul>--> <em>Deployment and Documentation</em>
2476 <li>2G and 1G options in launchApp have no effect on
2477 memory allocation</li>
2478 <li>launchApp service doesn't automatically open
2479 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2481 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2482 InstallAnywhere reports cannot find valid JVM when Java
2483 1.7_055 is available
2485 </ul> <em>Application Known issues</em>
2488 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2489 corrupted or unreadable alignment display when scrolling
2493 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2494 retrieval fails but progress bar continues for DAS retrieval
2495 with large number of ID
2498 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2499 flatfile output of visible region has incorrect sequence
2503 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2504 rna structure consensus doesn't update when secondary
2505 structure tracks are rearranged
2508 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2509 invalid rna structure positional highlighting does not
2510 highlight position of invalid base pairs
2513 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2514 out of memory errors are not raised when saving Jalview
2515 project from alignment window file menu
2518 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2519 Switching to RNA Helices colouring doesn't propagate to
2523 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2524 colour by RNA Helices not enabled when user created
2525 annotation added to alignment
2528 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2529 Jalview icon not shown on dock in Mountain Lion/Webstart
2531 </ul> <em>Applet Known Issues</em>
2534 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2535 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2539 Jalview and Jmol example not compatible with IE9
2542 <li>Sort by annotation score doesn't reverse order
2548 <td><div align="center">
2549 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2552 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2555 <li>Internationalisation of user interface (usually
2556 called i18n support) and translation for Spanish locale</li>
2557 <li>Define/Undefine group on current selection with
2558 Ctrl-G/Shift Ctrl-G</li>
2559 <li>Improved group creation/removal options in
2560 alignment/sequence Popup menu</li>
2561 <li>Sensible precision for symbol distribution
2562 percentages shown in logo tooltip.</li>
2563 <li>Annotation panel height set according to amount of
2564 annotation when alignment first opened</li>
2565 </ul> <em>Application</em>
2567 <li>Interactive consensus RNA secondary structure
2568 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2569 <li>Select columns containing particular features from
2570 Feature Settings dialog</li>
2571 <li>View all 'representative' PDB structures for selected
2573 <li>Update Jalview project format:
2575 <li>New file extension for Jalview projects '.jvp'</li>
2576 <li>Preserve sequence and annotation dataset (to
2577 store secondary structure annotation,etc)</li>
2578 <li>Per group and alignment annotation and RNA helix
2582 <li>New similarity measures for PCA and Tree calculation
2584 <li>Experimental support for retrieval and viewing of
2585 flanking regions for an alignment</li>
2589 <!-- issues resolved --> <em>Application</em>
2591 <li>logo keeps spinning and status remains at queued or
2592 running after job is cancelled</li>
2593 <li>cannot export features from alignments imported from
2594 Jalview/VAMSAS projects</li>
2595 <li>Buggy slider for web service parameters that take
2597 <li>Newly created RNA secondary structure line doesn't
2598 have 'display all symbols' flag set</li>
2599 <li>T-COFFEE alignment score shading scheme and other
2600 annotation shading not saved in Jalview project</li>
2601 <li>Local file cannot be loaded in freshly downloaded
2603 <li>Jalview icon not shown on dock in Mountain
2605 <li>Load file from desktop file browser fails</li>
2606 <li>Occasional NPE thrown when calculating large trees</li>
2607 <li>Cannot reorder or slide sequences after dragging an
2608 alignment onto desktop</li>
2609 <li>Colour by annotation dialog throws NPE after using
2610 'extract scores' function</li>
2611 <li>Loading/cut'n'pasting an empty file leads to a grey
2612 alignment window</li>
2613 <li>Disorder thresholds rendered incorrectly after
2614 performing IUPred disorder prediction</li>
2615 <li>Multiple group annotated consensus rows shown when
2616 changing 'normalise logo' display setting</li>
2617 <li>Find shows blank dialog after 'finished searching' if
2618 nothing matches query</li>
2619 <li>Null Pointer Exceptions raised when sorting by
2620 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2622 <li>Errors in Jmol console when structures in alignment
2623 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2625 <li>Not all working JABAWS services are shown in
2627 <li>JAVAWS version of Jalview fails to launch with
2628 'invalid literal/length code'</li>
2629 <li>Annotation/RNA Helix colourschemes cannot be applied
2630 to alignment with groups (actually fixed in 2.8.0b1)</li>
2631 <li>RNA Helices and T-Coffee Scores available as default
2634 </ul> <em>Applet</em>
2636 <li>Remove group option is shown even when selection is
2638 <li>Apply to all groups ticked but colourscheme changes
2639 don't affect groups</li>
2640 <li>Documented RNA Helices and T-Coffee Scores as valid
2641 colourscheme name</li>
2642 <li>Annotation labels drawn on sequence IDs when
2643 Annotation panel is not displayed</li>
2644 <li>Increased font size for dropdown menus on OSX and
2645 embedded windows</li>
2646 </ul> <em>Other</em>
2648 <li>Consensus sequence for alignments/groups with a
2649 single sequence were not calculated</li>
2650 <li>annotation files that contain only groups imported as
2651 annotation and junk sequences</li>
2652 <li>Fasta files with sequences containing '*' incorrectly
2653 recognised as PFAM or BLC</li>
2654 <li>conservation/PID slider apply all groups option
2655 doesn't affect background (2.8.0b1)
2657 <li>redundancy highlighting is erratic at 0% and 100%</li>
2658 <li>Remove gapped columns fails for sequences with ragged
2660 <li>AMSA annotation row with leading spaces is not
2661 registered correctly on import</li>
2662 <li>Jalview crashes when selecting PCA analysis for
2663 certain alignments</li>
2664 <li>Opening the colour by annotation dialog for an
2665 existing annotation based 'use original colours'
2666 colourscheme loses original colours setting</li>
2671 <td><div align="center">
2672 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2673 <em>30/1/2014</em></strong>
2677 <li>Trusted certificates for JalviewLite applet and
2678 Jalview Desktop application<br />Certificate was donated by
2679 <a href="https://www.certum.eu">Certum</a> to the Jalview
2680 open source project).
2682 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2683 <li>Output in Stockholm format</li>
2684 <li>Allow import of data from gzipped files</li>
2685 <li>Export/import group and sequence associated line
2686 graph thresholds</li>
2687 <li>Nucleotide substitution matrix that supports RNA and
2688 ambiguity codes</li>
2689 <li>Allow disorder predictions to be made on the current
2690 selection (or visible selection) in the same way that JPred
2692 <li>Groovy scripting for headless Jalview operation</li>
2693 </ul> <em>Other improvements</em>
2695 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2696 <li>COMBINE statement uses current SEQUENCE_REF and
2697 GROUP_REF scope to group annotation rows</li>
2698 <li>Support '' style escaping of quotes in Newick
2700 <li>Group options for JABAWS service by command line name</li>
2701 <li>Empty tooltip shown for JABA service options with a
2702 link but no description</li>
2703 <li>Select primary source when selecting authority in
2704 database fetcher GUI</li>
2705 <li>Add .mfa to FASTA file extensions recognised by
2707 <li>Annotation label tooltip text wrap</li>
2712 <li>Slow scrolling when lots of annotation rows are
2714 <li>Lots of NPE (and slowness) after creating RNA
2715 secondary structure annotation line</li>
2716 <li>Sequence database accessions not imported when
2717 fetching alignments from Rfam</li>
2718 <li>Incorrect SHMR submission for sequences with
2720 <li>View all structures does not always superpose
2722 <li>Option widgets in service parameters not updated to
2723 reflect user or preset settings</li>
2724 <li>Null pointer exceptions for some services without
2725 presets or adjustable parameters</li>
2726 <li>Discover PDB IDs entry in structure menu doesn't
2727 discover PDB xRefs</li>
2728 <li>Exception encountered while trying to retrieve
2729 features with DAS</li>
2730 <li>Lowest value in annotation row isn't coloured
2731 when colour by annotation (per sequence) is coloured</li>
2732 <li>Keyboard mode P jumps to start of gapped region when
2733 residue follows a gap</li>
2734 <li>Jalview appears to hang importing an alignment with
2735 Wrap as default or after enabling Wrap</li>
2736 <li>'Right click to add annotations' message
2737 shown in wrap mode when no annotations present</li>
2738 <li>Disorder predictions fail with NPE if no automatic
2739 annotation already exists on alignment</li>
2740 <li>oninit javascript function should be called after
2741 initialisation completes</li>
2742 <li>Remove redundancy after disorder prediction corrupts
2743 alignment window display</li>
2744 <li>Example annotation file in documentation is invalid</li>
2745 <li>Grouped line graph annotation rows are not exported
2746 to annotation file</li>
2747 <li>Multi-harmony analysis cannot be run when only two
2749 <li>Cannot create multiple groups of line graphs with
2750 several 'combine' statements in annotation file</li>
2751 <li>Pressing return several times causes Number Format
2752 exceptions in keyboard mode</li>
2753 <li>Multi-harmony (SHMMR) method doesn't submit
2754 correct partitions for input data</li>
2755 <li>Translation from DNA to Amino Acids fails</li>
2756 <li>Jalview fail to load newick tree with quoted label</li>
2757 <li>--headless flag isn't understood</li>
2758 <li>ClassCastException when generating EPS in headless
2760 <li>Adjusting sequence-associated shading threshold only
2761 changes one row's threshold</li>
2762 <li>Preferences and Feature settings panel panel
2763 doesn't open</li>
2764 <li>hide consensus histogram also hides conservation and
2765 quality histograms</li>
2770 <td><div align="center">
2771 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2773 <td><em>Application</em>
2775 <li>Support for JABAWS 2.0 Services (AACon alignment
2776 conservation, protein disorder and Clustal Omega)</li>
2777 <li>JABAWS server status indicator in Web Services
2779 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2780 in Jalview alignment window</li>
2781 <li>Updated Jalview build and deploy framework for OSX
2782 mountain lion, windows 7, and 8</li>
2783 <li>Nucleotide substitution matrix for PCA that supports
2784 RNA and ambiguity codes</li>
2786 <li>Improved sequence database retrieval GUI</li>
2787 <li>Support fetching and database reference look up
2788 against multiple DAS sources (Fetch all from in 'fetch db
2790 <li>Jalview project improvements
2792 <li>Store and retrieve the 'belowAlignment'
2793 flag for annotation</li>
2794 <li>calcId attribute to group annotation rows on the
2796 <li>Store AACon calculation settings for a view in
2797 Jalview project</li>
2801 <li>horizontal scrolling gesture support</li>
2802 <li>Visual progress indicator when PCA calculation is
2804 <li>Simpler JABA web services menus</li>
2805 <li>visual indication that web service results are still
2806 being retrieved from server</li>
2807 <li>Serialise the dialogs that are shown when Jalview
2808 starts up for first time</li>
2809 <li>Jalview user agent string for interacting with HTTP
2811 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2813 <li>Examples directory and Groovy library included in
2814 InstallAnywhere distribution</li>
2815 </ul> <em>Applet</em>
2817 <li>RNA alignment and secondary structure annotation
2818 visualization applet example</li>
2819 </ul> <em>General</em>
2821 <li>Normalise option for consensus sequence logo</li>
2822 <li>Reset button in PCA window to return dimensions to
2824 <li>Allow seqspace or Jalview variant of alignment PCA
2826 <li>PCA with either nucleic acid and protein substitution
2828 <li>Allow windows containing HTML reports to be exported
2830 <li>Interactive display and editing of RNA secondary
2831 structure contacts</li>
2832 <li>RNA Helix Alignment Colouring</li>
2833 <li>RNA base pair logo consensus</li>
2834 <li>Parse sequence associated secondary structure
2835 information in Stockholm files</li>
2836 <li>HTML Export database accessions and annotation
2837 information presented in tooltip for sequences</li>
2838 <li>Import secondary structure from LOCARNA clustalw
2839 style RNA alignment files</li>
2840 <li>import and visualise T-COFFEE quality scores for an
2842 <li>'colour by annotation' per sequence option to
2843 shade each sequence according to its associated alignment
2845 <li>New Jalview Logo</li>
2846 </ul> <em>Documentation and Development</em>
2848 <li>documentation for score matrices used in Jalview</li>
2849 <li>New Website!</li>
2851 <td><em>Application</em>
2853 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2854 wsdbfetch REST service</li>
2855 <li>Stop windows being moved outside desktop on OSX</li>
2856 <li>Filetype associations not installed for webstart
2858 <li>Jalview does not always retrieve progress of a JABAWS
2859 job execution in full once it is complete</li>
2860 <li>revise SHMR RSBS definition to ensure alignment is
2861 uploaded via ali_file parameter</li>
2862 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2863 <li>View all structures superposed fails with exception</li>
2864 <li>Jnet job queues forever if a very short sequence is
2865 submitted for prediction</li>
2866 <li>Cut and paste menu not opened when mouse clicked on
2868 <li>Putting fractional value into integer text box in
2869 alignment parameter dialog causes Jalview to hang</li>
2870 <li>Structure view highlighting doesn't work on
2872 <li>View all structures fails with exception shown in
2874 <li>Characters in filename associated with PDBEntry not
2875 escaped in a platform independent way</li>
2876 <li>Jalview desktop fails to launch with exception when
2878 <li>Tree calculation reports 'you must have 2 or more
2879 sequences selected' when selection is empty</li>
2880 <li>Jalview desktop fails to launch with jar signature
2881 failure when java web start temporary file caching is
2883 <li>DAS Sequence retrieval with range qualification
2884 results in sequence xref which includes range qualification</li>
2885 <li>Errors during processing of command line arguments
2886 cause progress bar (JAL-898) to be removed</li>
2887 <li>Replace comma for semi-colon option not disabled for
2888 DAS sources in sequence fetcher</li>
2889 <li>Cannot close news reader when JABAWS server warning
2890 dialog is shown</li>
2891 <li>Option widgets not updated to reflect user settings</li>
2892 <li>Edited sequence not submitted to web service</li>
2893 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2894 <li>InstallAnywhere installer doesn't unpack and run
2895 on OSX Mountain Lion</li>
2896 <li>Annotation panel not given a scroll bar when
2897 sequences with alignment annotation are pasted into the
2899 <li>Sequence associated annotation rows not associated
2900 when loaded from Jalview project</li>
2901 <li>Browser launch fails with NPE on java 1.7</li>
2902 <li>JABAWS alignment marked as finished when job was
2903 cancelled or job failed due to invalid input</li>
2904 <li>NPE with v2.7 example when clicking on Tree
2905 associated with all views</li>
2906 <li>Exceptions when copy/paste sequences with grouped
2907 annotation rows to new window</li>
2908 </ul> <em>Applet</em>
2910 <li>Sequence features are momentarily displayed before
2911 they are hidden using hidefeaturegroups applet parameter</li>
2912 <li>loading features via javascript API automatically
2913 enables feature display</li>
2914 <li>scrollToColumnIn javascript API method doesn't
2916 </ul> <em>General</em>
2918 <li>Redundancy removal fails for rna alignment</li>
2919 <li>PCA calculation fails when sequence has been selected
2920 and then deselected</li>
2921 <li>PCA window shows grey box when first opened on OSX</li>
2922 <li>Letters coloured pink in sequence logo when alignment
2923 coloured with clustalx</li>
2924 <li>Choosing fonts without letter symbols defined causes
2925 exceptions and redraw errors</li>
2926 <li>Initial PCA plot view is not same as manually
2927 reconfigured view</li>
2928 <li>Grouped annotation graph label has incorrect line
2930 <li>Grouped annotation graph label display is corrupted
2931 for lots of labels</li>
2936 <div align="center">
2937 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2940 <td><em>Application</em>
2942 <li>Jalview Desktop News Reader</li>
2943 <li>Tweaked default layout of web services menu</li>
2944 <li>View/alignment association menu to enable user to
2945 easily specify which alignment a multi-structure view takes
2946 its colours/correspondences from</li>
2947 <li>Allow properties file location to be specified as URL</li>
2948 <li>Extend Jalview project to preserve associations
2949 between many alignment views and a single Jmol display</li>
2950 <li>Store annotation row height in Jalview project file</li>
2951 <li>Annotation row column label formatting attributes
2952 stored in project file</li>
2953 <li>Annotation row order for auto-calculated annotation
2954 rows preserved in Jalview project file</li>
2955 <li>Visual progress indication when Jalview state is
2956 saved using Desktop window menu</li>
2957 <li>Visual indication that command line arguments are
2958 still being processed</li>
2959 <li>Groovy script execution from URL</li>
2960 <li>Colour by annotation default min and max colours in
2962 <li>Automatically associate PDB files dragged onto an
2963 alignment with sequences that have high similarity and
2965 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2966 <li>'view structures' option to open many
2967 structures in same window</li>
2968 <li>Sort associated views menu option for tree panel</li>
2969 <li>Group all JABA and non-JABA services for a particular
2970 analysis function in its own submenu</li>
2971 </ul> <em>Applet</em>
2973 <li>Userdefined and autogenerated annotation rows for
2975 <li>Adjustment of alignment annotation pane height</li>
2976 <li>Annotation scrollbar for annotation panel</li>
2977 <li>Drag to reorder annotation rows in annotation panel</li>
2978 <li>'automaticScrolling' parameter</li>
2979 <li>Allow sequences with partial ID string matches to be
2980 annotated from GFF/Jalview features files</li>
2981 <li>Sequence logo annotation row in applet</li>
2982 <li>Absolute paths relative to host server in applet
2983 parameters are treated as such</li>
2984 <li>New in the JalviewLite javascript API:
2986 <li>JalviewLite.js javascript library</li>
2987 <li>Javascript callbacks for
2989 <li>Applet initialisation</li>
2990 <li>Sequence/alignment mouse-overs and selections</li>
2993 <li>scrollTo row and column alignment scrolling
2995 <li>Select sequence/alignment regions from javascript</li>
2996 <li>javascript structure viewer harness to pass
2997 messages between Jmol and Jalview when running as
2998 distinct applets</li>
2999 <li>sortBy method</li>
3000 <li>Set of applet and application examples shipped
3001 with documentation</li>
3002 <li>New example to demonstrate JalviewLite and Jmol
3003 javascript message exchange</li>
3005 </ul> <em>General</em>
3007 <li>Enable Jmol displays to be associated with multiple
3008 multiple alignments</li>
3009 <li>Option to automatically sort alignment with new tree</li>
3010 <li>User configurable link to enable redirects to a
3011 www.Jalview.org mirror</li>
3012 <li>Jmol colours option for Jmol displays</li>
3013 <li>Configurable newline string when writing alignment
3014 and other flat files</li>
3015 <li>Allow alignment annotation description lines to
3016 contain html tags</li>
3017 </ul> <em>Documentation and Development</em>
3019 <li>Add groovy test harness for bulk load testing to
3021 <li>Groovy script to load and align a set of sequences
3022 using a web service before displaying the result in the
3023 Jalview desktop</li>
3024 <li>Restructured javascript and applet api documentation</li>
3025 <li>Ant target to publish example html files with applet
3027 <li>Netbeans project for building Jalview from source</li>
3028 <li>ant task to create online javadoc for Jalview source</li>
3030 <td><em>Application</em>
3032 <li>User defined colourscheme throws exception when
3033 current built in colourscheme is saved as new scheme</li>
3034 <li>AlignFrame->Save in application pops up save
3035 dialog for valid filename/format</li>
3036 <li>Cannot view associated structure for UniProt sequence</li>
3037 <li>PDB file association breaks for UniProt sequence
3039 <li>Associate PDB from file dialog does not tell you
3040 which sequence is to be associated with the file</li>
3041 <li>Find All raises null pointer exception when query
3042 only matches sequence IDs</li>
3043 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3044 <li>Jalview project with Jmol views created with Jalview
3045 2.4 cannot be loaded</li>
3046 <li>Filetype associations not installed for webstart
3048 <li>Two or more chains in a single PDB file associated
3049 with sequences in different alignments do not get coloured
3050 by their associated sequence</li>
3051 <li>Visibility status of autocalculated annotation row
3052 not preserved when project is loaded</li>
3053 <li>Annotation row height and visibility attributes not
3054 stored in Jalview project</li>
3055 <li>Tree bootstraps are not preserved when saved as a
3056 Jalview project</li>
3057 <li>Envision2 workflow tooltips are corrupted</li>
3058 <li>Enabling show group conservation also enables colour
3059 by conservation</li>
3060 <li>Duplicate group associated conservation or consensus
3061 created on new view</li>
3062 <li>Annotation scrollbar not displayed after 'show
3063 all hidden annotation rows' option selected</li>
3064 <li>Alignment quality not updated after alignment
3065 annotation row is hidden then shown</li>
3066 <li>Preserve colouring of structures coloured by
3067 sequences in pre Jalview 2.7 projects</li>
3068 <li>Web service job parameter dialog is not laid out
3070 <li>Web services menu not refreshed after 'reset
3071 services' button is pressed in preferences</li>
3072 <li>Annotation off by one in Jalview v2_3 example project</li>
3073 <li>Structures imported from file and saved in project
3074 get name like jalview_pdb1234.txt when reloaded</li>
3075 <li>Jalview does not always retrieve progress of a JABAWS
3076 job execution in full once it is complete</li>
3077 </ul> <em>Applet</em>
3079 <li>Alignment height set incorrectly when lots of
3080 annotation rows are displayed</li>
3081 <li>Relative URLs in feature HTML text not resolved to
3083 <li>View follows highlighting does not work for positions
3085 <li><= shown as = in tooltip</li>
3086 <li>Export features raises exception when no features
3088 <li>Separator string used for serialising lists of IDs
3089 for javascript api is modified when separator string
3090 provided as parameter</li>
3091 <li>Null pointer exception when selecting tree leaves for
3092 alignment with no existing selection</li>
3093 <li>Relative URLs for datasources assumed to be relative
3094 to applet's codebase</li>
3095 <li>Status bar not updated after finished searching and
3096 search wraps around to first result</li>
3097 <li>StructureSelectionManager instance shared between
3098 several Jalview applets causes race conditions and memory
3100 <li>Hover tooltip and mouseover of position on structure
3101 not sent from Jmol in applet</li>
3102 <li>Certain sequences of javascript method calls to
3103 applet API fatally hang browser</li>
3104 </ul> <em>General</em>
3106 <li>View follows structure mouseover scrolls beyond
3107 position with wrapped view and hidden regions</li>
3108 <li>Find sequence position moves to wrong residue
3109 with/without hidden columns</li>
3110 <li>Sequence length given in alignment properties window
3112 <li>InvalidNumberFormat exceptions thrown when trying to
3113 import PDB like structure files</li>
3114 <li>Positional search results are only highlighted
3115 between user-supplied sequence start/end bounds</li>
3116 <li>End attribute of sequence is not validated</li>
3117 <li>Find dialog only finds first sequence containing a
3118 given sequence position</li>
3119 <li>Sequence numbering not preserved in MSF alignment
3121 <li>Jalview PDB file reader does not extract sequence
3122 from nucleotide chains correctly</li>
3123 <li>Structure colours not updated when tree partition
3124 changed in alignment</li>
3125 <li>Sequence associated secondary structure not correctly
3126 parsed in interleaved stockholm</li>
3127 <li>Colour by annotation dialog does not restore current
3129 <li>Hiding (nearly) all sequences doesn't work
3131 <li>Sequences containing lowercase letters are not
3132 properly associated with their pdb files</li>
3133 </ul> <em>Documentation and Development</em>
3135 <li>schemas/JalviewWsParamSet.xsd corrupted by
3136 ApplyCopyright tool</li>
3141 <div align="center">
3142 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3145 <td><em>Application</em>
3147 <li>New warning dialog when the Jalview Desktop cannot
3148 contact web services</li>
3149 <li>JABA service parameters for a preset are shown in
3150 service job window</li>
3151 <li>JABA Service menu entries reworded</li>
3155 <li>Modeller PIR IO broken - cannot correctly import a
3156 pir file emitted by Jalview</li>
3157 <li>Existing feature settings transferred to new
3158 alignment view created from cut'n'paste</li>
3159 <li>Improved test for mixed amino/nucleotide chains when
3160 parsing PDB files</li>
3161 <li>Consensus and conservation annotation rows
3162 occasionally become blank for all new windows</li>
3163 <li>Exception raised when right clicking above sequences
3164 in wrapped view mode</li>
3165 </ul> <em>Application</em>
3167 <li>multiple multiply aligned structure views cause cpu
3168 usage to hit 100% and computer to hang</li>
3169 <li>Web Service parameter layout breaks for long user
3170 parameter names</li>
3171 <li>Jaba service discovery hangs desktop if Jaba server
3178 <div align="center">
3179 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3182 <td><em>Application</em>
3184 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3185 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3188 <li>Web Services preference tab</li>
3189 <li>Analysis parameters dialog box and user defined
3191 <li>Improved speed and layout of Envision2 service menu</li>
3192 <li>Superpose structures using associated sequence
3194 <li>Export coordinates and projection as CSV from PCA
3196 </ul> <em>Applet</em>
3198 <li>enable javascript: execution by the applet via the
3199 link out mechanism</li>
3200 </ul> <em>Other</em>
3202 <li>Updated the Jmol Jalview interface to work with Jmol
3204 <li>The Jalview Desktop and JalviewLite applet now
3205 require Java 1.5</li>
3206 <li>Allow Jalview feature colour specification for GFF
3207 sequence annotation files</li>
3208 <li>New 'colour by label' keword in Jalview feature file
3209 type colour specification</li>
3210 <li>New Jalview Desktop Groovy API method that allows a
3211 script to check if it being run in an interactive session or
3212 in a batch operation from the Jalview command line</li>
3216 <li>clustalx colourscheme colours Ds preferentially when
3217 both D+E are present in over 50% of the column</li>
3218 </ul> <em>Application</em>
3220 <li>typo in AlignmentFrame->View->Hide->all but
3221 selected Regions menu item</li>
3222 <li>sequence fetcher replaces ',' for ';' when the ',' is
3223 part of a valid accession ID</li>
3224 <li>fatal OOM if object retrieved by sequence fetcher
3225 runs out of memory</li>
3226 <li>unhandled Out of Memory Error when viewing pca
3227 analysis results</li>
3228 <li>InstallAnywhere builds fail to launch on OS X java
3229 10.5 update 4 (due to apple Java 1.6 update)</li>
3230 <li>Installanywhere Jalview silently fails to launch</li>
3231 </ul> <em>Applet</em>
3233 <li>Jalview.getFeatureGroups() raises an
3234 ArrayIndexOutOfBoundsException if no feature groups are
3241 <div align="center">
3242 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3248 <li>Alignment prettyprinter doesn't cope with long
3250 <li>clustalx colourscheme colours Ds preferentially when
3251 both D+E are present in over 50% of the column</li>
3252 <li>nucleic acid structures retrieved from PDB do not
3253 import correctly</li>
3254 <li>More columns get selected than were clicked on when a
3255 number of columns are hidden</li>
3256 <li>annotation label popup menu not providing correct
3257 add/hide/show options when rows are hidden or none are
3259 <li>Stockholm format shown in list of readable formats,
3260 and parser copes better with alignments from RFAM.</li>
3261 <li>CSV output of consensus only includes the percentage
3262 of all symbols if sequence logo display is enabled</li>
3264 </ul> <em>Applet</em>
3266 <li>annotation panel disappears when annotation is
3268 </ul> <em>Application</em>
3270 <li>Alignment view not redrawn properly when new
3271 alignment opened where annotation panel is visible but no
3272 annotations are present on alignment</li>
3273 <li>pasted region containing hidden columns is
3274 incorrectly displayed in new alignment window</li>
3275 <li>Jalview slow to complete operations when stdout is
3276 flooded (fix is to close the Jalview console)</li>
3277 <li>typo in AlignmentFrame->View->Hide->all but
3278 selected Rregions menu item.</li>
3279 <li>inconsistent group submenu and Format submenu entry
3280 'Un' or 'Non'conserved</li>
3281 <li>Sequence feature settings are being shared by
3282 multiple distinct alignments</li>
3283 <li>group annotation not recreated when tree partition is
3285 <li>double click on group annotation to select sequences
3286 does not propagate to associated trees</li>
3287 <li>Mac OSX specific issues:
3289 <li>exception raised when mouse clicked on desktop
3290 window background</li>
3291 <li>Desktop menu placed on menu bar and application
3292 name set correctly</li>
3293 <li>sequence feature settings not wide enough for the
3294 save feature colourscheme button</li>
3303 <div align="center">
3304 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3307 <td><em>New Capabilities</em>
3309 <li>URL links generated from description line for
3310 regular-expression based URL links (applet and application)
3312 <li>Non-positional feature URL links are shown in link
3314 <li>Linked viewing of nucleic acid sequences and
3316 <li>Automatic Scrolling option in View menu to display
3317 the currently highlighted region of an alignment.</li>
3318 <li>Order an alignment by sequence length, or using the
3319 average score or total feature count for each sequence.</li>
3320 <li>Shading features by score or associated description</li>
3321 <li>Subdivide alignment and groups based on identity of
3322 selected subsequence (Make Groups from Selection).</li>
3323 <li>New hide/show options including Shift+Control+H to
3324 hide everything but the currently selected region.</li>
3325 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3326 </ul> <em>Application</em>
3328 <li>Fetch DB References capabilities and UI expanded to
3329 support retrieval from DAS sequence sources</li>
3330 <li>Local DAS Sequence sources can be added via the
3331 command line or via the Add local source dialog box.</li>
3332 <li>DAS Dbref and DbxRef feature types are parsed as
3333 database references and protein_name is parsed as
3334 description line (BioSapiens terms).</li>
3335 <li>Enable or disable non-positional feature and database
3336 references in sequence ID tooltip from View menu in
3338 <!-- <li>New hidden columns and rows and representatives capabilities
3339 in annotations file (in progress - not yet fully implemented)</li> -->
3340 <li>Group-associated consensus, sequence logos and
3341 conservation plots</li>
3342 <li>Symbol distributions for each column can be exported
3343 and visualized as sequence logos</li>
3344 <li>Optionally scale multi-character column labels to fit
3345 within each column of annotation row<!-- todo for applet -->
3347 <li>Optional automatic sort of associated alignment view
3348 when a new tree is opened.</li>
3349 <li>Jalview Java Console</li>
3350 <li>Better placement of desktop window when moving
3351 between different screens.</li>
3352 <li>New preference items for sequence ID tooltip and
3353 consensus annotation</li>
3354 <li>Client to submit sequences and IDs to Envision2
3356 <li><em>Vamsas Capabilities</em>
3358 <li>Improved VAMSAS synchronization (Jalview archive
3359 used to preserve views, structures, and tree display
3361 <li>Import of vamsas documents from disk or URL via
3363 <li>Sharing of selected regions between views and
3364 with other VAMSAS applications (Experimental feature!)</li>
3365 <li>Updated API to VAMSAS version 0.2</li>
3367 </ul> <em>Applet</em>
3369 <li>Middle button resizes annotation row height</li>
3372 <li>sortByTree (true/false) - automatically sort the
3373 associated alignment view by the tree when a new tree is
3375 <li>showTreeBootstraps (true/false) - show or hide
3376 branch bootstraps (default is to show them if available)</li>
3377 <li>showTreeDistances (true/false) - show or hide
3378 branch lengths (default is to show them if available)</li>
3379 <li>showUnlinkedTreeNodes (true/false) - indicate if
3380 unassociated nodes should be highlighted in the tree
3382 <li>heightScale and widthScale (1.0 or more) -
3383 increase the height or width of a cell in the alignment
3384 grid relative to the current font size.</li>
3387 <li>Non-positional features displayed in sequence ID
3389 </ul> <em>Other</em>
3391 <li>Features format: graduated colour definitions and
3392 specification of feature scores</li>
3393 <li>Alignment Annotations format: new keywords for group
3394 associated annotation (GROUP_REF) and annotation row display
3395 properties (ROW_PROPERTIES)</li>
3396 <li>XML formats extended to support graduated feature
3397 colourschemes, group associated annotation, and profile
3398 visualization settings.</li></td>
3401 <li>Source field in GFF files parsed as feature source
3402 rather than description</li>
3403 <li>Non-positional features are now included in sequence
3404 feature and gff files (controlled via non-positional feature
3405 visibility in tooltip).</li>
3406 <li>URL links generated for all feature links (bugfix)</li>
3407 <li>Added URL embedding instructions to features file
3409 <li>Codons containing ambiguous nucleotides translated as
3410 'X' in peptide product</li>
3411 <li>Match case switch in find dialog box works for both
3412 sequence ID and sequence string and query strings do not
3413 have to be in upper case to match case-insensitively.</li>
3414 <li>AMSA files only contain first column of
3415 multi-character column annotation labels</li>
3416 <li>Jalview Annotation File generation/parsing consistent
3417 with documentation (e.g. Stockholm annotation can be
3418 exported and re-imported)</li>
3419 <li>PDB files without embedded PDB IDs given a friendly
3421 <li>Find incrementally searches ID string matches as well
3422 as subsequence matches, and correctly reports total number
3426 <li>Better handling of exceptions during sequence
3428 <li>Dasobert generated non-positional feature URL
3429 link text excludes the start_end suffix</li>
3430 <li>DAS feature and source retrieval buttons disabled
3431 when fetch or registry operations in progress.</li>
3432 <li>PDB files retrieved from URLs are cached properly</li>
3433 <li>Sequence description lines properly shared via
3435 <li>Sequence fetcher fetches multiple records for all
3437 <li>Ensured that command line das feature retrieval
3438 completes before alignment figures are generated.</li>
3439 <li>Reduced time taken when opening file browser for
3441 <li>isAligned check prior to calculating tree, PCA or
3442 submitting an MSA to JNet now excludes hidden sequences.</li>
3443 <li>User defined group colours properly recovered
3444 from Jalview projects.</li>
3453 <div align="center">
3454 <strong>2.4.0.b2</strong><br> 28/10/2009
3459 <li>Experimental support for google analytics usage
3461 <li>Jalview privacy settings (user preferences and docs).</li>
3466 <li>Race condition in applet preventing startup in
3468 <li>Exception when feature created from selection beyond
3469 length of sequence.</li>
3470 <li>Allow synthetic PDB files to be imported gracefully</li>
3471 <li>Sequence associated annotation rows associate with
3472 all sequences with a given id</li>
3473 <li>Find function matches case-insensitively for sequence
3474 ID string searches</li>
3475 <li>Non-standard characters do not cause pairwise
3476 alignment to fail with exception</li>
3477 </ul> <em>Application Issues</em>
3479 <li>Sequences are now validated against EMBL database</li>
3480 <li>Sequence fetcher fetches multiple records for all
3482 </ul> <em>InstallAnywhere Issues</em>
3484 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3485 issue with installAnywhere mechanism)</li>
3486 <li>Command line launching of JARs from InstallAnywhere
3487 version (java class versioning error fixed)</li>
3494 <div align="center">
3495 <strong>2.4</strong><br> 27/8/2008
3498 <td><em>User Interface</em>
3500 <li>Linked highlighting of codon and amino acid from
3501 translation and protein products</li>
3502 <li>Linked highlighting of structure associated with
3503 residue mapping to codon position</li>
3504 <li>Sequence Fetcher provides example accession numbers
3505 and 'clear' button</li>
3506 <li>MemoryMonitor added as an option under Desktop's
3508 <li>Extract score function to parse whitespace separated
3509 numeric data in description line</li>
3510 <li>Column labels in alignment annotation can be centred.</li>
3511 <li>Tooltip for sequence associated annotation give name
3513 </ul> <em>Web Services and URL fetching</em>
3515 <li>JPred3 web service</li>
3516 <li>Prototype sequence search client (no public services
3518 <li>Fetch either seed alignment or full alignment from
3520 <li>URL Links created for matching database cross
3521 references as well as sequence ID</li>
3522 <li>URL Links can be created using regular-expressions</li>
3523 </ul> <em>Sequence Database Connectivity</em>
3525 <li>Retrieval of cross-referenced sequences from other
3527 <li>Generalised database reference retrieval and
3528 validation to all fetchable databases</li>
3529 <li>Fetch sequences from DAS sources supporting the
3530 sequence command</li>
3531 </ul> <em>Import and Export</em>
3532 <li>export annotation rows as CSV for spreadsheet import</li>
3533 <li>Jalview projects record alignment dataset associations,
3534 EMBL products, and cDNA sequence mappings</li>
3535 <li>Sequence Group colour can be specified in Annotation
3537 <li>Ad-hoc colouring of group in Annotation File using RGB
3538 triplet as name of colourscheme</li>
3539 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3541 <li>treenode binding for VAMSAS tree exchange</li>
3542 <li>local editing and update of sequences in VAMSAS
3543 alignments (experimental)</li>
3544 <li>Create new or select existing session to join</li>
3545 <li>load and save of vamsas documents</li>
3546 </ul> <em>Application command line</em>
3548 <li>-tree parameter to open trees (introduced for passing
3550 <li>-fetchfrom command line argument to specify nicknames
3551 of DAS servers to query for alignment features</li>
3552 <li>-dasserver command line argument to add new servers
3553 that are also automatically queried for features</li>
3554 <li>-groovy command line argument executes a given groovy
3555 script after all input data has been loaded and parsed</li>
3556 </ul> <em>Applet-Application data exchange</em>
3558 <li>Trees passed as applet parameters can be passed to
3559 application (when using "View in full
3560 application")</li>
3561 </ul> <em>Applet Parameters</em>
3563 <li>feature group display control parameter</li>
3564 <li>debug parameter</li>
3565 <li>showbutton parameter</li>
3566 </ul> <em>Applet API methods</em>
3568 <li>newView public method</li>
3569 <li>Window (current view) specific get/set public methods</li>
3570 <li>Feature display control methods</li>
3571 <li>get list of currently selected sequences</li>
3572 </ul> <em>New Jalview distribution features</em>
3574 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3575 <li>RELEASE file gives build properties for the latest
3576 Jalview release.</li>
3577 <li>Java 1.1 Applet build made easier and donotobfuscate
3578 property controls execution of obfuscator</li>
3579 <li>Build target for generating source distribution</li>
3580 <li>Debug flag for javacc</li>
3581 <li>.jalview_properties file is documented (slightly) in
3582 jalview.bin.Cache</li>
3583 <li>Continuous Build Integration for stable and
3584 development version of Application, Applet and source
3589 <li>selected region output includes visible annotations
3590 (for certain formats)</li>
3591 <li>edit label/displaychar contains existing label/char
3593 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3594 <li>shorter peptide product names from EMBL records</li>
3595 <li>Newick string generator makes compact representations</li>
3596 <li>bootstrap values parsed correctly for tree files with
3598 <li>pathological filechooser bug avoided by not allowing
3599 filenames containing a ':'</li>
3600 <li>Fixed exception when parsing GFF files containing
3601 global sequence features</li>
3602 <li>Alignment datasets are finalized only when number of
3603 references from alignment sequences goes to zero</li>
3604 <li>Close of tree branch colour box without colour
3605 selection causes cascading exceptions</li>
3606 <li>occasional negative imgwidth exceptions</li>
3607 <li>better reporting of non-fatal warnings to user when
3608 file parsing fails.</li>
3609 <li>Save works when Jalview project is default format</li>
3610 <li>Save as dialog opened if current alignment format is
3611 not a valid output format</li>
3612 <li>UniProt canonical names introduced for both das and
3614 <li>Histidine should be midblue (not pink!) in Zappo</li>
3615 <li>error messages passed up and output when data read
3617 <li>edit undo recovers previous dataset sequence when
3618 sequence is edited</li>
3619 <li>allow PDB files without pdb ID HEADER lines (like
3620 those generated by MODELLER) to be read in properly</li>
3621 <li>allow reading of JPred concise files as a normal
3623 <li>Stockholm annotation parsing and alignment properties
3624 import fixed for PFAM records</li>
3625 <li>Structure view windows have correct name in Desktop
3627 <li>annotation consisting of sequence associated scores
3628 can be read and written correctly to annotation file</li>
3629 <li>Aligned cDNA translation to aligned peptide works
3631 <li>Fixed display of hidden sequence markers and
3632 non-italic font for representatives in Applet</li>
3633 <li>Applet Menus are always embedded in applet window on
3635 <li>Newly shown features appear at top of stack (in
3637 <li>Annotations added via parameter not drawn properly
3638 due to null pointer exceptions</li>
3639 <li>Secondary structure lines are drawn starting from
3640 first column of alignment</li>
3641 <li>UniProt XML import updated for new schema release in
3643 <li>Sequence feature to sequence ID match for Features
3644 file is case-insensitive</li>
3645 <li>Sequence features read from Features file appended to
3646 all sequences with matching IDs</li>
3647 <li>PDB structure coloured correctly for associated views
3648 containing a sub-sequence</li>
3649 <li>PDB files can be retrieved by applet from Jar files</li>
3650 <li>feature and annotation file applet parameters
3651 referring to different directories are retrieved correctly</li>
3652 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3653 <li>Fixed application hang whilst waiting for
3654 splash-screen version check to complete</li>
3655 <li>Applet properly URLencodes input parameter values
3656 when passing them to the launchApp service</li>
3657 <li>display name and local features preserved in results
3658 retrieved from web service</li>
3659 <li>Visual delay indication for sequence retrieval and
3660 sequence fetcher initialisation</li>
3661 <li>updated Application to use DAS 1.53e version of
3662 dasobert DAS client</li>
3663 <li>Re-instated Full AMSA support and .amsa file
3665 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3673 <div align="center">
3674 <strong>2.3</strong><br> 9/5/07
3679 <li>Jmol 11.0.2 integration</li>
3680 <li>PDB views stored in Jalview XML files</li>
3681 <li>Slide sequences</li>
3682 <li>Edit sequence in place</li>
3683 <li>EMBL CDS features</li>
3684 <li>DAS Feature mapping</li>
3685 <li>Feature ordering</li>
3686 <li>Alignment Properties</li>
3687 <li>Annotation Scores</li>
3688 <li>Sort by scores</li>
3689 <li>Feature/annotation editing in applet</li>
3694 <li>Headless state operation in 2.2.1</li>
3695 <li>Incorrect and unstable DNA pairwise alignment</li>
3696 <li>Cut and paste of sequences with annotation</li>
3697 <li>Feature group display state in XML</li>
3698 <li>Feature ordering in XML</li>
3699 <li>blc file iteration selection using filename # suffix</li>
3700 <li>Stockholm alignment properties</li>
3701 <li>Stockhom alignment secondary structure annotation</li>
3702 <li>2.2.1 applet had no feature transparency</li>
3703 <li>Number pad keys can be used in cursor mode</li>
3704 <li>Structure Viewer mirror image resolved</li>
3711 <div align="center">
3712 <strong>2.2.1</strong><br> 12/2/07
3717 <li>Non standard characters can be read and displayed
3718 <li>Annotations/Features can be imported/exported to the
3720 <li>Applet allows editing of sequence/annotation/group
3721 name & description
3722 <li>Preference setting to display sequence name in
3724 <li>Annotation file format extended to allow
3725 Sequence_groups to be defined
3726 <li>Default opening of alignment overview panel can be
3727 specified in preferences
3728 <li>PDB residue numbering annotation added to associated
3734 <li>Applet crash under certain Linux OS with Java 1.6
3736 <li>Annotation file export / import bugs fixed
3737 <li>PNG / EPS image output bugs fixed
3743 <div align="center">
3744 <strong>2.2</strong><br> 27/11/06
3749 <li>Multiple views on alignment
3750 <li>Sequence feature editing
3751 <li>"Reload" alignment
3752 <li>"Save" to current filename
3753 <li>Background dependent text colour
3754 <li>Right align sequence ids
3755 <li>User-defined lower case residue colours
3758 <li>Menu item accelerator keys
3759 <li>Control-V pastes to current alignment
3760 <li>Cancel button for DAS Feature Fetching
3761 <li>PCA and PDB Viewers zoom via mouse roller
3762 <li>User-defined sub-tree colours and sub-tree selection
3764 <li>'New Window' button on the 'Output to Text box'
3769 <li>New memory efficient Undo/Redo System
3770 <li>Optimised symbol lookups and conservation/consensus
3772 <li>Region Conservation/Consensus recalculated after
3774 <li>Fixed Remove Empty Columns Bug (empty columns at end
3776 <li>Slowed DAS Feature Fetching for increased robustness.
3778 <li>Made angle brackets in ASCII feature descriptions
3780 <li>Re-instated Zoom function for PCA
3781 <li>Sequence descriptions conserved in web service
3783 <li>UniProt ID discoverer uses any word separated by
3785 <li>WsDbFetch query/result association resolved
3786 <li>Tree leaf to sequence mapping improved
3787 <li>Smooth fonts switch moved to FontChooser dialog box.
3794 <div align="center">
3795 <strong>2.1.1</strong><br> 12/9/06
3800 <li>Copy consensus sequence to clipboard</li>
3805 <li>Image output - rightmost residues are rendered if
3806 sequence id panel has been resized</li>
3807 <li>Image output - all offscreen group boundaries are
3809 <li>Annotation files with sequence references - all
3810 elements in file are relative to sequence position</li>
3811 <li>Mac Applet users can use Alt key for group editing</li>
3817 <div align="center">
3818 <strong>2.1</strong><br> 22/8/06
3823 <li>MAFFT Multiple Alignment in default Web Service list</li>
3824 <li>DAS Feature fetching</li>
3825 <li>Hide sequences and columns</li>
3826 <li>Export Annotations and Features</li>
3827 <li>GFF file reading / writing</li>
3828 <li>Associate structures with sequences from local PDB
3830 <li>Add sequences to exisiting alignment</li>
3831 <li>Recently opened files / URL lists</li>
3832 <li>Applet can launch the full application</li>
3833 <li>Applet has transparency for features (Java 1.2
3835 <li>Applet has user defined colours parameter</li>
3836 <li>Applet can load sequences from parameter
3837 "sequence<em>x</em>"
3843 <li>Redundancy Panel reinstalled in the Applet</li>
3844 <li>Monospaced font - EPS / rescaling bug fixed</li>
3845 <li>Annotation files with sequence references bug fixed</li>
3851 <div align="center">
3852 <strong>2.08.1</strong><br> 2/5/06
3857 <li>Change case of selected region from Popup menu</li>
3858 <li>Choose to match case when searching</li>
3859 <li>Middle mouse button and mouse movement can compress /
3860 expand the visible width and height of the alignment</li>
3865 <li>Annotation Panel displays complete JNet results</li>
3871 <div align="center">
3872 <strong>2.08b</strong><br> 18/4/06
3878 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3879 <li>Righthand label on wrapped alignments shows correct
3886 <div align="center">
3887 <strong>2.08</strong><br> 10/4/06
3892 <li>Editing can be locked to the selection area</li>
3893 <li>Keyboard editing</li>
3894 <li>Create sequence features from searches</li>
3895 <li>Precalculated annotations can be loaded onto
3897 <li>Features file allows grouping of features</li>
3898 <li>Annotation Colouring scheme added</li>
3899 <li>Smooth fonts off by default - Faster rendering</li>
3900 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3905 <li>Drag & Drop fixed on Linux</li>
3906 <li>Jalview Archive file faster to load/save, sequence
3907 descriptions saved.</li>
3913 <div align="center">
3914 <strong>2.07</strong><br> 12/12/05
3919 <li>PDB Structure Viewer enhanced</li>
3920 <li>Sequence Feature retrieval and display enhanced</li>
3921 <li>Choose to output sequence start-end after sequence
3922 name for file output</li>
3923 <li>Sequence Fetcher WSDBFetch@EBI</li>
3924 <li>Applet can read feature files, PDB files and can be
3925 used for HTML form input</li>
3930 <li>HTML output writes groups and features</li>
3931 <li>Group editing is Control and mouse click</li>
3932 <li>File IO bugs</li>
3938 <div align="center">
3939 <strong>2.06</strong><br> 28/9/05
3944 <li>View annotations in wrapped mode</li>
3945 <li>More options for PCA viewer</li>
3950 <li>GUI bugs resolved</li>
3951 <li>Runs with -nodisplay from command line</li>
3957 <div align="center">
3958 <strong>2.05b</strong><br> 15/9/05
3963 <li>Choose EPS export as lineart or text</li>
3964 <li>Jar files are executable</li>
3965 <li>Can read in Uracil - maps to unknown residue</li>
3970 <li>Known OutOfMemory errors give warning message</li>
3971 <li>Overview window calculated more efficiently</li>
3972 <li>Several GUI bugs resolved</li>
3978 <div align="center">
3979 <strong>2.05</strong><br> 30/8/05
3984 <li>Edit and annotate in "Wrapped" view</li>
3989 <li>Several GUI bugs resolved</li>
3995 <div align="center">
3996 <strong>2.04</strong><br> 24/8/05
4001 <li>Hold down mouse wheel & scroll to change font
4007 <li>Improved JPred client reliability</li>
4008 <li>Improved loading of Jalview files</li>
4014 <div align="center">
4015 <strong>2.03</strong><br> 18/8/05
4020 <li>Set Proxy server name and port in preferences</li>
4021 <li>Multiple URL links from sequence ids</li>
4022 <li>User Defined Colours can have a scheme name and added
4024 <li>Choose to ignore gaps in consensus calculation</li>
4025 <li>Unix users can set default web browser</li>
4026 <li>Runs without GUI for batch processing</li>
4027 <li>Dynamically generated Web Service Menus</li>
4032 <li>InstallAnywhere download for Sparc Solaris</li>
4038 <div align="center">
4039 <strong>2.02</strong><br> 18/7/05
4045 <li>Copy & Paste order of sequences maintains
4046 alignment order.</li>
4052 <div align="center">
4053 <strong>2.01</strong><br> 12/7/05
4058 <li>Use delete key for deleting selection.</li>
4059 <li>Use Mouse wheel to scroll sequences.</li>
4060 <li>Help file updated to describe how to add alignment
4062 <li>Version and build date written to build properties
4064 <li>InstallAnywhere installation will check for updates
4065 at launch of Jalview.</li>
4070 <li>Delete gaps bug fixed.</li>
4071 <li>FileChooser sorts columns.</li>
4072 <li>Can remove groups one by one.</li>
4073 <li>Filechooser icons installed.</li>
4074 <li>Finder ignores return character when searching.
4075 Return key will initiate a search.<br>
4082 <div align="center">
4083 <strong>2.0</strong><br> 20/6/05
4088 <li>New codebase</li>