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>10/09/2018</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-3107 -->Group conservation/consensus not shown
124 for newly created group when 'Apply to all groups'
128 <!-- JAL-3087 -->Corrupted display when switching to
129 wrapped mode when sequence panel's vertical scrollbar is
133 <!-- JAL-3003 -->Alignment is black in exported EPS file
134 when sequences are selected in exported view.</em>
137 <!-- JAL-3059 -->Groups with different coloured borders
138 aren't rendered with correct colour.
141 <!-- JAL-3092 -->Jalview could hang when importing certain
142 types of knotted RNA secondary structure.
145 <!-- JAL-3095 -->Sequence highlight and selection in
146 trimmed VARNA 2D structure is incorrect for sequences that
150 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
151 annotation when columns are inserted into an alignment,
152 and when exporting as Stockholm flatfile.
155 <!-- JAL-3053 -->Jalview annotation rows containing upper
156 and lower-case 'E' and 'H' do not automatically get
157 treated as RNA secondary structure.
160 <!-- JAL-3106 -->.jvp should be used as default extension
161 (not .jar) when saving a jalview project file.
164 <!-- JAL-3105 -->Mac Users: closing a window correctly
165 transfers focus to previous window on OSX
168 <em>Java 10 Issues Resolved</em>
171 <!-- JAL-2988 -->OSX - Can't save new files via the File
172 or export menus by typing in a name into the Save dialog
176 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
177 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
178 'look and feel' which has improved compatibility with the
179 latest version of OSX.
186 <td width="60" nowrap>
188 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
189 <em>7/06/2018</em></strong>
192 <td><div align="left">
196 <!-- JAL-2920 -->Use HGVS nomenclature for variant
197 annotation retrieved from Uniprot
200 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
201 onto the Jalview Desktop
205 <td><div align="left">
209 <!-- JAL-3017 -->Cannot import features with multiple
210 variant elements (blocks import of some Uniprot records)
213 <!-- JAL-2997 -->Clustal files with sequence positions in
214 right-hand column parsed correctly
217 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
218 not alignment area in exported graphic
221 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
222 window has input focus
225 <!-- JAL-2992 -->Annotation panel set too high when
226 annotation added to view (Windows)
229 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
230 network connectivity is poor
233 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
234 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
235 the currently open URL and links from a page viewed in
236 Firefox or Chrome on Windows is now fully supported. If
237 you are using Edge, only links in the page can be
238 dragged, and with Internet Explorer, only the currently
239 open URL in the browser can be dropped onto Jalview.</em>
245 <td width="60" nowrap>
247 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
250 <td><div align="left">
254 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
255 for disabling automatic superposition of multiple
256 structures and open structures in existing views
259 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
260 ID and annotation area margins can be click-dragged to
264 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
268 <!-- JAL-2759 -->Improved performance for large alignments
269 and lots of hidden columns
272 <!-- JAL-2593 -->Improved performance when rendering lots
273 of features (particularly when transparency is disabled)
278 <td><div align="left">
281 <!-- JAL-2899 -->Structure and Overview aren't updated
282 when Colour By Annotation threshold slider is adjusted
285 <!-- JAL-2778 -->Slow redraw when Overview panel shown
286 overlapping alignment panel
289 <!-- JAL-2929 -->Overview doesn't show end of unpadded
293 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
294 improved: CDS not handled correctly if transcript has no
298 <!-- JAL-2321 -->Secondary structure and temperature
299 factor annotation not added to sequence when local PDB
300 file associated with it by drag'n'drop or structure
304 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
305 dialog doesn't import PDB files dropped on an alignment
308 <!-- JAL-2666 -->Linked scrolling via protein horizontal
309 scroll bar doesn't work for some CDS/Protein views
312 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
313 Java 1.8u153 onwards and Java 1.9u4+.
316 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
317 columns in annotation row
320 <!-- JAL-2913 -->Preferences panel's ID Width control is not
321 honored in batch mode
324 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
325 for structures added to existing Jmol view
328 <!-- JAL-2223 -->'View Mappings' includes duplicate
329 entries after importing project with multiple views
332 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
333 protein sequences via SIFTS from associated PDB entries
334 with negative residue numbers or missing residues fails
337 <!-- JAL-2952 -->Exception when shading sequence with negative
338 Temperature Factor values from annotated PDB files (e.g.
339 as generated by CONSURF)
342 <!-- JAL-2920 -->Uniprot 'sequence variant' features
343 tooltip doesn't include a text description of mutation
346 <!-- JAL-2922 -->Invert displayed features very slow when
347 structure and/or overview windows are also shown
350 <!-- JAL-2954 -->Selecting columns from highlighted regions
351 very slow for alignments with large numbers of sequences
354 <!-- JAL-2925 -->Copy Consensus fails for group consensus
355 with 'StringIndexOutOfBounds'
358 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
359 platforms running Java 10
362 <!-- JAL-2960 -->Adding a structure to existing structure
363 view appears to do nothing because the view is hidden behind the alignment view
369 <!-- JAL-2926 -->Copy consensus sequence option in applet
370 should copy the group consensus when popup is opened on it
376 <!-- JAL-2913 -->Fixed ID width preference is not respected
379 <em>New Known Defects</em>
382 <!-- JAL-2973 --> Exceptions occasionally raised when
383 editing a large alignment and overview is displayed
386 <!-- JAL-2974 -->'Overview updating' progress bar is shown
387 repeatedly after a series of edits even when the overview
388 is no longer reflecting updates
391 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
392 structures for protein subsequence (if 'Trim Retrieved
393 Sequences' enabled) or Ensembl isoforms (Workaround in
394 2.10.4 is to fail back to N&W mapping)
401 <td width="60" nowrap>
403 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
406 <td><div align="left">
407 <ul><li>Updated Certum Codesigning Certificate
408 (Valid till 30th November 2018)</li></ul></div></td>
409 <td><div align="left">
412 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
413 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
414 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
415 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
416 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
417 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
418 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
424 <td width="60" nowrap>
426 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
429 <td><div align="left">
433 <!-- JAL-2446 -->Faster and more efficient management and
434 rendering of sequence features
437 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
438 429 rate limit request hander
441 <!-- JAL-2773 -->Structure views don't get updated unless
442 their colours have changed
445 <!-- JAL-2495 -->All linked sequences are highlighted for
446 a structure mousover (Jmol) or selection (Chimera)
449 <!-- JAL-2790 -->'Cancel' button in progress bar for
450 JABAWS AACon, RNAAliFold and Disorder prediction jobs
453 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
454 view from Ensembl locus cross-references
457 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
461 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
462 feature can be disabled
465 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
466 PDB easier retrieval of sequences for lists of IDs
469 <!-- JAL-2758 -->Short names for sequences retrieved from
475 <li>Groovy interpreter updated to 2.4.12</li>
476 <li>Example groovy script for generating a matrix of
477 percent identity scores for current alignment.</li>
479 <em>Testing and Deployment</em>
482 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
486 <td><div align="left">
490 <!-- JAL-2643 -->Pressing tab after updating the colour
491 threshold text field doesn't trigger an update to the
495 <!-- JAL-2682 -->Race condition when parsing sequence ID
499 <!-- JAL-2608 -->Overview windows are also closed when
500 alignment window is closed
503 <!-- JAL-2548 -->Export of features doesn't always respect
507 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
508 takes a long time in Cursor mode
514 <!-- JAL-2777 -->Structures with whitespace chainCode
515 cannot be viewed in Chimera
518 <!-- JAL-2728 -->Protein annotation panel too high in
522 <!-- JAL-2757 -->Can't edit the query after the server
523 error warning icon is shown in Uniprot and PDB Free Text
527 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
530 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
533 <!-- JAL-2739 -->Hidden column marker in last column not
534 rendered when switching back from Wrapped to normal view
537 <!-- JAL-2768 -->Annotation display corrupted when
538 scrolling right in unwapped alignment view
541 <!-- JAL-2542 -->Existing features on subsequence
542 incorrectly relocated when full sequence retrieved from
546 <!-- JAL-2733 -->Last reported memory still shown when
547 Desktop->Show Memory is unticked (OSX only)
550 <!-- JAL-2658 -->Amend Features dialog doesn't allow
551 features of same type and group to be selected for
555 <!-- JAL-2524 -->Jalview becomes sluggish in wide
556 alignments when hidden columns are present
559 <!-- JAL-2392 -->Jalview freezes when loading and
560 displaying several structures
563 <!-- JAL-2732 -->Black outlines left after resizing or
567 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
568 within the Jalview desktop on OSX
571 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
572 when in wrapped alignment mode
575 <!-- JAL-2636 -->Scale mark not shown when close to right
576 hand end of alignment
579 <!-- JAL-2684 -->Pairwise alignment of selected regions of
580 each selected sequence do not have correct start/end
584 <!-- JAL-2793 -->Alignment ruler height set incorrectly
585 after canceling the Alignment Window's Font dialog
588 <!-- JAL-2036 -->Show cross-references not enabled after
589 restoring project until a new view is created
592 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
593 URL links appears when only default EMBL-EBI link is
594 configured (since 2.10.2b2)
597 <!-- JAL-2775 -->Overview redraws whole window when box
601 <!-- JAL-2225 -->Structure viewer doesn't map all chains
602 in a multi-chain structure when viewing alignment
603 involving more than one chain (since 2.10)
606 <!-- JAL-2811 -->Double residue highlights in cursor mode
607 if new selection moves alignment window
610 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
611 arrow key in cursor mode to pass hidden column marker
614 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
615 that produces correctly annotated transcripts and products
618 <!-- JAL-2776 -->Toggling a feature group after first time
619 doesn't update associated structure view
622 <em>Applet</em><br />
625 <!-- JAL-2687 -->Concurrent modification exception when
626 closing alignment panel
629 <em>BioJSON</em><br />
632 <!-- JAL-2546 -->BioJSON export does not preserve
633 non-positional features
636 <em>New Known Issues</em>
639 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
640 sequence features correctly (for many previous versions of
644 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
645 using cursor in wrapped panel other than top
648 <!-- JAL-2791 -->Select columns containing feature ignores
649 graduated colour threshold
652 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
653 always preserve numbering and sequence features
656 <em>Known Java 9 Issues</em>
659 <!-- JAL-2902 -->Groovy Console very slow to open and is
660 not responsive when entering characters (Webstart, Java
667 <td width="60" nowrap>
669 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
670 <em>2/10/2017</em></strong>
673 <td><div align="left">
674 <em>New features in Jalview Desktop</em>
677 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
679 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
683 <td><div align="left">
687 <td width="60" nowrap>
689 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
690 <em>7/9/2017</em></strong>
693 <td><div align="left">
697 <!-- JAL-2588 -->Show gaps in overview window by colouring
698 in grey (sequences used to be coloured grey, and gaps were
702 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
706 <!-- JAL-2587 -->Overview updates immediately on increase
707 in size and progress bar shown as higher resolution
708 overview is recalculated
713 <td><div align="left">
717 <!-- JAL-2664 -->Overview window redraws every hidden
718 column region row by row
721 <!-- JAL-2681 -->duplicate protein sequences shown after
722 retrieving Ensembl crossrefs for sequences from Uniprot
725 <!-- JAL-2603 -->Overview window throws NPE if show boxes
726 format setting is unticked
729 <!-- JAL-2610 -->Groups are coloured wrongly in overview
730 if group has show boxes format setting unticked
733 <!-- JAL-2672,JAL-2665 -->Redraw problems when
734 autoscrolling whilst dragging current selection group to
735 include sequences and columns not currently displayed
738 <!-- JAL-2691 -->Not all chains are mapped when multimeric
739 assemblies are imported via CIF file
742 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
743 displayed when threshold or conservation colouring is also
747 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
751 <!-- JAL-2673 -->Jalview continues to scroll after
752 dragging a selected region off the visible region of the
756 <!-- JAL-2724 -->Cannot apply annotation based
757 colourscheme to all groups in a view
760 <!-- JAL-2511 -->IDs don't line up with sequences
761 initially after font size change using the Font chooser or
768 <td width="60" nowrap>
770 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
773 <td><div align="left">
774 <em>Calculations</em>
778 <!-- JAL-1933 -->Occupancy annotation row shows number of
779 ungapped positions in each column of the alignment.
782 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
783 a calculation dialog box
786 <!-- JAL-2379 -->Revised implementation of PCA for speed
787 and memory efficiency (~30x faster)
790 <!-- JAL-2403 -->Revised implementation of sequence
791 similarity scores as used by Tree, PCA, Shading Consensus
792 and other calculations
795 <!-- JAL-2416 -->Score matrices are stored as resource
796 files within the Jalview codebase
799 <!-- JAL-2500 -->Trees computed on Sequence Feature
800 Similarity may have different topology due to increased
807 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
808 model for alignments and groups
811 <!-- JAL-384 -->Custom shading schemes created via groovy
818 <!-- JAL-2526 -->Efficiency improvements for interacting
819 with alignment and overview windows
822 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
826 <!-- JAL-2388 -->Hidden columns and sequences can be
830 <!-- JAL-2611 -->Click-drag in visible area allows fine
831 adjustment of visible position
835 <em>Data import/export</em>
838 <!-- JAL-2535 -->Posterior probability annotation from
839 Stockholm files imported as sequence associated annotation
842 <!-- JAL-2507 -->More robust per-sequence positional
843 annotation input/output via stockholm flatfile
846 <!-- JAL-2533 -->Sequence names don't include file
847 extension when importing structure files without embedded
848 names or PDB accessions
851 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
852 format sequence substitution matrices
855 <em>User Interface</em>
858 <!-- JAL-2447 --> Experimental Features Checkbox in
859 Desktop's Tools menu to hide or show untested features in
863 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
864 via Overview or sequence motif search operations
867 <!-- JAL-2547 -->Amend sequence features dialog box can be
868 opened by double clicking gaps within sequence feature
872 <!-- JAL-1476 -->Status bar message shown when not enough
873 aligned positions were available to create a 3D structure
877 <em>3D Structure</em>
880 <!-- JAL-2430 -->Hidden regions in alignment views are not
881 coloured in linked structure views
884 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
885 file-based command exchange
888 <!-- JAL-2375 -->Structure chooser automatically shows
889 Cached Structures rather than querying the PDBe if
890 structures are already available for sequences
893 <!-- JAL-2520 -->Structures imported via URL are cached in
894 the Jalview project rather than downloaded again when the
898 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
899 to transfer Chimera's structure attributes as Jalview
900 features, and vice-versa (<strong>Experimental
904 <em>Web Services</em>
907 <!-- JAL-2549 -->Updated JABAWS client to v2.2
910 <!-- JAL-2335 -->Filter non-standard amino acids and
911 nucleotides when submitting to AACon and other MSA
915 <!-- JAL-2316, -->URLs for viewing database
916 cross-references provided by identifiers.org and the
924 <!-- JAL-2344 -->FileFormatI interface for describing and
925 identifying file formats (instead of String constants)
928 <!-- JAL-2228 -->FeatureCounter script refactored for
929 efficiency when counting all displayed features (not
930 backwards compatible with 2.10.1)
933 <em>Example files</em>
936 <!-- JAL-2631 -->Graduated feature colour style example
937 included in the example feature file
940 <em>Documentation</em>
943 <!-- JAL-2339 -->Release notes reformatted for readability
944 with the built-in Java help viewer
947 <!-- JAL-1644 -->Find documentation updated with 'search
948 sequence description' option
954 <!-- JAL-2485, -->External service integration tests for
955 Uniprot REST Free Text Search Client
958 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
961 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
966 <td><div align="left">
967 <em>Calculations</em>
970 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
971 matrix - C->R should be '-3'<br />Old matrix restored
972 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
974 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
975 Jalview's treatment of gaps in PCA and substitution matrix
976 based Tree calculations.<br /> <br />In earlier versions
977 of Jalview, gaps matching gaps were penalised, and gaps
978 matching non-gaps penalised even more. In the PCA
979 calculation, gaps were actually treated as non-gaps - so
980 different costs were applied, which meant Jalview's PCAs
981 were different to those produced by SeqSpace.<br />Jalview
982 now treats gaps in the same way as SeqSpace (ie it scores
983 them as 0). <br /> <br />Enter the following in the
984 Groovy console to restore pre-2.10.2 behaviour:<br />
985 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
986 // for 2.10.1 mode <br />
987 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
988 // to restore 2.10.2 mode <br /> <br /> <em>Note:
989 these settings will affect all subsequent tree and PCA
990 calculations (not recommended)</em></li>
992 <!-- JAL-2424 -->Fixed off-by-one bug that affected
993 scaling of branch lengths for trees computed using
994 Sequence Feature Similarity.
997 <!-- JAL-2377 -->PCA calculation could hang when
998 generating output report when working with highly
1002 <!-- JAL-2544 --> Sort by features includes features to
1003 right of selected region when gaps present on right-hand
1007 <em>User Interface</em>
1010 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1011 doesn't reselect a specific sequence's associated
1012 annotation after it was used for colouring a view
1015 <!-- JAL-2419 -->Current selection lost if popup menu
1016 opened on a region of alignment without groups
1019 <!-- JAL-2374 -->Popup menu not always shown for regions
1020 of an alignment with overlapping groups
1023 <!-- JAL-2310 -->Finder double counts if both a sequence's
1024 name and description match
1027 <!-- JAL-2370 -->Hiding column selection containing two
1028 hidden regions results in incorrect hidden regions
1031 <!-- JAL-2386 -->'Apply to all groups' setting when
1032 changing colour does not apply Conservation slider value
1036 <!-- JAL-2373 -->Percentage identity and conservation menu
1037 items do not show a tick or allow shading to be disabled
1040 <!-- JAL-2385 -->Conservation shading or PID threshold
1041 lost when base colourscheme changed if slider not visible
1044 <!-- JAL-2547 -->Sequence features shown in tooltip for
1045 gaps before start of features
1048 <!-- JAL-2623 -->Graduated feature colour threshold not
1049 restored to UI when feature colour is edited
1052 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1053 a time when scrolling vertically in wrapped mode.
1056 <!-- JAL-2630 -->Structure and alignment overview update
1057 as graduate feature colour settings are modified via the
1061 <!-- JAL-2034 -->Overview window doesn't always update
1062 when a group defined on the alignment is resized
1065 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1066 wrapped view result in positional status updates
1070 <!-- JAL-2563 -->Status bar doesn't show position for
1071 ambiguous amino acid and nucleotide symbols
1074 <!-- JAL-2602 -->Copy consensus sequence failed if
1075 alignment included gapped columns
1078 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1079 widgets don't permanently disappear
1082 <!-- JAL-2503 -->Cannot select or filter quantitative
1083 annotation that are shown only as column labels (e.g.
1084 T-Coffee column reliability scores)
1087 <!-- JAL-2594 -->Exception thrown if trying to create a
1088 sequence feature on gaps only
1091 <!-- JAL-2504 -->Features created with 'New feature'
1092 button from a Find inherit previously defined feature type
1093 rather than the Find query string
1096 <!-- JAL-2423 -->incorrect title in output window when
1097 exporting tree calculated in Jalview
1100 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1101 and then revealing them reorders sequences on the
1105 <!-- JAL-964 -->Group panel in sequence feature settings
1106 doesn't update to reflect available set of groups after
1107 interactively adding or modifying features
1110 <!-- JAL-2225 -->Sequence Database chooser unusable on
1114 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1115 only excluded gaps in current sequence and ignored
1122 <!-- JAL-2421 -->Overview window visible region moves
1123 erratically when hidden rows or columns are present
1126 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1127 Structure Viewer's colour menu don't correspond to
1131 <!-- JAL-2405 -->Protein specific colours only offered in
1132 colour and group colour menu for protein alignments
1135 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1136 reflect currently selected view or group's shading
1140 <!-- JAL-2624 -->Feature colour thresholds not respected
1141 when rendered on overview and structures when opacity at
1145 <!-- JAL-2589 -->User defined gap colour not shown in
1146 overview when features overlaid on alignment
1149 <em>Data import/export</em>
1152 <!-- JAL-2576 -->Very large alignments take a long time to
1156 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1157 added after a sequence was imported are not written to
1161 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1162 when importing RNA secondary structure via Stockholm
1165 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1166 not shown in correct direction for simple pseudoknots
1169 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1170 with lightGray or darkGray via features file (but can
1174 <!-- JAL-2383 -->Above PID colour threshold not recovered
1175 when alignment view imported from project
1178 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1179 structure and sequences extracted from structure files
1180 imported via URL and viewed in Jmol
1183 <!-- JAL-2520 -->Structures loaded via URL are saved in
1184 Jalview Projects rather than fetched via URL again when
1185 the project is loaded and the structure viewed
1188 <em>Web Services</em>
1191 <!-- JAL-2519 -->EnsemblGenomes example failing after
1192 release of Ensembl v.88
1195 <!-- JAL-2366 -->Proxy server address and port always
1196 appear enabled in Preferences->Connections
1199 <!-- JAL-2461 -->DAS registry not found exceptions
1200 removed from console output
1203 <!-- JAL-2582 -->Cannot retrieve protein products from
1204 Ensembl by Peptide ID
1207 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1208 created from SIFTs, and spurious 'Couldn't open structure
1209 in Chimera' errors raised after April 2017 update (problem
1210 due to 'null' string rather than empty string used for
1211 residues with no corresponding PDB mapping).
1214 <em>Application UI</em>
1217 <!-- JAL-2361 -->User Defined Colours not added to Colour
1221 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1222 case' residues (button in colourscheme editor debugged and
1223 new documentation and tooltips added)
1226 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1227 doesn't restore group-specific text colour thresholds
1230 <!-- JAL-2243 -->Feature settings panel does not update as
1231 new features are added to alignment
1234 <!-- JAL-2532 -->Cancel in feature settings reverts
1235 changes to feature colours via the Amend features dialog
1238 <!-- JAL-2506 -->Null pointer exception when attempting to
1239 edit graduated feature colour via amend features dialog
1243 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1244 selection menu changes colours of alignment views
1247 <!-- JAL-2426 -->Spurious exceptions in console raised
1248 from alignment calculation workers after alignment has
1252 <!-- JAL-1608 -->Typo in selection popup menu - Create
1253 groups now 'Create Group'
1256 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1257 Create/Undefine group doesn't always work
1260 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1261 shown again after pressing 'Cancel'
1264 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1265 adjusts start position in wrap mode
1268 <!-- JAL-2563 -->Status bar doesn't show positions for
1269 ambiguous amino acids
1272 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1273 CDS/Protein view after CDS sequences added for aligned
1277 <!-- JAL-2592 -->User defined colourschemes called 'User
1278 Defined' don't appear in Colours menu
1284 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1285 score models doesn't always result in an updated PCA plot
1288 <!-- JAL-2442 -->Features not rendered as transparent on
1289 overview or linked structure view
1292 <!-- JAL-2372 -->Colour group by conservation doesn't
1296 <!-- JAL-2517 -->Hitting Cancel after applying
1297 user-defined colourscheme doesn't restore original
1304 <!-- JAL-2314 -->Unit test failure:
1305 jalview.ws.jabaws.RNAStructExportImport setup fails
1308 <!-- JAL-2307 -->Unit test failure:
1309 jalview.ws.sifts.SiftsClientTest due to compatibility
1310 problems with deep array comparison equality asserts in
1311 successive versions of TestNG
1314 <!-- JAL-2479 -->Relocated StructureChooserTest and
1315 ParameterUtilsTest Unit tests to Network suite
1318 <em>New Known Issues</em>
1321 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1322 phase after a sequence motif find operation
1325 <!-- JAL-2550 -->Importing annotation file with rows
1326 containing just upper and lower case letters are
1327 interpreted as WUSS RNA secondary structure symbols
1330 <!-- JAL-2590 -->Cannot load and display Newick trees
1331 reliably from eggnog Ortholog database
1334 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1335 containing features of type Highlight' when 'B' is pressed
1336 to mark columns containing highlighted regions.
1339 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1340 doesn't always add secondary structure annotation.
1345 <td width="60" nowrap>
1346 <div align="center">
1347 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1350 <td><div align="left">
1354 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1355 for all consensus calculations
1358 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1361 <li>Updated Jalview's Certum code signing certificate
1364 <em>Application</em>
1367 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1368 set of database cross-references, sorted alphabetically
1371 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1372 from database cross references. Users with custom links
1373 will receive a <a href="webServices/urllinks.html#warning">warning
1374 dialog</a> asking them to update their preferences.
1377 <!-- JAL-2287-->Cancel button and escape listener on
1378 dialog warning user about disconnecting Jalview from a
1382 <!-- JAL-2320-->Jalview's Chimera control window closes if
1383 the Chimera it is connected to is shut down
1386 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1387 columns menu item to mark columns containing highlighted
1388 regions (e.g. from structure selections or results of a
1392 <!-- JAL-2284-->Command line option for batch-generation
1393 of HTML pages rendering alignment data with the BioJS
1403 <!-- JAL-2286 -->Columns with more than one modal residue
1404 are not coloured or thresholded according to percent
1405 identity (first observed in Jalview 2.8.2)
1408 <!-- JAL-2301 -->Threonine incorrectly reported as not
1412 <!-- JAL-2318 -->Updates to documentation pages (above PID
1413 threshold, amino acid properties)
1416 <!-- JAL-2292 -->Lower case residues in sequences are not
1417 reported as mapped to residues in a structure file in the
1421 <!--JAL-2324 -->Identical features with non-numeric scores
1422 could be added multiple times to a sequence
1425 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1426 bond features shown as two highlighted residues rather
1427 than a range in linked structure views, and treated
1428 correctly when selecting and computing trees from features
1431 <!-- JAL-2281-->Custom URL links for database
1432 cross-references are matched to database name regardless
1437 <em>Application</em>
1440 <!-- JAL-2282-->Custom URL links for specific database
1441 names without regular expressions also offer links from
1445 <!-- JAL-2315-->Removing a single configured link in the
1446 URL links pane in Connections preferences doesn't actually
1447 update Jalview configuration
1450 <!-- JAL-2272-->CTRL-Click on a selected region to open
1451 the alignment area popup menu doesn't work on El-Capitan
1454 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1455 files with similarly named sequences if dropped onto the
1459 <!-- JAL-2312 -->Additional mappings are shown for PDB
1460 entries where more chains exist in the PDB accession than
1461 are reported in the SIFTS file
1464 <!-- JAL-2317-->Certain structures do not get mapped to
1465 the structure view when displayed with Chimera
1468 <!-- JAL-2317-->No chains shown in the Chimera view
1469 panel's View->Show Chains submenu
1472 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1473 work for wrapped alignment views
1476 <!--JAL-2197 -->Rename UI components for running JPred
1477 predictions from 'JNet' to 'JPred'
1480 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1481 corrupted when annotation panel vertical scroll is not at
1482 first annotation row
1485 <!--JAL-2332 -->Attempting to view structure for Hen
1486 lysozyme results in a PDB Client error dialog box
1489 <!-- JAL-2319 -->Structure View's mapping report switched
1490 ranges for PDB and sequence for SIFTS
1493 SIFTS 'Not_Observed' residues mapped to non-existant
1497 <!-- <em>New Known Issues</em>
1504 <td width="60" nowrap>
1505 <div align="center">
1506 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1507 <em>25/10/2016</em></strong>
1510 <td><em>Application</em>
1512 <li>3D Structure chooser opens with 'Cached structures'
1513 view if structures already loaded</li>
1514 <li>Progress bar reports models as they are loaded to
1515 structure views</li>
1521 <li>Colour by conservation always enabled and no tick
1522 shown in menu when BLOSUM or PID shading applied</li>
1523 <li>FER1_ARATH and FER2_ARATH labels were switched in
1524 example sequences/projects/trees</li>
1526 <em>Application</em>
1528 <li>Jalview projects with views of local PDB structure
1529 files saved on Windows cannot be opened on OSX</li>
1530 <li>Multiple structure views can be opened and superposed
1531 without timeout for structures with multiple models or
1532 multiple sequences in alignment</li>
1533 <li>Cannot import or associated local PDB files without a
1534 PDB ID HEADER line</li>
1535 <li>RMSD is not output in Jmol console when superposition
1537 <li>Drag and drop of URL from Browser fails for Linux and
1538 OSX versions earlier than El Capitan</li>
1539 <li>ENA client ignores invalid content from ENA server</li>
1540 <li>Exceptions are not raised in console when ENA client
1541 attempts to fetch non-existent IDs via Fetch DB Refs UI
1543 <li>Exceptions are not raised in console when a new view
1544 is created on the alignment</li>
1545 <li>OSX right-click fixed for group selections: CMD-click
1546 to insert/remove gaps in groups and CTRL-click to open group
1549 <em>Build and deployment</em>
1551 <li>URL link checker now copes with multi-line anchor
1554 <em>New Known Issues</em>
1556 <li>Drag and drop from URL links in browsers do not work
1563 <td width="60" nowrap>
1564 <div align="center">
1565 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1568 <td><em>General</em>
1571 <!-- JAL-2124 -->Updated Spanish translations.
1574 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1575 for importing structure data to Jalview. Enables mmCIF and
1579 <!-- JAL-192 --->Alignment ruler shows positions relative to
1583 <!-- JAL-2202 -->Position/residue shown in status bar when
1584 mousing over sequence associated annotation
1587 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1591 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1592 '()', canonical '[]' and invalid '{}' base pair populations
1596 <!-- JAL-2092 -->Feature settings popup menu options for
1597 showing or hiding columns containing a feature
1600 <!-- JAL-1557 -->Edit selected group by double clicking on
1601 group and sequence associated annotation labels
1604 <!-- JAL-2236 -->Sequence name added to annotation label in
1605 select/hide columns by annotation and colour by annotation
1609 </ul> <em>Application</em>
1612 <!-- JAL-2050-->Automatically hide introns when opening a
1613 gene/transcript view
1616 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1620 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1621 structure mappings with the EMBL-EBI PDBe SIFTS database
1624 <!-- JAL-2079 -->Updated download sites used for Rfam and
1625 Pfam sources to xfam.org
1628 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1631 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1632 over sequences in Jalview
1635 <!-- JAL-2027-->Support for reverse-complement coding
1636 regions in ENA and EMBL
1639 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1640 for record retrieval via ENA rest API
1643 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1647 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1648 groovy script execution
1651 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1652 alignment window's Calculate menu
1655 <!-- JAL-1812 -->Allow groovy scripts that call
1656 Jalview.getAlignFrames() to run in headless mode
1659 <!-- JAL-2068 -->Support for creating new alignment
1660 calculation workers from groovy scripts
1663 <!-- JAL-1369 --->Store/restore reference sequence in
1667 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1668 associations are now saved/restored from project
1671 <!-- JAL-1993 -->Database selection dialog always shown
1672 before sequence fetcher is opened
1675 <!-- JAL-2183 -->Double click on an entry in Jalview's
1676 database chooser opens a sequence fetcher
1679 <!-- JAL-1563 -->Free-text search client for UniProt using
1680 the UniProt REST API
1683 <!-- JAL-2168 -->-nonews command line parameter to prevent
1684 the news reader opening
1687 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1688 querying stored in preferences
1691 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1695 <!-- JAL-1977-->Tooltips shown on database chooser
1698 <!-- JAL-391 -->Reverse complement function in calculate
1699 menu for nucleotide sequences
1702 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1703 and feature counts preserves alignment ordering (and
1704 debugged for complex feature sets).
1707 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1708 viewing structures with Jalview 2.10
1711 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1712 genome, transcript CCDS and gene ids via the Ensembl and
1713 Ensembl Genomes REST API
1716 <!-- JAL-2049 -->Protein sequence variant annotation
1717 computed for 'sequence_variant' annotation on CDS regions
1721 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1725 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1726 Ref Fetcher fails to match, or otherwise updates sequence
1727 data from external database records.
1730 <!-- JAL-2154 -->Revised Jalview Project format for
1731 efficient recovery of sequence coding and alignment
1732 annotation relationships.
1734 </ul> <!-- <em>Applet</em>
1745 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1749 <!-- JAL-2018-->Export features in Jalview format (again)
1750 includes graduated colourschemes
1753 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1754 working with big alignments and lots of hidden columns
1757 <!-- JAL-2053-->Hidden column markers not always rendered
1758 at right of alignment window
1761 <!-- JAL-2067 -->Tidied up links in help file table of
1765 <!-- JAL-2072 -->Feature based tree calculation not shown
1769 <!-- JAL-2075 -->Hidden columns ignored during feature
1770 based tree calculation
1773 <!-- JAL-2065 -->Alignment view stops updating when show
1774 unconserved enabled for group on alignment
1777 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1781 <!-- JAL-2146 -->Alignment column in status incorrectly
1782 shown as "Sequence position" when mousing over
1786 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1787 hidden columns present
1790 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1791 user created annotation added to alignment
1794 <!-- JAL-1841 -->RNA Structure consensus only computed for
1795 '()' base pair annotation
1798 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1799 in zero scores for all base pairs in RNA Structure
1803 <!-- JAL-2174-->Extend selection with columns containing
1807 <!-- JAL-2275 -->Pfam format writer puts extra space at
1808 beginning of sequence
1811 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1815 <!-- JAL-2238 -->Cannot create groups on an alignment from
1816 from a tree when t-coffee scores are shown
1819 <!-- JAL-1836,1967 -->Cannot import and view PDB
1820 structures with chains containing negative resnums (4q4h)
1823 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1827 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1828 to Clustal, PIR and PileUp output
1831 <!-- JAL-2008 -->Reordering sequence features that are
1832 not visible causes alignment window to repaint
1835 <!-- JAL-2006 -->Threshold sliders don't work in
1836 graduated colour and colour by annotation row for e-value
1837 scores associated with features and annotation rows
1840 <!-- JAL-1797 -->amino acid physicochemical conservation
1841 calculation should be case independent
1844 <!-- JAL-2173 -->Remove annotation also updates hidden
1848 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1849 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1850 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1853 <!-- JAL-2065 -->Null pointer exceptions and redraw
1854 problems when reference sequence defined and 'show
1855 non-conserved' enabled
1858 <!-- JAL-1306 -->Quality and Conservation are now shown on
1859 load even when Consensus calculation is disabled
1862 <!-- JAL-1932 -->Remove right on penultimate column of
1863 alignment does nothing
1866 <em>Application</em>
1869 <!-- JAL-1552-->URLs and links can't be imported by
1870 drag'n'drop on OSX when launched via webstart (note - not
1871 yet fixed for El Capitan)
1874 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1875 output when running on non-gb/us i18n platforms
1878 <!-- JAL-1944 -->Error thrown when exporting a view with
1879 hidden sequences as flat-file alignment
1882 <!-- JAL-2030-->InstallAnywhere distribution fails when
1886 <!-- JAL-2080-->Jalview very slow to launch via webstart
1887 (also hotfix for 2.9.0b2)
1890 <!-- JAL-2085 -->Cannot save project when view has a
1891 reference sequence defined
1894 <!-- JAL-1011 -->Columns are suddenly selected in other
1895 alignments and views when revealing hidden columns
1898 <!-- JAL-1989 -->Hide columns not mirrored in complement
1899 view in a cDNA/Protein splitframe
1902 <!-- JAL-1369 -->Cannot save/restore representative
1903 sequence from project when only one sequence is
1907 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1908 in Structure Chooser
1911 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1912 structure consensus didn't refresh annotation panel
1915 <!-- JAL-1962 -->View mapping in structure view shows
1916 mappings between sequence and all chains in a PDB file
1919 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1920 dialogs format columns correctly, don't display array
1921 data, sort columns according to type
1924 <!-- JAL-1975 -->Export complete shown after destination
1925 file chooser is cancelled during an image export
1928 <!-- JAL-2025 -->Error when querying PDB Service with
1929 sequence name containing special characters
1932 <!-- JAL-2024 -->Manual PDB structure querying should be
1936 <!-- JAL-2104 -->Large tooltips with broken HTML
1937 formatting don't wrap
1940 <!-- JAL-1128 -->Figures exported from wrapped view are
1941 truncated so L looks like I in consensus annotation
1944 <!-- JAL-2003 -->Export features should only export the
1945 currently displayed features for the current selection or
1949 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1950 after fetching cross-references, and restoring from
1954 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1955 followed in the structure viewer
1958 <!-- JAL-2163 -->Titles for individual alignments in
1959 splitframe not restored from project
1962 <!-- JAL-2145 -->missing autocalculated annotation at
1963 trailing end of protein alignment in transcript/product
1964 splitview when pad-gaps not enabled by default
1967 <!-- JAL-1797 -->amino acid physicochemical conservation
1971 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1972 article has been read (reopened issue due to
1973 internationalisation problems)
1976 <!-- JAL-1960 -->Only offer PDB structures in structure
1977 viewer based on sequence name, PDB and UniProt
1982 <!-- JAL-1976 -->No progress bar shown during export of
1986 <!-- JAL-2213 -->Structures not always superimposed after
1987 multiple structures are shown for one or more sequences.
1990 <!-- JAL-1370 -->Reference sequence characters should not
1991 be replaced with '.' when 'Show unconserved' format option
1995 <!-- JAL-1823 -->Cannot specify chain code when entering
1996 specific PDB id for sequence
1999 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2000 'Export hidden sequences' is enabled, but 'export hidden
2001 columns' is disabled.
2004 <!--JAL-2026-->Best Quality option in structure chooser
2005 selects lowest rather than highest resolution structures
2009 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2010 to sequence mapping in 'View Mappings' report
2013 <!-- JAL-2284 -->Unable to read old Jalview projects that
2014 contain non-XML data added after Jalvew wrote project.
2017 <!-- JAL-2118 -->Newly created annotation row reorders
2018 after clicking on it to create new annotation for a
2022 <!-- JAL-1980 -->Null Pointer Exception raised when
2023 pressing Add on an orphaned cut'n'paste window.
2025 <!-- may exclude, this is an external service stability issue JAL-1941
2026 -- > RNA 3D structure not added via DSSR service</li> -->
2031 <!-- JAL-2151 -->Incorrect columns are selected when
2032 hidden columns present before start of sequence
2035 <!-- JAL-1986 -->Missing dependencies on applet pages
2039 <!-- JAL-1947 -->Overview pixel size changes when
2040 sequences are hidden in applet
2043 <!-- JAL-1996 -->Updated instructions for applet
2044 deployment on examples pages.
2051 <td width="60" nowrap>
2052 <div align="center">
2053 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2054 <em>16/10/2015</em></strong>
2057 <td><em>General</em>
2059 <li>Time stamps for signed Jalview application and applet
2064 <em>Application</em>
2066 <li>Duplicate group consensus and conservation rows
2067 shown when tree is partitioned</li>
2068 <li>Erratic behaviour when tree partitions made with
2069 multiple cDNA/Protein split views</li>
2075 <td width="60" nowrap>
2076 <div align="center">
2077 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2078 <em>8/10/2015</em></strong>
2081 <td><em>General</em>
2083 <li>Updated Spanish translations of localized text for
2085 </ul> <em>Application</em>
2087 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2088 <li>Signed OSX InstallAnywhere installer<br></li>
2089 <li>Support for per-sequence based annotations in BioJSON</li>
2090 </ul> <em>Applet</em>
2092 <li>Split frame example added to applet examples page</li>
2093 </ul> <em>Build and Deployment</em>
2096 <!-- JAL-1888 -->New ant target for running Jalview's test
2104 <li>Mapping of cDNA to protein in split frames
2105 incorrect when sequence start > 1</li>
2106 <li>Broken images in filter column by annotation dialog
2108 <li>Feature colours not parsed from features file</li>
2109 <li>Exceptions and incomplete link URLs recovered when
2110 loading a features file containing HTML tags in feature
2114 <em>Application</em>
2116 <li>Annotations corrupted after BioJS export and
2118 <li>Incorrect sequence limits after Fetch DB References
2119 with 'trim retrieved sequences'</li>
2120 <li>Incorrect warning about deleting all data when
2121 deleting selected columns</li>
2122 <li>Patch to build system for shipping properly signed
2123 JNLP templates for webstart launch</li>
2124 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2125 unreleased structures for download or viewing</li>
2126 <li>Tab/space/return keystroke operation of EMBL-PDBe
2127 fetcher/viewer dialogs works correctly</li>
2128 <li>Disabled 'minimise' button on Jalview windows
2129 running on OSX to workaround redraw hang bug</li>
2130 <li>Split cDNA/Protein view position and geometry not
2131 recovered from jalview project</li>
2132 <li>Initial enabled/disabled state of annotation menu
2133 sorter 'show autocalculated first/last' corresponds to
2135 <li>Restoring of Clustal, RNA Helices and T-Coffee
2136 color schemes from BioJSON</li>
2140 <li>Reorder sequences mirrored in cDNA/Protein split
2142 <li>Applet with Jmol examples not loading correctly</li>
2148 <td><div align="center">
2149 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2151 <td><em>General</em>
2153 <li>Linked visualisation and analysis of DNA and Protein
2156 <li>Translated cDNA alignments shown as split protein
2157 and DNA alignment views</li>
2158 <li>Codon consensus annotation for linked protein and
2159 cDNA alignment views</li>
2160 <li>Link cDNA or Protein product sequences by loading
2161 them onto Protein or cDNA alignments</li>
2162 <li>Reconstruct linked cDNA alignment from aligned
2163 protein sequences</li>
2166 <li>Jmol integration updated to Jmol v14.2.14</li>
2167 <li>Import and export of Jalview alignment views as <a
2168 href="features/bioJsonFormat.html">BioJSON</a></li>
2169 <li>New alignment annotation file statements for
2170 reference sequences and marking hidden columns</li>
2171 <li>Reference sequence based alignment shading to
2172 highlight variation</li>
2173 <li>Select or hide columns according to alignment
2175 <li>Find option for locating sequences by description</li>
2176 <li>Conserved physicochemical properties shown in amino
2177 acid conservation row</li>
2178 <li>Alignments can be sorted by number of RNA helices</li>
2179 </ul> <em>Application</em>
2181 <li>New cDNA/Protein analysis capabilities
2183 <li>Get Cross-References should open a Split Frame
2184 view with cDNA/Protein</li>
2185 <li>Detect when nucleotide sequences and protein
2186 sequences are placed in the same alignment</li>
2187 <li>Split cDNA/Protein views are saved in Jalview
2192 <li>Use REST API to talk to Chimera</li>
2193 <li>Selected regions in Chimera are highlighted in linked
2194 Jalview windows</li>
2196 <li>VARNA RNA viewer updated to v3.93</li>
2197 <li>VARNA views are saved in Jalview Projects</li>
2198 <li>Pseudoknots displayed as Jalview RNA annotation can
2199 be shown in VARNA</li>
2201 <li>Make groups for selection uses marked columns as well
2202 as the active selected region</li>
2204 <li>Calculate UPGMA and NJ trees using sequence feature
2206 <li>New Export options
2208 <li>New Export Settings dialog to control hidden
2209 region export in flat file generation</li>
2211 <li>Export alignment views for display with the <a
2212 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2214 <li>Export scrollable SVG in HTML page</li>
2215 <li>Optional embedding of BioJSON data when exporting
2216 alignment figures to HTML</li>
2218 <li>3D structure retrieval and display
2220 <li>Free text and structured queries with the PDBe
2222 <li>PDBe Search API based discovery and selection of
2223 PDB structures for a sequence set</li>
2227 <li>JPred4 employed for protein secondary structure
2229 <li>Hide Insertions menu option to hide unaligned columns
2230 for one or a group of sequences</li>
2231 <li>Automatically hide insertions in alignments imported
2232 from the JPred4 web server</li>
2233 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2234 system on OSX<br />LGPL libraries courtesy of <a
2235 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2237 <li>changed 'View nucleotide structure' submenu to 'View
2238 VARNA 2D Structure'</li>
2239 <li>change "View protein structure" menu option to "3D
2242 </ul> <em>Applet</em>
2244 <li>New layout for applet example pages</li>
2245 <li>New parameters to enable SplitFrame view
2246 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2247 <li>New example demonstrating linked viewing of cDNA and
2248 Protein alignments</li>
2249 </ul> <em>Development and deployment</em>
2251 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2252 <li>Include installation type and git revision in build
2253 properties and console log output</li>
2254 <li>Jalview Github organisation, and new github site for
2255 storing BioJsMSA Templates</li>
2256 <li>Jalview's unit tests now managed with TestNG</li>
2259 <!-- <em>General</em>
2261 </ul> --> <!-- issues resolved --> <em>Application</em>
2263 <li>Escape should close any open find dialogs</li>
2264 <li>Typo in select-by-features status report</li>
2265 <li>Consensus RNA secondary secondary structure
2266 predictions are not highlighted in amber</li>
2267 <li>Missing gap character in v2.7 example file means
2268 alignment appears unaligned when pad-gaps is not enabled</li>
2269 <li>First switch to RNA Helices colouring doesn't colour
2270 associated structure views</li>
2271 <li>ID width preference option is greyed out when auto
2272 width checkbox not enabled</li>
2273 <li>Stopped a warning dialog from being shown when
2274 creating user defined colours</li>
2275 <li>'View Mapping' in structure viewer shows sequence
2276 mappings for just that viewer's sequences</li>
2277 <li>Workaround for superposing PDB files containing
2278 multiple models in Chimera</li>
2279 <li>Report sequence position in status bar when hovering
2280 over Jmol structure</li>
2281 <li>Cannot output gaps as '.' symbols with Selection ->
2282 output to text box</li>
2283 <li>Flat file exports of alignments with hidden columns
2284 have incorrect sequence start/end</li>
2285 <li>'Aligning' a second chain to a Chimera structure from
2287 <li>Colour schemes applied to structure viewers don't
2288 work for nucleotide</li>
2289 <li>Loading/cut'n'pasting an empty or invalid file leads
2290 to a grey/invisible alignment window</li>
2291 <li>Exported Jpred annotation from a sequence region
2292 imports to different position</li>
2293 <li>Space at beginning of sequence feature tooltips shown
2294 on some platforms</li>
2295 <li>Chimera viewer 'View | Show Chain' menu is not
2297 <li>'New View' fails with a Null Pointer Exception in
2298 console if Chimera has been opened</li>
2299 <li>Mouseover to Chimera not working</li>
2300 <li>Miscellaneous ENA XML feature qualifiers not
2302 <li>NPE in annotation renderer after 'Extract Scores'</li>
2303 <li>If two structures in one Chimera window, mouseover of
2304 either sequence shows on first structure</li>
2305 <li>'Show annotations' options should not make
2306 non-positional annotations visible</li>
2307 <li>Subsequence secondary structure annotation not shown
2308 in right place after 'view flanking regions'</li>
2309 <li>File Save As type unset when current file format is
2311 <li>Save as '.jar' option removed for saving Jalview
2313 <li>Colour by Sequence colouring in Chimera more
2315 <li>Cannot 'add reference annotation' for a sequence in
2316 several views on same alignment</li>
2317 <li>Cannot show linked products for EMBL / ENA records</li>
2318 <li>Jalview's tooltip wraps long texts containing no
2320 </ul> <em>Applet</em>
2322 <li>Jmol to JalviewLite mouseover/link not working</li>
2323 <li>JalviewLite can't import sequences with ID
2324 descriptions containing angle brackets</li>
2325 </ul> <em>General</em>
2327 <li>Cannot export and reimport RNA secondary structure
2328 via jalview annotation file</li>
2329 <li>Random helix colour palette for colour by annotation
2330 with RNA secondary structure</li>
2331 <li>Mouseover to cDNA from STOP residue in protein
2332 translation doesn't work.</li>
2333 <li>hints when using the select by annotation dialog box</li>
2334 <li>Jmol alignment incorrect if PDB file has alternate CA
2336 <li>FontChooser message dialog appears to hang after
2337 choosing 1pt font</li>
2338 <li>Peptide secondary structure incorrectly imported from
2339 annotation file when annotation display text includes 'e' or
2341 <li>Cannot set colour of new feature type whilst creating
2343 <li>cDNA translation alignment should not be sequence
2344 order dependent</li>
2345 <li>'Show unconserved' doesn't work for lower case
2347 <li>Nucleotide ambiguity codes involving R not recognised</li>
2348 </ul> <em>Deployment and Documentation</em>
2350 <li>Applet example pages appear different to the rest of
2351 www.jalview.org</li>
2352 </ul> <em>Application Known issues</em>
2354 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2355 <li>Misleading message appears after trying to delete
2357 <li>Jalview icon not shown in dock after InstallAnywhere
2358 version launches</li>
2359 <li>Fetching EMBL reference for an RNA sequence results
2360 fails with a sequence mismatch</li>
2361 <li>Corrupted or unreadable alignment display when
2362 scrolling alignment to right</li>
2363 <li>ArrayIndexOutOfBoundsException thrown when remove
2364 empty columns called on alignment with ragged gapped ends</li>
2365 <li>auto calculated alignment annotation rows do not get
2366 placed above or below non-autocalculated rows</li>
2367 <li>Jalview dekstop becomes sluggish at full screen in
2368 ultra-high resolution</li>
2369 <li>Cannot disable consensus calculation independently of
2370 quality and conservation</li>
2371 <li>Mouseover highlighting between cDNA and protein can
2372 become sluggish with more than one splitframe shown</li>
2373 </ul> <em>Applet Known Issues</em>
2375 <li>Core PDB parsing code requires Jmol</li>
2376 <li>Sequence canvas panel goes white when alignment
2377 window is being resized</li>
2383 <td><div align="center">
2384 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2386 <td><em>General</em>
2388 <li>Updated Java code signing certificate donated by
2390 <li>Features and annotation preserved when performing
2391 pairwise alignment</li>
2392 <li>RNA pseudoknot annotation can be
2393 imported/exported/displayed</li>
2394 <li>'colour by annotation' can colour by RNA and
2395 protein secondary structure</li>
2396 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2397 post-hoc with 2.9 release</em>)
2400 </ul> <em>Application</em>
2402 <li>Extract and display secondary structure for sequences
2403 with 3D structures</li>
2404 <li>Support for parsing RNAML</li>
2405 <li>Annotations menu for layout
2407 <li>sort sequence annotation rows by alignment</li>
2408 <li>place sequence annotation above/below alignment
2411 <li>Output in Stockholm format</li>
2412 <li>Internationalisation: improved Spanish (es)
2414 <li>Structure viewer preferences tab</li>
2415 <li>Disorder and Secondary Structure annotation tracks
2416 shared between alignments</li>
2417 <li>UCSF Chimera launch and linked highlighting from
2419 <li>Show/hide all sequence associated annotation rows for
2420 all or current selection</li>
2421 <li>disorder and secondary structure predictions
2422 available as dataset annotation</li>
2423 <li>Per-sequence rna helices colouring</li>
2426 <li>Sequence database accessions imported when fetching
2427 alignments from Rfam</li>
2428 <li>update VARNA version to 3.91</li>
2430 <li>New groovy scripts for exporting aligned positions,
2431 conservation values, and calculating sum of pairs scores.</li>
2432 <li>Command line argument to set default JABAWS server</li>
2433 <li>include installation type in build properties and
2434 console log output</li>
2435 <li>Updated Jalview project format to preserve dataset
2439 <!-- issues resolved --> <em>Application</em>
2441 <li>Distinguish alignment and sequence associated RNA
2442 structure in structure->view->VARNA</li>
2443 <li>Raise dialog box if user deletes all sequences in an
2445 <li>Pressing F1 results in documentation opening twice</li>
2446 <li>Sequence feature tooltip is wrapped</li>
2447 <li>Double click on sequence associated annotation
2448 selects only first column</li>
2449 <li>Redundancy removal doesn't result in unlinked
2450 leaves shown in tree</li>
2451 <li>Undos after several redundancy removals don't undo
2453 <li>Hide sequence doesn't hide associated annotation</li>
2454 <li>User defined colours dialog box too big to fit on
2455 screen and buttons not visible</li>
2456 <li>author list isn't updated if already written to
2457 Jalview properties</li>
2458 <li>Popup menu won't open after retrieving sequence
2460 <li>File open window for associate PDB doesn't open</li>
2461 <li>Left-then-right click on a sequence id opens a
2462 browser search window</li>
2463 <li>Cannot open sequence feature shading/sort popup menu
2464 in feature settings dialog</li>
2465 <li>better tooltip placement for some areas of Jalview
2467 <li>Allow addition of JABAWS Server which doesn't
2468 pass validation</li>
2469 <li>Web services parameters dialog box is too large to
2471 <li>Muscle nucleotide alignment preset obscured by
2473 <li>JABAWS preset submenus don't contain newly
2474 defined user preset</li>
2475 <li>MSA web services warns user if they were launched
2476 with invalid input</li>
2477 <li>Jalview cannot contact DAS Registy when running on
2480 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2481 'Superpose with' submenu not shown when new view
2485 </ul> <!-- <em>Applet</em>
2487 </ul> <em>General</em>
2489 </ul>--> <em>Deployment and Documentation</em>
2491 <li>2G and 1G options in launchApp have no effect on
2492 memory allocation</li>
2493 <li>launchApp service doesn't automatically open
2494 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2496 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2497 InstallAnywhere reports cannot find valid JVM when Java
2498 1.7_055 is available
2500 </ul> <em>Application Known issues</em>
2503 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2504 corrupted or unreadable alignment display when scrolling
2508 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2509 retrieval fails but progress bar continues for DAS retrieval
2510 with large number of ID
2513 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2514 flatfile output of visible region has incorrect sequence
2518 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2519 rna structure consensus doesn't update when secondary
2520 structure tracks are rearranged
2523 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2524 invalid rna structure positional highlighting does not
2525 highlight position of invalid base pairs
2528 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2529 out of memory errors are not raised when saving Jalview
2530 project from alignment window file menu
2533 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2534 Switching to RNA Helices colouring doesn't propagate to
2538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2539 colour by RNA Helices not enabled when user created
2540 annotation added to alignment
2543 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2544 Jalview icon not shown on dock in Mountain Lion/Webstart
2546 </ul> <em>Applet Known Issues</em>
2549 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2550 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2553 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2554 Jalview and Jmol example not compatible with IE9
2557 <li>Sort by annotation score doesn't reverse order
2563 <td><div align="center">
2564 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2567 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2570 <li>Internationalisation of user interface (usually
2571 called i18n support) and translation for Spanish locale</li>
2572 <li>Define/Undefine group on current selection with
2573 Ctrl-G/Shift Ctrl-G</li>
2574 <li>Improved group creation/removal options in
2575 alignment/sequence Popup menu</li>
2576 <li>Sensible precision for symbol distribution
2577 percentages shown in logo tooltip.</li>
2578 <li>Annotation panel height set according to amount of
2579 annotation when alignment first opened</li>
2580 </ul> <em>Application</em>
2582 <li>Interactive consensus RNA secondary structure
2583 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2584 <li>Select columns containing particular features from
2585 Feature Settings dialog</li>
2586 <li>View all 'representative' PDB structures for selected
2588 <li>Update Jalview project format:
2590 <li>New file extension for Jalview projects '.jvp'</li>
2591 <li>Preserve sequence and annotation dataset (to
2592 store secondary structure annotation,etc)</li>
2593 <li>Per group and alignment annotation and RNA helix
2597 <li>New similarity measures for PCA and Tree calculation
2599 <li>Experimental support for retrieval and viewing of
2600 flanking regions for an alignment</li>
2604 <!-- issues resolved --> <em>Application</em>
2606 <li>logo keeps spinning and status remains at queued or
2607 running after job is cancelled</li>
2608 <li>cannot export features from alignments imported from
2609 Jalview/VAMSAS projects</li>
2610 <li>Buggy slider for web service parameters that take
2612 <li>Newly created RNA secondary structure line doesn't
2613 have 'display all symbols' flag set</li>
2614 <li>T-COFFEE alignment score shading scheme and other
2615 annotation shading not saved in Jalview project</li>
2616 <li>Local file cannot be loaded in freshly downloaded
2618 <li>Jalview icon not shown on dock in Mountain
2620 <li>Load file from desktop file browser fails</li>
2621 <li>Occasional NPE thrown when calculating large trees</li>
2622 <li>Cannot reorder or slide sequences after dragging an
2623 alignment onto desktop</li>
2624 <li>Colour by annotation dialog throws NPE after using
2625 'extract scores' function</li>
2626 <li>Loading/cut'n'pasting an empty file leads to a grey
2627 alignment window</li>
2628 <li>Disorder thresholds rendered incorrectly after
2629 performing IUPred disorder prediction</li>
2630 <li>Multiple group annotated consensus rows shown when
2631 changing 'normalise logo' display setting</li>
2632 <li>Find shows blank dialog after 'finished searching' if
2633 nothing matches query</li>
2634 <li>Null Pointer Exceptions raised when sorting by
2635 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2637 <li>Errors in Jmol console when structures in alignment
2638 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2640 <li>Not all working JABAWS services are shown in
2642 <li>JAVAWS version of Jalview fails to launch with
2643 'invalid literal/length code'</li>
2644 <li>Annotation/RNA Helix colourschemes cannot be applied
2645 to alignment with groups (actually fixed in 2.8.0b1)</li>
2646 <li>RNA Helices and T-Coffee Scores available as default
2649 </ul> <em>Applet</em>
2651 <li>Remove group option is shown even when selection is
2653 <li>Apply to all groups ticked but colourscheme changes
2654 don't affect groups</li>
2655 <li>Documented RNA Helices and T-Coffee Scores as valid
2656 colourscheme name</li>
2657 <li>Annotation labels drawn on sequence IDs when
2658 Annotation panel is not displayed</li>
2659 <li>Increased font size for dropdown menus on OSX and
2660 embedded windows</li>
2661 </ul> <em>Other</em>
2663 <li>Consensus sequence for alignments/groups with a
2664 single sequence were not calculated</li>
2665 <li>annotation files that contain only groups imported as
2666 annotation and junk sequences</li>
2667 <li>Fasta files with sequences containing '*' incorrectly
2668 recognised as PFAM or BLC</li>
2669 <li>conservation/PID slider apply all groups option
2670 doesn't affect background (2.8.0b1)
2672 <li>redundancy highlighting is erratic at 0% and 100%</li>
2673 <li>Remove gapped columns fails for sequences with ragged
2675 <li>AMSA annotation row with leading spaces is not
2676 registered correctly on import</li>
2677 <li>Jalview crashes when selecting PCA analysis for
2678 certain alignments</li>
2679 <li>Opening the colour by annotation dialog for an
2680 existing annotation based 'use original colours'
2681 colourscheme loses original colours setting</li>
2686 <td><div align="center">
2687 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2688 <em>30/1/2014</em></strong>
2692 <li>Trusted certificates for JalviewLite applet and
2693 Jalview Desktop application<br />Certificate was donated by
2694 <a href="https://www.certum.eu">Certum</a> to the Jalview
2695 open source project).
2697 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2698 <li>Output in Stockholm format</li>
2699 <li>Allow import of data from gzipped files</li>
2700 <li>Export/import group and sequence associated line
2701 graph thresholds</li>
2702 <li>Nucleotide substitution matrix that supports RNA and
2703 ambiguity codes</li>
2704 <li>Allow disorder predictions to be made on the current
2705 selection (or visible selection) in the same way that JPred
2707 <li>Groovy scripting for headless Jalview operation</li>
2708 </ul> <em>Other improvements</em>
2710 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2711 <li>COMBINE statement uses current SEQUENCE_REF and
2712 GROUP_REF scope to group annotation rows</li>
2713 <li>Support '' style escaping of quotes in Newick
2715 <li>Group options for JABAWS service by command line name</li>
2716 <li>Empty tooltip shown for JABA service options with a
2717 link but no description</li>
2718 <li>Select primary source when selecting authority in
2719 database fetcher GUI</li>
2720 <li>Add .mfa to FASTA file extensions recognised by
2722 <li>Annotation label tooltip text wrap</li>
2727 <li>Slow scrolling when lots of annotation rows are
2729 <li>Lots of NPE (and slowness) after creating RNA
2730 secondary structure annotation line</li>
2731 <li>Sequence database accessions not imported when
2732 fetching alignments from Rfam</li>
2733 <li>Incorrect SHMR submission for sequences with
2735 <li>View all structures does not always superpose
2737 <li>Option widgets in service parameters not updated to
2738 reflect user or preset settings</li>
2739 <li>Null pointer exceptions for some services without
2740 presets or adjustable parameters</li>
2741 <li>Discover PDB IDs entry in structure menu doesn't
2742 discover PDB xRefs</li>
2743 <li>Exception encountered while trying to retrieve
2744 features with DAS</li>
2745 <li>Lowest value in annotation row isn't coloured
2746 when colour by annotation (per sequence) is coloured</li>
2747 <li>Keyboard mode P jumps to start of gapped region when
2748 residue follows a gap</li>
2749 <li>Jalview appears to hang importing an alignment with
2750 Wrap as default or after enabling Wrap</li>
2751 <li>'Right click to add annotations' message
2752 shown in wrap mode when no annotations present</li>
2753 <li>Disorder predictions fail with NPE if no automatic
2754 annotation already exists on alignment</li>
2755 <li>oninit javascript function should be called after
2756 initialisation completes</li>
2757 <li>Remove redundancy after disorder prediction corrupts
2758 alignment window display</li>
2759 <li>Example annotation file in documentation is invalid</li>
2760 <li>Grouped line graph annotation rows are not exported
2761 to annotation file</li>
2762 <li>Multi-harmony analysis cannot be run when only two
2764 <li>Cannot create multiple groups of line graphs with
2765 several 'combine' statements in annotation file</li>
2766 <li>Pressing return several times causes Number Format
2767 exceptions in keyboard mode</li>
2768 <li>Multi-harmony (SHMMR) method doesn't submit
2769 correct partitions for input data</li>
2770 <li>Translation from DNA to Amino Acids fails</li>
2771 <li>Jalview fail to load newick tree with quoted label</li>
2772 <li>--headless flag isn't understood</li>
2773 <li>ClassCastException when generating EPS in headless
2775 <li>Adjusting sequence-associated shading threshold only
2776 changes one row's threshold</li>
2777 <li>Preferences and Feature settings panel panel
2778 doesn't open</li>
2779 <li>hide consensus histogram also hides conservation and
2780 quality histograms</li>
2785 <td><div align="center">
2786 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2788 <td><em>Application</em>
2790 <li>Support for JABAWS 2.0 Services (AACon alignment
2791 conservation, protein disorder and Clustal Omega)</li>
2792 <li>JABAWS server status indicator in Web Services
2794 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2795 in Jalview alignment window</li>
2796 <li>Updated Jalview build and deploy framework for OSX
2797 mountain lion, windows 7, and 8</li>
2798 <li>Nucleotide substitution matrix for PCA that supports
2799 RNA and ambiguity codes</li>
2801 <li>Improved sequence database retrieval GUI</li>
2802 <li>Support fetching and database reference look up
2803 against multiple DAS sources (Fetch all from in 'fetch db
2805 <li>Jalview project improvements
2807 <li>Store and retrieve the 'belowAlignment'
2808 flag for annotation</li>
2809 <li>calcId attribute to group annotation rows on the
2811 <li>Store AACon calculation settings for a view in
2812 Jalview project</li>
2816 <li>horizontal scrolling gesture support</li>
2817 <li>Visual progress indicator when PCA calculation is
2819 <li>Simpler JABA web services menus</li>
2820 <li>visual indication that web service results are still
2821 being retrieved from server</li>
2822 <li>Serialise the dialogs that are shown when Jalview
2823 starts up for first time</li>
2824 <li>Jalview user agent string for interacting with HTTP
2826 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2828 <li>Examples directory and Groovy library included in
2829 InstallAnywhere distribution</li>
2830 </ul> <em>Applet</em>
2832 <li>RNA alignment and secondary structure annotation
2833 visualization applet example</li>
2834 </ul> <em>General</em>
2836 <li>Normalise option for consensus sequence logo</li>
2837 <li>Reset button in PCA window to return dimensions to
2839 <li>Allow seqspace or Jalview variant of alignment PCA
2841 <li>PCA with either nucleic acid and protein substitution
2843 <li>Allow windows containing HTML reports to be exported
2845 <li>Interactive display and editing of RNA secondary
2846 structure contacts</li>
2847 <li>RNA Helix Alignment Colouring</li>
2848 <li>RNA base pair logo consensus</li>
2849 <li>Parse sequence associated secondary structure
2850 information in Stockholm files</li>
2851 <li>HTML Export database accessions and annotation
2852 information presented in tooltip for sequences</li>
2853 <li>Import secondary structure from LOCARNA clustalw
2854 style RNA alignment files</li>
2855 <li>import and visualise T-COFFEE quality scores for an
2857 <li>'colour by annotation' per sequence option to
2858 shade each sequence according to its associated alignment
2860 <li>New Jalview Logo</li>
2861 </ul> <em>Documentation and Development</em>
2863 <li>documentation for score matrices used in Jalview</li>
2864 <li>New Website!</li>
2866 <td><em>Application</em>
2868 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2869 wsdbfetch REST service</li>
2870 <li>Stop windows being moved outside desktop on OSX</li>
2871 <li>Filetype associations not installed for webstart
2873 <li>Jalview does not always retrieve progress of a JABAWS
2874 job execution in full once it is complete</li>
2875 <li>revise SHMR RSBS definition to ensure alignment is
2876 uploaded via ali_file parameter</li>
2877 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2878 <li>View all structures superposed fails with exception</li>
2879 <li>Jnet job queues forever if a very short sequence is
2880 submitted for prediction</li>
2881 <li>Cut and paste menu not opened when mouse clicked on
2883 <li>Putting fractional value into integer text box in
2884 alignment parameter dialog causes Jalview to hang</li>
2885 <li>Structure view highlighting doesn't work on
2887 <li>View all structures fails with exception shown in
2889 <li>Characters in filename associated with PDBEntry not
2890 escaped in a platform independent way</li>
2891 <li>Jalview desktop fails to launch with exception when
2893 <li>Tree calculation reports 'you must have 2 or more
2894 sequences selected' when selection is empty</li>
2895 <li>Jalview desktop fails to launch with jar signature
2896 failure when java web start temporary file caching is
2898 <li>DAS Sequence retrieval with range qualification
2899 results in sequence xref which includes range qualification</li>
2900 <li>Errors during processing of command line arguments
2901 cause progress bar (JAL-898) to be removed</li>
2902 <li>Replace comma for semi-colon option not disabled for
2903 DAS sources in sequence fetcher</li>
2904 <li>Cannot close news reader when JABAWS server warning
2905 dialog is shown</li>
2906 <li>Option widgets not updated to reflect user settings</li>
2907 <li>Edited sequence not submitted to web service</li>
2908 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2909 <li>InstallAnywhere installer doesn't unpack and run
2910 on OSX Mountain Lion</li>
2911 <li>Annotation panel not given a scroll bar when
2912 sequences with alignment annotation are pasted into the
2914 <li>Sequence associated annotation rows not associated
2915 when loaded from Jalview project</li>
2916 <li>Browser launch fails with NPE on java 1.7</li>
2917 <li>JABAWS alignment marked as finished when job was
2918 cancelled or job failed due to invalid input</li>
2919 <li>NPE with v2.7 example when clicking on Tree
2920 associated with all views</li>
2921 <li>Exceptions when copy/paste sequences with grouped
2922 annotation rows to new window</li>
2923 </ul> <em>Applet</em>
2925 <li>Sequence features are momentarily displayed before
2926 they are hidden using hidefeaturegroups applet parameter</li>
2927 <li>loading features via javascript API automatically
2928 enables feature display</li>
2929 <li>scrollToColumnIn javascript API method doesn't
2931 </ul> <em>General</em>
2933 <li>Redundancy removal fails for rna alignment</li>
2934 <li>PCA calculation fails when sequence has been selected
2935 and then deselected</li>
2936 <li>PCA window shows grey box when first opened on OSX</li>
2937 <li>Letters coloured pink in sequence logo when alignment
2938 coloured with clustalx</li>
2939 <li>Choosing fonts without letter symbols defined causes
2940 exceptions and redraw errors</li>
2941 <li>Initial PCA plot view is not same as manually
2942 reconfigured view</li>
2943 <li>Grouped annotation graph label has incorrect line
2945 <li>Grouped annotation graph label display is corrupted
2946 for lots of labels</li>
2951 <div align="center">
2952 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2955 <td><em>Application</em>
2957 <li>Jalview Desktop News Reader</li>
2958 <li>Tweaked default layout of web services menu</li>
2959 <li>View/alignment association menu to enable user to
2960 easily specify which alignment a multi-structure view takes
2961 its colours/correspondences from</li>
2962 <li>Allow properties file location to be specified as URL</li>
2963 <li>Extend Jalview project to preserve associations
2964 between many alignment views and a single Jmol display</li>
2965 <li>Store annotation row height in Jalview project file</li>
2966 <li>Annotation row column label formatting attributes
2967 stored in project file</li>
2968 <li>Annotation row order for auto-calculated annotation
2969 rows preserved in Jalview project file</li>
2970 <li>Visual progress indication when Jalview state is
2971 saved using Desktop window menu</li>
2972 <li>Visual indication that command line arguments are
2973 still being processed</li>
2974 <li>Groovy script execution from URL</li>
2975 <li>Colour by annotation default min and max colours in
2977 <li>Automatically associate PDB files dragged onto an
2978 alignment with sequences that have high similarity and
2980 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2981 <li>'view structures' option to open many
2982 structures in same window</li>
2983 <li>Sort associated views menu option for tree panel</li>
2984 <li>Group all JABA and non-JABA services for a particular
2985 analysis function in its own submenu</li>
2986 </ul> <em>Applet</em>
2988 <li>Userdefined and autogenerated annotation rows for
2990 <li>Adjustment of alignment annotation pane height</li>
2991 <li>Annotation scrollbar for annotation panel</li>
2992 <li>Drag to reorder annotation rows in annotation panel</li>
2993 <li>'automaticScrolling' parameter</li>
2994 <li>Allow sequences with partial ID string matches to be
2995 annotated from GFF/Jalview features files</li>
2996 <li>Sequence logo annotation row in applet</li>
2997 <li>Absolute paths relative to host server in applet
2998 parameters are treated as such</li>
2999 <li>New in the JalviewLite javascript API:
3001 <li>JalviewLite.js javascript library</li>
3002 <li>Javascript callbacks for
3004 <li>Applet initialisation</li>
3005 <li>Sequence/alignment mouse-overs and selections</li>
3008 <li>scrollTo row and column alignment scrolling
3010 <li>Select sequence/alignment regions from javascript</li>
3011 <li>javascript structure viewer harness to pass
3012 messages between Jmol and Jalview when running as
3013 distinct applets</li>
3014 <li>sortBy method</li>
3015 <li>Set of applet and application examples shipped
3016 with documentation</li>
3017 <li>New example to demonstrate JalviewLite and Jmol
3018 javascript message exchange</li>
3020 </ul> <em>General</em>
3022 <li>Enable Jmol displays to be associated with multiple
3023 multiple alignments</li>
3024 <li>Option to automatically sort alignment with new tree</li>
3025 <li>User configurable link to enable redirects to a
3026 www.Jalview.org mirror</li>
3027 <li>Jmol colours option for Jmol displays</li>
3028 <li>Configurable newline string when writing alignment
3029 and other flat files</li>
3030 <li>Allow alignment annotation description lines to
3031 contain html tags</li>
3032 </ul> <em>Documentation and Development</em>
3034 <li>Add groovy test harness for bulk load testing to
3036 <li>Groovy script to load and align a set of sequences
3037 using a web service before displaying the result in the
3038 Jalview desktop</li>
3039 <li>Restructured javascript and applet api documentation</li>
3040 <li>Ant target to publish example html files with applet
3042 <li>Netbeans project for building Jalview from source</li>
3043 <li>ant task to create online javadoc for Jalview source</li>
3045 <td><em>Application</em>
3047 <li>User defined colourscheme throws exception when
3048 current built in colourscheme is saved as new scheme</li>
3049 <li>AlignFrame->Save in application pops up save
3050 dialog for valid filename/format</li>
3051 <li>Cannot view associated structure for UniProt sequence</li>
3052 <li>PDB file association breaks for UniProt sequence
3054 <li>Associate PDB from file dialog does not tell you
3055 which sequence is to be associated with the file</li>
3056 <li>Find All raises null pointer exception when query
3057 only matches sequence IDs</li>
3058 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3059 <li>Jalview project with Jmol views created with Jalview
3060 2.4 cannot be loaded</li>
3061 <li>Filetype associations not installed for webstart
3063 <li>Two or more chains in a single PDB file associated
3064 with sequences in different alignments do not get coloured
3065 by their associated sequence</li>
3066 <li>Visibility status of autocalculated annotation row
3067 not preserved when project is loaded</li>
3068 <li>Annotation row height and visibility attributes not
3069 stored in Jalview project</li>
3070 <li>Tree bootstraps are not preserved when saved as a
3071 Jalview project</li>
3072 <li>Envision2 workflow tooltips are corrupted</li>
3073 <li>Enabling show group conservation also enables colour
3074 by conservation</li>
3075 <li>Duplicate group associated conservation or consensus
3076 created on new view</li>
3077 <li>Annotation scrollbar not displayed after 'show
3078 all hidden annotation rows' option selected</li>
3079 <li>Alignment quality not updated after alignment
3080 annotation row is hidden then shown</li>
3081 <li>Preserve colouring of structures coloured by
3082 sequences in pre Jalview 2.7 projects</li>
3083 <li>Web service job parameter dialog is not laid out
3085 <li>Web services menu not refreshed after 'reset
3086 services' button is pressed in preferences</li>
3087 <li>Annotation off by one in Jalview v2_3 example project</li>
3088 <li>Structures imported from file and saved in project
3089 get name like jalview_pdb1234.txt when reloaded</li>
3090 <li>Jalview does not always retrieve progress of a JABAWS
3091 job execution in full once it is complete</li>
3092 </ul> <em>Applet</em>
3094 <li>Alignment height set incorrectly when lots of
3095 annotation rows are displayed</li>
3096 <li>Relative URLs in feature HTML text not resolved to
3098 <li>View follows highlighting does not work for positions
3100 <li><= shown as = in tooltip</li>
3101 <li>Export features raises exception when no features
3103 <li>Separator string used for serialising lists of IDs
3104 for javascript api is modified when separator string
3105 provided as parameter</li>
3106 <li>Null pointer exception when selecting tree leaves for
3107 alignment with no existing selection</li>
3108 <li>Relative URLs for datasources assumed to be relative
3109 to applet's codebase</li>
3110 <li>Status bar not updated after finished searching and
3111 search wraps around to first result</li>
3112 <li>StructureSelectionManager instance shared between
3113 several Jalview applets causes race conditions and memory
3115 <li>Hover tooltip and mouseover of position on structure
3116 not sent from Jmol in applet</li>
3117 <li>Certain sequences of javascript method calls to
3118 applet API fatally hang browser</li>
3119 </ul> <em>General</em>
3121 <li>View follows structure mouseover scrolls beyond
3122 position with wrapped view and hidden regions</li>
3123 <li>Find sequence position moves to wrong residue
3124 with/without hidden columns</li>
3125 <li>Sequence length given in alignment properties window
3127 <li>InvalidNumberFormat exceptions thrown when trying to
3128 import PDB like structure files</li>
3129 <li>Positional search results are only highlighted
3130 between user-supplied sequence start/end bounds</li>
3131 <li>End attribute of sequence is not validated</li>
3132 <li>Find dialog only finds first sequence containing a
3133 given sequence position</li>
3134 <li>Sequence numbering not preserved in MSF alignment
3136 <li>Jalview PDB file reader does not extract sequence
3137 from nucleotide chains correctly</li>
3138 <li>Structure colours not updated when tree partition
3139 changed in alignment</li>
3140 <li>Sequence associated secondary structure not correctly
3141 parsed in interleaved stockholm</li>
3142 <li>Colour by annotation dialog does not restore current
3144 <li>Hiding (nearly) all sequences doesn't work
3146 <li>Sequences containing lowercase letters are not
3147 properly associated with their pdb files</li>
3148 </ul> <em>Documentation and Development</em>
3150 <li>schemas/JalviewWsParamSet.xsd corrupted by
3151 ApplyCopyright tool</li>
3156 <div align="center">
3157 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3160 <td><em>Application</em>
3162 <li>New warning dialog when the Jalview Desktop cannot
3163 contact web services</li>
3164 <li>JABA service parameters for a preset are shown in
3165 service job window</li>
3166 <li>JABA Service menu entries reworded</li>
3170 <li>Modeller PIR IO broken - cannot correctly import a
3171 pir file emitted by Jalview</li>
3172 <li>Existing feature settings transferred to new
3173 alignment view created from cut'n'paste</li>
3174 <li>Improved test for mixed amino/nucleotide chains when
3175 parsing PDB files</li>
3176 <li>Consensus and conservation annotation rows
3177 occasionally become blank for all new windows</li>
3178 <li>Exception raised when right clicking above sequences
3179 in wrapped view mode</li>
3180 </ul> <em>Application</em>
3182 <li>multiple multiply aligned structure views cause cpu
3183 usage to hit 100% and computer to hang</li>
3184 <li>Web Service parameter layout breaks for long user
3185 parameter names</li>
3186 <li>Jaba service discovery hangs desktop if Jaba server
3193 <div align="center">
3194 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3197 <td><em>Application</em>
3199 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3200 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3203 <li>Web Services preference tab</li>
3204 <li>Analysis parameters dialog box and user defined
3206 <li>Improved speed and layout of Envision2 service menu</li>
3207 <li>Superpose structures using associated sequence
3209 <li>Export coordinates and projection as CSV from PCA
3211 </ul> <em>Applet</em>
3213 <li>enable javascript: execution by the applet via the
3214 link out mechanism</li>
3215 </ul> <em>Other</em>
3217 <li>Updated the Jmol Jalview interface to work with Jmol
3219 <li>The Jalview Desktop and JalviewLite applet now
3220 require Java 1.5</li>
3221 <li>Allow Jalview feature colour specification for GFF
3222 sequence annotation files</li>
3223 <li>New 'colour by label' keword in Jalview feature file
3224 type colour specification</li>
3225 <li>New Jalview Desktop Groovy API method that allows a
3226 script to check if it being run in an interactive session or
3227 in a batch operation from the Jalview command line</li>
3231 <li>clustalx colourscheme colours Ds preferentially when
3232 both D+E are present in over 50% of the column</li>
3233 </ul> <em>Application</em>
3235 <li>typo in AlignmentFrame->View->Hide->all but
3236 selected Regions menu item</li>
3237 <li>sequence fetcher replaces ',' for ';' when the ',' is
3238 part of a valid accession ID</li>
3239 <li>fatal OOM if object retrieved by sequence fetcher
3240 runs out of memory</li>
3241 <li>unhandled Out of Memory Error when viewing pca
3242 analysis results</li>
3243 <li>InstallAnywhere builds fail to launch on OS X java
3244 10.5 update 4 (due to apple Java 1.6 update)</li>
3245 <li>Installanywhere Jalview silently fails to launch</li>
3246 </ul> <em>Applet</em>
3248 <li>Jalview.getFeatureGroups() raises an
3249 ArrayIndexOutOfBoundsException if no feature groups are
3256 <div align="center">
3257 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3263 <li>Alignment prettyprinter doesn't cope with long
3265 <li>clustalx colourscheme colours Ds preferentially when
3266 both D+E are present in over 50% of the column</li>
3267 <li>nucleic acid structures retrieved from PDB do not
3268 import correctly</li>
3269 <li>More columns get selected than were clicked on when a
3270 number of columns are hidden</li>
3271 <li>annotation label popup menu not providing correct
3272 add/hide/show options when rows are hidden or none are
3274 <li>Stockholm format shown in list of readable formats,
3275 and parser copes better with alignments from RFAM.</li>
3276 <li>CSV output of consensus only includes the percentage
3277 of all symbols if sequence logo display is enabled</li>
3279 </ul> <em>Applet</em>
3281 <li>annotation panel disappears when annotation is
3283 </ul> <em>Application</em>
3285 <li>Alignment view not redrawn properly when new
3286 alignment opened where annotation panel is visible but no
3287 annotations are present on alignment</li>
3288 <li>pasted region containing hidden columns is
3289 incorrectly displayed in new alignment window</li>
3290 <li>Jalview slow to complete operations when stdout is
3291 flooded (fix is to close the Jalview console)</li>
3292 <li>typo in AlignmentFrame->View->Hide->all but
3293 selected Rregions menu item.</li>
3294 <li>inconsistent group submenu and Format submenu entry
3295 'Un' or 'Non'conserved</li>
3296 <li>Sequence feature settings are being shared by
3297 multiple distinct alignments</li>
3298 <li>group annotation not recreated when tree partition is
3300 <li>double click on group annotation to select sequences
3301 does not propagate to associated trees</li>
3302 <li>Mac OSX specific issues:
3304 <li>exception raised when mouse clicked on desktop
3305 window background</li>
3306 <li>Desktop menu placed on menu bar and application
3307 name set correctly</li>
3308 <li>sequence feature settings not wide enough for the
3309 save feature colourscheme button</li>
3318 <div align="center">
3319 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3322 <td><em>New Capabilities</em>
3324 <li>URL links generated from description line for
3325 regular-expression based URL links (applet and application)
3327 <li>Non-positional feature URL links are shown in link
3329 <li>Linked viewing of nucleic acid sequences and
3331 <li>Automatic Scrolling option in View menu to display
3332 the currently highlighted region of an alignment.</li>
3333 <li>Order an alignment by sequence length, or using the
3334 average score or total feature count for each sequence.</li>
3335 <li>Shading features by score or associated description</li>
3336 <li>Subdivide alignment and groups based on identity of
3337 selected subsequence (Make Groups from Selection).</li>
3338 <li>New hide/show options including Shift+Control+H to
3339 hide everything but the currently selected region.</li>
3340 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3341 </ul> <em>Application</em>
3343 <li>Fetch DB References capabilities and UI expanded to
3344 support retrieval from DAS sequence sources</li>
3345 <li>Local DAS Sequence sources can be added via the
3346 command line or via the Add local source dialog box.</li>
3347 <li>DAS Dbref and DbxRef feature types are parsed as
3348 database references and protein_name is parsed as
3349 description line (BioSapiens terms).</li>
3350 <li>Enable or disable non-positional feature and database
3351 references in sequence ID tooltip from View menu in
3353 <!-- <li>New hidden columns and rows and representatives capabilities
3354 in annotations file (in progress - not yet fully implemented)</li> -->
3355 <li>Group-associated consensus, sequence logos and
3356 conservation plots</li>
3357 <li>Symbol distributions for each column can be exported
3358 and visualized as sequence logos</li>
3359 <li>Optionally scale multi-character column labels to fit
3360 within each column of annotation row<!-- todo for applet -->
3362 <li>Optional automatic sort of associated alignment view
3363 when a new tree is opened.</li>
3364 <li>Jalview Java Console</li>
3365 <li>Better placement of desktop window when moving
3366 between different screens.</li>
3367 <li>New preference items for sequence ID tooltip and
3368 consensus annotation</li>
3369 <li>Client to submit sequences and IDs to Envision2
3371 <li><em>Vamsas Capabilities</em>
3373 <li>Improved VAMSAS synchronization (Jalview archive
3374 used to preserve views, structures, and tree display
3376 <li>Import of vamsas documents from disk or URL via
3378 <li>Sharing of selected regions between views and
3379 with other VAMSAS applications (Experimental feature!)</li>
3380 <li>Updated API to VAMSAS version 0.2</li>
3382 </ul> <em>Applet</em>
3384 <li>Middle button resizes annotation row height</li>
3387 <li>sortByTree (true/false) - automatically sort the
3388 associated alignment view by the tree when a new tree is
3390 <li>showTreeBootstraps (true/false) - show or hide
3391 branch bootstraps (default is to show them if available)</li>
3392 <li>showTreeDistances (true/false) - show or hide
3393 branch lengths (default is to show them if available)</li>
3394 <li>showUnlinkedTreeNodes (true/false) - indicate if
3395 unassociated nodes should be highlighted in the tree
3397 <li>heightScale and widthScale (1.0 or more) -
3398 increase the height or width of a cell in the alignment
3399 grid relative to the current font size.</li>
3402 <li>Non-positional features displayed in sequence ID
3404 </ul> <em>Other</em>
3406 <li>Features format: graduated colour definitions and
3407 specification of feature scores</li>
3408 <li>Alignment Annotations format: new keywords for group
3409 associated annotation (GROUP_REF) and annotation row display
3410 properties (ROW_PROPERTIES)</li>
3411 <li>XML formats extended to support graduated feature
3412 colourschemes, group associated annotation, and profile
3413 visualization settings.</li></td>
3416 <li>Source field in GFF files parsed as feature source
3417 rather than description</li>
3418 <li>Non-positional features are now included in sequence
3419 feature and gff files (controlled via non-positional feature
3420 visibility in tooltip).</li>
3421 <li>URL links generated for all feature links (bugfix)</li>
3422 <li>Added URL embedding instructions to features file
3424 <li>Codons containing ambiguous nucleotides translated as
3425 'X' in peptide product</li>
3426 <li>Match case switch in find dialog box works for both
3427 sequence ID and sequence string and query strings do not
3428 have to be in upper case to match case-insensitively.</li>
3429 <li>AMSA files only contain first column of
3430 multi-character column annotation labels</li>
3431 <li>Jalview Annotation File generation/parsing consistent
3432 with documentation (e.g. Stockholm annotation can be
3433 exported and re-imported)</li>
3434 <li>PDB files without embedded PDB IDs given a friendly
3436 <li>Find incrementally searches ID string matches as well
3437 as subsequence matches, and correctly reports total number
3441 <li>Better handling of exceptions during sequence
3443 <li>Dasobert generated non-positional feature URL
3444 link text excludes the start_end suffix</li>
3445 <li>DAS feature and source retrieval buttons disabled
3446 when fetch or registry operations in progress.</li>
3447 <li>PDB files retrieved from URLs are cached properly</li>
3448 <li>Sequence description lines properly shared via
3450 <li>Sequence fetcher fetches multiple records for all
3452 <li>Ensured that command line das feature retrieval
3453 completes before alignment figures are generated.</li>
3454 <li>Reduced time taken when opening file browser for
3456 <li>isAligned check prior to calculating tree, PCA or
3457 submitting an MSA to JNet now excludes hidden sequences.</li>
3458 <li>User defined group colours properly recovered
3459 from Jalview projects.</li>
3468 <div align="center">
3469 <strong>2.4.0.b2</strong><br> 28/10/2009
3474 <li>Experimental support for google analytics usage
3476 <li>Jalview privacy settings (user preferences and docs).</li>
3481 <li>Race condition in applet preventing startup in
3483 <li>Exception when feature created from selection beyond
3484 length of sequence.</li>
3485 <li>Allow synthetic PDB files to be imported gracefully</li>
3486 <li>Sequence associated annotation rows associate with
3487 all sequences with a given id</li>
3488 <li>Find function matches case-insensitively for sequence
3489 ID string searches</li>
3490 <li>Non-standard characters do not cause pairwise
3491 alignment to fail with exception</li>
3492 </ul> <em>Application Issues</em>
3494 <li>Sequences are now validated against EMBL database</li>
3495 <li>Sequence fetcher fetches multiple records for all
3497 </ul> <em>InstallAnywhere Issues</em>
3499 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3500 issue with installAnywhere mechanism)</li>
3501 <li>Command line launching of JARs from InstallAnywhere
3502 version (java class versioning error fixed)</li>
3509 <div align="center">
3510 <strong>2.4</strong><br> 27/8/2008
3513 <td><em>User Interface</em>
3515 <li>Linked highlighting of codon and amino acid from
3516 translation and protein products</li>
3517 <li>Linked highlighting of structure associated with
3518 residue mapping to codon position</li>
3519 <li>Sequence Fetcher provides example accession numbers
3520 and 'clear' button</li>
3521 <li>MemoryMonitor added as an option under Desktop's
3523 <li>Extract score function to parse whitespace separated
3524 numeric data in description line</li>
3525 <li>Column labels in alignment annotation can be centred.</li>
3526 <li>Tooltip for sequence associated annotation give name
3528 </ul> <em>Web Services and URL fetching</em>
3530 <li>JPred3 web service</li>
3531 <li>Prototype sequence search client (no public services
3533 <li>Fetch either seed alignment or full alignment from
3535 <li>URL Links created for matching database cross
3536 references as well as sequence ID</li>
3537 <li>URL Links can be created using regular-expressions</li>
3538 </ul> <em>Sequence Database Connectivity</em>
3540 <li>Retrieval of cross-referenced sequences from other
3542 <li>Generalised database reference retrieval and
3543 validation to all fetchable databases</li>
3544 <li>Fetch sequences from DAS sources supporting the
3545 sequence command</li>
3546 </ul> <em>Import and Export</em>
3547 <li>export annotation rows as CSV for spreadsheet import</li>
3548 <li>Jalview projects record alignment dataset associations,
3549 EMBL products, and cDNA sequence mappings</li>
3550 <li>Sequence Group colour can be specified in Annotation
3552 <li>Ad-hoc colouring of group in Annotation File using RGB
3553 triplet as name of colourscheme</li>
3554 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3556 <li>treenode binding for VAMSAS tree exchange</li>
3557 <li>local editing and update of sequences in VAMSAS
3558 alignments (experimental)</li>
3559 <li>Create new or select existing session to join</li>
3560 <li>load and save of vamsas documents</li>
3561 </ul> <em>Application command line</em>
3563 <li>-tree parameter to open trees (introduced for passing
3565 <li>-fetchfrom command line argument to specify nicknames
3566 of DAS servers to query for alignment features</li>
3567 <li>-dasserver command line argument to add new servers
3568 that are also automatically queried for features</li>
3569 <li>-groovy command line argument executes a given groovy
3570 script after all input data has been loaded and parsed</li>
3571 </ul> <em>Applet-Application data exchange</em>
3573 <li>Trees passed as applet parameters can be passed to
3574 application (when using "View in full
3575 application")</li>
3576 </ul> <em>Applet Parameters</em>
3578 <li>feature group display control parameter</li>
3579 <li>debug parameter</li>
3580 <li>showbutton parameter</li>
3581 </ul> <em>Applet API methods</em>
3583 <li>newView public method</li>
3584 <li>Window (current view) specific get/set public methods</li>
3585 <li>Feature display control methods</li>
3586 <li>get list of currently selected sequences</li>
3587 </ul> <em>New Jalview distribution features</em>
3589 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3590 <li>RELEASE file gives build properties for the latest
3591 Jalview release.</li>
3592 <li>Java 1.1 Applet build made easier and donotobfuscate
3593 property controls execution of obfuscator</li>
3594 <li>Build target for generating source distribution</li>
3595 <li>Debug flag for javacc</li>
3596 <li>.jalview_properties file is documented (slightly) in
3597 jalview.bin.Cache</li>
3598 <li>Continuous Build Integration for stable and
3599 development version of Application, Applet and source
3604 <li>selected region output includes visible annotations
3605 (for certain formats)</li>
3606 <li>edit label/displaychar contains existing label/char
3608 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3609 <li>shorter peptide product names from EMBL records</li>
3610 <li>Newick string generator makes compact representations</li>
3611 <li>bootstrap values parsed correctly for tree files with
3613 <li>pathological filechooser bug avoided by not allowing
3614 filenames containing a ':'</li>
3615 <li>Fixed exception when parsing GFF files containing
3616 global sequence features</li>
3617 <li>Alignment datasets are finalized only when number of
3618 references from alignment sequences goes to zero</li>
3619 <li>Close of tree branch colour box without colour
3620 selection causes cascading exceptions</li>
3621 <li>occasional negative imgwidth exceptions</li>
3622 <li>better reporting of non-fatal warnings to user when
3623 file parsing fails.</li>
3624 <li>Save works when Jalview project is default format</li>
3625 <li>Save as dialog opened if current alignment format is
3626 not a valid output format</li>
3627 <li>UniProt canonical names introduced for both das and
3629 <li>Histidine should be midblue (not pink!) in Zappo</li>
3630 <li>error messages passed up and output when data read
3632 <li>edit undo recovers previous dataset sequence when
3633 sequence is edited</li>
3634 <li>allow PDB files without pdb ID HEADER lines (like
3635 those generated by MODELLER) to be read in properly</li>
3636 <li>allow reading of JPred concise files as a normal
3638 <li>Stockholm annotation parsing and alignment properties
3639 import fixed for PFAM records</li>
3640 <li>Structure view windows have correct name in Desktop
3642 <li>annotation consisting of sequence associated scores
3643 can be read and written correctly to annotation file</li>
3644 <li>Aligned cDNA translation to aligned peptide works
3646 <li>Fixed display of hidden sequence markers and
3647 non-italic font for representatives in Applet</li>
3648 <li>Applet Menus are always embedded in applet window on
3650 <li>Newly shown features appear at top of stack (in
3652 <li>Annotations added via parameter not drawn properly
3653 due to null pointer exceptions</li>
3654 <li>Secondary structure lines are drawn starting from
3655 first column of alignment</li>
3656 <li>UniProt XML import updated for new schema release in
3658 <li>Sequence feature to sequence ID match for Features
3659 file is case-insensitive</li>
3660 <li>Sequence features read from Features file appended to
3661 all sequences with matching IDs</li>
3662 <li>PDB structure coloured correctly for associated views
3663 containing a sub-sequence</li>
3664 <li>PDB files can be retrieved by applet from Jar files</li>
3665 <li>feature and annotation file applet parameters
3666 referring to different directories are retrieved correctly</li>
3667 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3668 <li>Fixed application hang whilst waiting for
3669 splash-screen version check to complete</li>
3670 <li>Applet properly URLencodes input parameter values
3671 when passing them to the launchApp service</li>
3672 <li>display name and local features preserved in results
3673 retrieved from web service</li>
3674 <li>Visual delay indication for sequence retrieval and
3675 sequence fetcher initialisation</li>
3676 <li>updated Application to use DAS 1.53e version of
3677 dasobert DAS client</li>
3678 <li>Re-instated Full AMSA support and .amsa file
3680 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3688 <div align="center">
3689 <strong>2.3</strong><br> 9/5/07
3694 <li>Jmol 11.0.2 integration</li>
3695 <li>PDB views stored in Jalview XML files</li>
3696 <li>Slide sequences</li>
3697 <li>Edit sequence in place</li>
3698 <li>EMBL CDS features</li>
3699 <li>DAS Feature mapping</li>
3700 <li>Feature ordering</li>
3701 <li>Alignment Properties</li>
3702 <li>Annotation Scores</li>
3703 <li>Sort by scores</li>
3704 <li>Feature/annotation editing in applet</li>
3709 <li>Headless state operation in 2.2.1</li>
3710 <li>Incorrect and unstable DNA pairwise alignment</li>
3711 <li>Cut and paste of sequences with annotation</li>
3712 <li>Feature group display state in XML</li>
3713 <li>Feature ordering in XML</li>
3714 <li>blc file iteration selection using filename # suffix</li>
3715 <li>Stockholm alignment properties</li>
3716 <li>Stockhom alignment secondary structure annotation</li>
3717 <li>2.2.1 applet had no feature transparency</li>
3718 <li>Number pad keys can be used in cursor mode</li>
3719 <li>Structure Viewer mirror image resolved</li>
3726 <div align="center">
3727 <strong>2.2.1</strong><br> 12/2/07
3732 <li>Non standard characters can be read and displayed
3733 <li>Annotations/Features can be imported/exported to the
3735 <li>Applet allows editing of sequence/annotation/group
3736 name & description
3737 <li>Preference setting to display sequence name in
3739 <li>Annotation file format extended to allow
3740 Sequence_groups to be defined
3741 <li>Default opening of alignment overview panel can be
3742 specified in preferences
3743 <li>PDB residue numbering annotation added to associated
3749 <li>Applet crash under certain Linux OS with Java 1.6
3751 <li>Annotation file export / import bugs fixed
3752 <li>PNG / EPS image output bugs fixed
3758 <div align="center">
3759 <strong>2.2</strong><br> 27/11/06
3764 <li>Multiple views on alignment
3765 <li>Sequence feature editing
3766 <li>"Reload" alignment
3767 <li>"Save" to current filename
3768 <li>Background dependent text colour
3769 <li>Right align sequence ids
3770 <li>User-defined lower case residue colours
3773 <li>Menu item accelerator keys
3774 <li>Control-V pastes to current alignment
3775 <li>Cancel button for DAS Feature Fetching
3776 <li>PCA and PDB Viewers zoom via mouse roller
3777 <li>User-defined sub-tree colours and sub-tree selection
3779 <li>'New Window' button on the 'Output to Text box'
3784 <li>New memory efficient Undo/Redo System
3785 <li>Optimised symbol lookups and conservation/consensus
3787 <li>Region Conservation/Consensus recalculated after
3789 <li>Fixed Remove Empty Columns Bug (empty columns at end
3791 <li>Slowed DAS Feature Fetching for increased robustness.
3793 <li>Made angle brackets in ASCII feature descriptions
3795 <li>Re-instated Zoom function for PCA
3796 <li>Sequence descriptions conserved in web service
3798 <li>UniProt ID discoverer uses any word separated by
3800 <li>WsDbFetch query/result association resolved
3801 <li>Tree leaf to sequence mapping improved
3802 <li>Smooth fonts switch moved to FontChooser dialog box.
3809 <div align="center">
3810 <strong>2.1.1</strong><br> 12/9/06
3815 <li>Copy consensus sequence to clipboard</li>
3820 <li>Image output - rightmost residues are rendered if
3821 sequence id panel has been resized</li>
3822 <li>Image output - all offscreen group boundaries are
3824 <li>Annotation files with sequence references - all
3825 elements in file are relative to sequence position</li>
3826 <li>Mac Applet users can use Alt key for group editing</li>
3832 <div align="center">
3833 <strong>2.1</strong><br> 22/8/06
3838 <li>MAFFT Multiple Alignment in default Web Service list</li>
3839 <li>DAS Feature fetching</li>
3840 <li>Hide sequences and columns</li>
3841 <li>Export Annotations and Features</li>
3842 <li>GFF file reading / writing</li>
3843 <li>Associate structures with sequences from local PDB
3845 <li>Add sequences to exisiting alignment</li>
3846 <li>Recently opened files / URL lists</li>
3847 <li>Applet can launch the full application</li>
3848 <li>Applet has transparency for features (Java 1.2
3850 <li>Applet has user defined colours parameter</li>
3851 <li>Applet can load sequences from parameter
3852 "sequence<em>x</em>"
3858 <li>Redundancy Panel reinstalled in the Applet</li>
3859 <li>Monospaced font - EPS / rescaling bug fixed</li>
3860 <li>Annotation files with sequence references bug fixed</li>
3866 <div align="center">
3867 <strong>2.08.1</strong><br> 2/5/06
3872 <li>Change case of selected region from Popup menu</li>
3873 <li>Choose to match case when searching</li>
3874 <li>Middle mouse button and mouse movement can compress /
3875 expand the visible width and height of the alignment</li>
3880 <li>Annotation Panel displays complete JNet results</li>
3886 <div align="center">
3887 <strong>2.08b</strong><br> 18/4/06
3893 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3894 <li>Righthand label on wrapped alignments shows correct
3901 <div align="center">
3902 <strong>2.08</strong><br> 10/4/06
3907 <li>Editing can be locked to the selection area</li>
3908 <li>Keyboard editing</li>
3909 <li>Create sequence features from searches</li>
3910 <li>Precalculated annotations can be loaded onto
3912 <li>Features file allows grouping of features</li>
3913 <li>Annotation Colouring scheme added</li>
3914 <li>Smooth fonts off by default - Faster rendering</li>
3915 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3920 <li>Drag & Drop fixed on Linux</li>
3921 <li>Jalview Archive file faster to load/save, sequence
3922 descriptions saved.</li>
3928 <div align="center">
3929 <strong>2.07</strong><br> 12/12/05
3934 <li>PDB Structure Viewer enhanced</li>
3935 <li>Sequence Feature retrieval and display enhanced</li>
3936 <li>Choose to output sequence start-end after sequence
3937 name for file output</li>
3938 <li>Sequence Fetcher WSDBFetch@EBI</li>
3939 <li>Applet can read feature files, PDB files and can be
3940 used for HTML form input</li>
3945 <li>HTML output writes groups and features</li>
3946 <li>Group editing is Control and mouse click</li>
3947 <li>File IO bugs</li>
3953 <div align="center">
3954 <strong>2.06</strong><br> 28/9/05
3959 <li>View annotations in wrapped mode</li>
3960 <li>More options for PCA viewer</li>
3965 <li>GUI bugs resolved</li>
3966 <li>Runs with -nodisplay from command line</li>
3972 <div align="center">
3973 <strong>2.05b</strong><br> 15/9/05
3978 <li>Choose EPS export as lineart or text</li>
3979 <li>Jar files are executable</li>
3980 <li>Can read in Uracil - maps to unknown residue</li>
3985 <li>Known OutOfMemory errors give warning message</li>
3986 <li>Overview window calculated more efficiently</li>
3987 <li>Several GUI bugs resolved</li>
3993 <div align="center">
3994 <strong>2.05</strong><br> 30/8/05
3999 <li>Edit and annotate in "Wrapped" view</li>
4004 <li>Several GUI bugs resolved</li>
4010 <div align="center">
4011 <strong>2.04</strong><br> 24/8/05
4016 <li>Hold down mouse wheel & scroll to change font
4022 <li>Improved JPred client reliability</li>
4023 <li>Improved loading of Jalview files</li>
4029 <div align="center">
4030 <strong>2.03</strong><br> 18/8/05
4035 <li>Set Proxy server name and port in preferences</li>
4036 <li>Multiple URL links from sequence ids</li>
4037 <li>User Defined Colours can have a scheme name and added
4039 <li>Choose to ignore gaps in consensus calculation</li>
4040 <li>Unix users can set default web browser</li>
4041 <li>Runs without GUI for batch processing</li>
4042 <li>Dynamically generated Web Service Menus</li>
4047 <li>InstallAnywhere download for Sparc Solaris</li>
4053 <div align="center">
4054 <strong>2.02</strong><br> 18/7/05
4060 <li>Copy & Paste order of sequences maintains
4061 alignment order.</li>
4067 <div align="center">
4068 <strong>2.01</strong><br> 12/7/05
4073 <li>Use delete key for deleting selection.</li>
4074 <li>Use Mouse wheel to scroll sequences.</li>
4075 <li>Help file updated to describe how to add alignment
4077 <li>Version and build date written to build properties
4079 <li>InstallAnywhere installation will check for updates
4080 at launch of Jalview.</li>
4085 <li>Delete gaps bug fixed.</li>
4086 <li>FileChooser sorts columns.</li>
4087 <li>Can remove groups one by one.</li>
4088 <li>Filechooser icons installed.</li>
4089 <li>Finder ignores return character when searching.
4090 Return key will initiate a search.<br>
4097 <div align="center">
4098 <strong>2.0</strong><br> 20/6/05
4103 <li>New codebase</li>