3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>6/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-3101 -->Default memory for Jalview webstart and
81 InstallAnywhere increased to 1G.
84 <!-- JAL-247 -->Hidden sequence markers and representative
85 sequence bolding included when exporting alignment as EPS,
86 SVG, PNG or HTML. <em>Display is configured via the
87 Format menu, or for command-line use via a jalview
91 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
92 API and sequence data now imported as JSON.
95 <!-- JAL-3065 -->Change in recommended way of starting
96 Jalview via a Java command line: add jars in lib directory
97 to CLASSPATH, rather than via the deprecated java.ext.dirs
104 <!-- JAL-3047 -->Support added to execute test suite
105 instrumented with <a href="http://openclover.org/">Open
110 <td><div align="left">
114 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
115 row shown in Feredoxin Structure alignment view of example
119 <!-- JAL-2854 -->Annotation obscures sequences if lots of
120 annotation displayed.
123 <!-- JAL-3087 -->Corrupted display when switching to
124 wrapped mode when sequence panel's vertical scrollbar is
128 <!-- JAL-3003 -->Alignment is black in exported EPS file
129 when sequences are selected in exported view.</em>
132 <!-- JAL-3059 -->Groups with different coloured borders
133 aren't rendered with correct colour.
136 <!-- JAL-3092 -->Jalview could hang when importing certain
137 types of knotted RNA secondary structure.
140 <!-- JAL-3095 -->Sequence highlight and selection in
141 trimmed VARNA 2D structure is incorrect for sequences that
145 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
146 annotation when columns are inserted into an alignment,
147 and when exporting as Stockholm flatfile.
150 <!-- JAL-3053 -->Jalview annotation rows containing upper
151 and lower-case 'E' and 'H' do not automatically get
152 treated as RNA secondary structure.
155 <!-- JAL-3106 -->.jvp should be used as default extension
156 (not .jar) when saving a jalview project file.
159 <!-- JAL-3105 -->Mac Users: closing a window correctly
160 transfers focus to previous window on OSX
163 <em>Java 10 Issues</em>
166 <!-- JAL-2988 -->OSX - Can't save new files via the File
167 or export menus by typing in a name into the Save dialog
175 <td width="60" nowrap>
177 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
178 <em>7/06/2018</em></strong>
181 <td><div align="left">
185 <!-- JAL-2920 -->Use HGVS nomenclature for variant
186 annotation retrieved from Uniprot
189 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
190 onto the Jalview Desktop
194 <td><div align="left">
198 <!-- JAL-3017 -->Cannot import features with multiple
199 variant elements (blocks import of some Uniprot records)
202 <!-- JAL-2997 -->Clustal files with sequence positions in
203 right-hand column parsed correctly
206 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
207 not alignment area in exported graphic
210 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
211 window has input focus
214 <!-- JAL-2992 -->Annotation panel set too high when
215 annotation added to view (Windows)
218 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
219 network connectivity is poor
222 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
223 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
224 the currently open URL and links from a page viewed in
225 Firefox or Chrome on Windows is now fully supported. If
226 you are using Edge, only links in the page can be
227 dragged, and with Internet Explorer, only the currently
228 open URL in the browser can be dropped onto Jalview.</em>
234 <td width="60" nowrap>
236 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
239 <td><div align="left">
243 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
244 for disabling automatic superposition of multiple
245 structures and open structures in existing views
248 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
249 ID and annotation area margins can be click-dragged to
253 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
257 <!-- JAL-2759 -->Improved performance for large alignments
258 and lots of hidden columns
261 <!-- JAL-2593 -->Improved performance when rendering lots
262 of features (particularly when transparency is disabled)
267 <td><div align="left">
270 <!-- JAL-2899 -->Structure and Overview aren't updated
271 when Colour By Annotation threshold slider is adjusted
274 <!-- JAL-2778 -->Slow redraw when Overview panel shown
275 overlapping alignment panel
278 <!-- JAL-2929 -->Overview doesn't show end of unpadded
282 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
283 improved: CDS not handled correctly if transcript has no
287 <!-- JAL-2321 -->Secondary structure and temperature
288 factor annotation not added to sequence when local PDB
289 file associated with it by drag'n'drop or structure
293 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
294 dialog doesn't import PDB files dropped on an alignment
297 <!-- JAL-2666 -->Linked scrolling via protein horizontal
298 scroll bar doesn't work for some CDS/Protein views
301 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
302 Java 1.8u153 onwards and Java 1.9u4+.
305 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
306 columns in annotation row
309 <!-- JAL-2913 -->Preferences panel's ID Width control is not
310 honored in batch mode
313 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
314 for structures added to existing Jmol view
317 <!-- JAL-2223 -->'View Mappings' includes duplicate
318 entries after importing project with multiple views
321 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
322 protein sequences via SIFTS from associated PDB entries
323 with negative residue numbers or missing residues fails
326 <!-- JAL-2952 -->Exception when shading sequence with negative
327 Temperature Factor values from annotated PDB files (e.g.
328 as generated by CONSURF)
331 <!-- JAL-2920 -->Uniprot 'sequence variant' features
332 tooltip doesn't include a text description of mutation
335 <!-- JAL-2922 -->Invert displayed features very slow when
336 structure and/or overview windows are also shown
339 <!-- JAL-2954 -->Selecting columns from highlighted regions
340 very slow for alignments with large numbers of sequences
343 <!-- JAL-2925 -->Copy Consensus fails for group consensus
344 with 'StringIndexOutOfBounds'
347 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
348 platforms running Java 10
351 <!-- JAL-2960 -->Adding a structure to existing structure
352 view appears to do nothing because the view is hidden behind the alignment view
358 <!-- JAL-2926 -->Copy consensus sequence option in applet
359 should copy the group consensus when popup is opened on it
365 <!-- JAL-2913 -->Fixed ID width preference is not respected
368 <em>New Known Defects</em>
371 <!-- JAL-2973 --> Exceptions occasionally raised when
372 editing a large alignment and overview is displayed
375 <!-- JAL-2974 -->'Overview updating' progress bar is shown
376 repeatedly after a series of edits even when the overview
377 is no longer reflecting updates
380 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
381 structures for protein subsequence (if 'Trim Retrieved
382 Sequences' enabled) or Ensembl isoforms (Workaround in
383 2.10.4 is to fail back to N&W mapping)
390 <td width="60" nowrap>
392 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
395 <td><div align="left">
396 <ul><li>Updated Certum Codesigning Certificate
397 (Valid till 30th November 2018)</li></ul></div></td>
398 <td><div align="left">
401 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
402 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
403 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
404 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
405 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
406 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
407 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
413 <td width="60" nowrap>
415 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
418 <td><div align="left">
422 <!-- JAL-2446 -->Faster and more efficient management and
423 rendering of sequence features
426 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
427 429 rate limit request hander
430 <!-- JAL-2773 -->Structure views don't get updated unless
431 their colours have changed
434 <!-- JAL-2495 -->All linked sequences are highlighted for
435 a structure mousover (Jmol) or selection (Chimera)
438 <!-- JAL-2790 -->'Cancel' button in progress bar for
439 JABAWS AACon, RNAAliFold and Disorder prediction jobs
442 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
443 view from Ensembl locus cross-references
446 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
450 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
451 feature can be disabled
454 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
455 PDB easier retrieval of sequences for lists of IDs
458 <!-- JAL-2758 -->Short names for sequences retrieved from
464 <li>Groovy interpreter updated to 2.4.12</li>
465 <li>Example groovy script for generating a matrix of
466 percent identity scores for current alignment.</li>
468 <em>Testing and Deployment</em>
471 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
475 <td><div align="left">
479 <!-- JAL-2643 -->Pressing tab after updating the colour
480 threshold text field doesn't trigger an update to the
484 <!-- JAL-2682 -->Race condition when parsing sequence ID
488 <!-- JAL-2608 -->Overview windows are also closed when
489 alignment window is closed
492 <!-- JAL-2548 -->Export of features doesn't always respect
496 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
497 takes a long time in Cursor mode
503 <!-- JAL-2777 -->Structures with whitespace chainCode
504 cannot be viewed in Chimera
507 <!-- JAL-2728 -->Protein annotation panel too high in
511 <!-- JAL-2757 -->Can't edit the query after the server
512 error warning icon is shown in Uniprot and PDB Free Text
516 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
519 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
522 <!-- JAL-2739 -->Hidden column marker in last column not
523 rendered when switching back from Wrapped to normal view
526 <!-- JAL-2768 -->Annotation display corrupted when
527 scrolling right in unwapped alignment view
530 <!-- JAL-2542 -->Existing features on subsequence
531 incorrectly relocated when full sequence retrieved from
535 <!-- JAL-2733 -->Last reported memory still shown when
536 Desktop->Show Memory is unticked (OSX only)
539 <!-- JAL-2658 -->Amend Features dialog doesn't allow
540 features of same type and group to be selected for
544 <!-- JAL-2524 -->Jalview becomes sluggish in wide
545 alignments when hidden columns are present
548 <!-- JAL-2392 -->Jalview freezes when loading and
549 displaying several structures
552 <!-- JAL-2732 -->Black outlines left after resizing or
556 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
557 within the Jalview desktop on OSX
560 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
561 when in wrapped alignment mode
564 <!-- JAL-2636 -->Scale mark not shown when close to right
565 hand end of alignment
568 <!-- JAL-2684 -->Pairwise alignment of selected regions of
569 each selected sequence do not have correct start/end
573 <!-- JAL-2793 -->Alignment ruler height set incorrectly
574 after canceling the Alignment Window's Font dialog
577 <!-- JAL-2036 -->Show cross-references not enabled after
578 restoring project until a new view is created
581 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
582 URL links appears when only default EMBL-EBI link is
583 configured (since 2.10.2b2)
586 <!-- JAL-2775 -->Overview redraws whole window when box
590 <!-- JAL-2225 -->Structure viewer doesn't map all chains
591 in a multi-chain structure when viewing alignment
592 involving more than one chain (since 2.10)
595 <!-- JAL-2811 -->Double residue highlights in cursor mode
596 if new selection moves alignment window
599 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
600 arrow key in cursor mode to pass hidden column marker
603 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
604 that produces correctly annotated transcripts and products
607 <!-- JAL-2776 -->Toggling a feature group after first time
608 doesn't update associated structure view
611 <em>Applet</em><br />
614 <!-- JAL-2687 -->Concurrent modification exception when
615 closing alignment panel
618 <em>BioJSON</em><br />
621 <!-- JAL-2546 -->BioJSON export does not preserve
622 non-positional features
625 <em>New Known Issues</em>
628 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
629 sequence features correctly (for many previous versions of
633 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
634 using cursor in wrapped panel other than top
637 <!-- JAL-2791 -->Select columns containing feature ignores
638 graduated colour threshold
641 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
642 always preserve numbering and sequence features
645 <em>Known Java 9 Issues</em>
648 <!-- JAL-2902 -->Groovy Console very slow to open and is
649 not responsive when entering characters (Webstart, Java
656 <td width="60" nowrap>
658 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
659 <em>2/10/2017</em></strong>
662 <td><div align="left">
663 <em>New features in Jalview Desktop</em>
666 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
668 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
672 <td><div align="left">
676 <td width="60" nowrap>
678 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
679 <em>7/9/2017</em></strong>
682 <td><div align="left">
686 <!-- JAL-2588 -->Show gaps in overview window by colouring
687 in grey (sequences used to be coloured grey, and gaps were
691 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
695 <!-- JAL-2587 -->Overview updates immediately on increase
696 in size and progress bar shown as higher resolution
697 overview is recalculated
702 <td><div align="left">
706 <!-- JAL-2664 -->Overview window redraws every hidden
707 column region row by row
710 <!-- JAL-2681 -->duplicate protein sequences shown after
711 retrieving Ensembl crossrefs for sequences from Uniprot
714 <!-- JAL-2603 -->Overview window throws NPE if show boxes
715 format setting is unticked
718 <!-- JAL-2610 -->Groups are coloured wrongly in overview
719 if group has show boxes format setting unticked
722 <!-- JAL-2672,JAL-2665 -->Redraw problems when
723 autoscrolling whilst dragging current selection group to
724 include sequences and columns not currently displayed
727 <!-- JAL-2691 -->Not all chains are mapped when multimeric
728 assemblies are imported via CIF file
731 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
732 displayed when threshold or conservation colouring is also
736 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
740 <!-- JAL-2673 -->Jalview continues to scroll after
741 dragging a selected region off the visible region of the
745 <!-- JAL-2724 -->Cannot apply annotation based
746 colourscheme to all groups in a view
749 <!-- JAL-2511 -->IDs don't line up with sequences
750 initially after font size change using the Font chooser or
757 <td width="60" nowrap>
759 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
762 <td><div align="left">
763 <em>Calculations</em>
767 <!-- JAL-1933 -->Occupancy annotation row shows number of
768 ungapped positions in each column of the alignment.
771 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
772 a calculation dialog box
775 <!-- JAL-2379 -->Revised implementation of PCA for speed
776 and memory efficiency (~30x faster)
779 <!-- JAL-2403 -->Revised implementation of sequence
780 similarity scores as used by Tree, PCA, Shading Consensus
781 and other calculations
784 <!-- JAL-2416 -->Score matrices are stored as resource
785 files within the Jalview codebase
788 <!-- JAL-2500 -->Trees computed on Sequence Feature
789 Similarity may have different topology due to increased
796 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
797 model for alignments and groups
800 <!-- JAL-384 -->Custom shading schemes created via groovy
807 <!-- JAL-2526 -->Efficiency improvements for interacting
808 with alignment and overview windows
811 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
815 <!-- JAL-2388 -->Hidden columns and sequences can be
819 <!-- JAL-2611 -->Click-drag in visible area allows fine
820 adjustment of visible position
824 <em>Data import/export</em>
827 <!-- JAL-2535 -->Posterior probability annotation from
828 Stockholm files imported as sequence associated annotation
831 <!-- JAL-2507 -->More robust per-sequence positional
832 annotation input/output via stockholm flatfile
835 <!-- JAL-2533 -->Sequence names don't include file
836 extension when importing structure files without embedded
837 names or PDB accessions
840 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
841 format sequence substitution matrices
844 <em>User Interface</em>
847 <!-- JAL-2447 --> Experimental Features Checkbox in
848 Desktop's Tools menu to hide or show untested features in
852 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
853 via Overview or sequence motif search operations
856 <!-- JAL-2547 -->Amend sequence features dialog box can be
857 opened by double clicking gaps within sequence feature
861 <!-- JAL-1476 -->Status bar message shown when not enough
862 aligned positions were available to create a 3D structure
866 <em>3D Structure</em>
869 <!-- JAL-2430 -->Hidden regions in alignment views are not
870 coloured in linked structure views
873 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
874 file-based command exchange
877 <!-- JAL-2375 -->Structure chooser automatically shows
878 Cached Structures rather than querying the PDBe if
879 structures are already available for sequences
882 <!-- JAL-2520 -->Structures imported via URL are cached in
883 the Jalview project rather than downloaded again when the
887 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
888 to transfer Chimera's structure attributes as Jalview
889 features, and vice-versa (<strong>Experimental
893 <em>Web Services</em>
896 <!-- JAL-2549 -->Updated JABAWS client to v2.2
899 <!-- JAL-2335 -->Filter non-standard amino acids and
900 nucleotides when submitting to AACon and other MSA
904 <!-- JAL-2316, -->URLs for viewing database
905 cross-references provided by identifiers.org and the
913 <!-- JAL-2344 -->FileFormatI interface for describing and
914 identifying file formats (instead of String constants)
917 <!-- JAL-2228 -->FeatureCounter script refactored for
918 efficiency when counting all displayed features (not
919 backwards compatible with 2.10.1)
922 <em>Example files</em>
925 <!-- JAL-2631 -->Graduated feature colour style example
926 included in the example feature file
929 <em>Documentation</em>
932 <!-- JAL-2339 -->Release notes reformatted for readability
933 with the built-in Java help viewer
936 <!-- JAL-1644 -->Find documentation updated with 'search
937 sequence description' option
943 <!-- JAL-2485, -->External service integration tests for
944 Uniprot REST Free Text Search Client
947 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
950 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
955 <td><div align="left">
956 <em>Calculations</em>
959 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
960 matrix - C->R should be '-3'<br />Old matrix restored
961 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
963 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
964 Jalview's treatment of gaps in PCA and substitution matrix
965 based Tree calculations.<br /> <br />In earlier versions
966 of Jalview, gaps matching gaps were penalised, and gaps
967 matching non-gaps penalised even more. In the PCA
968 calculation, gaps were actually treated as non-gaps - so
969 different costs were applied, which meant Jalview's PCAs
970 were different to those produced by SeqSpace.<br />Jalview
971 now treats gaps in the same way as SeqSpace (ie it scores
972 them as 0). <br /> <br />Enter the following in the
973 Groovy console to restore pre-2.10.2 behaviour:<br />
974 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
975 // for 2.10.1 mode <br />
976 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
977 // to restore 2.10.2 mode <br /> <br /> <em>Note:
978 these settings will affect all subsequent tree and PCA
979 calculations (not recommended)</em></li>
981 <!-- JAL-2424 -->Fixed off-by-one bug that affected
982 scaling of branch lengths for trees computed using
983 Sequence Feature Similarity.
986 <!-- JAL-2377 -->PCA calculation could hang when
987 generating output report when working with highly
991 <!-- JAL-2544 --> Sort by features includes features to
992 right of selected region when gaps present on right-hand
996 <em>User Interface</em>
999 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1000 doesn't reselect a specific sequence's associated
1001 annotation after it was used for colouring a view
1004 <!-- JAL-2419 -->Current selection lost if popup menu
1005 opened on a region of alignment without groups
1008 <!-- JAL-2374 -->Popup menu not always shown for regions
1009 of an alignment with overlapping groups
1012 <!-- JAL-2310 -->Finder double counts if both a sequence's
1013 name and description match
1016 <!-- JAL-2370 -->Hiding column selection containing two
1017 hidden regions results in incorrect hidden regions
1020 <!-- JAL-2386 -->'Apply to all groups' setting when
1021 changing colour does not apply Conservation slider value
1025 <!-- JAL-2373 -->Percentage identity and conservation menu
1026 items do not show a tick or allow shading to be disabled
1029 <!-- JAL-2385 -->Conservation shading or PID threshold
1030 lost when base colourscheme changed if slider not visible
1033 <!-- JAL-2547 -->Sequence features shown in tooltip for
1034 gaps before start of features
1037 <!-- JAL-2623 -->Graduated feature colour threshold not
1038 restored to UI when feature colour is edited
1041 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1042 a time when scrolling vertically in wrapped mode.
1045 <!-- JAL-2630 -->Structure and alignment overview update
1046 as graduate feature colour settings are modified via the
1050 <!-- JAL-2034 -->Overview window doesn't always update
1051 when a group defined on the alignment is resized
1054 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1055 wrapped view result in positional status updates
1059 <!-- JAL-2563 -->Status bar doesn't show position for
1060 ambiguous amino acid and nucleotide symbols
1063 <!-- JAL-2602 -->Copy consensus sequence failed if
1064 alignment included gapped columns
1067 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1068 widgets don't permanently disappear
1071 <!-- JAL-2503 -->Cannot select or filter quantitative
1072 annotation that are shown only as column labels (e.g.
1073 T-Coffee column reliability scores)
1076 <!-- JAL-2594 -->Exception thrown if trying to create a
1077 sequence feature on gaps only
1080 <!-- JAL-2504 -->Features created with 'New feature'
1081 button from a Find inherit previously defined feature type
1082 rather than the Find query string
1085 <!-- JAL-2423 -->incorrect title in output window when
1086 exporting tree calculated in Jalview
1089 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1090 and then revealing them reorders sequences on the
1094 <!-- JAL-964 -->Group panel in sequence feature settings
1095 doesn't update to reflect available set of groups after
1096 interactively adding or modifying features
1099 <!-- JAL-2225 -->Sequence Database chooser unusable on
1103 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1104 only excluded gaps in current sequence and ignored
1111 <!-- JAL-2421 -->Overview window visible region moves
1112 erratically when hidden rows or columns are present
1115 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1116 Structure Viewer's colour menu don't correspond to
1120 <!-- JAL-2405 -->Protein specific colours only offered in
1121 colour and group colour menu for protein alignments
1124 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1125 reflect currently selected view or group's shading
1129 <!-- JAL-2624 -->Feature colour thresholds not respected
1130 when rendered on overview and structures when opacity at
1134 <!-- JAL-2589 -->User defined gap colour not shown in
1135 overview when features overlaid on alignment
1138 <em>Data import/export</em>
1141 <!-- JAL-2576 -->Very large alignments take a long time to
1145 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1146 added after a sequence was imported are not written to
1150 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1151 when importing RNA secondary structure via Stockholm
1154 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1155 not shown in correct direction for simple pseudoknots
1158 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1159 with lightGray or darkGray via features file (but can
1163 <!-- JAL-2383 -->Above PID colour threshold not recovered
1164 when alignment view imported from project
1167 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1168 structure and sequences extracted from structure files
1169 imported via URL and viewed in Jmol
1172 <!-- JAL-2520 -->Structures loaded via URL are saved in
1173 Jalview Projects rather than fetched via URL again when
1174 the project is loaded and the structure viewed
1177 <em>Web Services</em>
1180 <!-- JAL-2519 -->EnsemblGenomes example failing after
1181 release of Ensembl v.88
1184 <!-- JAL-2366 -->Proxy server address and port always
1185 appear enabled in Preferences->Connections
1188 <!-- JAL-2461 -->DAS registry not found exceptions
1189 removed from console output
1192 <!-- JAL-2582 -->Cannot retrieve protein products from
1193 Ensembl by Peptide ID
1196 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1197 created from SIFTs, and spurious 'Couldn't open structure
1198 in Chimera' errors raised after April 2017 update (problem
1199 due to 'null' string rather than empty string used for
1200 residues with no corresponding PDB mapping).
1203 <em>Application UI</em>
1206 <!-- JAL-2361 -->User Defined Colours not added to Colour
1210 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1211 case' residues (button in colourscheme editor debugged and
1212 new documentation and tooltips added)
1215 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1216 doesn't restore group-specific text colour thresholds
1219 <!-- JAL-2243 -->Feature settings panel does not update as
1220 new features are added to alignment
1223 <!-- JAL-2532 -->Cancel in feature settings reverts
1224 changes to feature colours via the Amend features dialog
1227 <!-- JAL-2506 -->Null pointer exception when attempting to
1228 edit graduated feature colour via amend features dialog
1232 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1233 selection menu changes colours of alignment views
1236 <!-- JAL-2426 -->Spurious exceptions in console raised
1237 from alignment calculation workers after alignment has
1241 <!-- JAL-1608 -->Typo in selection popup menu - Create
1242 groups now 'Create Group'
1245 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1246 Create/Undefine group doesn't always work
1249 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1250 shown again after pressing 'Cancel'
1253 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1254 adjusts start position in wrap mode
1257 <!-- JAL-2563 -->Status bar doesn't show positions for
1258 ambiguous amino acids
1261 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1262 CDS/Protein view after CDS sequences added for aligned
1266 <!-- JAL-2592 -->User defined colourschemes called 'User
1267 Defined' don't appear in Colours menu
1273 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1274 score models doesn't always result in an updated PCA plot
1277 <!-- JAL-2442 -->Features not rendered as transparent on
1278 overview or linked structure view
1281 <!-- JAL-2372 -->Colour group by conservation doesn't
1285 <!-- JAL-2517 -->Hitting Cancel after applying
1286 user-defined colourscheme doesn't restore original
1293 <!-- JAL-2314 -->Unit test failure:
1294 jalview.ws.jabaws.RNAStructExportImport setup fails
1297 <!-- JAL-2307 -->Unit test failure:
1298 jalview.ws.sifts.SiftsClientTest due to compatibility
1299 problems with deep array comparison equality asserts in
1300 successive versions of TestNG
1303 <!-- JAL-2479 -->Relocated StructureChooserTest and
1304 ParameterUtilsTest Unit tests to Network suite
1307 <em>New Known Issues</em>
1310 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1311 phase after a sequence motif find operation
1314 <!-- JAL-2550 -->Importing annotation file with rows
1315 containing just upper and lower case letters are
1316 interpreted as WUSS RNA secondary structure symbols
1319 <!-- JAL-2590 -->Cannot load and display Newick trees
1320 reliably from eggnog Ortholog database
1323 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1324 containing features of type Highlight' when 'B' is pressed
1325 to mark columns containing highlighted regions.
1328 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1329 doesn't always add secondary structure annotation.
1334 <td width="60" nowrap>
1335 <div align="center">
1336 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1339 <td><div align="left">
1343 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1344 for all consensus calculations
1347 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1350 <li>Updated Jalview's Certum code signing certificate
1353 <em>Application</em>
1356 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1357 set of database cross-references, sorted alphabetically
1360 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1361 from database cross references. Users with custom links
1362 will receive a <a href="webServices/urllinks.html#warning">warning
1363 dialog</a> asking them to update their preferences.
1366 <!-- JAL-2287-->Cancel button and escape listener on
1367 dialog warning user about disconnecting Jalview from a
1371 <!-- JAL-2320-->Jalview's Chimera control window closes if
1372 the Chimera it is connected to is shut down
1375 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1376 columns menu item to mark columns containing highlighted
1377 regions (e.g. from structure selections or results of a
1381 <!-- JAL-2284-->Command line option for batch-generation
1382 of HTML pages rendering alignment data with the BioJS
1392 <!-- JAL-2286 -->Columns with more than one modal residue
1393 are not coloured or thresholded according to percent
1394 identity (first observed in Jalview 2.8.2)
1397 <!-- JAL-2301 -->Threonine incorrectly reported as not
1401 <!-- JAL-2318 -->Updates to documentation pages (above PID
1402 threshold, amino acid properties)
1405 <!-- JAL-2292 -->Lower case residues in sequences are not
1406 reported as mapped to residues in a structure file in the
1410 <!--JAL-2324 -->Identical features with non-numeric scores
1411 could be added multiple times to a sequence
1414 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1415 bond features shown as two highlighted residues rather
1416 than a range in linked structure views, and treated
1417 correctly when selecting and computing trees from features
1420 <!-- JAL-2281-->Custom URL links for database
1421 cross-references are matched to database name regardless
1426 <em>Application</em>
1429 <!-- JAL-2282-->Custom URL links for specific database
1430 names without regular expressions also offer links from
1434 <!-- JAL-2315-->Removing a single configured link in the
1435 URL links pane in Connections preferences doesn't actually
1436 update Jalview configuration
1439 <!-- JAL-2272-->CTRL-Click on a selected region to open
1440 the alignment area popup menu doesn't work on El-Capitan
1443 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1444 files with similarly named sequences if dropped onto the
1448 <!-- JAL-2312 -->Additional mappings are shown for PDB
1449 entries where more chains exist in the PDB accession than
1450 are reported in the SIFTS file
1453 <!-- JAL-2317-->Certain structures do not get mapped to
1454 the structure view when displayed with Chimera
1457 <!-- JAL-2317-->No chains shown in the Chimera view
1458 panel's View->Show Chains submenu
1461 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1462 work for wrapped alignment views
1465 <!--JAL-2197 -->Rename UI components for running JPred
1466 predictions from 'JNet' to 'JPred'
1469 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1470 corrupted when annotation panel vertical scroll is not at
1471 first annotation row
1474 <!--JAL-2332 -->Attempting to view structure for Hen
1475 lysozyme results in a PDB Client error dialog box
1478 <!-- JAL-2319 -->Structure View's mapping report switched
1479 ranges for PDB and sequence for SIFTS
1482 SIFTS 'Not_Observed' residues mapped to non-existant
1486 <!-- <em>New Known Issues</em>
1493 <td width="60" nowrap>
1494 <div align="center">
1495 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1496 <em>25/10/2016</em></strong>
1499 <td><em>Application</em>
1501 <li>3D Structure chooser opens with 'Cached structures'
1502 view if structures already loaded</li>
1503 <li>Progress bar reports models as they are loaded to
1504 structure views</li>
1510 <li>Colour by conservation always enabled and no tick
1511 shown in menu when BLOSUM or PID shading applied</li>
1512 <li>FER1_ARATH and FER2_ARATH labels were switched in
1513 example sequences/projects/trees</li>
1515 <em>Application</em>
1517 <li>Jalview projects with views of local PDB structure
1518 files saved on Windows cannot be opened on OSX</li>
1519 <li>Multiple structure views can be opened and superposed
1520 without timeout for structures with multiple models or
1521 multiple sequences in alignment</li>
1522 <li>Cannot import or associated local PDB files without a
1523 PDB ID HEADER line</li>
1524 <li>RMSD is not output in Jmol console when superposition
1526 <li>Drag and drop of URL from Browser fails for Linux and
1527 OSX versions earlier than El Capitan</li>
1528 <li>ENA client ignores invalid content from ENA server</li>
1529 <li>Exceptions are not raised in console when ENA client
1530 attempts to fetch non-existent IDs via Fetch DB Refs UI
1532 <li>Exceptions are not raised in console when a new view
1533 is created on the alignment</li>
1534 <li>OSX right-click fixed for group selections: CMD-click
1535 to insert/remove gaps in groups and CTRL-click to open group
1538 <em>Build and deployment</em>
1540 <li>URL link checker now copes with multi-line anchor
1543 <em>New Known Issues</em>
1545 <li>Drag and drop from URL links in browsers do not work
1552 <td width="60" nowrap>
1553 <div align="center">
1554 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1557 <td><em>General</em>
1560 <!-- JAL-2124 -->Updated Spanish translations.
1563 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1564 for importing structure data to Jalview. Enables mmCIF and
1568 <!-- JAL-192 --->Alignment ruler shows positions relative to
1572 <!-- JAL-2202 -->Position/residue shown in status bar when
1573 mousing over sequence associated annotation
1576 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1580 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1581 '()', canonical '[]' and invalid '{}' base pair populations
1585 <!-- JAL-2092 -->Feature settings popup menu options for
1586 showing or hiding columns containing a feature
1589 <!-- JAL-1557 -->Edit selected group by double clicking on
1590 group and sequence associated annotation labels
1593 <!-- JAL-2236 -->Sequence name added to annotation label in
1594 select/hide columns by annotation and colour by annotation
1598 </ul> <em>Application</em>
1601 <!-- JAL-2050-->Automatically hide introns when opening a
1602 gene/transcript view
1605 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1609 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1610 structure mappings with the EMBL-EBI PDBe SIFTS database
1613 <!-- JAL-2079 -->Updated download sites used for Rfam and
1614 Pfam sources to xfam.org
1617 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1620 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1621 over sequences in Jalview
1624 <!-- JAL-2027-->Support for reverse-complement coding
1625 regions in ENA and EMBL
1628 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1629 for record retrieval via ENA rest API
1632 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1636 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1637 groovy script execution
1640 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1641 alignment window's Calculate menu
1644 <!-- JAL-1812 -->Allow groovy scripts that call
1645 Jalview.getAlignFrames() to run in headless mode
1648 <!-- JAL-2068 -->Support for creating new alignment
1649 calculation workers from groovy scripts
1652 <!-- JAL-1369 --->Store/restore reference sequence in
1656 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1657 associations are now saved/restored from project
1660 <!-- JAL-1993 -->Database selection dialog always shown
1661 before sequence fetcher is opened
1664 <!-- JAL-2183 -->Double click on an entry in Jalview's
1665 database chooser opens a sequence fetcher
1668 <!-- JAL-1563 -->Free-text search client for UniProt using
1669 the UniProt REST API
1672 <!-- JAL-2168 -->-nonews command line parameter to prevent
1673 the news reader opening
1676 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1677 querying stored in preferences
1680 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1684 <!-- JAL-1977-->Tooltips shown on database chooser
1687 <!-- JAL-391 -->Reverse complement function in calculate
1688 menu for nucleotide sequences
1691 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1692 and feature counts preserves alignment ordering (and
1693 debugged for complex feature sets).
1696 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1697 viewing structures with Jalview 2.10
1700 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1701 genome, transcript CCDS and gene ids via the Ensembl and
1702 Ensembl Genomes REST API
1705 <!-- JAL-2049 -->Protein sequence variant annotation
1706 computed for 'sequence_variant' annotation on CDS regions
1710 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1714 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1715 Ref Fetcher fails to match, or otherwise updates sequence
1716 data from external database records.
1719 <!-- JAL-2154 -->Revised Jalview Project format for
1720 efficient recovery of sequence coding and alignment
1721 annotation relationships.
1723 </ul> <!-- <em>Applet</em>
1734 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1738 <!-- JAL-2018-->Export features in Jalview format (again)
1739 includes graduated colourschemes
1742 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1743 working with big alignments and lots of hidden columns
1746 <!-- JAL-2053-->Hidden column markers not always rendered
1747 at right of alignment window
1750 <!-- JAL-2067 -->Tidied up links in help file table of
1754 <!-- JAL-2072 -->Feature based tree calculation not shown
1758 <!-- JAL-2075 -->Hidden columns ignored during feature
1759 based tree calculation
1762 <!-- JAL-2065 -->Alignment view stops updating when show
1763 unconserved enabled for group on alignment
1766 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1770 <!-- JAL-2146 -->Alignment column in status incorrectly
1771 shown as "Sequence position" when mousing over
1775 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1776 hidden columns present
1779 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1780 user created annotation added to alignment
1783 <!-- JAL-1841 -->RNA Structure consensus only computed for
1784 '()' base pair annotation
1787 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1788 in zero scores for all base pairs in RNA Structure
1792 <!-- JAL-2174-->Extend selection with columns containing
1796 <!-- JAL-2275 -->Pfam format writer puts extra space at
1797 beginning of sequence
1800 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1804 <!-- JAL-2238 -->Cannot create groups on an alignment from
1805 from a tree when t-coffee scores are shown
1808 <!-- JAL-1836,1967 -->Cannot import and view PDB
1809 structures with chains containing negative resnums (4q4h)
1812 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1816 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1817 to Clustal, PIR and PileUp output
1820 <!-- JAL-2008 -->Reordering sequence features that are
1821 not visible causes alignment window to repaint
1824 <!-- JAL-2006 -->Threshold sliders don't work in
1825 graduated colour and colour by annotation row for e-value
1826 scores associated with features and annotation rows
1829 <!-- JAL-1797 -->amino acid physicochemical conservation
1830 calculation should be case independent
1833 <!-- JAL-2173 -->Remove annotation also updates hidden
1837 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1838 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1839 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1842 <!-- JAL-2065 -->Null pointer exceptions and redraw
1843 problems when reference sequence defined and 'show
1844 non-conserved' enabled
1847 <!-- JAL-1306 -->Quality and Conservation are now shown on
1848 load even when Consensus calculation is disabled
1851 <!-- JAL-1932 -->Remove right on penultimate column of
1852 alignment does nothing
1855 <em>Application</em>
1858 <!-- JAL-1552-->URLs and links can't be imported by
1859 drag'n'drop on OSX when launched via webstart (note - not
1860 yet fixed for El Capitan)
1863 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1864 output when running on non-gb/us i18n platforms
1867 <!-- JAL-1944 -->Error thrown when exporting a view with
1868 hidden sequences as flat-file alignment
1871 <!-- JAL-2030-->InstallAnywhere distribution fails when
1875 <!-- JAL-2080-->Jalview very slow to launch via webstart
1876 (also hotfix for 2.9.0b2)
1879 <!-- JAL-2085 -->Cannot save project when view has a
1880 reference sequence defined
1883 <!-- JAL-1011 -->Columns are suddenly selected in other
1884 alignments and views when revealing hidden columns
1887 <!-- JAL-1989 -->Hide columns not mirrored in complement
1888 view in a cDNA/Protein splitframe
1891 <!-- JAL-1369 -->Cannot save/restore representative
1892 sequence from project when only one sequence is
1896 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1897 in Structure Chooser
1900 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1901 structure consensus didn't refresh annotation panel
1904 <!-- JAL-1962 -->View mapping in structure view shows
1905 mappings between sequence and all chains in a PDB file
1908 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1909 dialogs format columns correctly, don't display array
1910 data, sort columns according to type
1913 <!-- JAL-1975 -->Export complete shown after destination
1914 file chooser is cancelled during an image export
1917 <!-- JAL-2025 -->Error when querying PDB Service with
1918 sequence name containing special characters
1921 <!-- JAL-2024 -->Manual PDB structure querying should be
1925 <!-- JAL-2104 -->Large tooltips with broken HTML
1926 formatting don't wrap
1929 <!-- JAL-1128 -->Figures exported from wrapped view are
1930 truncated so L looks like I in consensus annotation
1933 <!-- JAL-2003 -->Export features should only export the
1934 currently displayed features for the current selection or
1938 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1939 after fetching cross-references, and restoring from
1943 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1944 followed in the structure viewer
1947 <!-- JAL-2163 -->Titles for individual alignments in
1948 splitframe not restored from project
1951 <!-- JAL-2145 -->missing autocalculated annotation at
1952 trailing end of protein alignment in transcript/product
1953 splitview when pad-gaps not enabled by default
1956 <!-- JAL-1797 -->amino acid physicochemical conservation
1960 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1961 article has been read (reopened issue due to
1962 internationalisation problems)
1965 <!-- JAL-1960 -->Only offer PDB structures in structure
1966 viewer based on sequence name, PDB and UniProt
1971 <!-- JAL-1976 -->No progress bar shown during export of
1975 <!-- JAL-2213 -->Structures not always superimposed after
1976 multiple structures are shown for one or more sequences.
1979 <!-- JAL-1370 -->Reference sequence characters should not
1980 be replaced with '.' when 'Show unconserved' format option
1984 <!-- JAL-1823 -->Cannot specify chain code when entering
1985 specific PDB id for sequence
1988 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1989 'Export hidden sequences' is enabled, but 'export hidden
1990 columns' is disabled.
1993 <!--JAL-2026-->Best Quality option in structure chooser
1994 selects lowest rather than highest resolution structures
1998 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1999 to sequence mapping in 'View Mappings' report
2002 <!-- JAL-2284 -->Unable to read old Jalview projects that
2003 contain non-XML data added after Jalvew wrote project.
2006 <!-- JAL-2118 -->Newly created annotation row reorders
2007 after clicking on it to create new annotation for a
2011 <!-- JAL-1980 -->Null Pointer Exception raised when
2012 pressing Add on an orphaned cut'n'paste window.
2014 <!-- may exclude, this is an external service stability issue JAL-1941
2015 -- > RNA 3D structure not added via DSSR service</li> -->
2020 <!-- JAL-2151 -->Incorrect columns are selected when
2021 hidden columns present before start of sequence
2024 <!-- JAL-1986 -->Missing dependencies on applet pages
2028 <!-- JAL-1947 -->Overview pixel size changes when
2029 sequences are hidden in applet
2032 <!-- JAL-1996 -->Updated instructions for applet
2033 deployment on examples pages.
2040 <td width="60" nowrap>
2041 <div align="center">
2042 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2043 <em>16/10/2015</em></strong>
2046 <td><em>General</em>
2048 <li>Time stamps for signed Jalview application and applet
2053 <em>Application</em>
2055 <li>Duplicate group consensus and conservation rows
2056 shown when tree is partitioned</li>
2057 <li>Erratic behaviour when tree partitions made with
2058 multiple cDNA/Protein split views</li>
2064 <td width="60" nowrap>
2065 <div align="center">
2066 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2067 <em>8/10/2015</em></strong>
2070 <td><em>General</em>
2072 <li>Updated Spanish translations of localized text for
2074 </ul> <em>Application</em>
2076 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2077 <li>Signed OSX InstallAnywhere installer<br></li>
2078 <li>Support for per-sequence based annotations in BioJSON</li>
2079 </ul> <em>Applet</em>
2081 <li>Split frame example added to applet examples page</li>
2082 </ul> <em>Build and Deployment</em>
2085 <!-- JAL-1888 -->New ant target for running Jalview's test
2093 <li>Mapping of cDNA to protein in split frames
2094 incorrect when sequence start > 1</li>
2095 <li>Broken images in filter column by annotation dialog
2097 <li>Feature colours not parsed from features file</li>
2098 <li>Exceptions and incomplete link URLs recovered when
2099 loading a features file containing HTML tags in feature
2103 <em>Application</em>
2105 <li>Annotations corrupted after BioJS export and
2107 <li>Incorrect sequence limits after Fetch DB References
2108 with 'trim retrieved sequences'</li>
2109 <li>Incorrect warning about deleting all data when
2110 deleting selected columns</li>
2111 <li>Patch to build system for shipping properly signed
2112 JNLP templates for webstart launch</li>
2113 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2114 unreleased structures for download or viewing</li>
2115 <li>Tab/space/return keystroke operation of EMBL-PDBe
2116 fetcher/viewer dialogs works correctly</li>
2117 <li>Disabled 'minimise' button on Jalview windows
2118 running on OSX to workaround redraw hang bug</li>
2119 <li>Split cDNA/Protein view position and geometry not
2120 recovered from jalview project</li>
2121 <li>Initial enabled/disabled state of annotation menu
2122 sorter 'show autocalculated first/last' corresponds to
2124 <li>Restoring of Clustal, RNA Helices and T-Coffee
2125 color schemes from BioJSON</li>
2129 <li>Reorder sequences mirrored in cDNA/Protein split
2131 <li>Applet with Jmol examples not loading correctly</li>
2137 <td><div align="center">
2138 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2140 <td><em>General</em>
2142 <li>Linked visualisation and analysis of DNA and Protein
2145 <li>Translated cDNA alignments shown as split protein
2146 and DNA alignment views</li>
2147 <li>Codon consensus annotation for linked protein and
2148 cDNA alignment views</li>
2149 <li>Link cDNA or Protein product sequences by loading
2150 them onto Protein or cDNA alignments</li>
2151 <li>Reconstruct linked cDNA alignment from aligned
2152 protein sequences</li>
2155 <li>Jmol integration updated to Jmol v14.2.14</li>
2156 <li>Import and export of Jalview alignment views as <a
2157 href="features/bioJsonFormat.html">BioJSON</a></li>
2158 <li>New alignment annotation file statements for
2159 reference sequences and marking hidden columns</li>
2160 <li>Reference sequence based alignment shading to
2161 highlight variation</li>
2162 <li>Select or hide columns according to alignment
2164 <li>Find option for locating sequences by description</li>
2165 <li>Conserved physicochemical properties shown in amino
2166 acid conservation row</li>
2167 <li>Alignments can be sorted by number of RNA helices</li>
2168 </ul> <em>Application</em>
2170 <li>New cDNA/Protein analysis capabilities
2172 <li>Get Cross-References should open a Split Frame
2173 view with cDNA/Protein</li>
2174 <li>Detect when nucleotide sequences and protein
2175 sequences are placed in the same alignment</li>
2176 <li>Split cDNA/Protein views are saved in Jalview
2181 <li>Use REST API to talk to Chimera</li>
2182 <li>Selected regions in Chimera are highlighted in linked
2183 Jalview windows</li>
2185 <li>VARNA RNA viewer updated to v3.93</li>
2186 <li>VARNA views are saved in Jalview Projects</li>
2187 <li>Pseudoknots displayed as Jalview RNA annotation can
2188 be shown in VARNA</li>
2190 <li>Make groups for selection uses marked columns as well
2191 as the active selected region</li>
2193 <li>Calculate UPGMA and NJ trees using sequence feature
2195 <li>New Export options
2197 <li>New Export Settings dialog to control hidden
2198 region export in flat file generation</li>
2200 <li>Export alignment views for display with the <a
2201 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2203 <li>Export scrollable SVG in HTML page</li>
2204 <li>Optional embedding of BioJSON data when exporting
2205 alignment figures to HTML</li>
2207 <li>3D structure retrieval and display
2209 <li>Free text and structured queries with the PDBe
2211 <li>PDBe Search API based discovery and selection of
2212 PDB structures for a sequence set</li>
2216 <li>JPred4 employed for protein secondary structure
2218 <li>Hide Insertions menu option to hide unaligned columns
2219 for one or a group of sequences</li>
2220 <li>Automatically hide insertions in alignments imported
2221 from the JPred4 web server</li>
2222 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2223 system on OSX<br />LGPL libraries courtesy of <a
2224 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2226 <li>changed 'View nucleotide structure' submenu to 'View
2227 VARNA 2D Structure'</li>
2228 <li>change "View protein structure" menu option to "3D
2231 </ul> <em>Applet</em>
2233 <li>New layout for applet example pages</li>
2234 <li>New parameters to enable SplitFrame view
2235 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2236 <li>New example demonstrating linked viewing of cDNA and
2237 Protein alignments</li>
2238 </ul> <em>Development and deployment</em>
2240 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2241 <li>Include installation type and git revision in build
2242 properties and console log output</li>
2243 <li>Jalview Github organisation, and new github site for
2244 storing BioJsMSA Templates</li>
2245 <li>Jalview's unit tests now managed with TestNG</li>
2248 <!-- <em>General</em>
2250 </ul> --> <!-- issues resolved --> <em>Application</em>
2252 <li>Escape should close any open find dialogs</li>
2253 <li>Typo in select-by-features status report</li>
2254 <li>Consensus RNA secondary secondary structure
2255 predictions are not highlighted in amber</li>
2256 <li>Missing gap character in v2.7 example file means
2257 alignment appears unaligned when pad-gaps is not enabled</li>
2258 <li>First switch to RNA Helices colouring doesn't colour
2259 associated structure views</li>
2260 <li>ID width preference option is greyed out when auto
2261 width checkbox not enabled</li>
2262 <li>Stopped a warning dialog from being shown when
2263 creating user defined colours</li>
2264 <li>'View Mapping' in structure viewer shows sequence
2265 mappings for just that viewer's sequences</li>
2266 <li>Workaround for superposing PDB files containing
2267 multiple models in Chimera</li>
2268 <li>Report sequence position in status bar when hovering
2269 over Jmol structure</li>
2270 <li>Cannot output gaps as '.' symbols with Selection ->
2271 output to text box</li>
2272 <li>Flat file exports of alignments with hidden columns
2273 have incorrect sequence start/end</li>
2274 <li>'Aligning' a second chain to a Chimera structure from
2276 <li>Colour schemes applied to structure viewers don't
2277 work for nucleotide</li>
2278 <li>Loading/cut'n'pasting an empty or invalid file leads
2279 to a grey/invisible alignment window</li>
2280 <li>Exported Jpred annotation from a sequence region
2281 imports to different position</li>
2282 <li>Space at beginning of sequence feature tooltips shown
2283 on some platforms</li>
2284 <li>Chimera viewer 'View | Show Chain' menu is not
2286 <li>'New View' fails with a Null Pointer Exception in
2287 console if Chimera has been opened</li>
2288 <li>Mouseover to Chimera not working</li>
2289 <li>Miscellaneous ENA XML feature qualifiers not
2291 <li>NPE in annotation renderer after 'Extract Scores'</li>
2292 <li>If two structures in one Chimera window, mouseover of
2293 either sequence shows on first structure</li>
2294 <li>'Show annotations' options should not make
2295 non-positional annotations visible</li>
2296 <li>Subsequence secondary structure annotation not shown
2297 in right place after 'view flanking regions'</li>
2298 <li>File Save As type unset when current file format is
2300 <li>Save as '.jar' option removed for saving Jalview
2302 <li>Colour by Sequence colouring in Chimera more
2304 <li>Cannot 'add reference annotation' for a sequence in
2305 several views on same alignment</li>
2306 <li>Cannot show linked products for EMBL / ENA records</li>
2307 <li>Jalview's tooltip wraps long texts containing no
2309 </ul> <em>Applet</em>
2311 <li>Jmol to JalviewLite mouseover/link not working</li>
2312 <li>JalviewLite can't import sequences with ID
2313 descriptions containing angle brackets</li>
2314 </ul> <em>General</em>
2316 <li>Cannot export and reimport RNA secondary structure
2317 via jalview annotation file</li>
2318 <li>Random helix colour palette for colour by annotation
2319 with RNA secondary structure</li>
2320 <li>Mouseover to cDNA from STOP residue in protein
2321 translation doesn't work.</li>
2322 <li>hints when using the select by annotation dialog box</li>
2323 <li>Jmol alignment incorrect if PDB file has alternate CA
2325 <li>FontChooser message dialog appears to hang after
2326 choosing 1pt font</li>
2327 <li>Peptide secondary structure incorrectly imported from
2328 annotation file when annotation display text includes 'e' or
2330 <li>Cannot set colour of new feature type whilst creating
2332 <li>cDNA translation alignment should not be sequence
2333 order dependent</li>
2334 <li>'Show unconserved' doesn't work for lower case
2336 <li>Nucleotide ambiguity codes involving R not recognised</li>
2337 </ul> <em>Deployment and Documentation</em>
2339 <li>Applet example pages appear different to the rest of
2340 www.jalview.org</li>
2341 </ul> <em>Application Known issues</em>
2343 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2344 <li>Misleading message appears after trying to delete
2346 <li>Jalview icon not shown in dock after InstallAnywhere
2347 version launches</li>
2348 <li>Fetching EMBL reference for an RNA sequence results
2349 fails with a sequence mismatch</li>
2350 <li>Corrupted or unreadable alignment display when
2351 scrolling alignment to right</li>
2352 <li>ArrayIndexOutOfBoundsException thrown when remove
2353 empty columns called on alignment with ragged gapped ends</li>
2354 <li>auto calculated alignment annotation rows do not get
2355 placed above or below non-autocalculated rows</li>
2356 <li>Jalview dekstop becomes sluggish at full screen in
2357 ultra-high resolution</li>
2358 <li>Cannot disable consensus calculation independently of
2359 quality and conservation</li>
2360 <li>Mouseover highlighting between cDNA and protein can
2361 become sluggish with more than one splitframe shown</li>
2362 </ul> <em>Applet Known Issues</em>
2364 <li>Core PDB parsing code requires Jmol</li>
2365 <li>Sequence canvas panel goes white when alignment
2366 window is being resized</li>
2372 <td><div align="center">
2373 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2375 <td><em>General</em>
2377 <li>Updated Java code signing certificate donated by
2379 <li>Features and annotation preserved when performing
2380 pairwise alignment</li>
2381 <li>RNA pseudoknot annotation can be
2382 imported/exported/displayed</li>
2383 <li>'colour by annotation' can colour by RNA and
2384 protein secondary structure</li>
2385 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2386 post-hoc with 2.9 release</em>)
2389 </ul> <em>Application</em>
2391 <li>Extract and display secondary structure for sequences
2392 with 3D structures</li>
2393 <li>Support for parsing RNAML</li>
2394 <li>Annotations menu for layout
2396 <li>sort sequence annotation rows by alignment</li>
2397 <li>place sequence annotation above/below alignment
2400 <li>Output in Stockholm format</li>
2401 <li>Internationalisation: improved Spanish (es)
2403 <li>Structure viewer preferences tab</li>
2404 <li>Disorder and Secondary Structure annotation tracks
2405 shared between alignments</li>
2406 <li>UCSF Chimera launch and linked highlighting from
2408 <li>Show/hide all sequence associated annotation rows for
2409 all or current selection</li>
2410 <li>disorder and secondary structure predictions
2411 available as dataset annotation</li>
2412 <li>Per-sequence rna helices colouring</li>
2415 <li>Sequence database accessions imported when fetching
2416 alignments from Rfam</li>
2417 <li>update VARNA version to 3.91</li>
2419 <li>New groovy scripts for exporting aligned positions,
2420 conservation values, and calculating sum of pairs scores.</li>
2421 <li>Command line argument to set default JABAWS server</li>
2422 <li>include installation type in build properties and
2423 console log output</li>
2424 <li>Updated Jalview project format to preserve dataset
2428 <!-- issues resolved --> <em>Application</em>
2430 <li>Distinguish alignment and sequence associated RNA
2431 structure in structure->view->VARNA</li>
2432 <li>Raise dialog box if user deletes all sequences in an
2434 <li>Pressing F1 results in documentation opening twice</li>
2435 <li>Sequence feature tooltip is wrapped</li>
2436 <li>Double click on sequence associated annotation
2437 selects only first column</li>
2438 <li>Redundancy removal doesn't result in unlinked
2439 leaves shown in tree</li>
2440 <li>Undos after several redundancy removals don't undo
2442 <li>Hide sequence doesn't hide associated annotation</li>
2443 <li>User defined colours dialog box too big to fit on
2444 screen and buttons not visible</li>
2445 <li>author list isn't updated if already written to
2446 Jalview properties</li>
2447 <li>Popup menu won't open after retrieving sequence
2449 <li>File open window for associate PDB doesn't open</li>
2450 <li>Left-then-right click on a sequence id opens a
2451 browser search window</li>
2452 <li>Cannot open sequence feature shading/sort popup menu
2453 in feature settings dialog</li>
2454 <li>better tooltip placement for some areas of Jalview
2456 <li>Allow addition of JABAWS Server which doesn't
2457 pass validation</li>
2458 <li>Web services parameters dialog box is too large to
2460 <li>Muscle nucleotide alignment preset obscured by
2462 <li>JABAWS preset submenus don't contain newly
2463 defined user preset</li>
2464 <li>MSA web services warns user if they were launched
2465 with invalid input</li>
2466 <li>Jalview cannot contact DAS Registy when running on
2469 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2470 'Superpose with' submenu not shown when new view
2474 </ul> <!-- <em>Applet</em>
2476 </ul> <em>General</em>
2478 </ul>--> <em>Deployment and Documentation</em>
2480 <li>2G and 1G options in launchApp have no effect on
2481 memory allocation</li>
2482 <li>launchApp service doesn't automatically open
2483 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2485 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2486 InstallAnywhere reports cannot find valid JVM when Java
2487 1.7_055 is available
2489 </ul> <em>Application Known issues</em>
2492 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2493 corrupted or unreadable alignment display when scrolling
2497 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2498 retrieval fails but progress bar continues for DAS retrieval
2499 with large number of ID
2502 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2503 flatfile output of visible region has incorrect sequence
2507 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2508 rna structure consensus doesn't update when secondary
2509 structure tracks are rearranged
2512 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2513 invalid rna structure positional highlighting does not
2514 highlight position of invalid base pairs
2517 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2518 out of memory errors are not raised when saving Jalview
2519 project from alignment window file menu
2522 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2523 Switching to RNA Helices colouring doesn't propagate to
2527 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2528 colour by RNA Helices not enabled when user created
2529 annotation added to alignment
2532 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2533 Jalview icon not shown on dock in Mountain Lion/Webstart
2535 </ul> <em>Applet Known Issues</em>
2538 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2539 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2542 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2543 Jalview and Jmol example not compatible with IE9
2546 <li>Sort by annotation score doesn't reverse order
2552 <td><div align="center">
2553 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2556 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2559 <li>Internationalisation of user interface (usually
2560 called i18n support) and translation for Spanish locale</li>
2561 <li>Define/Undefine group on current selection with
2562 Ctrl-G/Shift Ctrl-G</li>
2563 <li>Improved group creation/removal options in
2564 alignment/sequence Popup menu</li>
2565 <li>Sensible precision for symbol distribution
2566 percentages shown in logo tooltip.</li>
2567 <li>Annotation panel height set according to amount of
2568 annotation when alignment first opened</li>
2569 </ul> <em>Application</em>
2571 <li>Interactive consensus RNA secondary structure
2572 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2573 <li>Select columns containing particular features from
2574 Feature Settings dialog</li>
2575 <li>View all 'representative' PDB structures for selected
2577 <li>Update Jalview project format:
2579 <li>New file extension for Jalview projects '.jvp'</li>
2580 <li>Preserve sequence and annotation dataset (to
2581 store secondary structure annotation,etc)</li>
2582 <li>Per group and alignment annotation and RNA helix
2586 <li>New similarity measures for PCA and Tree calculation
2588 <li>Experimental support for retrieval and viewing of
2589 flanking regions for an alignment</li>
2593 <!-- issues resolved --> <em>Application</em>
2595 <li>logo keeps spinning and status remains at queued or
2596 running after job is cancelled</li>
2597 <li>cannot export features from alignments imported from
2598 Jalview/VAMSAS projects</li>
2599 <li>Buggy slider for web service parameters that take
2601 <li>Newly created RNA secondary structure line doesn't
2602 have 'display all symbols' flag set</li>
2603 <li>T-COFFEE alignment score shading scheme and other
2604 annotation shading not saved in Jalview project</li>
2605 <li>Local file cannot be loaded in freshly downloaded
2607 <li>Jalview icon not shown on dock in Mountain
2609 <li>Load file from desktop file browser fails</li>
2610 <li>Occasional NPE thrown when calculating large trees</li>
2611 <li>Cannot reorder or slide sequences after dragging an
2612 alignment onto desktop</li>
2613 <li>Colour by annotation dialog throws NPE after using
2614 'extract scores' function</li>
2615 <li>Loading/cut'n'pasting an empty file leads to a grey
2616 alignment window</li>
2617 <li>Disorder thresholds rendered incorrectly after
2618 performing IUPred disorder prediction</li>
2619 <li>Multiple group annotated consensus rows shown when
2620 changing 'normalise logo' display setting</li>
2621 <li>Find shows blank dialog after 'finished searching' if
2622 nothing matches query</li>
2623 <li>Null Pointer Exceptions raised when sorting by
2624 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2626 <li>Errors in Jmol console when structures in alignment
2627 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2629 <li>Not all working JABAWS services are shown in
2631 <li>JAVAWS version of Jalview fails to launch with
2632 'invalid literal/length code'</li>
2633 <li>Annotation/RNA Helix colourschemes cannot be applied
2634 to alignment with groups (actually fixed in 2.8.0b1)</li>
2635 <li>RNA Helices and T-Coffee Scores available as default
2638 </ul> <em>Applet</em>
2640 <li>Remove group option is shown even when selection is
2642 <li>Apply to all groups ticked but colourscheme changes
2643 don't affect groups</li>
2644 <li>Documented RNA Helices and T-Coffee Scores as valid
2645 colourscheme name</li>
2646 <li>Annotation labels drawn on sequence IDs when
2647 Annotation panel is not displayed</li>
2648 <li>Increased font size for dropdown menus on OSX and
2649 embedded windows</li>
2650 </ul> <em>Other</em>
2652 <li>Consensus sequence for alignments/groups with a
2653 single sequence were not calculated</li>
2654 <li>annotation files that contain only groups imported as
2655 annotation and junk sequences</li>
2656 <li>Fasta files with sequences containing '*' incorrectly
2657 recognised as PFAM or BLC</li>
2658 <li>conservation/PID slider apply all groups option
2659 doesn't affect background (2.8.0b1)
2661 <li>redundancy highlighting is erratic at 0% and 100%</li>
2662 <li>Remove gapped columns fails for sequences with ragged
2664 <li>AMSA annotation row with leading spaces is not
2665 registered correctly on import</li>
2666 <li>Jalview crashes when selecting PCA analysis for
2667 certain alignments</li>
2668 <li>Opening the colour by annotation dialog for an
2669 existing annotation based 'use original colours'
2670 colourscheme loses original colours setting</li>
2675 <td><div align="center">
2676 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2677 <em>30/1/2014</em></strong>
2681 <li>Trusted certificates for JalviewLite applet and
2682 Jalview Desktop application<br />Certificate was donated by
2683 <a href="https://www.certum.eu">Certum</a> to the Jalview
2684 open source project).
2686 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2687 <li>Output in Stockholm format</li>
2688 <li>Allow import of data from gzipped files</li>
2689 <li>Export/import group and sequence associated line
2690 graph thresholds</li>
2691 <li>Nucleotide substitution matrix that supports RNA and
2692 ambiguity codes</li>
2693 <li>Allow disorder predictions to be made on the current
2694 selection (or visible selection) in the same way that JPred
2696 <li>Groovy scripting for headless Jalview operation</li>
2697 </ul> <em>Other improvements</em>
2699 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2700 <li>COMBINE statement uses current SEQUENCE_REF and
2701 GROUP_REF scope to group annotation rows</li>
2702 <li>Support '' style escaping of quotes in Newick
2704 <li>Group options for JABAWS service by command line name</li>
2705 <li>Empty tooltip shown for JABA service options with a
2706 link but no description</li>
2707 <li>Select primary source when selecting authority in
2708 database fetcher GUI</li>
2709 <li>Add .mfa to FASTA file extensions recognised by
2711 <li>Annotation label tooltip text wrap</li>
2716 <li>Slow scrolling when lots of annotation rows are
2718 <li>Lots of NPE (and slowness) after creating RNA
2719 secondary structure annotation line</li>
2720 <li>Sequence database accessions not imported when
2721 fetching alignments from Rfam</li>
2722 <li>Incorrect SHMR submission for sequences with
2724 <li>View all structures does not always superpose
2726 <li>Option widgets in service parameters not updated to
2727 reflect user or preset settings</li>
2728 <li>Null pointer exceptions for some services without
2729 presets or adjustable parameters</li>
2730 <li>Discover PDB IDs entry in structure menu doesn't
2731 discover PDB xRefs</li>
2732 <li>Exception encountered while trying to retrieve
2733 features with DAS</li>
2734 <li>Lowest value in annotation row isn't coloured
2735 when colour by annotation (per sequence) is coloured</li>
2736 <li>Keyboard mode P jumps to start of gapped region when
2737 residue follows a gap</li>
2738 <li>Jalview appears to hang importing an alignment with
2739 Wrap as default or after enabling Wrap</li>
2740 <li>'Right click to add annotations' message
2741 shown in wrap mode when no annotations present</li>
2742 <li>Disorder predictions fail with NPE if no automatic
2743 annotation already exists on alignment</li>
2744 <li>oninit javascript function should be called after
2745 initialisation completes</li>
2746 <li>Remove redundancy after disorder prediction corrupts
2747 alignment window display</li>
2748 <li>Example annotation file in documentation is invalid</li>
2749 <li>Grouped line graph annotation rows are not exported
2750 to annotation file</li>
2751 <li>Multi-harmony analysis cannot be run when only two
2753 <li>Cannot create multiple groups of line graphs with
2754 several 'combine' statements in annotation file</li>
2755 <li>Pressing return several times causes Number Format
2756 exceptions in keyboard mode</li>
2757 <li>Multi-harmony (SHMMR) method doesn't submit
2758 correct partitions for input data</li>
2759 <li>Translation from DNA to Amino Acids fails</li>
2760 <li>Jalview fail to load newick tree with quoted label</li>
2761 <li>--headless flag isn't understood</li>
2762 <li>ClassCastException when generating EPS in headless
2764 <li>Adjusting sequence-associated shading threshold only
2765 changes one row's threshold</li>
2766 <li>Preferences and Feature settings panel panel
2767 doesn't open</li>
2768 <li>hide consensus histogram also hides conservation and
2769 quality histograms</li>
2774 <td><div align="center">
2775 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2777 <td><em>Application</em>
2779 <li>Support for JABAWS 2.0 Services (AACon alignment
2780 conservation, protein disorder and Clustal Omega)</li>
2781 <li>JABAWS server status indicator in Web Services
2783 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2784 in Jalview alignment window</li>
2785 <li>Updated Jalview build and deploy framework for OSX
2786 mountain lion, windows 7, and 8</li>
2787 <li>Nucleotide substitution matrix for PCA that supports
2788 RNA and ambiguity codes</li>
2790 <li>Improved sequence database retrieval GUI</li>
2791 <li>Support fetching and database reference look up
2792 against multiple DAS sources (Fetch all from in 'fetch db
2794 <li>Jalview project improvements
2796 <li>Store and retrieve the 'belowAlignment'
2797 flag for annotation</li>
2798 <li>calcId attribute to group annotation rows on the
2800 <li>Store AACon calculation settings for a view in
2801 Jalview project</li>
2805 <li>horizontal scrolling gesture support</li>
2806 <li>Visual progress indicator when PCA calculation is
2808 <li>Simpler JABA web services menus</li>
2809 <li>visual indication that web service results are still
2810 being retrieved from server</li>
2811 <li>Serialise the dialogs that are shown when Jalview
2812 starts up for first time</li>
2813 <li>Jalview user agent string for interacting with HTTP
2815 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2817 <li>Examples directory and Groovy library included in
2818 InstallAnywhere distribution</li>
2819 </ul> <em>Applet</em>
2821 <li>RNA alignment and secondary structure annotation
2822 visualization applet example</li>
2823 </ul> <em>General</em>
2825 <li>Normalise option for consensus sequence logo</li>
2826 <li>Reset button in PCA window to return dimensions to
2828 <li>Allow seqspace or Jalview variant of alignment PCA
2830 <li>PCA with either nucleic acid and protein substitution
2832 <li>Allow windows containing HTML reports to be exported
2834 <li>Interactive display and editing of RNA secondary
2835 structure contacts</li>
2836 <li>RNA Helix Alignment Colouring</li>
2837 <li>RNA base pair logo consensus</li>
2838 <li>Parse sequence associated secondary structure
2839 information in Stockholm files</li>
2840 <li>HTML Export database accessions and annotation
2841 information presented in tooltip for sequences</li>
2842 <li>Import secondary structure from LOCARNA clustalw
2843 style RNA alignment files</li>
2844 <li>import and visualise T-COFFEE quality scores for an
2846 <li>'colour by annotation' per sequence option to
2847 shade each sequence according to its associated alignment
2849 <li>New Jalview Logo</li>
2850 </ul> <em>Documentation and Development</em>
2852 <li>documentation for score matrices used in Jalview</li>
2853 <li>New Website!</li>
2855 <td><em>Application</em>
2857 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2858 wsdbfetch REST service</li>
2859 <li>Stop windows being moved outside desktop on OSX</li>
2860 <li>Filetype associations not installed for webstart
2862 <li>Jalview does not always retrieve progress of a JABAWS
2863 job execution in full once it is complete</li>
2864 <li>revise SHMR RSBS definition to ensure alignment is
2865 uploaded via ali_file parameter</li>
2866 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2867 <li>View all structures superposed fails with exception</li>
2868 <li>Jnet job queues forever if a very short sequence is
2869 submitted for prediction</li>
2870 <li>Cut and paste menu not opened when mouse clicked on
2872 <li>Putting fractional value into integer text box in
2873 alignment parameter dialog causes Jalview to hang</li>
2874 <li>Structure view highlighting doesn't work on
2876 <li>View all structures fails with exception shown in
2878 <li>Characters in filename associated with PDBEntry not
2879 escaped in a platform independent way</li>
2880 <li>Jalview desktop fails to launch with exception when
2882 <li>Tree calculation reports 'you must have 2 or more
2883 sequences selected' when selection is empty</li>
2884 <li>Jalview desktop fails to launch with jar signature
2885 failure when java web start temporary file caching is
2887 <li>DAS Sequence retrieval with range qualification
2888 results in sequence xref which includes range qualification</li>
2889 <li>Errors during processing of command line arguments
2890 cause progress bar (JAL-898) to be removed</li>
2891 <li>Replace comma for semi-colon option not disabled for
2892 DAS sources in sequence fetcher</li>
2893 <li>Cannot close news reader when JABAWS server warning
2894 dialog is shown</li>
2895 <li>Option widgets not updated to reflect user settings</li>
2896 <li>Edited sequence not submitted to web service</li>
2897 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2898 <li>InstallAnywhere installer doesn't unpack and run
2899 on OSX Mountain Lion</li>
2900 <li>Annotation panel not given a scroll bar when
2901 sequences with alignment annotation are pasted into the
2903 <li>Sequence associated annotation rows not associated
2904 when loaded from Jalview project</li>
2905 <li>Browser launch fails with NPE on java 1.7</li>
2906 <li>JABAWS alignment marked as finished when job was
2907 cancelled or job failed due to invalid input</li>
2908 <li>NPE with v2.7 example when clicking on Tree
2909 associated with all views</li>
2910 <li>Exceptions when copy/paste sequences with grouped
2911 annotation rows to new window</li>
2912 </ul> <em>Applet</em>
2914 <li>Sequence features are momentarily displayed before
2915 they are hidden using hidefeaturegroups applet parameter</li>
2916 <li>loading features via javascript API automatically
2917 enables feature display</li>
2918 <li>scrollToColumnIn javascript API method doesn't
2920 </ul> <em>General</em>
2922 <li>Redundancy removal fails for rna alignment</li>
2923 <li>PCA calculation fails when sequence has been selected
2924 and then deselected</li>
2925 <li>PCA window shows grey box when first opened on OSX</li>
2926 <li>Letters coloured pink in sequence logo when alignment
2927 coloured with clustalx</li>
2928 <li>Choosing fonts without letter symbols defined causes
2929 exceptions and redraw errors</li>
2930 <li>Initial PCA plot view is not same as manually
2931 reconfigured view</li>
2932 <li>Grouped annotation graph label has incorrect line
2934 <li>Grouped annotation graph label display is corrupted
2935 for lots of labels</li>
2940 <div align="center">
2941 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2944 <td><em>Application</em>
2946 <li>Jalview Desktop News Reader</li>
2947 <li>Tweaked default layout of web services menu</li>
2948 <li>View/alignment association menu to enable user to
2949 easily specify which alignment a multi-structure view takes
2950 its colours/correspondences from</li>
2951 <li>Allow properties file location to be specified as URL</li>
2952 <li>Extend Jalview project to preserve associations
2953 between many alignment views and a single Jmol display</li>
2954 <li>Store annotation row height in Jalview project file</li>
2955 <li>Annotation row column label formatting attributes
2956 stored in project file</li>
2957 <li>Annotation row order for auto-calculated annotation
2958 rows preserved in Jalview project file</li>
2959 <li>Visual progress indication when Jalview state is
2960 saved using Desktop window menu</li>
2961 <li>Visual indication that command line arguments are
2962 still being processed</li>
2963 <li>Groovy script execution from URL</li>
2964 <li>Colour by annotation default min and max colours in
2966 <li>Automatically associate PDB files dragged onto an
2967 alignment with sequences that have high similarity and
2969 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2970 <li>'view structures' option to open many
2971 structures in same window</li>
2972 <li>Sort associated views menu option for tree panel</li>
2973 <li>Group all JABA and non-JABA services for a particular
2974 analysis function in its own submenu</li>
2975 </ul> <em>Applet</em>
2977 <li>Userdefined and autogenerated annotation rows for
2979 <li>Adjustment of alignment annotation pane height</li>
2980 <li>Annotation scrollbar for annotation panel</li>
2981 <li>Drag to reorder annotation rows in annotation panel</li>
2982 <li>'automaticScrolling' parameter</li>
2983 <li>Allow sequences with partial ID string matches to be
2984 annotated from GFF/Jalview features files</li>
2985 <li>Sequence logo annotation row in applet</li>
2986 <li>Absolute paths relative to host server in applet
2987 parameters are treated as such</li>
2988 <li>New in the JalviewLite javascript API:
2990 <li>JalviewLite.js javascript library</li>
2991 <li>Javascript callbacks for
2993 <li>Applet initialisation</li>
2994 <li>Sequence/alignment mouse-overs and selections</li>
2997 <li>scrollTo row and column alignment scrolling
2999 <li>Select sequence/alignment regions from javascript</li>
3000 <li>javascript structure viewer harness to pass
3001 messages between Jmol and Jalview when running as
3002 distinct applets</li>
3003 <li>sortBy method</li>
3004 <li>Set of applet and application examples shipped
3005 with documentation</li>
3006 <li>New example to demonstrate JalviewLite and Jmol
3007 javascript message exchange</li>
3009 </ul> <em>General</em>
3011 <li>Enable Jmol displays to be associated with multiple
3012 multiple alignments</li>
3013 <li>Option to automatically sort alignment with new tree</li>
3014 <li>User configurable link to enable redirects to a
3015 www.Jalview.org mirror</li>
3016 <li>Jmol colours option for Jmol displays</li>
3017 <li>Configurable newline string when writing alignment
3018 and other flat files</li>
3019 <li>Allow alignment annotation description lines to
3020 contain html tags</li>
3021 </ul> <em>Documentation and Development</em>
3023 <li>Add groovy test harness for bulk load testing to
3025 <li>Groovy script to load and align a set of sequences
3026 using a web service before displaying the result in the
3027 Jalview desktop</li>
3028 <li>Restructured javascript and applet api documentation</li>
3029 <li>Ant target to publish example html files with applet
3031 <li>Netbeans project for building Jalview from source</li>
3032 <li>ant task to create online javadoc for Jalview source</li>
3034 <td><em>Application</em>
3036 <li>User defined colourscheme throws exception when
3037 current built in colourscheme is saved as new scheme</li>
3038 <li>AlignFrame->Save in application pops up save
3039 dialog for valid filename/format</li>
3040 <li>Cannot view associated structure for UniProt sequence</li>
3041 <li>PDB file association breaks for UniProt sequence
3043 <li>Associate PDB from file dialog does not tell you
3044 which sequence is to be associated with the file</li>
3045 <li>Find All raises null pointer exception when query
3046 only matches sequence IDs</li>
3047 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3048 <li>Jalview project with Jmol views created with Jalview
3049 2.4 cannot be loaded</li>
3050 <li>Filetype associations not installed for webstart
3052 <li>Two or more chains in a single PDB file associated
3053 with sequences in different alignments do not get coloured
3054 by their associated sequence</li>
3055 <li>Visibility status of autocalculated annotation row
3056 not preserved when project is loaded</li>
3057 <li>Annotation row height and visibility attributes not
3058 stored in Jalview project</li>
3059 <li>Tree bootstraps are not preserved when saved as a
3060 Jalview project</li>
3061 <li>Envision2 workflow tooltips are corrupted</li>
3062 <li>Enabling show group conservation also enables colour
3063 by conservation</li>
3064 <li>Duplicate group associated conservation or consensus
3065 created on new view</li>
3066 <li>Annotation scrollbar not displayed after 'show
3067 all hidden annotation rows' option selected</li>
3068 <li>Alignment quality not updated after alignment
3069 annotation row is hidden then shown</li>
3070 <li>Preserve colouring of structures coloured by
3071 sequences in pre Jalview 2.7 projects</li>
3072 <li>Web service job parameter dialog is not laid out
3074 <li>Web services menu not refreshed after 'reset
3075 services' button is pressed in preferences</li>
3076 <li>Annotation off by one in Jalview v2_3 example project</li>
3077 <li>Structures imported from file and saved in project
3078 get name like jalview_pdb1234.txt when reloaded</li>
3079 <li>Jalview does not always retrieve progress of a JABAWS
3080 job execution in full once it is complete</li>
3081 </ul> <em>Applet</em>
3083 <li>Alignment height set incorrectly when lots of
3084 annotation rows are displayed</li>
3085 <li>Relative URLs in feature HTML text not resolved to
3087 <li>View follows highlighting does not work for positions
3089 <li><= shown as = in tooltip</li>
3090 <li>Export features raises exception when no features
3092 <li>Separator string used for serialising lists of IDs
3093 for javascript api is modified when separator string
3094 provided as parameter</li>
3095 <li>Null pointer exception when selecting tree leaves for
3096 alignment with no existing selection</li>
3097 <li>Relative URLs for datasources assumed to be relative
3098 to applet's codebase</li>
3099 <li>Status bar not updated after finished searching and
3100 search wraps around to first result</li>
3101 <li>StructureSelectionManager instance shared between
3102 several Jalview applets causes race conditions and memory
3104 <li>Hover tooltip and mouseover of position on structure
3105 not sent from Jmol in applet</li>
3106 <li>Certain sequences of javascript method calls to
3107 applet API fatally hang browser</li>
3108 </ul> <em>General</em>
3110 <li>View follows structure mouseover scrolls beyond
3111 position with wrapped view and hidden regions</li>
3112 <li>Find sequence position moves to wrong residue
3113 with/without hidden columns</li>
3114 <li>Sequence length given in alignment properties window
3116 <li>InvalidNumberFormat exceptions thrown when trying to
3117 import PDB like structure files</li>
3118 <li>Positional search results are only highlighted
3119 between user-supplied sequence start/end bounds</li>
3120 <li>End attribute of sequence is not validated</li>
3121 <li>Find dialog only finds first sequence containing a
3122 given sequence position</li>
3123 <li>Sequence numbering not preserved in MSF alignment
3125 <li>Jalview PDB file reader does not extract sequence
3126 from nucleotide chains correctly</li>
3127 <li>Structure colours not updated when tree partition
3128 changed in alignment</li>
3129 <li>Sequence associated secondary structure not correctly
3130 parsed in interleaved stockholm</li>
3131 <li>Colour by annotation dialog does not restore current
3133 <li>Hiding (nearly) all sequences doesn't work
3135 <li>Sequences containing lowercase letters are not
3136 properly associated with their pdb files</li>
3137 </ul> <em>Documentation and Development</em>
3139 <li>schemas/JalviewWsParamSet.xsd corrupted by
3140 ApplyCopyright tool</li>
3145 <div align="center">
3146 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3149 <td><em>Application</em>
3151 <li>New warning dialog when the Jalview Desktop cannot
3152 contact web services</li>
3153 <li>JABA service parameters for a preset are shown in
3154 service job window</li>
3155 <li>JABA Service menu entries reworded</li>
3159 <li>Modeller PIR IO broken - cannot correctly import a
3160 pir file emitted by Jalview</li>
3161 <li>Existing feature settings transferred to new
3162 alignment view created from cut'n'paste</li>
3163 <li>Improved test for mixed amino/nucleotide chains when
3164 parsing PDB files</li>
3165 <li>Consensus and conservation annotation rows
3166 occasionally become blank for all new windows</li>
3167 <li>Exception raised when right clicking above sequences
3168 in wrapped view mode</li>
3169 </ul> <em>Application</em>
3171 <li>multiple multiply aligned structure views cause cpu
3172 usage to hit 100% and computer to hang</li>
3173 <li>Web Service parameter layout breaks for long user
3174 parameter names</li>
3175 <li>Jaba service discovery hangs desktop if Jaba server
3182 <div align="center">
3183 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3186 <td><em>Application</em>
3188 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3189 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3192 <li>Web Services preference tab</li>
3193 <li>Analysis parameters dialog box and user defined
3195 <li>Improved speed and layout of Envision2 service menu</li>
3196 <li>Superpose structures using associated sequence
3198 <li>Export coordinates and projection as CSV from PCA
3200 </ul> <em>Applet</em>
3202 <li>enable javascript: execution by the applet via the
3203 link out mechanism</li>
3204 </ul> <em>Other</em>
3206 <li>Updated the Jmol Jalview interface to work with Jmol
3208 <li>The Jalview Desktop and JalviewLite applet now
3209 require Java 1.5</li>
3210 <li>Allow Jalview feature colour specification for GFF
3211 sequence annotation files</li>
3212 <li>New 'colour by label' keword in Jalview feature file
3213 type colour specification</li>
3214 <li>New Jalview Desktop Groovy API method that allows a
3215 script to check if it being run in an interactive session or
3216 in a batch operation from the Jalview command line</li>
3220 <li>clustalx colourscheme colours Ds preferentially when
3221 both D+E are present in over 50% of the column</li>
3222 </ul> <em>Application</em>
3224 <li>typo in AlignmentFrame->View->Hide->all but
3225 selected Regions menu item</li>
3226 <li>sequence fetcher replaces ',' for ';' when the ',' is
3227 part of a valid accession ID</li>
3228 <li>fatal OOM if object retrieved by sequence fetcher
3229 runs out of memory</li>
3230 <li>unhandled Out of Memory Error when viewing pca
3231 analysis results</li>
3232 <li>InstallAnywhere builds fail to launch on OS X java
3233 10.5 update 4 (due to apple Java 1.6 update)</li>
3234 <li>Installanywhere Jalview silently fails to launch</li>
3235 </ul> <em>Applet</em>
3237 <li>Jalview.getFeatureGroups() raises an
3238 ArrayIndexOutOfBoundsException if no feature groups are
3245 <div align="center">
3246 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3252 <li>Alignment prettyprinter doesn't cope with long
3254 <li>clustalx colourscheme colours Ds preferentially when
3255 both D+E are present in over 50% of the column</li>
3256 <li>nucleic acid structures retrieved from PDB do not
3257 import correctly</li>
3258 <li>More columns get selected than were clicked on when a
3259 number of columns are hidden</li>
3260 <li>annotation label popup menu not providing correct
3261 add/hide/show options when rows are hidden or none are
3263 <li>Stockholm format shown in list of readable formats,
3264 and parser copes better with alignments from RFAM.</li>
3265 <li>CSV output of consensus only includes the percentage
3266 of all symbols if sequence logo display is enabled</li>
3268 </ul> <em>Applet</em>
3270 <li>annotation panel disappears when annotation is
3272 </ul> <em>Application</em>
3274 <li>Alignment view not redrawn properly when new
3275 alignment opened where annotation panel is visible but no
3276 annotations are present on alignment</li>
3277 <li>pasted region containing hidden columns is
3278 incorrectly displayed in new alignment window</li>
3279 <li>Jalview slow to complete operations when stdout is
3280 flooded (fix is to close the Jalview console)</li>
3281 <li>typo in AlignmentFrame->View->Hide->all but
3282 selected Rregions menu item.</li>
3283 <li>inconsistent group submenu and Format submenu entry
3284 'Un' or 'Non'conserved</li>
3285 <li>Sequence feature settings are being shared by
3286 multiple distinct alignments</li>
3287 <li>group annotation not recreated when tree partition is
3289 <li>double click on group annotation to select sequences
3290 does not propagate to associated trees</li>
3291 <li>Mac OSX specific issues:
3293 <li>exception raised when mouse clicked on desktop
3294 window background</li>
3295 <li>Desktop menu placed on menu bar and application
3296 name set correctly</li>
3297 <li>sequence feature settings not wide enough for the
3298 save feature colourscheme button</li>
3307 <div align="center">
3308 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3311 <td><em>New Capabilities</em>
3313 <li>URL links generated from description line for
3314 regular-expression based URL links (applet and application)
3316 <li>Non-positional feature URL links are shown in link
3318 <li>Linked viewing of nucleic acid sequences and
3320 <li>Automatic Scrolling option in View menu to display
3321 the currently highlighted region of an alignment.</li>
3322 <li>Order an alignment by sequence length, or using the
3323 average score or total feature count for each sequence.</li>
3324 <li>Shading features by score or associated description</li>
3325 <li>Subdivide alignment and groups based on identity of
3326 selected subsequence (Make Groups from Selection).</li>
3327 <li>New hide/show options including Shift+Control+H to
3328 hide everything but the currently selected region.</li>
3329 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3330 </ul> <em>Application</em>
3332 <li>Fetch DB References capabilities and UI expanded to
3333 support retrieval from DAS sequence sources</li>
3334 <li>Local DAS Sequence sources can be added via the
3335 command line or via the Add local source dialog box.</li>
3336 <li>DAS Dbref and DbxRef feature types are parsed as
3337 database references and protein_name is parsed as
3338 description line (BioSapiens terms).</li>
3339 <li>Enable or disable non-positional feature and database
3340 references in sequence ID tooltip from View menu in
3342 <!-- <li>New hidden columns and rows and representatives capabilities
3343 in annotations file (in progress - not yet fully implemented)</li> -->
3344 <li>Group-associated consensus, sequence logos and
3345 conservation plots</li>
3346 <li>Symbol distributions for each column can be exported
3347 and visualized as sequence logos</li>
3348 <li>Optionally scale multi-character column labels to fit
3349 within each column of annotation row<!-- todo for applet -->
3351 <li>Optional automatic sort of associated alignment view
3352 when a new tree is opened.</li>
3353 <li>Jalview Java Console</li>
3354 <li>Better placement of desktop window when moving
3355 between different screens.</li>
3356 <li>New preference items for sequence ID tooltip and
3357 consensus annotation</li>
3358 <li>Client to submit sequences and IDs to Envision2
3360 <li><em>Vamsas Capabilities</em>
3362 <li>Improved VAMSAS synchronization (Jalview archive
3363 used to preserve views, structures, and tree display
3365 <li>Import of vamsas documents from disk or URL via
3367 <li>Sharing of selected regions between views and
3368 with other VAMSAS applications (Experimental feature!)</li>
3369 <li>Updated API to VAMSAS version 0.2</li>
3371 </ul> <em>Applet</em>
3373 <li>Middle button resizes annotation row height</li>
3376 <li>sortByTree (true/false) - automatically sort the
3377 associated alignment view by the tree when a new tree is
3379 <li>showTreeBootstraps (true/false) - show or hide
3380 branch bootstraps (default is to show them if available)</li>
3381 <li>showTreeDistances (true/false) - show or hide
3382 branch lengths (default is to show them if available)</li>
3383 <li>showUnlinkedTreeNodes (true/false) - indicate if
3384 unassociated nodes should be highlighted in the tree
3386 <li>heightScale and widthScale (1.0 or more) -
3387 increase the height or width of a cell in the alignment
3388 grid relative to the current font size.</li>
3391 <li>Non-positional features displayed in sequence ID
3393 </ul> <em>Other</em>
3395 <li>Features format: graduated colour definitions and
3396 specification of feature scores</li>
3397 <li>Alignment Annotations format: new keywords for group
3398 associated annotation (GROUP_REF) and annotation row display
3399 properties (ROW_PROPERTIES)</li>
3400 <li>XML formats extended to support graduated feature
3401 colourschemes, group associated annotation, and profile
3402 visualization settings.</li></td>
3405 <li>Source field in GFF files parsed as feature source
3406 rather than description</li>
3407 <li>Non-positional features are now included in sequence
3408 feature and gff files (controlled via non-positional feature
3409 visibility in tooltip).</li>
3410 <li>URL links generated for all feature links (bugfix)</li>
3411 <li>Added URL embedding instructions to features file
3413 <li>Codons containing ambiguous nucleotides translated as
3414 'X' in peptide product</li>
3415 <li>Match case switch in find dialog box works for both
3416 sequence ID and sequence string and query strings do not
3417 have to be in upper case to match case-insensitively.</li>
3418 <li>AMSA files only contain first column of
3419 multi-character column annotation labels</li>
3420 <li>Jalview Annotation File generation/parsing consistent
3421 with documentation (e.g. Stockholm annotation can be
3422 exported and re-imported)</li>
3423 <li>PDB files without embedded PDB IDs given a friendly
3425 <li>Find incrementally searches ID string matches as well
3426 as subsequence matches, and correctly reports total number
3430 <li>Better handling of exceptions during sequence
3432 <li>Dasobert generated non-positional feature URL
3433 link text excludes the start_end suffix</li>
3434 <li>DAS feature and source retrieval buttons disabled
3435 when fetch or registry operations in progress.</li>
3436 <li>PDB files retrieved from URLs are cached properly</li>
3437 <li>Sequence description lines properly shared via
3439 <li>Sequence fetcher fetches multiple records for all
3441 <li>Ensured that command line das feature retrieval
3442 completes before alignment figures are generated.</li>
3443 <li>Reduced time taken when opening file browser for
3445 <li>isAligned check prior to calculating tree, PCA or
3446 submitting an MSA to JNet now excludes hidden sequences.</li>
3447 <li>User defined group colours properly recovered
3448 from Jalview projects.</li>
3457 <div align="center">
3458 <strong>2.4.0.b2</strong><br> 28/10/2009
3463 <li>Experimental support for google analytics usage
3465 <li>Jalview privacy settings (user preferences and docs).</li>
3470 <li>Race condition in applet preventing startup in
3472 <li>Exception when feature created from selection beyond
3473 length of sequence.</li>
3474 <li>Allow synthetic PDB files to be imported gracefully</li>
3475 <li>Sequence associated annotation rows associate with
3476 all sequences with a given id</li>
3477 <li>Find function matches case-insensitively for sequence
3478 ID string searches</li>
3479 <li>Non-standard characters do not cause pairwise
3480 alignment to fail with exception</li>
3481 </ul> <em>Application Issues</em>
3483 <li>Sequences are now validated against EMBL database</li>
3484 <li>Sequence fetcher fetches multiple records for all
3486 </ul> <em>InstallAnywhere Issues</em>
3488 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3489 issue with installAnywhere mechanism)</li>
3490 <li>Command line launching of JARs from InstallAnywhere
3491 version (java class versioning error fixed)</li>
3498 <div align="center">
3499 <strong>2.4</strong><br> 27/8/2008
3502 <td><em>User Interface</em>
3504 <li>Linked highlighting of codon and amino acid from
3505 translation and protein products</li>
3506 <li>Linked highlighting of structure associated with
3507 residue mapping to codon position</li>
3508 <li>Sequence Fetcher provides example accession numbers
3509 and 'clear' button</li>
3510 <li>MemoryMonitor added as an option under Desktop's
3512 <li>Extract score function to parse whitespace separated
3513 numeric data in description line</li>
3514 <li>Column labels in alignment annotation can be centred.</li>
3515 <li>Tooltip for sequence associated annotation give name
3517 </ul> <em>Web Services and URL fetching</em>
3519 <li>JPred3 web service</li>
3520 <li>Prototype sequence search client (no public services
3522 <li>Fetch either seed alignment or full alignment from
3524 <li>URL Links created for matching database cross
3525 references as well as sequence ID</li>
3526 <li>URL Links can be created using regular-expressions</li>
3527 </ul> <em>Sequence Database Connectivity</em>
3529 <li>Retrieval of cross-referenced sequences from other
3531 <li>Generalised database reference retrieval and
3532 validation to all fetchable databases</li>
3533 <li>Fetch sequences from DAS sources supporting the
3534 sequence command</li>
3535 </ul> <em>Import and Export</em>
3536 <li>export annotation rows as CSV for spreadsheet import</li>
3537 <li>Jalview projects record alignment dataset associations,
3538 EMBL products, and cDNA sequence mappings</li>
3539 <li>Sequence Group colour can be specified in Annotation
3541 <li>Ad-hoc colouring of group in Annotation File using RGB
3542 triplet as name of colourscheme</li>
3543 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3545 <li>treenode binding for VAMSAS tree exchange</li>
3546 <li>local editing and update of sequences in VAMSAS
3547 alignments (experimental)</li>
3548 <li>Create new or select existing session to join</li>
3549 <li>load and save of vamsas documents</li>
3550 </ul> <em>Application command line</em>
3552 <li>-tree parameter to open trees (introduced for passing
3554 <li>-fetchfrom command line argument to specify nicknames
3555 of DAS servers to query for alignment features</li>
3556 <li>-dasserver command line argument to add new servers
3557 that are also automatically queried for features</li>
3558 <li>-groovy command line argument executes a given groovy
3559 script after all input data has been loaded and parsed</li>
3560 </ul> <em>Applet-Application data exchange</em>
3562 <li>Trees passed as applet parameters can be passed to
3563 application (when using "View in full
3564 application")</li>
3565 </ul> <em>Applet Parameters</em>
3567 <li>feature group display control parameter</li>
3568 <li>debug parameter</li>
3569 <li>showbutton parameter</li>
3570 </ul> <em>Applet API methods</em>
3572 <li>newView public method</li>
3573 <li>Window (current view) specific get/set public methods</li>
3574 <li>Feature display control methods</li>
3575 <li>get list of currently selected sequences</li>
3576 </ul> <em>New Jalview distribution features</em>
3578 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3579 <li>RELEASE file gives build properties for the latest
3580 Jalview release.</li>
3581 <li>Java 1.1 Applet build made easier and donotobfuscate
3582 property controls execution of obfuscator</li>
3583 <li>Build target for generating source distribution</li>
3584 <li>Debug flag for javacc</li>
3585 <li>.jalview_properties file is documented (slightly) in
3586 jalview.bin.Cache</li>
3587 <li>Continuous Build Integration for stable and
3588 development version of Application, Applet and source
3593 <li>selected region output includes visible annotations
3594 (for certain formats)</li>
3595 <li>edit label/displaychar contains existing label/char
3597 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3598 <li>shorter peptide product names from EMBL records</li>
3599 <li>Newick string generator makes compact representations</li>
3600 <li>bootstrap values parsed correctly for tree files with
3602 <li>pathological filechooser bug avoided by not allowing
3603 filenames containing a ':'</li>
3604 <li>Fixed exception when parsing GFF files containing
3605 global sequence features</li>
3606 <li>Alignment datasets are finalized only when number of
3607 references from alignment sequences goes to zero</li>
3608 <li>Close of tree branch colour box without colour
3609 selection causes cascading exceptions</li>
3610 <li>occasional negative imgwidth exceptions</li>
3611 <li>better reporting of non-fatal warnings to user when
3612 file parsing fails.</li>
3613 <li>Save works when Jalview project is default format</li>
3614 <li>Save as dialog opened if current alignment format is
3615 not a valid output format</li>
3616 <li>UniProt canonical names introduced for both das and
3618 <li>Histidine should be midblue (not pink!) in Zappo</li>
3619 <li>error messages passed up and output when data read
3621 <li>edit undo recovers previous dataset sequence when
3622 sequence is edited</li>
3623 <li>allow PDB files without pdb ID HEADER lines (like
3624 those generated by MODELLER) to be read in properly</li>
3625 <li>allow reading of JPred concise files as a normal
3627 <li>Stockholm annotation parsing and alignment properties
3628 import fixed for PFAM records</li>
3629 <li>Structure view windows have correct name in Desktop
3631 <li>annotation consisting of sequence associated scores
3632 can be read and written correctly to annotation file</li>
3633 <li>Aligned cDNA translation to aligned peptide works
3635 <li>Fixed display of hidden sequence markers and
3636 non-italic font for representatives in Applet</li>
3637 <li>Applet Menus are always embedded in applet window on
3639 <li>Newly shown features appear at top of stack (in
3641 <li>Annotations added via parameter not drawn properly
3642 due to null pointer exceptions</li>
3643 <li>Secondary structure lines are drawn starting from
3644 first column of alignment</li>
3645 <li>UniProt XML import updated for new schema release in
3647 <li>Sequence feature to sequence ID match for Features
3648 file is case-insensitive</li>
3649 <li>Sequence features read from Features file appended to
3650 all sequences with matching IDs</li>
3651 <li>PDB structure coloured correctly for associated views
3652 containing a sub-sequence</li>
3653 <li>PDB files can be retrieved by applet from Jar files</li>
3654 <li>feature and annotation file applet parameters
3655 referring to different directories are retrieved correctly</li>
3656 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3657 <li>Fixed application hang whilst waiting for
3658 splash-screen version check to complete</li>
3659 <li>Applet properly URLencodes input parameter values
3660 when passing them to the launchApp service</li>
3661 <li>display name and local features preserved in results
3662 retrieved from web service</li>
3663 <li>Visual delay indication for sequence retrieval and
3664 sequence fetcher initialisation</li>
3665 <li>updated Application to use DAS 1.53e version of
3666 dasobert DAS client</li>
3667 <li>Re-instated Full AMSA support and .amsa file
3669 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3677 <div align="center">
3678 <strong>2.3</strong><br> 9/5/07
3683 <li>Jmol 11.0.2 integration</li>
3684 <li>PDB views stored in Jalview XML files</li>
3685 <li>Slide sequences</li>
3686 <li>Edit sequence in place</li>
3687 <li>EMBL CDS features</li>
3688 <li>DAS Feature mapping</li>
3689 <li>Feature ordering</li>
3690 <li>Alignment Properties</li>
3691 <li>Annotation Scores</li>
3692 <li>Sort by scores</li>
3693 <li>Feature/annotation editing in applet</li>
3698 <li>Headless state operation in 2.2.1</li>
3699 <li>Incorrect and unstable DNA pairwise alignment</li>
3700 <li>Cut and paste of sequences with annotation</li>
3701 <li>Feature group display state in XML</li>
3702 <li>Feature ordering in XML</li>
3703 <li>blc file iteration selection using filename # suffix</li>
3704 <li>Stockholm alignment properties</li>
3705 <li>Stockhom alignment secondary structure annotation</li>
3706 <li>2.2.1 applet had no feature transparency</li>
3707 <li>Number pad keys can be used in cursor mode</li>
3708 <li>Structure Viewer mirror image resolved</li>
3715 <div align="center">
3716 <strong>2.2.1</strong><br> 12/2/07
3721 <li>Non standard characters can be read and displayed
3722 <li>Annotations/Features can be imported/exported to the
3724 <li>Applet allows editing of sequence/annotation/group
3725 name & description
3726 <li>Preference setting to display sequence name in
3728 <li>Annotation file format extended to allow
3729 Sequence_groups to be defined
3730 <li>Default opening of alignment overview panel can be
3731 specified in preferences
3732 <li>PDB residue numbering annotation added to associated
3738 <li>Applet crash under certain Linux OS with Java 1.6
3740 <li>Annotation file export / import bugs fixed
3741 <li>PNG / EPS image output bugs fixed
3747 <div align="center">
3748 <strong>2.2</strong><br> 27/11/06
3753 <li>Multiple views on alignment
3754 <li>Sequence feature editing
3755 <li>"Reload" alignment
3756 <li>"Save" to current filename
3757 <li>Background dependent text colour
3758 <li>Right align sequence ids
3759 <li>User-defined lower case residue colours
3762 <li>Menu item accelerator keys
3763 <li>Control-V pastes to current alignment
3764 <li>Cancel button for DAS Feature Fetching
3765 <li>PCA and PDB Viewers zoom via mouse roller
3766 <li>User-defined sub-tree colours and sub-tree selection
3768 <li>'New Window' button on the 'Output to Text box'
3773 <li>New memory efficient Undo/Redo System
3774 <li>Optimised symbol lookups and conservation/consensus
3776 <li>Region Conservation/Consensus recalculated after
3778 <li>Fixed Remove Empty Columns Bug (empty columns at end
3780 <li>Slowed DAS Feature Fetching for increased robustness.
3782 <li>Made angle brackets in ASCII feature descriptions
3784 <li>Re-instated Zoom function for PCA
3785 <li>Sequence descriptions conserved in web service
3787 <li>UniProt ID discoverer uses any word separated by
3789 <li>WsDbFetch query/result association resolved
3790 <li>Tree leaf to sequence mapping improved
3791 <li>Smooth fonts switch moved to FontChooser dialog box.
3798 <div align="center">
3799 <strong>2.1.1</strong><br> 12/9/06
3804 <li>Copy consensus sequence to clipboard</li>
3809 <li>Image output - rightmost residues are rendered if
3810 sequence id panel has been resized</li>
3811 <li>Image output - all offscreen group boundaries are
3813 <li>Annotation files with sequence references - all
3814 elements in file are relative to sequence position</li>
3815 <li>Mac Applet users can use Alt key for group editing</li>
3821 <div align="center">
3822 <strong>2.1</strong><br> 22/8/06
3827 <li>MAFFT Multiple Alignment in default Web Service list</li>
3828 <li>DAS Feature fetching</li>
3829 <li>Hide sequences and columns</li>
3830 <li>Export Annotations and Features</li>
3831 <li>GFF file reading / writing</li>
3832 <li>Associate structures with sequences from local PDB
3834 <li>Add sequences to exisiting alignment</li>
3835 <li>Recently opened files / URL lists</li>
3836 <li>Applet can launch the full application</li>
3837 <li>Applet has transparency for features (Java 1.2
3839 <li>Applet has user defined colours parameter</li>
3840 <li>Applet can load sequences from parameter
3841 "sequence<em>x</em>"
3847 <li>Redundancy Panel reinstalled in the Applet</li>
3848 <li>Monospaced font - EPS / rescaling bug fixed</li>
3849 <li>Annotation files with sequence references bug fixed</li>
3855 <div align="center">
3856 <strong>2.08.1</strong><br> 2/5/06
3861 <li>Change case of selected region from Popup menu</li>
3862 <li>Choose to match case when searching</li>
3863 <li>Middle mouse button and mouse movement can compress /
3864 expand the visible width and height of the alignment</li>
3869 <li>Annotation Panel displays complete JNet results</li>
3875 <div align="center">
3876 <strong>2.08b</strong><br> 18/4/06
3882 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3883 <li>Righthand label on wrapped alignments shows correct
3890 <div align="center">
3891 <strong>2.08</strong><br> 10/4/06
3896 <li>Editing can be locked to the selection area</li>
3897 <li>Keyboard editing</li>
3898 <li>Create sequence features from searches</li>
3899 <li>Precalculated annotations can be loaded onto
3901 <li>Features file allows grouping of features</li>
3902 <li>Annotation Colouring scheme added</li>
3903 <li>Smooth fonts off by default - Faster rendering</li>
3904 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3909 <li>Drag & Drop fixed on Linux</li>
3910 <li>Jalview Archive file faster to load/save, sequence
3911 descriptions saved.</li>
3917 <div align="center">
3918 <strong>2.07</strong><br> 12/12/05
3923 <li>PDB Structure Viewer enhanced</li>
3924 <li>Sequence Feature retrieval and display enhanced</li>
3925 <li>Choose to output sequence start-end after sequence
3926 name for file output</li>
3927 <li>Sequence Fetcher WSDBFetch@EBI</li>
3928 <li>Applet can read feature files, PDB files and can be
3929 used for HTML form input</li>
3934 <li>HTML output writes groups and features</li>
3935 <li>Group editing is Control and mouse click</li>
3936 <li>File IO bugs</li>
3942 <div align="center">
3943 <strong>2.06</strong><br> 28/9/05
3948 <li>View annotations in wrapped mode</li>
3949 <li>More options for PCA viewer</li>
3954 <li>GUI bugs resolved</li>
3955 <li>Runs with -nodisplay from command line</li>
3961 <div align="center">
3962 <strong>2.05b</strong><br> 15/9/05
3967 <li>Choose EPS export as lineart or text</li>
3968 <li>Jar files are executable</li>
3969 <li>Can read in Uracil - maps to unknown residue</li>
3974 <li>Known OutOfMemory errors give warning message</li>
3975 <li>Overview window calculated more efficiently</li>
3976 <li>Several GUI bugs resolved</li>
3982 <div align="center">
3983 <strong>2.05</strong><br> 30/8/05
3988 <li>Edit and annotate in "Wrapped" view</li>
3993 <li>Several GUI bugs resolved</li>
3999 <div align="center">
4000 <strong>2.04</strong><br> 24/8/05
4005 <li>Hold down mouse wheel & scroll to change font
4011 <li>Improved JPred client reliability</li>
4012 <li>Improved loading of Jalview files</li>
4018 <div align="center">
4019 <strong>2.03</strong><br> 18/8/05
4024 <li>Set Proxy server name and port in preferences</li>
4025 <li>Multiple URL links from sequence ids</li>
4026 <li>User Defined Colours can have a scheme name and added
4028 <li>Choose to ignore gaps in consensus calculation</li>
4029 <li>Unix users can set default web browser</li>
4030 <li>Runs without GUI for batch processing</li>
4031 <li>Dynamically generated Web Service Menus</li>
4036 <li>InstallAnywhere download for Sparc Solaris</li>
4042 <div align="center">
4043 <strong>2.02</strong><br> 18/7/05
4049 <li>Copy & Paste order of sequences maintains
4050 alignment order.</li>
4056 <div align="center">
4057 <strong>2.01</strong><br> 12/7/05
4062 <li>Use delete key for deleting selection.</li>
4063 <li>Use Mouse wheel to scroll sequences.</li>
4064 <li>Help file updated to describe how to add alignment
4066 <li>Version and build date written to build properties
4068 <li>InstallAnywhere installation will check for updates
4069 at launch of Jalview.</li>
4074 <li>Delete gaps bug fixed.</li>
4075 <li>FileChooser sorts columns.</li>
4076 <li>Can remove groups one by one.</li>
4077 <li>Filechooser icons installed.</li>
4078 <li>Finder ignores return character when searching.
4079 Return key will initiate a search.<br>
4086 <div align="center">
4087 <strong>2.0</strong><br> 20/6/05
4092 <li>New codebase</li>