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>
26 /* remove bullets, narrower indent */
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.2.11.0">2.11.0</a><br />
74 <em>8/09/2018</em></strong>
77 <td><div align="left">
81 <!-- JAL-2865 -->Jalview doesn't hang when closing windows or the overview updates with large alignments.
85 <td><div align="left">
89 <!-- JAL-3035 -->DAS sequence retrieval and annotation capabilities removed from the Jalview Desktop
95 <td width="60" nowrap>
97 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
100 <td><div align="left">
104 <!-- JAL-3101 -->Default memory for Jalview webstart and
105 InstallAnywhere increased to 1G.
108 <!-- JAL-247 -->Hidden sequence markers and representative
109 sequence bolding included when exporting alignment as EPS,
110 SVG, PNG or HTML. <em>Display is configured via the
111 Format menu, or for command-line use via a jalview
112 properties file.</em>
115 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
116 API and sequence data now imported as JSON.
119 <!-- JAL-3065 -->Change in recommended way of starting
120 Jalview via a Java command line: add jars in lib directory
121 to CLASSPATH, rather than via the deprecated java.ext.dirs
128 <!-- JAL-3047 -->Support added to execute test suite
129 instrumented with <a href="http://openclover.org/">Open
134 <td><div align="left">
138 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
139 row shown in Feredoxin Structure alignment view of example
143 <!-- JAL-2854 -->Annotation obscures sequences if lots of
144 annotation displayed.
147 <!-- JAL-3107 -->Group conservation/consensus not shown
148 for newly created group when 'Apply to all groups'
152 <!-- JAL-3087 -->Corrupted display when switching to
153 wrapped mode when sequence panel's vertical scrollbar is
157 <!-- JAL-3003 -->Alignment is black in exported EPS file
158 when sequences are selected in exported view.</em>
161 <!-- JAL-3059 -->Groups with different coloured borders
162 aren't rendered with correct colour.
165 <!-- JAL-3092 -->Jalview could hang when importing certain
166 types of knotted RNA secondary structure.
169 <!-- JAL-3095 -->Sequence highlight and selection in
170 trimmed VARNA 2D structure is incorrect for sequences that
174 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
175 annotation when columns are inserted into an alignment,
176 and when exporting as Stockholm flatfile.
179 <!-- JAL-3053 -->Jalview annotation rows containing upper
180 and lower-case 'E' and 'H' do not automatically get
181 treated as RNA secondary structure.
184 <!-- JAL-3106 -->.jvp should be used as default extension
185 (not .jar) when saving a jalview project file.
188 <!-- JAL-3105 -->Mac Users: closing a window correctly
189 transfers focus to previous window on OSX
192 <em>Java 10 Issues Resolved</em>
195 <!-- JAL-2988 -->OSX - Can't save new files via the File
196 or export menus by typing in a name into the Save dialog
200 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
201 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
202 'look and feel' which has improved compatibility with the
203 latest version of OSX.
210 <td width="60" nowrap>
212 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
213 <em>7/06/2018</em></strong>
216 <td><div align="left">
220 <!-- JAL-2920 -->Use HGVS nomenclature for variant
221 annotation retrieved from Uniprot
224 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
225 onto the Jalview Desktop
229 <td><div align="left">
233 <!-- JAL-3017 -->Cannot import features with multiple
234 variant elements (blocks import of some Uniprot records)
237 <!-- JAL-2997 -->Clustal files with sequence positions in
238 right-hand column parsed correctly
241 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
242 not alignment area in exported graphic
245 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
246 window has input focus
249 <!-- JAL-2992 -->Annotation panel set too high when
250 annotation added to view (Windows)
253 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
254 network connectivity is poor
257 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
258 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
259 the currently open URL and links from a page viewed in
260 Firefox or Chrome on Windows is now fully supported. If
261 you are using Edge, only links in the page can be
262 dragged, and with Internet Explorer, only the currently
263 open URL in the browser can be dropped onto Jalview.</em>
269 <td width="60" nowrap>
271 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
274 <td><div align="left">
278 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
279 for disabling automatic superposition of multiple
280 structures and open structures in existing views
283 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
284 ID and annotation area margins can be click-dragged to
288 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
292 <!-- JAL-2759 -->Improved performance for large alignments
293 and lots of hidden columns
296 <!-- JAL-2593 -->Improved performance when rendering lots
297 of features (particularly when transparency is disabled)
302 <td><div align="left">
305 <!-- JAL-2899 -->Structure and Overview aren't updated
306 when Colour By Annotation threshold slider is adjusted
309 <!-- JAL-2778 -->Slow redraw when Overview panel shown
310 overlapping alignment panel
313 <!-- JAL-2929 -->Overview doesn't show end of unpadded
317 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
318 improved: CDS not handled correctly if transcript has no
322 <!-- JAL-2321 -->Secondary structure and temperature
323 factor annotation not added to sequence when local PDB
324 file associated with it by drag'n'drop or structure
328 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
329 dialog doesn't import PDB files dropped on an alignment
332 <!-- JAL-2666 -->Linked scrolling via protein horizontal
333 scroll bar doesn't work for some CDS/Protein views
336 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
337 Java 1.8u153 onwards and Java 1.9u4+.
340 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
341 columns in annotation row
344 <!-- JAL-2913 -->Preferences panel's ID Width control is not
345 honored in batch mode
348 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
349 for structures added to existing Jmol view
352 <!-- JAL-2223 -->'View Mappings' includes duplicate
353 entries after importing project with multiple views
356 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
357 protein sequences via SIFTS from associated PDB entries
358 with negative residue numbers or missing residues fails
361 <!-- JAL-2952 -->Exception when shading sequence with negative
362 Temperature Factor values from annotated PDB files (e.g.
363 as generated by CONSURF)
366 <!-- JAL-2920 -->Uniprot 'sequence variant' features
367 tooltip doesn't include a text description of mutation
370 <!-- JAL-2922 -->Invert displayed features very slow when
371 structure and/or overview windows are also shown
374 <!-- JAL-2954 -->Selecting columns from highlighted regions
375 very slow for alignments with large numbers of sequences
378 <!-- JAL-2925 -->Copy Consensus fails for group consensus
379 with 'StringIndexOutOfBounds'
382 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
383 platforms running Java 10
386 <!-- JAL-2960 -->Adding a structure to existing structure
387 view appears to do nothing because the view is hidden behind the alignment view
393 <!-- JAL-2926 -->Copy consensus sequence option in applet
394 should copy the group consensus when popup is opened on it
400 <!-- JAL-2913 -->Fixed ID width preference is not respected
403 <em>New Known Defects</em>
406 <!-- JAL-2973 --> Exceptions occasionally raised when
407 editing a large alignment and overview is displayed
410 <!-- JAL-2974 -->'Overview updating' progress bar is shown
411 repeatedly after a series of edits even when the overview
412 is no longer reflecting updates
415 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
416 structures for protein subsequence (if 'Trim Retrieved
417 Sequences' enabled) or Ensembl isoforms (Workaround in
418 2.10.4 is to fail back to N&W mapping)
425 <td width="60" nowrap>
427 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
430 <td><div align="left">
431 <ul><li>Updated Certum Codesigning Certificate
432 (Valid till 30th November 2018)</li></ul></div></td>
433 <td><div align="left">
436 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
437 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
438 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
439 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
440 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
441 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
442 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
448 <td width="60" nowrap>
450 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
453 <td><div align="left">
457 <!-- JAL-2446 -->Faster and more efficient management and
458 rendering of sequence features
461 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
462 429 rate limit request hander
465 <!-- JAL-2773 -->Structure views don't get updated unless
466 their colours have changed
469 <!-- JAL-2495 -->All linked sequences are highlighted for
470 a structure mousover (Jmol) or selection (Chimera)
473 <!-- JAL-2790 -->'Cancel' button in progress bar for
474 JABAWS AACon, RNAAliFold and Disorder prediction jobs
477 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
478 view from Ensembl locus cross-references
481 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
485 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
486 feature can be disabled
489 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
490 PDB easier retrieval of sequences for lists of IDs
493 <!-- JAL-2758 -->Short names for sequences retrieved from
499 <li>Groovy interpreter updated to 2.4.12</li>
500 <li>Example groovy script for generating a matrix of
501 percent identity scores for current alignment.</li>
503 <em>Testing and Deployment</em>
506 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
510 <td><div align="left">
514 <!-- JAL-2643 -->Pressing tab after updating the colour
515 threshold text field doesn't trigger an update to the
519 <!-- JAL-2682 -->Race condition when parsing sequence ID
523 <!-- JAL-2608 -->Overview windows are also closed when
524 alignment window is closed
527 <!-- JAL-2548 -->Export of features doesn't always respect
531 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
532 takes a long time in Cursor mode
538 <!-- JAL-2777 -->Structures with whitespace chainCode
539 cannot be viewed in Chimera
542 <!-- JAL-2728 -->Protein annotation panel too high in
546 <!-- JAL-2757 -->Can't edit the query after the server
547 error warning icon is shown in Uniprot and PDB Free Text
551 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
554 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
557 <!-- JAL-2739 -->Hidden column marker in last column not
558 rendered when switching back from Wrapped to normal view
561 <!-- JAL-2768 -->Annotation display corrupted when
562 scrolling right in unwapped alignment view
565 <!-- JAL-2542 -->Existing features on subsequence
566 incorrectly relocated when full sequence retrieved from
570 <!-- JAL-2733 -->Last reported memory still shown when
571 Desktop->Show Memory is unticked (OSX only)
574 <!-- JAL-2658 -->Amend Features dialog doesn't allow
575 features of same type and group to be selected for
579 <!-- JAL-2524 -->Jalview becomes sluggish in wide
580 alignments when hidden columns are present
583 <!-- JAL-2392 -->Jalview freezes when loading and
584 displaying several structures
587 <!-- JAL-2732 -->Black outlines left after resizing or
591 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
592 within the Jalview desktop on OSX
595 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
596 when in wrapped alignment mode
599 <!-- JAL-2636 -->Scale mark not shown when close to right
600 hand end of alignment
603 <!-- JAL-2684 -->Pairwise alignment of selected regions of
604 each selected sequence do not have correct start/end
608 <!-- JAL-2793 -->Alignment ruler height set incorrectly
609 after canceling the Alignment Window's Font dialog
612 <!-- JAL-2036 -->Show cross-references not enabled after
613 restoring project until a new view is created
616 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
617 URL links appears when only default EMBL-EBI link is
618 configured (since 2.10.2b2)
621 <!-- JAL-2775 -->Overview redraws whole window when box
625 <!-- JAL-2225 -->Structure viewer doesn't map all chains
626 in a multi-chain structure when viewing alignment
627 involving more than one chain (since 2.10)
630 <!-- JAL-2811 -->Double residue highlights in cursor mode
631 if new selection moves alignment window
634 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
635 arrow key in cursor mode to pass hidden column marker
638 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
639 that produces correctly annotated transcripts and products
642 <!-- JAL-2776 -->Toggling a feature group after first time
643 doesn't update associated structure view
646 <em>Applet</em><br />
649 <!-- JAL-2687 -->Concurrent modification exception when
650 closing alignment panel
653 <em>BioJSON</em><br />
656 <!-- JAL-2546 -->BioJSON export does not preserve
657 non-positional features
660 <em>New Known Issues</em>
663 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
664 sequence features correctly (for many previous versions of
668 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
669 using cursor in wrapped panel other than top
672 <!-- JAL-2791 -->Select columns containing feature ignores
673 graduated colour threshold
676 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
677 always preserve numbering and sequence features
680 <em>Known Java 9 Issues</em>
683 <!-- JAL-2902 -->Groovy Console very slow to open and is
684 not responsive when entering characters (Webstart, Java
691 <td width="60" nowrap>
693 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
694 <em>2/10/2017</em></strong>
697 <td><div align="left">
698 <em>New features in Jalview Desktop</em>
701 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
703 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
707 <td><div align="left">
711 <td width="60" nowrap>
713 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
714 <em>7/9/2017</em></strong>
717 <td><div align="left">
721 <!-- JAL-2588 -->Show gaps in overview window by colouring
722 in grey (sequences used to be coloured grey, and gaps were
726 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
730 <!-- JAL-2587 -->Overview updates immediately on increase
731 in size and progress bar shown as higher resolution
732 overview is recalculated
737 <td><div align="left">
741 <!-- JAL-2664 -->Overview window redraws every hidden
742 column region row by row
745 <!-- JAL-2681 -->duplicate protein sequences shown after
746 retrieving Ensembl crossrefs for sequences from Uniprot
749 <!-- JAL-2603 -->Overview window throws NPE if show boxes
750 format setting is unticked
753 <!-- JAL-2610 -->Groups are coloured wrongly in overview
754 if group has show boxes format setting unticked
757 <!-- JAL-2672,JAL-2665 -->Redraw problems when
758 autoscrolling whilst dragging current selection group to
759 include sequences and columns not currently displayed
762 <!-- JAL-2691 -->Not all chains are mapped when multimeric
763 assemblies are imported via CIF file
766 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
767 displayed when threshold or conservation colouring is also
771 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
775 <!-- JAL-2673 -->Jalview continues to scroll after
776 dragging a selected region off the visible region of the
780 <!-- JAL-2724 -->Cannot apply annotation based
781 colourscheme to all groups in a view
784 <!-- JAL-2511 -->IDs don't line up with sequences
785 initially after font size change using the Font chooser or
792 <td width="60" nowrap>
794 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
797 <td><div align="left">
798 <em>Calculations</em>
802 <!-- JAL-1933 -->Occupancy annotation row shows number of
803 ungapped positions in each column of the alignment.
806 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
807 a calculation dialog box
810 <!-- JAL-2379 -->Revised implementation of PCA for speed
811 and memory efficiency (~30x faster)
814 <!-- JAL-2403 -->Revised implementation of sequence
815 similarity scores as used by Tree, PCA, Shading Consensus
816 and other calculations
819 <!-- JAL-2416 -->Score matrices are stored as resource
820 files within the Jalview codebase
823 <!-- JAL-2500 -->Trees computed on Sequence Feature
824 Similarity may have different topology due to increased
831 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
832 model for alignments and groups
835 <!-- JAL-384 -->Custom shading schemes created via groovy
842 <!-- JAL-2526 -->Efficiency improvements for interacting
843 with alignment and overview windows
846 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
850 <!-- JAL-2388 -->Hidden columns and sequences can be
854 <!-- JAL-2611 -->Click-drag in visible area allows fine
855 adjustment of visible position
859 <em>Data import/export</em>
862 <!-- JAL-2535 -->Posterior probability annotation from
863 Stockholm files imported as sequence associated annotation
866 <!-- JAL-2507 -->More robust per-sequence positional
867 annotation input/output via stockholm flatfile
870 <!-- JAL-2533 -->Sequence names don't include file
871 extension when importing structure files without embedded
872 names or PDB accessions
875 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
876 format sequence substitution matrices
879 <em>User Interface</em>
882 <!-- JAL-2447 --> Experimental Features Checkbox in
883 Desktop's Tools menu to hide or show untested features in
887 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
888 via Overview or sequence motif search operations
891 <!-- JAL-2547 -->Amend sequence features dialog box can be
892 opened by double clicking gaps within sequence feature
896 <!-- JAL-1476 -->Status bar message shown when not enough
897 aligned positions were available to create a 3D structure
901 <em>3D Structure</em>
904 <!-- JAL-2430 -->Hidden regions in alignment views are not
905 coloured in linked structure views
908 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
909 file-based command exchange
912 <!-- JAL-2375 -->Structure chooser automatically shows
913 Cached Structures rather than querying the PDBe if
914 structures are already available for sequences
917 <!-- JAL-2520 -->Structures imported via URL are cached in
918 the Jalview project rather than downloaded again when the
922 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
923 to transfer Chimera's structure attributes as Jalview
924 features, and vice-versa (<strong>Experimental
928 <em>Web Services</em>
931 <!-- JAL-2549 -->Updated JABAWS client to v2.2
934 <!-- JAL-2335 -->Filter non-standard amino acids and
935 nucleotides when submitting to AACon and other MSA
939 <!-- JAL-2316, -->URLs for viewing database
940 cross-references provided by identifiers.org and the
948 <!-- JAL-2344 -->FileFormatI interface for describing and
949 identifying file formats (instead of String constants)
952 <!-- JAL-2228 -->FeatureCounter script refactored for
953 efficiency when counting all displayed features (not
954 backwards compatible with 2.10.1)
957 <em>Example files</em>
960 <!-- JAL-2631 -->Graduated feature colour style example
961 included in the example feature file
964 <em>Documentation</em>
967 <!-- JAL-2339 -->Release notes reformatted for readability
968 with the built-in Java help viewer
971 <!-- JAL-1644 -->Find documentation updated with 'search
972 sequence description' option
978 <!-- JAL-2485, -->External service integration tests for
979 Uniprot REST Free Text Search Client
982 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
985 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
990 <td><div align="left">
991 <em>Calculations</em>
994 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
995 matrix - C->R should be '-3'<br />Old matrix restored
996 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
998 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
999 Jalview's treatment of gaps in PCA and substitution matrix
1000 based Tree calculations.<br /> <br />In earlier versions
1001 of Jalview, gaps matching gaps were penalised, and gaps
1002 matching non-gaps penalised even more. In the PCA
1003 calculation, gaps were actually treated as non-gaps - so
1004 different costs were applied, which meant Jalview's PCAs
1005 were different to those produced by SeqSpace.<br />Jalview
1006 now treats gaps in the same way as SeqSpace (ie it scores
1007 them as 0). <br /> <br />Enter the following in the
1008 Groovy console to restore pre-2.10.2 behaviour:<br />
1009 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1010 // for 2.10.1 mode <br />
1011 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1012 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1013 these settings will affect all subsequent tree and PCA
1014 calculations (not recommended)</em></li>
1016 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1017 scaling of branch lengths for trees computed using
1018 Sequence Feature Similarity.
1021 <!-- JAL-2377 -->PCA calculation could hang when
1022 generating output report when working with highly
1023 redundant alignments
1026 <!-- JAL-2544 --> Sort by features includes features to
1027 right of selected region when gaps present on right-hand
1031 <em>User Interface</em>
1034 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1035 doesn't reselect a specific sequence's associated
1036 annotation after it was used for colouring a view
1039 <!-- JAL-2419 -->Current selection lost if popup menu
1040 opened on a region of alignment without groups
1043 <!-- JAL-2374 -->Popup menu not always shown for regions
1044 of an alignment with overlapping groups
1047 <!-- JAL-2310 -->Finder double counts if both a sequence's
1048 name and description match
1051 <!-- JAL-2370 -->Hiding column selection containing two
1052 hidden regions results in incorrect hidden regions
1055 <!-- JAL-2386 -->'Apply to all groups' setting when
1056 changing colour does not apply Conservation slider value
1060 <!-- JAL-2373 -->Percentage identity and conservation menu
1061 items do not show a tick or allow shading to be disabled
1064 <!-- JAL-2385 -->Conservation shading or PID threshold
1065 lost when base colourscheme changed if slider not visible
1068 <!-- JAL-2547 -->Sequence features shown in tooltip for
1069 gaps before start of features
1072 <!-- JAL-2623 -->Graduated feature colour threshold not
1073 restored to UI when feature colour is edited
1076 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1077 a time when scrolling vertically in wrapped mode.
1080 <!-- JAL-2630 -->Structure and alignment overview update
1081 as graduate feature colour settings are modified via the
1085 <!-- JAL-2034 -->Overview window doesn't always update
1086 when a group defined on the alignment is resized
1089 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1090 wrapped view result in positional status updates
1094 <!-- JAL-2563 -->Status bar doesn't show position for
1095 ambiguous amino acid and nucleotide symbols
1098 <!-- JAL-2602 -->Copy consensus sequence failed if
1099 alignment included gapped columns
1102 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1103 widgets don't permanently disappear
1106 <!-- JAL-2503 -->Cannot select or filter quantitative
1107 annotation that are shown only as column labels (e.g.
1108 T-Coffee column reliability scores)
1111 <!-- JAL-2594 -->Exception thrown if trying to create a
1112 sequence feature on gaps only
1115 <!-- JAL-2504 -->Features created with 'New feature'
1116 button from a Find inherit previously defined feature type
1117 rather than the Find query string
1120 <!-- JAL-2423 -->incorrect title in output window when
1121 exporting tree calculated in Jalview
1124 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1125 and then revealing them reorders sequences on the
1129 <!-- JAL-964 -->Group panel in sequence feature settings
1130 doesn't update to reflect available set of groups after
1131 interactively adding or modifying features
1134 <!-- JAL-2225 -->Sequence Database chooser unusable on
1138 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1139 only excluded gaps in current sequence and ignored
1146 <!-- JAL-2421 -->Overview window visible region moves
1147 erratically when hidden rows or columns are present
1150 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1151 Structure Viewer's colour menu don't correspond to
1155 <!-- JAL-2405 -->Protein specific colours only offered in
1156 colour and group colour menu for protein alignments
1159 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1160 reflect currently selected view or group's shading
1164 <!-- JAL-2624 -->Feature colour thresholds not respected
1165 when rendered on overview and structures when opacity at
1169 <!-- JAL-2589 -->User defined gap colour not shown in
1170 overview when features overlaid on alignment
1173 <em>Data import/export</em>
1176 <!-- JAL-2576 -->Very large alignments take a long time to
1180 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1181 added after a sequence was imported are not written to
1185 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1186 when importing RNA secondary structure via Stockholm
1189 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1190 not shown in correct direction for simple pseudoknots
1193 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1194 with lightGray or darkGray via features file (but can
1198 <!-- JAL-2383 -->Above PID colour threshold not recovered
1199 when alignment view imported from project
1202 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1203 structure and sequences extracted from structure files
1204 imported via URL and viewed in Jmol
1207 <!-- JAL-2520 -->Structures loaded via URL are saved in
1208 Jalview Projects rather than fetched via URL again when
1209 the project is loaded and the structure viewed
1212 <em>Web Services</em>
1215 <!-- JAL-2519 -->EnsemblGenomes example failing after
1216 release of Ensembl v.88
1219 <!-- JAL-2366 -->Proxy server address and port always
1220 appear enabled in Preferences->Connections
1223 <!-- JAL-2461 -->DAS registry not found exceptions
1224 removed from console output
1227 <!-- JAL-2582 -->Cannot retrieve protein products from
1228 Ensembl by Peptide ID
1231 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1232 created from SIFTs, and spurious 'Couldn't open structure
1233 in Chimera' errors raised after April 2017 update (problem
1234 due to 'null' string rather than empty string used for
1235 residues with no corresponding PDB mapping).
1238 <em>Application UI</em>
1241 <!-- JAL-2361 -->User Defined Colours not added to Colour
1245 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1246 case' residues (button in colourscheme editor debugged and
1247 new documentation and tooltips added)
1250 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1251 doesn't restore group-specific text colour thresholds
1254 <!-- JAL-2243 -->Feature settings panel does not update as
1255 new features are added to alignment
1258 <!-- JAL-2532 -->Cancel in feature settings reverts
1259 changes to feature colours via the Amend features dialog
1262 <!-- JAL-2506 -->Null pointer exception when attempting to
1263 edit graduated feature colour via amend features dialog
1267 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1268 selection menu changes colours of alignment views
1271 <!-- JAL-2426 -->Spurious exceptions in console raised
1272 from alignment calculation workers after alignment has
1276 <!-- JAL-1608 -->Typo in selection popup menu - Create
1277 groups now 'Create Group'
1280 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1281 Create/Undefine group doesn't always work
1284 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1285 shown again after pressing 'Cancel'
1288 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1289 adjusts start position in wrap mode
1292 <!-- JAL-2563 -->Status bar doesn't show positions for
1293 ambiguous amino acids
1296 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1297 CDS/Protein view after CDS sequences added for aligned
1301 <!-- JAL-2592 -->User defined colourschemes called 'User
1302 Defined' don't appear in Colours menu
1308 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1309 score models doesn't always result in an updated PCA plot
1312 <!-- JAL-2442 -->Features not rendered as transparent on
1313 overview or linked structure view
1316 <!-- JAL-2372 -->Colour group by conservation doesn't
1320 <!-- JAL-2517 -->Hitting Cancel after applying
1321 user-defined colourscheme doesn't restore original
1328 <!-- JAL-2314 -->Unit test failure:
1329 jalview.ws.jabaws.RNAStructExportImport setup fails
1332 <!-- JAL-2307 -->Unit test failure:
1333 jalview.ws.sifts.SiftsClientTest due to compatibility
1334 problems with deep array comparison equality asserts in
1335 successive versions of TestNG
1338 <!-- JAL-2479 -->Relocated StructureChooserTest and
1339 ParameterUtilsTest Unit tests to Network suite
1342 <em>New Known Issues</em>
1345 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1346 phase after a sequence motif find operation
1349 <!-- JAL-2550 -->Importing annotation file with rows
1350 containing just upper and lower case letters are
1351 interpreted as WUSS RNA secondary structure symbols
1354 <!-- JAL-2590 -->Cannot load and display Newick trees
1355 reliably from eggnog Ortholog database
1358 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1359 containing features of type Highlight' when 'B' is pressed
1360 to mark columns containing highlighted regions.
1363 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1364 doesn't always add secondary structure annotation.
1369 <td width="60" nowrap>
1370 <div align="center">
1371 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1374 <td><div align="left">
1378 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1379 for all consensus calculations
1382 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1385 <li>Updated Jalview's Certum code signing certificate
1388 <em>Application</em>
1391 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1392 set of database cross-references, sorted alphabetically
1395 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1396 from database cross references. Users with custom links
1397 will receive a <a href="webServices/urllinks.html#warning">warning
1398 dialog</a> asking them to update their preferences.
1401 <!-- JAL-2287-->Cancel button and escape listener on
1402 dialog warning user about disconnecting Jalview from a
1406 <!-- JAL-2320-->Jalview's Chimera control window closes if
1407 the Chimera it is connected to is shut down
1410 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1411 columns menu item to mark columns containing highlighted
1412 regions (e.g. from structure selections or results of a
1416 <!-- JAL-2284-->Command line option for batch-generation
1417 of HTML pages rendering alignment data with the BioJS
1427 <!-- JAL-2286 -->Columns with more than one modal residue
1428 are not coloured or thresholded according to percent
1429 identity (first observed in Jalview 2.8.2)
1432 <!-- JAL-2301 -->Threonine incorrectly reported as not
1436 <!-- JAL-2318 -->Updates to documentation pages (above PID
1437 threshold, amino acid properties)
1440 <!-- JAL-2292 -->Lower case residues in sequences are not
1441 reported as mapped to residues in a structure file in the
1445 <!--JAL-2324 -->Identical features with non-numeric scores
1446 could be added multiple times to a sequence
1449 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1450 bond features shown as two highlighted residues rather
1451 than a range in linked structure views, and treated
1452 correctly when selecting and computing trees from features
1455 <!-- JAL-2281-->Custom URL links for database
1456 cross-references are matched to database name regardless
1461 <em>Application</em>
1464 <!-- JAL-2282-->Custom URL links for specific database
1465 names without regular expressions also offer links from
1469 <!-- JAL-2315-->Removing a single configured link in the
1470 URL links pane in Connections preferences doesn't actually
1471 update Jalview configuration
1474 <!-- JAL-2272-->CTRL-Click on a selected region to open
1475 the alignment area popup menu doesn't work on El-Capitan
1478 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1479 files with similarly named sequences if dropped onto the
1483 <!-- JAL-2312 -->Additional mappings are shown for PDB
1484 entries where more chains exist in the PDB accession than
1485 are reported in the SIFTS file
1488 <!-- JAL-2317-->Certain structures do not get mapped to
1489 the structure view when displayed with Chimera
1492 <!-- JAL-2317-->No chains shown in the Chimera view
1493 panel's View->Show Chains submenu
1496 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1497 work for wrapped alignment views
1500 <!--JAL-2197 -->Rename UI components for running JPred
1501 predictions from 'JNet' to 'JPred'
1504 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1505 corrupted when annotation panel vertical scroll is not at
1506 first annotation row
1509 <!--JAL-2332 -->Attempting to view structure for Hen
1510 lysozyme results in a PDB Client error dialog box
1513 <!-- JAL-2319 -->Structure View's mapping report switched
1514 ranges for PDB and sequence for SIFTS
1517 SIFTS 'Not_Observed' residues mapped to non-existant
1521 <!-- <em>New Known Issues</em>
1528 <td width="60" nowrap>
1529 <div align="center">
1530 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1531 <em>25/10/2016</em></strong>
1534 <td><em>Application</em>
1536 <li>3D Structure chooser opens with 'Cached structures'
1537 view if structures already loaded</li>
1538 <li>Progress bar reports models as they are loaded to
1539 structure views</li>
1545 <li>Colour by conservation always enabled and no tick
1546 shown in menu when BLOSUM or PID shading applied</li>
1547 <li>FER1_ARATH and FER2_ARATH labels were switched in
1548 example sequences/projects/trees</li>
1550 <em>Application</em>
1552 <li>Jalview projects with views of local PDB structure
1553 files saved on Windows cannot be opened on OSX</li>
1554 <li>Multiple structure views can be opened and superposed
1555 without timeout for structures with multiple models or
1556 multiple sequences in alignment</li>
1557 <li>Cannot import or associated local PDB files without a
1558 PDB ID HEADER line</li>
1559 <li>RMSD is not output in Jmol console when superposition
1561 <li>Drag and drop of URL from Browser fails for Linux and
1562 OSX versions earlier than El Capitan</li>
1563 <li>ENA client ignores invalid content from ENA server</li>
1564 <li>Exceptions are not raised in console when ENA client
1565 attempts to fetch non-existent IDs via Fetch DB Refs UI
1567 <li>Exceptions are not raised in console when a new view
1568 is created on the alignment</li>
1569 <li>OSX right-click fixed for group selections: CMD-click
1570 to insert/remove gaps in groups and CTRL-click to open group
1573 <em>Build and deployment</em>
1575 <li>URL link checker now copes with multi-line anchor
1578 <em>New Known Issues</em>
1580 <li>Drag and drop from URL links in browsers do not work
1587 <td width="60" nowrap>
1588 <div align="center">
1589 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1592 <td><em>General</em>
1595 <!-- JAL-2124 -->Updated Spanish translations.
1598 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1599 for importing structure data to Jalview. Enables mmCIF and
1603 <!-- JAL-192 --->Alignment ruler shows positions relative to
1607 <!-- JAL-2202 -->Position/residue shown in status bar when
1608 mousing over sequence associated annotation
1611 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1615 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1616 '()', canonical '[]' and invalid '{}' base pair populations
1620 <!-- JAL-2092 -->Feature settings popup menu options for
1621 showing or hiding columns containing a feature
1624 <!-- JAL-1557 -->Edit selected group by double clicking on
1625 group and sequence associated annotation labels
1628 <!-- JAL-2236 -->Sequence name added to annotation label in
1629 select/hide columns by annotation and colour by annotation
1633 </ul> <em>Application</em>
1636 <!-- JAL-2050-->Automatically hide introns when opening a
1637 gene/transcript view
1640 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1644 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1645 structure mappings with the EMBL-EBI PDBe SIFTS database
1648 <!-- JAL-2079 -->Updated download sites used for Rfam and
1649 Pfam sources to xfam.org
1652 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1655 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1656 over sequences in Jalview
1659 <!-- JAL-2027-->Support for reverse-complement coding
1660 regions in ENA and EMBL
1663 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1664 for record retrieval via ENA rest API
1667 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1671 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1672 groovy script execution
1675 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1676 alignment window's Calculate menu
1679 <!-- JAL-1812 -->Allow groovy scripts that call
1680 Jalview.getAlignFrames() to run in headless mode
1683 <!-- JAL-2068 -->Support for creating new alignment
1684 calculation workers from groovy scripts
1687 <!-- JAL-1369 --->Store/restore reference sequence in
1691 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1692 associations are now saved/restored from project
1695 <!-- JAL-1993 -->Database selection dialog always shown
1696 before sequence fetcher is opened
1699 <!-- JAL-2183 -->Double click on an entry in Jalview's
1700 database chooser opens a sequence fetcher
1703 <!-- JAL-1563 -->Free-text search client for UniProt using
1704 the UniProt REST API
1707 <!-- JAL-2168 -->-nonews command line parameter to prevent
1708 the news reader opening
1711 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1712 querying stored in preferences
1715 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1719 <!-- JAL-1977-->Tooltips shown on database chooser
1722 <!-- JAL-391 -->Reverse complement function in calculate
1723 menu for nucleotide sequences
1726 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1727 and feature counts preserves alignment ordering (and
1728 debugged for complex feature sets).
1731 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1732 viewing structures with Jalview 2.10
1735 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1736 genome, transcript CCDS and gene ids via the Ensembl and
1737 Ensembl Genomes REST API
1740 <!-- JAL-2049 -->Protein sequence variant annotation
1741 computed for 'sequence_variant' annotation on CDS regions
1745 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1749 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1750 Ref Fetcher fails to match, or otherwise updates sequence
1751 data from external database records.
1754 <!-- JAL-2154 -->Revised Jalview Project format for
1755 efficient recovery of sequence coding and alignment
1756 annotation relationships.
1758 </ul> <!-- <em>Applet</em>
1769 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1773 <!-- JAL-2018-->Export features in Jalview format (again)
1774 includes graduated colourschemes
1777 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1778 working with big alignments and lots of hidden columns
1781 <!-- JAL-2053-->Hidden column markers not always rendered
1782 at right of alignment window
1785 <!-- JAL-2067 -->Tidied up links in help file table of
1789 <!-- JAL-2072 -->Feature based tree calculation not shown
1793 <!-- JAL-2075 -->Hidden columns ignored during feature
1794 based tree calculation
1797 <!-- JAL-2065 -->Alignment view stops updating when show
1798 unconserved enabled for group on alignment
1801 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1805 <!-- JAL-2146 -->Alignment column in status incorrectly
1806 shown as "Sequence position" when mousing over
1810 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1811 hidden columns present
1814 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1815 user created annotation added to alignment
1818 <!-- JAL-1841 -->RNA Structure consensus only computed for
1819 '()' base pair annotation
1822 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1823 in zero scores for all base pairs in RNA Structure
1827 <!-- JAL-2174-->Extend selection with columns containing
1831 <!-- JAL-2275 -->Pfam format writer puts extra space at
1832 beginning of sequence
1835 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1839 <!-- JAL-2238 -->Cannot create groups on an alignment from
1840 from a tree when t-coffee scores are shown
1843 <!-- JAL-1836,1967 -->Cannot import and view PDB
1844 structures with chains containing negative resnums (4q4h)
1847 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1851 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1852 to Clustal, PIR and PileUp output
1855 <!-- JAL-2008 -->Reordering sequence features that are
1856 not visible causes alignment window to repaint
1859 <!-- JAL-2006 -->Threshold sliders don't work in
1860 graduated colour and colour by annotation row for e-value
1861 scores associated with features and annotation rows
1864 <!-- JAL-1797 -->amino acid physicochemical conservation
1865 calculation should be case independent
1868 <!-- JAL-2173 -->Remove annotation also updates hidden
1872 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1873 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1874 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1877 <!-- JAL-2065 -->Null pointer exceptions and redraw
1878 problems when reference sequence defined and 'show
1879 non-conserved' enabled
1882 <!-- JAL-1306 -->Quality and Conservation are now shown on
1883 load even when Consensus calculation is disabled
1886 <!-- JAL-1932 -->Remove right on penultimate column of
1887 alignment does nothing
1890 <em>Application</em>
1893 <!-- JAL-1552-->URLs and links can't be imported by
1894 drag'n'drop on OSX when launched via webstart (note - not
1895 yet fixed for El Capitan)
1898 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1899 output when running on non-gb/us i18n platforms
1902 <!-- JAL-1944 -->Error thrown when exporting a view with
1903 hidden sequences as flat-file alignment
1906 <!-- JAL-2030-->InstallAnywhere distribution fails when
1910 <!-- JAL-2080-->Jalview very slow to launch via webstart
1911 (also hotfix for 2.9.0b2)
1914 <!-- JAL-2085 -->Cannot save project when view has a
1915 reference sequence defined
1918 <!-- JAL-1011 -->Columns are suddenly selected in other
1919 alignments and views when revealing hidden columns
1922 <!-- JAL-1989 -->Hide columns not mirrored in complement
1923 view in a cDNA/Protein splitframe
1926 <!-- JAL-1369 -->Cannot save/restore representative
1927 sequence from project when only one sequence is
1931 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1932 in Structure Chooser
1935 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1936 structure consensus didn't refresh annotation panel
1939 <!-- JAL-1962 -->View mapping in structure view shows
1940 mappings between sequence and all chains in a PDB file
1943 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1944 dialogs format columns correctly, don't display array
1945 data, sort columns according to type
1948 <!-- JAL-1975 -->Export complete shown after destination
1949 file chooser is cancelled during an image export
1952 <!-- JAL-2025 -->Error when querying PDB Service with
1953 sequence name containing special characters
1956 <!-- JAL-2024 -->Manual PDB structure querying should be
1960 <!-- JAL-2104 -->Large tooltips with broken HTML
1961 formatting don't wrap
1964 <!-- JAL-1128 -->Figures exported from wrapped view are
1965 truncated so L looks like I in consensus annotation
1968 <!-- JAL-2003 -->Export features should only export the
1969 currently displayed features for the current selection or
1973 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1974 after fetching cross-references, and restoring from
1978 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1979 followed in the structure viewer
1982 <!-- JAL-2163 -->Titles for individual alignments in
1983 splitframe not restored from project
1986 <!-- JAL-2145 -->missing autocalculated annotation at
1987 trailing end of protein alignment in transcript/product
1988 splitview when pad-gaps not enabled by default
1991 <!-- JAL-1797 -->amino acid physicochemical conservation
1995 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1996 article has been read (reopened issue due to
1997 internationalisation problems)
2000 <!-- JAL-1960 -->Only offer PDB structures in structure
2001 viewer based on sequence name, PDB and UniProt
2006 <!-- JAL-1976 -->No progress bar shown during export of
2010 <!-- JAL-2213 -->Structures not always superimposed after
2011 multiple structures are shown for one or more sequences.
2014 <!-- JAL-1370 -->Reference sequence characters should not
2015 be replaced with '.' when 'Show unconserved' format option
2019 <!-- JAL-1823 -->Cannot specify chain code when entering
2020 specific PDB id for sequence
2023 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2024 'Export hidden sequences' is enabled, but 'export hidden
2025 columns' is disabled.
2028 <!--JAL-2026-->Best Quality option in structure chooser
2029 selects lowest rather than highest resolution structures
2033 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2034 to sequence mapping in 'View Mappings' report
2037 <!-- JAL-2284 -->Unable to read old Jalview projects that
2038 contain non-XML data added after Jalvew wrote project.
2041 <!-- JAL-2118 -->Newly created annotation row reorders
2042 after clicking on it to create new annotation for a
2046 <!-- JAL-1980 -->Null Pointer Exception raised when
2047 pressing Add on an orphaned cut'n'paste window.
2049 <!-- may exclude, this is an external service stability issue JAL-1941
2050 -- > RNA 3D structure not added via DSSR service</li> -->
2055 <!-- JAL-2151 -->Incorrect columns are selected when
2056 hidden columns present before start of sequence
2059 <!-- JAL-1986 -->Missing dependencies on applet pages
2063 <!-- JAL-1947 -->Overview pixel size changes when
2064 sequences are hidden in applet
2067 <!-- JAL-1996 -->Updated instructions for applet
2068 deployment on examples pages.
2075 <td width="60" nowrap>
2076 <div align="center">
2077 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2078 <em>16/10/2015</em></strong>
2081 <td><em>General</em>
2083 <li>Time stamps for signed Jalview application and applet
2088 <em>Application</em>
2090 <li>Duplicate group consensus and conservation rows
2091 shown when tree is partitioned</li>
2092 <li>Erratic behaviour when tree partitions made with
2093 multiple cDNA/Protein split views</li>
2099 <td width="60" nowrap>
2100 <div align="center">
2101 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2102 <em>8/10/2015</em></strong>
2105 <td><em>General</em>
2107 <li>Updated Spanish translations of localized text for
2109 </ul> <em>Application</em>
2111 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2112 <li>Signed OSX InstallAnywhere installer<br></li>
2113 <li>Support for per-sequence based annotations in BioJSON</li>
2114 </ul> <em>Applet</em>
2116 <li>Split frame example added to applet examples page</li>
2117 </ul> <em>Build and Deployment</em>
2120 <!-- JAL-1888 -->New ant target for running Jalview's test
2128 <li>Mapping of cDNA to protein in split frames
2129 incorrect when sequence start > 1</li>
2130 <li>Broken images in filter column by annotation dialog
2132 <li>Feature colours not parsed from features file</li>
2133 <li>Exceptions and incomplete link URLs recovered when
2134 loading a features file containing HTML tags in feature
2138 <em>Application</em>
2140 <li>Annotations corrupted after BioJS export and
2142 <li>Incorrect sequence limits after Fetch DB References
2143 with 'trim retrieved sequences'</li>
2144 <li>Incorrect warning about deleting all data when
2145 deleting selected columns</li>
2146 <li>Patch to build system for shipping properly signed
2147 JNLP templates for webstart launch</li>
2148 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2149 unreleased structures for download or viewing</li>
2150 <li>Tab/space/return keystroke operation of EMBL-PDBe
2151 fetcher/viewer dialogs works correctly</li>
2152 <li>Disabled 'minimise' button on Jalview windows
2153 running on OSX to workaround redraw hang bug</li>
2154 <li>Split cDNA/Protein view position and geometry not
2155 recovered from jalview project</li>
2156 <li>Initial enabled/disabled state of annotation menu
2157 sorter 'show autocalculated first/last' corresponds to
2159 <li>Restoring of Clustal, RNA Helices and T-Coffee
2160 color schemes from BioJSON</li>
2164 <li>Reorder sequences mirrored in cDNA/Protein split
2166 <li>Applet with Jmol examples not loading correctly</li>
2172 <td><div align="center">
2173 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2175 <td><em>General</em>
2177 <li>Linked visualisation and analysis of DNA and Protein
2180 <li>Translated cDNA alignments shown as split protein
2181 and DNA alignment views</li>
2182 <li>Codon consensus annotation for linked protein and
2183 cDNA alignment views</li>
2184 <li>Link cDNA or Protein product sequences by loading
2185 them onto Protein or cDNA alignments</li>
2186 <li>Reconstruct linked cDNA alignment from aligned
2187 protein sequences</li>
2190 <li>Jmol integration updated to Jmol v14.2.14</li>
2191 <li>Import and export of Jalview alignment views as <a
2192 href="features/bioJsonFormat.html">BioJSON</a></li>
2193 <li>New alignment annotation file statements for
2194 reference sequences and marking hidden columns</li>
2195 <li>Reference sequence based alignment shading to
2196 highlight variation</li>
2197 <li>Select or hide columns according to alignment
2199 <li>Find option for locating sequences by description</li>
2200 <li>Conserved physicochemical properties shown in amino
2201 acid conservation row</li>
2202 <li>Alignments can be sorted by number of RNA helices</li>
2203 </ul> <em>Application</em>
2205 <li>New cDNA/Protein analysis capabilities
2207 <li>Get Cross-References should open a Split Frame
2208 view with cDNA/Protein</li>
2209 <li>Detect when nucleotide sequences and protein
2210 sequences are placed in the same alignment</li>
2211 <li>Split cDNA/Protein views are saved in Jalview
2216 <li>Use REST API to talk to Chimera</li>
2217 <li>Selected regions in Chimera are highlighted in linked
2218 Jalview windows</li>
2220 <li>VARNA RNA viewer updated to v3.93</li>
2221 <li>VARNA views are saved in Jalview Projects</li>
2222 <li>Pseudoknots displayed as Jalview RNA annotation can
2223 be shown in VARNA</li>
2225 <li>Make groups for selection uses marked columns as well
2226 as the active selected region</li>
2228 <li>Calculate UPGMA and NJ trees using sequence feature
2230 <li>New Export options
2232 <li>New Export Settings dialog to control hidden
2233 region export in flat file generation</li>
2235 <li>Export alignment views for display with the <a
2236 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2238 <li>Export scrollable SVG in HTML page</li>
2239 <li>Optional embedding of BioJSON data when exporting
2240 alignment figures to HTML</li>
2242 <li>3D structure retrieval and display
2244 <li>Free text and structured queries with the PDBe
2246 <li>PDBe Search API based discovery and selection of
2247 PDB structures for a sequence set</li>
2251 <li>JPred4 employed for protein secondary structure
2253 <li>Hide Insertions menu option to hide unaligned columns
2254 for one or a group of sequences</li>
2255 <li>Automatically hide insertions in alignments imported
2256 from the JPred4 web server</li>
2257 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2258 system on OSX<br />LGPL libraries courtesy of <a
2259 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2261 <li>changed 'View nucleotide structure' submenu to 'View
2262 VARNA 2D Structure'</li>
2263 <li>change "View protein structure" menu option to "3D
2266 </ul> <em>Applet</em>
2268 <li>New layout for applet example pages</li>
2269 <li>New parameters to enable SplitFrame view
2270 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2271 <li>New example demonstrating linked viewing of cDNA and
2272 Protein alignments</li>
2273 </ul> <em>Development and deployment</em>
2275 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2276 <li>Include installation type and git revision in build
2277 properties and console log output</li>
2278 <li>Jalview Github organisation, and new github site for
2279 storing BioJsMSA Templates</li>
2280 <li>Jalview's unit tests now managed with TestNG</li>
2283 <!-- <em>General</em>
2285 </ul> --> <!-- issues resolved --> <em>Application</em>
2287 <li>Escape should close any open find dialogs</li>
2288 <li>Typo in select-by-features status report</li>
2289 <li>Consensus RNA secondary secondary structure
2290 predictions are not highlighted in amber</li>
2291 <li>Missing gap character in v2.7 example file means
2292 alignment appears unaligned when pad-gaps is not enabled</li>
2293 <li>First switch to RNA Helices colouring doesn't colour
2294 associated structure views</li>
2295 <li>ID width preference option is greyed out when auto
2296 width checkbox not enabled</li>
2297 <li>Stopped a warning dialog from being shown when
2298 creating user defined colours</li>
2299 <li>'View Mapping' in structure viewer shows sequence
2300 mappings for just that viewer's sequences</li>
2301 <li>Workaround for superposing PDB files containing
2302 multiple models in Chimera</li>
2303 <li>Report sequence position in status bar when hovering
2304 over Jmol structure</li>
2305 <li>Cannot output gaps as '.' symbols with Selection ->
2306 output to text box</li>
2307 <li>Flat file exports of alignments with hidden columns
2308 have incorrect sequence start/end</li>
2309 <li>'Aligning' a second chain to a Chimera structure from
2311 <li>Colour schemes applied to structure viewers don't
2312 work for nucleotide</li>
2313 <li>Loading/cut'n'pasting an empty or invalid file leads
2314 to a grey/invisible alignment window</li>
2315 <li>Exported Jpred annotation from a sequence region
2316 imports to different position</li>
2317 <li>Space at beginning of sequence feature tooltips shown
2318 on some platforms</li>
2319 <li>Chimera viewer 'View | Show Chain' menu is not
2321 <li>'New View' fails with a Null Pointer Exception in
2322 console if Chimera has been opened</li>
2323 <li>Mouseover to Chimera not working</li>
2324 <li>Miscellaneous ENA XML feature qualifiers not
2326 <li>NPE in annotation renderer after 'Extract Scores'</li>
2327 <li>If two structures in one Chimera window, mouseover of
2328 either sequence shows on first structure</li>
2329 <li>'Show annotations' options should not make
2330 non-positional annotations visible</li>
2331 <li>Subsequence secondary structure annotation not shown
2332 in right place after 'view flanking regions'</li>
2333 <li>File Save As type unset when current file format is
2335 <li>Save as '.jar' option removed for saving Jalview
2337 <li>Colour by Sequence colouring in Chimera more
2339 <li>Cannot 'add reference annotation' for a sequence in
2340 several views on same alignment</li>
2341 <li>Cannot show linked products for EMBL / ENA records</li>
2342 <li>Jalview's tooltip wraps long texts containing no
2344 </ul> <em>Applet</em>
2346 <li>Jmol to JalviewLite mouseover/link not working</li>
2347 <li>JalviewLite can't import sequences with ID
2348 descriptions containing angle brackets</li>
2349 </ul> <em>General</em>
2351 <li>Cannot export and reimport RNA secondary structure
2352 via jalview annotation file</li>
2353 <li>Random helix colour palette for colour by annotation
2354 with RNA secondary structure</li>
2355 <li>Mouseover to cDNA from STOP residue in protein
2356 translation doesn't work.</li>
2357 <li>hints when using the select by annotation dialog box</li>
2358 <li>Jmol alignment incorrect if PDB file has alternate CA
2360 <li>FontChooser message dialog appears to hang after
2361 choosing 1pt font</li>
2362 <li>Peptide secondary structure incorrectly imported from
2363 annotation file when annotation display text includes 'e' or
2365 <li>Cannot set colour of new feature type whilst creating
2367 <li>cDNA translation alignment should not be sequence
2368 order dependent</li>
2369 <li>'Show unconserved' doesn't work for lower case
2371 <li>Nucleotide ambiguity codes involving R not recognised</li>
2372 </ul> <em>Deployment and Documentation</em>
2374 <li>Applet example pages appear different to the rest of
2375 www.jalview.org</li>
2376 </ul> <em>Application Known issues</em>
2378 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2379 <li>Misleading message appears after trying to delete
2381 <li>Jalview icon not shown in dock after InstallAnywhere
2382 version launches</li>
2383 <li>Fetching EMBL reference for an RNA sequence results
2384 fails with a sequence mismatch</li>
2385 <li>Corrupted or unreadable alignment display when
2386 scrolling alignment to right</li>
2387 <li>ArrayIndexOutOfBoundsException thrown when remove
2388 empty columns called on alignment with ragged gapped ends</li>
2389 <li>auto calculated alignment annotation rows do not get
2390 placed above or below non-autocalculated rows</li>
2391 <li>Jalview dekstop becomes sluggish at full screen in
2392 ultra-high resolution</li>
2393 <li>Cannot disable consensus calculation independently of
2394 quality and conservation</li>
2395 <li>Mouseover highlighting between cDNA and protein can
2396 become sluggish with more than one splitframe shown</li>
2397 </ul> <em>Applet Known Issues</em>
2399 <li>Core PDB parsing code requires Jmol</li>
2400 <li>Sequence canvas panel goes white when alignment
2401 window is being resized</li>
2407 <td><div align="center">
2408 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2410 <td><em>General</em>
2412 <li>Updated Java code signing certificate donated by
2414 <li>Features and annotation preserved when performing
2415 pairwise alignment</li>
2416 <li>RNA pseudoknot annotation can be
2417 imported/exported/displayed</li>
2418 <li>'colour by annotation' can colour by RNA and
2419 protein secondary structure</li>
2420 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2421 post-hoc with 2.9 release</em>)
2424 </ul> <em>Application</em>
2426 <li>Extract and display secondary structure for sequences
2427 with 3D structures</li>
2428 <li>Support for parsing RNAML</li>
2429 <li>Annotations menu for layout
2431 <li>sort sequence annotation rows by alignment</li>
2432 <li>place sequence annotation above/below alignment
2435 <li>Output in Stockholm format</li>
2436 <li>Internationalisation: improved Spanish (es)
2438 <li>Structure viewer preferences tab</li>
2439 <li>Disorder and Secondary Structure annotation tracks
2440 shared between alignments</li>
2441 <li>UCSF Chimera launch and linked highlighting from
2443 <li>Show/hide all sequence associated annotation rows for
2444 all or current selection</li>
2445 <li>disorder and secondary structure predictions
2446 available as dataset annotation</li>
2447 <li>Per-sequence rna helices colouring</li>
2450 <li>Sequence database accessions imported when fetching
2451 alignments from Rfam</li>
2452 <li>update VARNA version to 3.91</li>
2454 <li>New groovy scripts for exporting aligned positions,
2455 conservation values, and calculating sum of pairs scores.</li>
2456 <li>Command line argument to set default JABAWS server</li>
2457 <li>include installation type in build properties and
2458 console log output</li>
2459 <li>Updated Jalview project format to preserve dataset
2463 <!-- issues resolved --> <em>Application</em>
2465 <li>Distinguish alignment and sequence associated RNA
2466 structure in structure->view->VARNA</li>
2467 <li>Raise dialog box if user deletes all sequences in an
2469 <li>Pressing F1 results in documentation opening twice</li>
2470 <li>Sequence feature tooltip is wrapped</li>
2471 <li>Double click on sequence associated annotation
2472 selects only first column</li>
2473 <li>Redundancy removal doesn't result in unlinked
2474 leaves shown in tree</li>
2475 <li>Undos after several redundancy removals don't undo
2477 <li>Hide sequence doesn't hide associated annotation</li>
2478 <li>User defined colours dialog box too big to fit on
2479 screen and buttons not visible</li>
2480 <li>author list isn't updated if already written to
2481 Jalview properties</li>
2482 <li>Popup menu won't open after retrieving sequence
2484 <li>File open window for associate PDB doesn't open</li>
2485 <li>Left-then-right click on a sequence id opens a
2486 browser search window</li>
2487 <li>Cannot open sequence feature shading/sort popup menu
2488 in feature settings dialog</li>
2489 <li>better tooltip placement for some areas of Jalview
2491 <li>Allow addition of JABAWS Server which doesn't
2492 pass validation</li>
2493 <li>Web services parameters dialog box is too large to
2495 <li>Muscle nucleotide alignment preset obscured by
2497 <li>JABAWS preset submenus don't contain newly
2498 defined user preset</li>
2499 <li>MSA web services warns user if they were launched
2500 with invalid input</li>
2501 <li>Jalview cannot contact DAS Registy when running on
2504 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2505 'Superpose with' submenu not shown when new view
2509 </ul> <!-- <em>Applet</em>
2511 </ul> <em>General</em>
2513 </ul>--> <em>Deployment and Documentation</em>
2515 <li>2G and 1G options in launchApp have no effect on
2516 memory allocation</li>
2517 <li>launchApp service doesn't automatically open
2518 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2520 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2521 InstallAnywhere reports cannot find valid JVM when Java
2522 1.7_055 is available
2524 </ul> <em>Application Known issues</em>
2527 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2528 corrupted or unreadable alignment display when scrolling
2532 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2533 retrieval fails but progress bar continues for DAS retrieval
2534 with large number of ID
2537 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2538 flatfile output of visible region has incorrect sequence
2542 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2543 rna structure consensus doesn't update when secondary
2544 structure tracks are rearranged
2547 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2548 invalid rna structure positional highlighting does not
2549 highlight position of invalid base pairs
2552 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2553 out of memory errors are not raised when saving Jalview
2554 project from alignment window file menu
2557 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2558 Switching to RNA Helices colouring doesn't propagate to
2562 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2563 colour by RNA Helices not enabled when user created
2564 annotation added to alignment
2567 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2568 Jalview icon not shown on dock in Mountain Lion/Webstart
2570 </ul> <em>Applet Known Issues</em>
2573 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2574 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2577 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2578 Jalview and Jmol example not compatible with IE9
2581 <li>Sort by annotation score doesn't reverse order
2587 <td><div align="center">
2588 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2591 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2594 <li>Internationalisation of user interface (usually
2595 called i18n support) and translation for Spanish locale</li>
2596 <li>Define/Undefine group on current selection with
2597 Ctrl-G/Shift Ctrl-G</li>
2598 <li>Improved group creation/removal options in
2599 alignment/sequence Popup menu</li>
2600 <li>Sensible precision for symbol distribution
2601 percentages shown in logo tooltip.</li>
2602 <li>Annotation panel height set according to amount of
2603 annotation when alignment first opened</li>
2604 </ul> <em>Application</em>
2606 <li>Interactive consensus RNA secondary structure
2607 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2608 <li>Select columns containing particular features from
2609 Feature Settings dialog</li>
2610 <li>View all 'representative' PDB structures for selected
2612 <li>Update Jalview project format:
2614 <li>New file extension for Jalview projects '.jvp'</li>
2615 <li>Preserve sequence and annotation dataset (to
2616 store secondary structure annotation,etc)</li>
2617 <li>Per group and alignment annotation and RNA helix
2621 <li>New similarity measures for PCA and Tree calculation
2623 <li>Experimental support for retrieval and viewing of
2624 flanking regions for an alignment</li>
2628 <!-- issues resolved --> <em>Application</em>
2630 <li>logo keeps spinning and status remains at queued or
2631 running after job is cancelled</li>
2632 <li>cannot export features from alignments imported from
2633 Jalview/VAMSAS projects</li>
2634 <li>Buggy slider for web service parameters that take
2636 <li>Newly created RNA secondary structure line doesn't
2637 have 'display all symbols' flag set</li>
2638 <li>T-COFFEE alignment score shading scheme and other
2639 annotation shading not saved in Jalview project</li>
2640 <li>Local file cannot be loaded in freshly downloaded
2642 <li>Jalview icon not shown on dock in Mountain
2644 <li>Load file from desktop file browser fails</li>
2645 <li>Occasional NPE thrown when calculating large trees</li>
2646 <li>Cannot reorder or slide sequences after dragging an
2647 alignment onto desktop</li>
2648 <li>Colour by annotation dialog throws NPE after using
2649 'extract scores' function</li>
2650 <li>Loading/cut'n'pasting an empty file leads to a grey
2651 alignment window</li>
2652 <li>Disorder thresholds rendered incorrectly after
2653 performing IUPred disorder prediction</li>
2654 <li>Multiple group annotated consensus rows shown when
2655 changing 'normalise logo' display setting</li>
2656 <li>Find shows blank dialog after 'finished searching' if
2657 nothing matches query</li>
2658 <li>Null Pointer Exceptions raised when sorting by
2659 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2661 <li>Errors in Jmol console when structures in alignment
2662 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2664 <li>Not all working JABAWS services are shown in
2666 <li>JAVAWS version of Jalview fails to launch with
2667 'invalid literal/length code'</li>
2668 <li>Annotation/RNA Helix colourschemes cannot be applied
2669 to alignment with groups (actually fixed in 2.8.0b1)</li>
2670 <li>RNA Helices and T-Coffee Scores available as default
2673 </ul> <em>Applet</em>
2675 <li>Remove group option is shown even when selection is
2677 <li>Apply to all groups ticked but colourscheme changes
2678 don't affect groups</li>
2679 <li>Documented RNA Helices and T-Coffee Scores as valid
2680 colourscheme name</li>
2681 <li>Annotation labels drawn on sequence IDs when
2682 Annotation panel is not displayed</li>
2683 <li>Increased font size for dropdown menus on OSX and
2684 embedded windows</li>
2685 </ul> <em>Other</em>
2687 <li>Consensus sequence for alignments/groups with a
2688 single sequence were not calculated</li>
2689 <li>annotation files that contain only groups imported as
2690 annotation and junk sequences</li>
2691 <li>Fasta files with sequences containing '*' incorrectly
2692 recognised as PFAM or BLC</li>
2693 <li>conservation/PID slider apply all groups option
2694 doesn't affect background (2.8.0b1)
2696 <li>redundancy highlighting is erratic at 0% and 100%</li>
2697 <li>Remove gapped columns fails for sequences with ragged
2699 <li>AMSA annotation row with leading spaces is not
2700 registered correctly on import</li>
2701 <li>Jalview crashes when selecting PCA analysis for
2702 certain alignments</li>
2703 <li>Opening the colour by annotation dialog for an
2704 existing annotation based 'use original colours'
2705 colourscheme loses original colours setting</li>
2710 <td><div align="center">
2711 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2712 <em>30/1/2014</em></strong>
2716 <li>Trusted certificates for JalviewLite applet and
2717 Jalview Desktop application<br />Certificate was donated by
2718 <a href="https://www.certum.eu">Certum</a> to the Jalview
2719 open source project).
2721 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2722 <li>Output in Stockholm format</li>
2723 <li>Allow import of data from gzipped files</li>
2724 <li>Export/import group and sequence associated line
2725 graph thresholds</li>
2726 <li>Nucleotide substitution matrix that supports RNA and
2727 ambiguity codes</li>
2728 <li>Allow disorder predictions to be made on the current
2729 selection (or visible selection) in the same way that JPred
2731 <li>Groovy scripting for headless Jalview operation</li>
2732 </ul> <em>Other improvements</em>
2734 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2735 <li>COMBINE statement uses current SEQUENCE_REF and
2736 GROUP_REF scope to group annotation rows</li>
2737 <li>Support '' style escaping of quotes in Newick
2739 <li>Group options for JABAWS service by command line name</li>
2740 <li>Empty tooltip shown for JABA service options with a
2741 link but no description</li>
2742 <li>Select primary source when selecting authority in
2743 database fetcher GUI</li>
2744 <li>Add .mfa to FASTA file extensions recognised by
2746 <li>Annotation label tooltip text wrap</li>
2751 <li>Slow scrolling when lots of annotation rows are
2753 <li>Lots of NPE (and slowness) after creating RNA
2754 secondary structure annotation line</li>
2755 <li>Sequence database accessions not imported when
2756 fetching alignments from Rfam</li>
2757 <li>Incorrect SHMR submission for sequences with
2759 <li>View all structures does not always superpose
2761 <li>Option widgets in service parameters not updated to
2762 reflect user or preset settings</li>
2763 <li>Null pointer exceptions for some services without
2764 presets or adjustable parameters</li>
2765 <li>Discover PDB IDs entry in structure menu doesn't
2766 discover PDB xRefs</li>
2767 <li>Exception encountered while trying to retrieve
2768 features with DAS</li>
2769 <li>Lowest value in annotation row isn't coloured
2770 when colour by annotation (per sequence) is coloured</li>
2771 <li>Keyboard mode P jumps to start of gapped region when
2772 residue follows a gap</li>
2773 <li>Jalview appears to hang importing an alignment with
2774 Wrap as default or after enabling Wrap</li>
2775 <li>'Right click to add annotations' message
2776 shown in wrap mode when no annotations present</li>
2777 <li>Disorder predictions fail with NPE if no automatic
2778 annotation already exists on alignment</li>
2779 <li>oninit javascript function should be called after
2780 initialisation completes</li>
2781 <li>Remove redundancy after disorder prediction corrupts
2782 alignment window display</li>
2783 <li>Example annotation file in documentation is invalid</li>
2784 <li>Grouped line graph annotation rows are not exported
2785 to annotation file</li>
2786 <li>Multi-harmony analysis cannot be run when only two
2788 <li>Cannot create multiple groups of line graphs with
2789 several 'combine' statements in annotation file</li>
2790 <li>Pressing return several times causes Number Format
2791 exceptions in keyboard mode</li>
2792 <li>Multi-harmony (SHMMR) method doesn't submit
2793 correct partitions for input data</li>
2794 <li>Translation from DNA to Amino Acids fails</li>
2795 <li>Jalview fail to load newick tree with quoted label</li>
2796 <li>--headless flag isn't understood</li>
2797 <li>ClassCastException when generating EPS in headless
2799 <li>Adjusting sequence-associated shading threshold only
2800 changes one row's threshold</li>
2801 <li>Preferences and Feature settings panel panel
2802 doesn't open</li>
2803 <li>hide consensus histogram also hides conservation and
2804 quality histograms</li>
2809 <td><div align="center">
2810 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2812 <td><em>Application</em>
2814 <li>Support for JABAWS 2.0 Services (AACon alignment
2815 conservation, protein disorder and Clustal Omega)</li>
2816 <li>JABAWS server status indicator in Web Services
2818 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2819 in Jalview alignment window</li>
2820 <li>Updated Jalview build and deploy framework for OSX
2821 mountain lion, windows 7, and 8</li>
2822 <li>Nucleotide substitution matrix for PCA that supports
2823 RNA and ambiguity codes</li>
2825 <li>Improved sequence database retrieval GUI</li>
2826 <li>Support fetching and database reference look up
2827 against multiple DAS sources (Fetch all from in 'fetch db
2829 <li>Jalview project improvements
2831 <li>Store and retrieve the 'belowAlignment'
2832 flag for annotation</li>
2833 <li>calcId attribute to group annotation rows on the
2835 <li>Store AACon calculation settings for a view in
2836 Jalview project</li>
2840 <li>horizontal scrolling gesture support</li>
2841 <li>Visual progress indicator when PCA calculation is
2843 <li>Simpler JABA web services menus</li>
2844 <li>visual indication that web service results are still
2845 being retrieved from server</li>
2846 <li>Serialise the dialogs that are shown when Jalview
2847 starts up for first time</li>
2848 <li>Jalview user agent string for interacting with HTTP
2850 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2852 <li>Examples directory and Groovy library included in
2853 InstallAnywhere distribution</li>
2854 </ul> <em>Applet</em>
2856 <li>RNA alignment and secondary structure annotation
2857 visualization applet example</li>
2858 </ul> <em>General</em>
2860 <li>Normalise option for consensus sequence logo</li>
2861 <li>Reset button in PCA window to return dimensions to
2863 <li>Allow seqspace or Jalview variant of alignment PCA
2865 <li>PCA with either nucleic acid and protein substitution
2867 <li>Allow windows containing HTML reports to be exported
2869 <li>Interactive display and editing of RNA secondary
2870 structure contacts</li>
2871 <li>RNA Helix Alignment Colouring</li>
2872 <li>RNA base pair logo consensus</li>
2873 <li>Parse sequence associated secondary structure
2874 information in Stockholm files</li>
2875 <li>HTML Export database accessions and annotation
2876 information presented in tooltip for sequences</li>
2877 <li>Import secondary structure from LOCARNA clustalw
2878 style RNA alignment files</li>
2879 <li>import and visualise T-COFFEE quality scores for an
2881 <li>'colour by annotation' per sequence option to
2882 shade each sequence according to its associated alignment
2884 <li>New Jalview Logo</li>
2885 </ul> <em>Documentation and Development</em>
2887 <li>documentation for score matrices used in Jalview</li>
2888 <li>New Website!</li>
2890 <td><em>Application</em>
2892 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2893 wsdbfetch REST service</li>
2894 <li>Stop windows being moved outside desktop on OSX</li>
2895 <li>Filetype associations not installed for webstart
2897 <li>Jalview does not always retrieve progress of a JABAWS
2898 job execution in full once it is complete</li>
2899 <li>revise SHMR RSBS definition to ensure alignment is
2900 uploaded via ali_file parameter</li>
2901 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2902 <li>View all structures superposed fails with exception</li>
2903 <li>Jnet job queues forever if a very short sequence is
2904 submitted for prediction</li>
2905 <li>Cut and paste menu not opened when mouse clicked on
2907 <li>Putting fractional value into integer text box in
2908 alignment parameter dialog causes Jalview to hang</li>
2909 <li>Structure view highlighting doesn't work on
2911 <li>View all structures fails with exception shown in
2913 <li>Characters in filename associated with PDBEntry not
2914 escaped in a platform independent way</li>
2915 <li>Jalview desktop fails to launch with exception when
2917 <li>Tree calculation reports 'you must have 2 or more
2918 sequences selected' when selection is empty</li>
2919 <li>Jalview desktop fails to launch with jar signature
2920 failure when java web start temporary file caching is
2922 <li>DAS Sequence retrieval with range qualification
2923 results in sequence xref which includes range qualification</li>
2924 <li>Errors during processing of command line arguments
2925 cause progress bar (JAL-898) to be removed</li>
2926 <li>Replace comma for semi-colon option not disabled for
2927 DAS sources in sequence fetcher</li>
2928 <li>Cannot close news reader when JABAWS server warning
2929 dialog is shown</li>
2930 <li>Option widgets not updated to reflect user settings</li>
2931 <li>Edited sequence not submitted to web service</li>
2932 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2933 <li>InstallAnywhere installer doesn't unpack and run
2934 on OSX Mountain Lion</li>
2935 <li>Annotation panel not given a scroll bar when
2936 sequences with alignment annotation are pasted into the
2938 <li>Sequence associated annotation rows not associated
2939 when loaded from Jalview project</li>
2940 <li>Browser launch fails with NPE on java 1.7</li>
2941 <li>JABAWS alignment marked as finished when job was
2942 cancelled or job failed due to invalid input</li>
2943 <li>NPE with v2.7 example when clicking on Tree
2944 associated with all views</li>
2945 <li>Exceptions when copy/paste sequences with grouped
2946 annotation rows to new window</li>
2947 </ul> <em>Applet</em>
2949 <li>Sequence features are momentarily displayed before
2950 they are hidden using hidefeaturegroups applet parameter</li>
2951 <li>loading features via javascript API automatically
2952 enables feature display</li>
2953 <li>scrollToColumnIn javascript API method doesn't
2955 </ul> <em>General</em>
2957 <li>Redundancy removal fails for rna alignment</li>
2958 <li>PCA calculation fails when sequence has been selected
2959 and then deselected</li>
2960 <li>PCA window shows grey box when first opened on OSX</li>
2961 <li>Letters coloured pink in sequence logo when alignment
2962 coloured with clustalx</li>
2963 <li>Choosing fonts without letter symbols defined causes
2964 exceptions and redraw errors</li>
2965 <li>Initial PCA plot view is not same as manually
2966 reconfigured view</li>
2967 <li>Grouped annotation graph label has incorrect line
2969 <li>Grouped annotation graph label display is corrupted
2970 for lots of labels</li>
2975 <div align="center">
2976 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2979 <td><em>Application</em>
2981 <li>Jalview Desktop News Reader</li>
2982 <li>Tweaked default layout of web services menu</li>
2983 <li>View/alignment association menu to enable user to
2984 easily specify which alignment a multi-structure view takes
2985 its colours/correspondences from</li>
2986 <li>Allow properties file location to be specified as URL</li>
2987 <li>Extend Jalview project to preserve associations
2988 between many alignment views and a single Jmol display</li>
2989 <li>Store annotation row height in Jalview project file</li>
2990 <li>Annotation row column label formatting attributes
2991 stored in project file</li>
2992 <li>Annotation row order for auto-calculated annotation
2993 rows preserved in Jalview project file</li>
2994 <li>Visual progress indication when Jalview state is
2995 saved using Desktop window menu</li>
2996 <li>Visual indication that command line arguments are
2997 still being processed</li>
2998 <li>Groovy script execution from URL</li>
2999 <li>Colour by annotation default min and max colours in
3001 <li>Automatically associate PDB files dragged onto an
3002 alignment with sequences that have high similarity and
3004 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3005 <li>'view structures' option to open many
3006 structures in same window</li>
3007 <li>Sort associated views menu option for tree panel</li>
3008 <li>Group all JABA and non-JABA services for a particular
3009 analysis function in its own submenu</li>
3010 </ul> <em>Applet</em>
3012 <li>Userdefined and autogenerated annotation rows for
3014 <li>Adjustment of alignment annotation pane height</li>
3015 <li>Annotation scrollbar for annotation panel</li>
3016 <li>Drag to reorder annotation rows in annotation panel</li>
3017 <li>'automaticScrolling' parameter</li>
3018 <li>Allow sequences with partial ID string matches to be
3019 annotated from GFF/Jalview features files</li>
3020 <li>Sequence logo annotation row in applet</li>
3021 <li>Absolute paths relative to host server in applet
3022 parameters are treated as such</li>
3023 <li>New in the JalviewLite javascript API:
3025 <li>JalviewLite.js javascript library</li>
3026 <li>Javascript callbacks for
3028 <li>Applet initialisation</li>
3029 <li>Sequence/alignment mouse-overs and selections</li>
3032 <li>scrollTo row and column alignment scrolling
3034 <li>Select sequence/alignment regions from javascript</li>
3035 <li>javascript structure viewer harness to pass
3036 messages between Jmol and Jalview when running as
3037 distinct applets</li>
3038 <li>sortBy method</li>
3039 <li>Set of applet and application examples shipped
3040 with documentation</li>
3041 <li>New example to demonstrate JalviewLite and Jmol
3042 javascript message exchange</li>
3044 </ul> <em>General</em>
3046 <li>Enable Jmol displays to be associated with multiple
3047 multiple alignments</li>
3048 <li>Option to automatically sort alignment with new tree</li>
3049 <li>User configurable link to enable redirects to a
3050 www.Jalview.org mirror</li>
3051 <li>Jmol colours option for Jmol displays</li>
3052 <li>Configurable newline string when writing alignment
3053 and other flat files</li>
3054 <li>Allow alignment annotation description lines to
3055 contain html tags</li>
3056 </ul> <em>Documentation and Development</em>
3058 <li>Add groovy test harness for bulk load testing to
3060 <li>Groovy script to load and align a set of sequences
3061 using a web service before displaying the result in the
3062 Jalview desktop</li>
3063 <li>Restructured javascript and applet api documentation</li>
3064 <li>Ant target to publish example html files with applet
3066 <li>Netbeans project for building Jalview from source</li>
3067 <li>ant task to create online javadoc for Jalview source</li>
3069 <td><em>Application</em>
3071 <li>User defined colourscheme throws exception when
3072 current built in colourscheme is saved as new scheme</li>
3073 <li>AlignFrame->Save in application pops up save
3074 dialog for valid filename/format</li>
3075 <li>Cannot view associated structure for UniProt sequence</li>
3076 <li>PDB file association breaks for UniProt sequence
3078 <li>Associate PDB from file dialog does not tell you
3079 which sequence is to be associated with the file</li>
3080 <li>Find All raises null pointer exception when query
3081 only matches sequence IDs</li>
3082 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3083 <li>Jalview project with Jmol views created with Jalview
3084 2.4 cannot be loaded</li>
3085 <li>Filetype associations not installed for webstart
3087 <li>Two or more chains in a single PDB file associated
3088 with sequences in different alignments do not get coloured
3089 by their associated sequence</li>
3090 <li>Visibility status of autocalculated annotation row
3091 not preserved when project is loaded</li>
3092 <li>Annotation row height and visibility attributes not
3093 stored in Jalview project</li>
3094 <li>Tree bootstraps are not preserved when saved as a
3095 Jalview project</li>
3096 <li>Envision2 workflow tooltips are corrupted</li>
3097 <li>Enabling show group conservation also enables colour
3098 by conservation</li>
3099 <li>Duplicate group associated conservation or consensus
3100 created on new view</li>
3101 <li>Annotation scrollbar not displayed after 'show
3102 all hidden annotation rows' option selected</li>
3103 <li>Alignment quality not updated after alignment
3104 annotation row is hidden then shown</li>
3105 <li>Preserve colouring of structures coloured by
3106 sequences in pre Jalview 2.7 projects</li>
3107 <li>Web service job parameter dialog is not laid out
3109 <li>Web services menu not refreshed after 'reset
3110 services' button is pressed in preferences</li>
3111 <li>Annotation off by one in Jalview v2_3 example project</li>
3112 <li>Structures imported from file and saved in project
3113 get name like jalview_pdb1234.txt when reloaded</li>
3114 <li>Jalview does not always retrieve progress of a JABAWS
3115 job execution in full once it is complete</li>
3116 </ul> <em>Applet</em>
3118 <li>Alignment height set incorrectly when lots of
3119 annotation rows are displayed</li>
3120 <li>Relative URLs in feature HTML text not resolved to
3122 <li>View follows highlighting does not work for positions
3124 <li><= shown as = in tooltip</li>
3125 <li>Export features raises exception when no features
3127 <li>Separator string used for serialising lists of IDs
3128 for javascript api is modified when separator string
3129 provided as parameter</li>
3130 <li>Null pointer exception when selecting tree leaves for
3131 alignment with no existing selection</li>
3132 <li>Relative URLs for datasources assumed to be relative
3133 to applet's codebase</li>
3134 <li>Status bar not updated after finished searching and
3135 search wraps around to first result</li>
3136 <li>StructureSelectionManager instance shared between
3137 several Jalview applets causes race conditions and memory
3139 <li>Hover tooltip and mouseover of position on structure
3140 not sent from Jmol in applet</li>
3141 <li>Certain sequences of javascript method calls to
3142 applet API fatally hang browser</li>
3143 </ul> <em>General</em>
3145 <li>View follows structure mouseover scrolls beyond
3146 position with wrapped view and hidden regions</li>
3147 <li>Find sequence position moves to wrong residue
3148 with/without hidden columns</li>
3149 <li>Sequence length given in alignment properties window
3151 <li>InvalidNumberFormat exceptions thrown when trying to
3152 import PDB like structure files</li>
3153 <li>Positional search results are only highlighted
3154 between user-supplied sequence start/end bounds</li>
3155 <li>End attribute of sequence is not validated</li>
3156 <li>Find dialog only finds first sequence containing a
3157 given sequence position</li>
3158 <li>Sequence numbering not preserved in MSF alignment
3160 <li>Jalview PDB file reader does not extract sequence
3161 from nucleotide chains correctly</li>
3162 <li>Structure colours not updated when tree partition
3163 changed in alignment</li>
3164 <li>Sequence associated secondary structure not correctly
3165 parsed in interleaved stockholm</li>
3166 <li>Colour by annotation dialog does not restore current
3168 <li>Hiding (nearly) all sequences doesn't work
3170 <li>Sequences containing lowercase letters are not
3171 properly associated with their pdb files</li>
3172 </ul> <em>Documentation and Development</em>
3174 <li>schemas/JalviewWsParamSet.xsd corrupted by
3175 ApplyCopyright tool</li>
3180 <div align="center">
3181 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3184 <td><em>Application</em>
3186 <li>New warning dialog when the Jalview Desktop cannot
3187 contact web services</li>
3188 <li>JABA service parameters for a preset are shown in
3189 service job window</li>
3190 <li>JABA Service menu entries reworded</li>
3194 <li>Modeller PIR IO broken - cannot correctly import a
3195 pir file emitted by Jalview</li>
3196 <li>Existing feature settings transferred to new
3197 alignment view created from cut'n'paste</li>
3198 <li>Improved test for mixed amino/nucleotide chains when
3199 parsing PDB files</li>
3200 <li>Consensus and conservation annotation rows
3201 occasionally become blank for all new windows</li>
3202 <li>Exception raised when right clicking above sequences
3203 in wrapped view mode</li>
3204 </ul> <em>Application</em>
3206 <li>multiple multiply aligned structure views cause cpu
3207 usage to hit 100% and computer to hang</li>
3208 <li>Web Service parameter layout breaks for long user
3209 parameter names</li>
3210 <li>Jaba service discovery hangs desktop if Jaba server
3217 <div align="center">
3218 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3221 <td><em>Application</em>
3223 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3224 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3227 <li>Web Services preference tab</li>
3228 <li>Analysis parameters dialog box and user defined
3230 <li>Improved speed and layout of Envision2 service menu</li>
3231 <li>Superpose structures using associated sequence
3233 <li>Export coordinates and projection as CSV from PCA
3235 </ul> <em>Applet</em>
3237 <li>enable javascript: execution by the applet via the
3238 link out mechanism</li>
3239 </ul> <em>Other</em>
3241 <li>Updated the Jmol Jalview interface to work with Jmol
3243 <li>The Jalview Desktop and JalviewLite applet now
3244 require Java 1.5</li>
3245 <li>Allow Jalview feature colour specification for GFF
3246 sequence annotation files</li>
3247 <li>New 'colour by label' keword in Jalview feature file
3248 type colour specification</li>
3249 <li>New Jalview Desktop Groovy API method that allows a
3250 script to check if it being run in an interactive session or
3251 in a batch operation from the Jalview command line</li>
3255 <li>clustalx colourscheme colours Ds preferentially when
3256 both D+E are present in over 50% of the column</li>
3257 </ul> <em>Application</em>
3259 <li>typo in AlignmentFrame->View->Hide->all but
3260 selected Regions menu item</li>
3261 <li>sequence fetcher replaces ',' for ';' when the ',' is
3262 part of a valid accession ID</li>
3263 <li>fatal OOM if object retrieved by sequence fetcher
3264 runs out of memory</li>
3265 <li>unhandled Out of Memory Error when viewing pca
3266 analysis results</li>
3267 <li>InstallAnywhere builds fail to launch on OS X java
3268 10.5 update 4 (due to apple Java 1.6 update)</li>
3269 <li>Installanywhere Jalview silently fails to launch</li>
3270 </ul> <em>Applet</em>
3272 <li>Jalview.getFeatureGroups() raises an
3273 ArrayIndexOutOfBoundsException if no feature groups are
3280 <div align="center">
3281 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3287 <li>Alignment prettyprinter doesn't cope with long
3289 <li>clustalx colourscheme colours Ds preferentially when
3290 both D+E are present in over 50% of the column</li>
3291 <li>nucleic acid structures retrieved from PDB do not
3292 import correctly</li>
3293 <li>More columns get selected than were clicked on when a
3294 number of columns are hidden</li>
3295 <li>annotation label popup menu not providing correct
3296 add/hide/show options when rows are hidden or none are
3298 <li>Stockholm format shown in list of readable formats,
3299 and parser copes better with alignments from RFAM.</li>
3300 <li>CSV output of consensus only includes the percentage
3301 of all symbols if sequence logo display is enabled</li>
3303 </ul> <em>Applet</em>
3305 <li>annotation panel disappears when annotation is
3307 </ul> <em>Application</em>
3309 <li>Alignment view not redrawn properly when new
3310 alignment opened where annotation panel is visible but no
3311 annotations are present on alignment</li>
3312 <li>pasted region containing hidden columns is
3313 incorrectly displayed in new alignment window</li>
3314 <li>Jalview slow to complete operations when stdout is
3315 flooded (fix is to close the Jalview console)</li>
3316 <li>typo in AlignmentFrame->View->Hide->all but
3317 selected Rregions menu item.</li>
3318 <li>inconsistent group submenu and Format submenu entry
3319 'Un' or 'Non'conserved</li>
3320 <li>Sequence feature settings are being shared by
3321 multiple distinct alignments</li>
3322 <li>group annotation not recreated when tree partition is
3324 <li>double click on group annotation to select sequences
3325 does not propagate to associated trees</li>
3326 <li>Mac OSX specific issues:
3328 <li>exception raised when mouse clicked on desktop
3329 window background</li>
3330 <li>Desktop menu placed on menu bar and application
3331 name set correctly</li>
3332 <li>sequence feature settings not wide enough for the
3333 save feature colourscheme button</li>
3342 <div align="center">
3343 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3346 <td><em>New Capabilities</em>
3348 <li>URL links generated from description line for
3349 regular-expression based URL links (applet and application)
3351 <li>Non-positional feature URL links are shown in link
3353 <li>Linked viewing of nucleic acid sequences and
3355 <li>Automatic Scrolling option in View menu to display
3356 the currently highlighted region of an alignment.</li>
3357 <li>Order an alignment by sequence length, or using the
3358 average score or total feature count for each sequence.</li>
3359 <li>Shading features by score or associated description</li>
3360 <li>Subdivide alignment and groups based on identity of
3361 selected subsequence (Make Groups from Selection).</li>
3362 <li>New hide/show options including Shift+Control+H to
3363 hide everything but the currently selected region.</li>
3364 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3365 </ul> <em>Application</em>
3367 <li>Fetch DB References capabilities and UI expanded to
3368 support retrieval from DAS sequence sources</li>
3369 <li>Local DAS Sequence sources can be added via the
3370 command line or via the Add local source dialog box.</li>
3371 <li>DAS Dbref and DbxRef feature types are parsed as
3372 database references and protein_name is parsed as
3373 description line (BioSapiens terms).</li>
3374 <li>Enable or disable non-positional feature and database
3375 references in sequence ID tooltip from View menu in
3377 <!-- <li>New hidden columns and rows and representatives capabilities
3378 in annotations file (in progress - not yet fully implemented)</li> -->
3379 <li>Group-associated consensus, sequence logos and
3380 conservation plots</li>
3381 <li>Symbol distributions for each column can be exported
3382 and visualized as sequence logos</li>
3383 <li>Optionally scale multi-character column labels to fit
3384 within each column of annotation row<!-- todo for applet -->
3386 <li>Optional automatic sort of associated alignment view
3387 when a new tree is opened.</li>
3388 <li>Jalview Java Console</li>
3389 <li>Better placement of desktop window when moving
3390 between different screens.</li>
3391 <li>New preference items for sequence ID tooltip and
3392 consensus annotation</li>
3393 <li>Client to submit sequences and IDs to Envision2
3395 <li><em>Vamsas Capabilities</em>
3397 <li>Improved VAMSAS synchronization (Jalview archive
3398 used to preserve views, structures, and tree display
3400 <li>Import of vamsas documents from disk or URL via
3402 <li>Sharing of selected regions between views and
3403 with other VAMSAS applications (Experimental feature!)</li>
3404 <li>Updated API to VAMSAS version 0.2</li>
3406 </ul> <em>Applet</em>
3408 <li>Middle button resizes annotation row height</li>
3411 <li>sortByTree (true/false) - automatically sort the
3412 associated alignment view by the tree when a new tree is
3414 <li>showTreeBootstraps (true/false) - show or hide
3415 branch bootstraps (default is to show them if available)</li>
3416 <li>showTreeDistances (true/false) - show or hide
3417 branch lengths (default is to show them if available)</li>
3418 <li>showUnlinkedTreeNodes (true/false) - indicate if
3419 unassociated nodes should be highlighted in the tree
3421 <li>heightScale and widthScale (1.0 or more) -
3422 increase the height or width of a cell in the alignment
3423 grid relative to the current font size.</li>
3426 <li>Non-positional features displayed in sequence ID
3428 </ul> <em>Other</em>
3430 <li>Features format: graduated colour definitions and
3431 specification of feature scores</li>
3432 <li>Alignment Annotations format: new keywords for group
3433 associated annotation (GROUP_REF) and annotation row display
3434 properties (ROW_PROPERTIES)</li>
3435 <li>XML formats extended to support graduated feature
3436 colourschemes, group associated annotation, and profile
3437 visualization settings.</li></td>
3440 <li>Source field in GFF files parsed as feature source
3441 rather than description</li>
3442 <li>Non-positional features are now included in sequence
3443 feature and gff files (controlled via non-positional feature
3444 visibility in tooltip).</li>
3445 <li>URL links generated for all feature links (bugfix)</li>
3446 <li>Added URL embedding instructions to features file
3448 <li>Codons containing ambiguous nucleotides translated as
3449 'X' in peptide product</li>
3450 <li>Match case switch in find dialog box works for both
3451 sequence ID and sequence string and query strings do not
3452 have to be in upper case to match case-insensitively.</li>
3453 <li>AMSA files only contain first column of
3454 multi-character column annotation labels</li>
3455 <li>Jalview Annotation File generation/parsing consistent
3456 with documentation (e.g. Stockholm annotation can be
3457 exported and re-imported)</li>
3458 <li>PDB files without embedded PDB IDs given a friendly
3460 <li>Find incrementally searches ID string matches as well
3461 as subsequence matches, and correctly reports total number
3465 <li>Better handling of exceptions during sequence
3467 <li>Dasobert generated non-positional feature URL
3468 link text excludes the start_end suffix</li>
3469 <li>DAS feature and source retrieval buttons disabled
3470 when fetch or registry operations in progress.</li>
3471 <li>PDB files retrieved from URLs are cached properly</li>
3472 <li>Sequence description lines properly shared via
3474 <li>Sequence fetcher fetches multiple records for all
3476 <li>Ensured that command line das feature retrieval
3477 completes before alignment figures are generated.</li>
3478 <li>Reduced time taken when opening file browser for
3480 <li>isAligned check prior to calculating tree, PCA or
3481 submitting an MSA to JNet now excludes hidden sequences.</li>
3482 <li>User defined group colours properly recovered
3483 from Jalview projects.</li>
3492 <div align="center">
3493 <strong>2.4.0.b2</strong><br> 28/10/2009
3498 <li>Experimental support for google analytics usage
3500 <li>Jalview privacy settings (user preferences and docs).</li>
3505 <li>Race condition in applet preventing startup in
3507 <li>Exception when feature created from selection beyond
3508 length of sequence.</li>
3509 <li>Allow synthetic PDB files to be imported gracefully</li>
3510 <li>Sequence associated annotation rows associate with
3511 all sequences with a given id</li>
3512 <li>Find function matches case-insensitively for sequence
3513 ID string searches</li>
3514 <li>Non-standard characters do not cause pairwise
3515 alignment to fail with exception</li>
3516 </ul> <em>Application Issues</em>
3518 <li>Sequences are now validated against EMBL database</li>
3519 <li>Sequence fetcher fetches multiple records for all
3521 </ul> <em>InstallAnywhere Issues</em>
3523 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3524 issue with installAnywhere mechanism)</li>
3525 <li>Command line launching of JARs from InstallAnywhere
3526 version (java class versioning error fixed)</li>
3533 <div align="center">
3534 <strong>2.4</strong><br> 27/8/2008
3537 <td><em>User Interface</em>
3539 <li>Linked highlighting of codon and amino acid from
3540 translation and protein products</li>
3541 <li>Linked highlighting of structure associated with
3542 residue mapping to codon position</li>
3543 <li>Sequence Fetcher provides example accession numbers
3544 and 'clear' button</li>
3545 <li>MemoryMonitor added as an option under Desktop's
3547 <li>Extract score function to parse whitespace separated
3548 numeric data in description line</li>
3549 <li>Column labels in alignment annotation can be centred.</li>
3550 <li>Tooltip for sequence associated annotation give name
3552 </ul> <em>Web Services and URL fetching</em>
3554 <li>JPred3 web service</li>
3555 <li>Prototype sequence search client (no public services
3557 <li>Fetch either seed alignment or full alignment from
3559 <li>URL Links created for matching database cross
3560 references as well as sequence ID</li>
3561 <li>URL Links can be created using regular-expressions</li>
3562 </ul> <em>Sequence Database Connectivity</em>
3564 <li>Retrieval of cross-referenced sequences from other
3566 <li>Generalised database reference retrieval and
3567 validation to all fetchable databases</li>
3568 <li>Fetch sequences from DAS sources supporting the
3569 sequence command</li>
3570 </ul> <em>Import and Export</em>
3571 <li>export annotation rows as CSV for spreadsheet import</li>
3572 <li>Jalview projects record alignment dataset associations,
3573 EMBL products, and cDNA sequence mappings</li>
3574 <li>Sequence Group colour can be specified in Annotation
3576 <li>Ad-hoc colouring of group in Annotation File using RGB
3577 triplet as name of colourscheme</li>
3578 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3580 <li>treenode binding for VAMSAS tree exchange</li>
3581 <li>local editing and update of sequences in VAMSAS
3582 alignments (experimental)</li>
3583 <li>Create new or select existing session to join</li>
3584 <li>load and save of vamsas documents</li>
3585 </ul> <em>Application command line</em>
3587 <li>-tree parameter to open trees (introduced for passing
3589 <li>-fetchfrom command line argument to specify nicknames
3590 of DAS servers to query for alignment features</li>
3591 <li>-dasserver command line argument to add new servers
3592 that are also automatically queried for features</li>
3593 <li>-groovy command line argument executes a given groovy
3594 script after all input data has been loaded and parsed</li>
3595 </ul> <em>Applet-Application data exchange</em>
3597 <li>Trees passed as applet parameters can be passed to
3598 application (when using "View in full
3599 application")</li>
3600 </ul> <em>Applet Parameters</em>
3602 <li>feature group display control parameter</li>
3603 <li>debug parameter</li>
3604 <li>showbutton parameter</li>
3605 </ul> <em>Applet API methods</em>
3607 <li>newView public method</li>
3608 <li>Window (current view) specific get/set public methods</li>
3609 <li>Feature display control methods</li>
3610 <li>get list of currently selected sequences</li>
3611 </ul> <em>New Jalview distribution features</em>
3613 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3614 <li>RELEASE file gives build properties for the latest
3615 Jalview release.</li>
3616 <li>Java 1.1 Applet build made easier and donotobfuscate
3617 property controls execution of obfuscator</li>
3618 <li>Build target for generating source distribution</li>
3619 <li>Debug flag for javacc</li>
3620 <li>.jalview_properties file is documented (slightly) in
3621 jalview.bin.Cache</li>
3622 <li>Continuous Build Integration for stable and
3623 development version of Application, Applet and source
3628 <li>selected region output includes visible annotations
3629 (for certain formats)</li>
3630 <li>edit label/displaychar contains existing label/char
3632 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3633 <li>shorter peptide product names from EMBL records</li>
3634 <li>Newick string generator makes compact representations</li>
3635 <li>bootstrap values parsed correctly for tree files with
3637 <li>pathological filechooser bug avoided by not allowing
3638 filenames containing a ':'</li>
3639 <li>Fixed exception when parsing GFF files containing
3640 global sequence features</li>
3641 <li>Alignment datasets are finalized only when number of
3642 references from alignment sequences goes to zero</li>
3643 <li>Close of tree branch colour box without colour
3644 selection causes cascading exceptions</li>
3645 <li>occasional negative imgwidth exceptions</li>
3646 <li>better reporting of non-fatal warnings to user when
3647 file parsing fails.</li>
3648 <li>Save works when Jalview project is default format</li>
3649 <li>Save as dialog opened if current alignment format is
3650 not a valid output format</li>
3651 <li>UniProt canonical names introduced for both das and
3653 <li>Histidine should be midblue (not pink!) in Zappo</li>
3654 <li>error messages passed up and output when data read
3656 <li>edit undo recovers previous dataset sequence when
3657 sequence is edited</li>
3658 <li>allow PDB files without pdb ID HEADER lines (like
3659 those generated by MODELLER) to be read in properly</li>
3660 <li>allow reading of JPred concise files as a normal
3662 <li>Stockholm annotation parsing and alignment properties
3663 import fixed for PFAM records</li>
3664 <li>Structure view windows have correct name in Desktop
3666 <li>annotation consisting of sequence associated scores
3667 can be read and written correctly to annotation file</li>
3668 <li>Aligned cDNA translation to aligned peptide works
3670 <li>Fixed display of hidden sequence markers and
3671 non-italic font for representatives in Applet</li>
3672 <li>Applet Menus are always embedded in applet window on
3674 <li>Newly shown features appear at top of stack (in
3676 <li>Annotations added via parameter not drawn properly
3677 due to null pointer exceptions</li>
3678 <li>Secondary structure lines are drawn starting from
3679 first column of alignment</li>
3680 <li>UniProt XML import updated for new schema release in
3682 <li>Sequence feature to sequence ID match for Features
3683 file is case-insensitive</li>
3684 <li>Sequence features read from Features file appended to
3685 all sequences with matching IDs</li>
3686 <li>PDB structure coloured correctly for associated views
3687 containing a sub-sequence</li>
3688 <li>PDB files can be retrieved by applet from Jar files</li>
3689 <li>feature and annotation file applet parameters
3690 referring to different directories are retrieved correctly</li>
3691 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3692 <li>Fixed application hang whilst waiting for
3693 splash-screen version check to complete</li>
3694 <li>Applet properly URLencodes input parameter values
3695 when passing them to the launchApp service</li>
3696 <li>display name and local features preserved in results
3697 retrieved from web service</li>
3698 <li>Visual delay indication for sequence retrieval and
3699 sequence fetcher initialisation</li>
3700 <li>updated Application to use DAS 1.53e version of
3701 dasobert DAS client</li>
3702 <li>Re-instated Full AMSA support and .amsa file
3704 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3712 <div align="center">
3713 <strong>2.3</strong><br> 9/5/07
3718 <li>Jmol 11.0.2 integration</li>
3719 <li>PDB views stored in Jalview XML files</li>
3720 <li>Slide sequences</li>
3721 <li>Edit sequence in place</li>
3722 <li>EMBL CDS features</li>
3723 <li>DAS Feature mapping</li>
3724 <li>Feature ordering</li>
3725 <li>Alignment Properties</li>
3726 <li>Annotation Scores</li>
3727 <li>Sort by scores</li>
3728 <li>Feature/annotation editing in applet</li>
3733 <li>Headless state operation in 2.2.1</li>
3734 <li>Incorrect and unstable DNA pairwise alignment</li>
3735 <li>Cut and paste of sequences with annotation</li>
3736 <li>Feature group display state in XML</li>
3737 <li>Feature ordering in XML</li>
3738 <li>blc file iteration selection using filename # suffix</li>
3739 <li>Stockholm alignment properties</li>
3740 <li>Stockhom alignment secondary structure annotation</li>
3741 <li>2.2.1 applet had no feature transparency</li>
3742 <li>Number pad keys can be used in cursor mode</li>
3743 <li>Structure Viewer mirror image resolved</li>
3750 <div align="center">
3751 <strong>2.2.1</strong><br> 12/2/07
3756 <li>Non standard characters can be read and displayed
3757 <li>Annotations/Features can be imported/exported to the
3759 <li>Applet allows editing of sequence/annotation/group
3760 name & description
3761 <li>Preference setting to display sequence name in
3763 <li>Annotation file format extended to allow
3764 Sequence_groups to be defined
3765 <li>Default opening of alignment overview panel can be
3766 specified in preferences
3767 <li>PDB residue numbering annotation added to associated
3773 <li>Applet crash under certain Linux OS with Java 1.6
3775 <li>Annotation file export / import bugs fixed
3776 <li>PNG / EPS image output bugs fixed
3782 <div align="center">
3783 <strong>2.2</strong><br> 27/11/06
3788 <li>Multiple views on alignment
3789 <li>Sequence feature editing
3790 <li>"Reload" alignment
3791 <li>"Save" to current filename
3792 <li>Background dependent text colour
3793 <li>Right align sequence ids
3794 <li>User-defined lower case residue colours
3797 <li>Menu item accelerator keys
3798 <li>Control-V pastes to current alignment
3799 <li>Cancel button for DAS Feature Fetching
3800 <li>PCA and PDB Viewers zoom via mouse roller
3801 <li>User-defined sub-tree colours and sub-tree selection
3803 <li>'New Window' button on the 'Output to Text box'
3808 <li>New memory efficient Undo/Redo System
3809 <li>Optimised symbol lookups and conservation/consensus
3811 <li>Region Conservation/Consensus recalculated after
3813 <li>Fixed Remove Empty Columns Bug (empty columns at end
3815 <li>Slowed DAS Feature Fetching for increased robustness.
3817 <li>Made angle brackets in ASCII feature descriptions
3819 <li>Re-instated Zoom function for PCA
3820 <li>Sequence descriptions conserved in web service
3822 <li>UniProt ID discoverer uses any word separated by
3824 <li>WsDbFetch query/result association resolved
3825 <li>Tree leaf to sequence mapping improved
3826 <li>Smooth fonts switch moved to FontChooser dialog box.
3833 <div align="center">
3834 <strong>2.1.1</strong><br> 12/9/06
3839 <li>Copy consensus sequence to clipboard</li>
3844 <li>Image output - rightmost residues are rendered if
3845 sequence id panel has been resized</li>
3846 <li>Image output - all offscreen group boundaries are
3848 <li>Annotation files with sequence references - all
3849 elements in file are relative to sequence position</li>
3850 <li>Mac Applet users can use Alt key for group editing</li>
3856 <div align="center">
3857 <strong>2.1</strong><br> 22/8/06
3862 <li>MAFFT Multiple Alignment in default Web Service list</li>
3863 <li>DAS Feature fetching</li>
3864 <li>Hide sequences and columns</li>
3865 <li>Export Annotations and Features</li>
3866 <li>GFF file reading / writing</li>
3867 <li>Associate structures with sequences from local PDB
3869 <li>Add sequences to exisiting alignment</li>
3870 <li>Recently opened files / URL lists</li>
3871 <li>Applet can launch the full application</li>
3872 <li>Applet has transparency for features (Java 1.2
3874 <li>Applet has user defined colours parameter</li>
3875 <li>Applet can load sequences from parameter
3876 "sequence<em>x</em>"
3882 <li>Redundancy Panel reinstalled in the Applet</li>
3883 <li>Monospaced font - EPS / rescaling bug fixed</li>
3884 <li>Annotation files with sequence references bug fixed</li>
3890 <div align="center">
3891 <strong>2.08.1</strong><br> 2/5/06
3896 <li>Change case of selected region from Popup menu</li>
3897 <li>Choose to match case when searching</li>
3898 <li>Middle mouse button and mouse movement can compress /
3899 expand the visible width and height of the alignment</li>
3904 <li>Annotation Panel displays complete JNet results</li>
3910 <div align="center">
3911 <strong>2.08b</strong><br> 18/4/06
3917 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3918 <li>Righthand label on wrapped alignments shows correct
3925 <div align="center">
3926 <strong>2.08</strong><br> 10/4/06
3931 <li>Editing can be locked to the selection area</li>
3932 <li>Keyboard editing</li>
3933 <li>Create sequence features from searches</li>
3934 <li>Precalculated annotations can be loaded onto
3936 <li>Features file allows grouping of features</li>
3937 <li>Annotation Colouring scheme added</li>
3938 <li>Smooth fonts off by default - Faster rendering</li>
3939 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3944 <li>Drag & Drop fixed on Linux</li>
3945 <li>Jalview Archive file faster to load/save, sequence
3946 descriptions saved.</li>
3952 <div align="center">
3953 <strong>2.07</strong><br> 12/12/05
3958 <li>PDB Structure Viewer enhanced</li>
3959 <li>Sequence Feature retrieval and display enhanced</li>
3960 <li>Choose to output sequence start-end after sequence
3961 name for file output</li>
3962 <li>Sequence Fetcher WSDBFetch@EBI</li>
3963 <li>Applet can read feature files, PDB files and can be
3964 used for HTML form input</li>
3969 <li>HTML output writes groups and features</li>
3970 <li>Group editing is Control and mouse click</li>
3971 <li>File IO bugs</li>
3977 <div align="center">
3978 <strong>2.06</strong><br> 28/9/05
3983 <li>View annotations in wrapped mode</li>
3984 <li>More options for PCA viewer</li>
3989 <li>GUI bugs resolved</li>
3990 <li>Runs with -nodisplay from command line</li>
3996 <div align="center">
3997 <strong>2.05b</strong><br> 15/9/05
4002 <li>Choose EPS export as lineart or text</li>
4003 <li>Jar files are executable</li>
4004 <li>Can read in Uracil - maps to unknown residue</li>
4009 <li>Known OutOfMemory errors give warning message</li>
4010 <li>Overview window calculated more efficiently</li>
4011 <li>Several GUI bugs resolved</li>
4017 <div align="center">
4018 <strong>2.05</strong><br> 30/8/05
4023 <li>Edit and annotate in "Wrapped" view</li>
4028 <li>Several GUI bugs resolved</li>
4034 <div align="center">
4035 <strong>2.04</strong><br> 24/8/05
4040 <li>Hold down mouse wheel & scroll to change font
4046 <li>Improved JPred client reliability</li>
4047 <li>Improved loading of Jalview files</li>
4053 <div align="center">
4054 <strong>2.03</strong><br> 18/8/05
4059 <li>Set Proxy server name and port in preferences</li>
4060 <li>Multiple URL links from sequence ids</li>
4061 <li>User Defined Colours can have a scheme name and added
4063 <li>Choose to ignore gaps in consensus calculation</li>
4064 <li>Unix users can set default web browser</li>
4065 <li>Runs without GUI for batch processing</li>
4066 <li>Dynamically generated Web Service Menus</li>
4071 <li>InstallAnywhere download for Sparc Solaris</li>
4077 <div align="center">
4078 <strong>2.02</strong><br> 18/7/05
4084 <li>Copy & Paste order of sequences maintains
4085 alignment order.</li>
4091 <div align="center">
4092 <strong>2.01</strong><br> 12/7/05
4097 <li>Use delete key for deleting selection.</li>
4098 <li>Use Mouse wheel to scroll sequences.</li>
4099 <li>Help file updated to describe how to add alignment
4101 <li>Version and build date written to build properties
4103 <li>InstallAnywhere installation will check for updates
4104 at launch of Jalview.</li>
4109 <li>Delete gaps bug fixed.</li>
4110 <li>FileChooser sorts columns.</li>
4111 <li>Can remove groups one by one.</li>
4112 <li>Filechooser icons installed.</li>
4113 <li>Finder ignores return character when searching.
4114 Return key will initiate a search.<br>
4121 <div align="center">
4122 <strong>2.0</strong><br> 20/6/05
4127 <li>New codebase</li>