3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
74 <em>29/01/2019</em></strong>
77 <td><div align="left">
81 <!-- JAL-3035 -->DAS sequence retrieval and annotation
82 capabilities removed from the Jalview Desktop
85 <em>Release Processes</em>
87 <li>Atlassian Bamboo continuous integration server for unattended Test Suite execution</li>
88 <li><!-- JAL-2864 -->Memory test suite to detect leaks in common operations</li>
91 <td><div align="left">
95 <!-- JAL-2865 -->Jalview hangs when closing windows
96 or the overview updates with large alignments.
99 <!-- JAL-2865 -->Tree and PCA calculation fails for selected
100 region if columns were selected by dragging right-to-left
101 and the mouse moved to the left of the first column.
107 <!-- JAL-2822 -->Start and End should be updated when
108 sequence data at beginning or end of alignment added/removed
112 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
113 sequence features correctly when start of sequence is
114 removed (Known defect since 2.10)
117 <!-- JAL-2846, -->Avoided use of apostrophe in dialog box
126 <td width="60" nowrap>
128 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
131 <td><div align="left">
135 <!-- JAL-3101 -->Default memory for Jalview webstart and
136 InstallAnywhere increased to 1G.
139 <!-- JAL-247 -->Hidden sequence markers and representative
140 sequence bolding included when exporting alignment as EPS,
141 SVG, PNG or HTML. <em>Display is configured via the
142 Format menu, or for command-line use via a jalview
143 properties file.</em>
146 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
147 API and sequence data now imported as JSON.
150 <!-- JAL-3065 -->Change in recommended way of starting
151 Jalview via a Java command line: add jars in lib directory
152 to CLASSPATH, rather than via the deprecated java.ext.dirs
159 <!-- JAL-3047 -->Support added to execute test suite
160 instrumented with <a href="http://openclover.org/">Open
165 <td><div align="left">
169 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
170 row shown in Feredoxin Structure alignment view of example
174 <!-- JAL-2854 -->Annotation obscures sequences if lots of
175 annotation displayed.
178 <!-- JAL-3107 -->Group conservation/consensus not shown
179 for newly created group when 'Apply to all groups'
183 <!-- JAL-3087 -->Corrupted display when switching to
184 wrapped mode when sequence panel's vertical scrollbar is
188 <!-- JAL-3003 -->Alignment is black in exported EPS file
189 when sequences are selected in exported view.</em>
192 <!-- JAL-3059 -->Groups with different coloured borders
193 aren't rendered with correct colour.
196 <!-- JAL-3092 -->Jalview could hang when importing certain
197 types of knotted RNA secondary structure.
200 <!-- JAL-3095 -->Sequence highlight and selection in
201 trimmed VARNA 2D structure is incorrect for sequences that
205 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
206 annotation when columns are inserted into an alignment,
207 and when exporting as Stockholm flatfile.
210 <!-- JAL-3053 -->Jalview annotation rows containing upper
211 and lower-case 'E' and 'H' do not automatically get
212 treated as RNA secondary structure.
215 <!-- JAL-3106 -->.jvp should be used as default extension
216 (not .jar) when saving a jalview project file.
219 <!-- JAL-3105 -->Mac Users: closing a window correctly
220 transfers focus to previous window on OSX
223 <em>Java 10 Issues Resolved</em>
226 <!-- JAL-2988 -->OSX - Can't save new files via the File
227 or export menus by typing in a name into the Save dialog
231 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
232 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
233 'look and feel' which has improved compatibility with the
234 latest version of OSX.
241 <td width="60" nowrap>
243 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
244 <em>7/06/2018</em></strong>
247 <td><div align="left">
251 <!-- JAL-2920 -->Use HGVS nomenclature for variant
252 annotation retrieved from Uniprot
255 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
256 onto the Jalview Desktop
260 <td><div align="left">
264 <!-- JAL-3017 -->Cannot import features with multiple
265 variant elements (blocks import of some Uniprot records)
268 <!-- JAL-2997 -->Clustal files with sequence positions in
269 right-hand column parsed correctly
272 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
273 not alignment area in exported graphic
276 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
277 window has input focus
280 <!-- JAL-2992 -->Annotation panel set too high when
281 annotation added to view (Windows)
284 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
285 network connectivity is poor
288 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
289 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
290 the currently open URL and links from a page viewed in
291 Firefox or Chrome on Windows is now fully supported. If
292 you are using Edge, only links in the page can be
293 dragged, and with Internet Explorer, only the currently
294 open URL in the browser can be dropped onto Jalview.</em>
300 <td width="60" nowrap>
302 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
305 <td><div align="left">
309 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
310 for disabling automatic superposition of multiple
311 structures and open structures in existing views
314 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
315 ID and annotation area margins can be click-dragged to
319 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
323 <!-- JAL-2759 -->Improved performance for large alignments
324 and lots of hidden columns
327 <!-- JAL-2593 -->Improved performance when rendering lots
328 of features (particularly when transparency is disabled)
333 <td><div align="left">
336 <!-- JAL-2899 -->Structure and Overview aren't updated
337 when Colour By Annotation threshold slider is adjusted
340 <!-- JAL-2778 -->Slow redraw when Overview panel shown
341 overlapping alignment panel
344 <!-- JAL-2929 -->Overview doesn't show end of unpadded
348 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
349 improved: CDS not handled correctly if transcript has no
353 <!-- JAL-2321 -->Secondary structure and temperature
354 factor annotation not added to sequence when local PDB
355 file associated with it by drag'n'drop or structure
359 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
360 dialog doesn't import PDB files dropped on an alignment
363 <!-- JAL-2666 -->Linked scrolling via protein horizontal
364 scroll bar doesn't work for some CDS/Protein views
367 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
368 Java 1.8u153 onwards and Java 1.9u4+.
371 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
372 columns in annotation row
375 <!-- JAL-2913 -->Preferences panel's ID Width control is not
376 honored in batch mode
379 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
380 for structures added to existing Jmol view
383 <!-- JAL-2223 -->'View Mappings' includes duplicate
384 entries after importing project with multiple views
387 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
388 protein sequences via SIFTS from associated PDB entries
389 with negative residue numbers or missing residues fails
392 <!-- JAL-2952 -->Exception when shading sequence with negative
393 Temperature Factor values from annotated PDB files (e.g.
394 as generated by CONSURF)
397 <!-- JAL-2920 -->Uniprot 'sequence variant' features
398 tooltip doesn't include a text description of mutation
401 <!-- JAL-2922 -->Invert displayed features very slow when
402 structure and/or overview windows are also shown
405 <!-- JAL-2954 -->Selecting columns from highlighted regions
406 very slow for alignments with large numbers of sequences
409 <!-- JAL-2925 -->Copy Consensus fails for group consensus
410 with 'StringIndexOutOfBounds'
413 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
414 platforms running Java 10
417 <!-- JAL-2960 -->Adding a structure to existing structure
418 view appears to do nothing because the view is hidden behind the alignment view
424 <!-- JAL-2926 -->Copy consensus sequence option in applet
425 should copy the group consensus when popup is opened on it
431 <!-- JAL-2913 -->Fixed ID width preference is not respected
434 <em>New Known Defects</em>
437 <!-- JAL-2973 --> Exceptions occasionally raised when
438 editing a large alignment and overview is displayed
441 <!-- JAL-2974 -->'Overview updating' progress bar is shown
442 repeatedly after a series of edits even when the overview
443 is no longer reflecting updates
446 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
447 structures for protein subsequence (if 'Trim Retrieved
448 Sequences' enabled) or Ensembl isoforms (Workaround in
449 2.10.4 is to fail back to N&W mapping)
456 <td width="60" nowrap>
458 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
461 <td><div align="left">
462 <ul><li>Updated Certum Codesigning Certificate
463 (Valid till 30th November 2018)</li></ul></div></td>
464 <td><div align="left">
467 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
468 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
469 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
470 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
471 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
472 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
473 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
479 <td width="60" nowrap>
481 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
484 <td><div align="left">
488 <!-- JAL-2446 -->Faster and more efficient management and
489 rendering of sequence features
492 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
493 429 rate limit request hander
496 <!-- JAL-2773 -->Structure views don't get updated unless
497 their colours have changed
500 <!-- JAL-2495 -->All linked sequences are highlighted for
501 a structure mousover (Jmol) or selection (Chimera)
504 <!-- JAL-2790 -->'Cancel' button in progress bar for
505 JABAWS AACon, RNAAliFold and Disorder prediction jobs
508 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
509 view from Ensembl locus cross-references
512 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
516 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
517 feature can be disabled
520 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
521 PDB easier retrieval of sequences for lists of IDs
524 <!-- JAL-2758 -->Short names for sequences retrieved from
530 <li>Groovy interpreter updated to 2.4.12</li>
531 <li>Example groovy script for generating a matrix of
532 percent identity scores for current alignment.</li>
534 <em>Testing and Deployment</em>
537 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
541 <td><div align="left">
545 <!-- JAL-2643 -->Pressing tab after updating the colour
546 threshold text field doesn't trigger an update to the
550 <!-- JAL-2682 -->Race condition when parsing sequence ID
554 <!-- JAL-2608 -->Overview windows are also closed when
555 alignment window is closed
558 <!-- JAL-2548 -->Export of features doesn't always respect
562 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
563 takes a long time in Cursor mode
569 <!-- JAL-2777 -->Structures with whitespace chainCode
570 cannot be viewed in Chimera
573 <!-- JAL-2728 -->Protein annotation panel too high in
577 <!-- JAL-2757 -->Can't edit the query after the server
578 error warning icon is shown in Uniprot and PDB Free Text
582 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
585 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
588 <!-- JAL-2739 -->Hidden column marker in last column not
589 rendered when switching back from Wrapped to normal view
592 <!-- JAL-2768 -->Annotation display corrupted when
593 scrolling right in unwapped alignment view
596 <!-- JAL-2542 -->Existing features on subsequence
597 incorrectly relocated when full sequence retrieved from
601 <!-- JAL-2733 -->Last reported memory still shown when
602 Desktop->Show Memory is unticked (OSX only)
605 <!-- JAL-2658 -->Amend Features dialog doesn't allow
606 features of same type and group to be selected for
610 <!-- JAL-2524 -->Jalview becomes sluggish in wide
611 alignments when hidden columns are present
614 <!-- JAL-2392 -->Jalview freezes when loading and
615 displaying several structures
618 <!-- JAL-2732 -->Black outlines left after resizing or
622 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
623 within the Jalview desktop on OSX
626 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
627 when in wrapped alignment mode
630 <!-- JAL-2636 -->Scale mark not shown when close to right
631 hand end of alignment
634 <!-- JAL-2684 -->Pairwise alignment of selected regions of
635 each selected sequence do not have correct start/end
639 <!-- JAL-2793 -->Alignment ruler height set incorrectly
640 after canceling the Alignment Window's Font dialog
643 <!-- JAL-2036 -->Show cross-references not enabled after
644 restoring project until a new view is created
647 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
648 URL links appears when only default EMBL-EBI link is
649 configured (since 2.10.2b2)
652 <!-- JAL-2775 -->Overview redraws whole window when box
656 <!-- JAL-2225 -->Structure viewer doesn't map all chains
657 in a multi-chain structure when viewing alignment
658 involving more than one chain (since 2.10)
661 <!-- JAL-2811 -->Double residue highlights in cursor mode
662 if new selection moves alignment window
665 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
666 arrow key in cursor mode to pass hidden column marker
669 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
670 that produces correctly annotated transcripts and products
673 <!-- JAL-2776 -->Toggling a feature group after first time
674 doesn't update associated structure view
677 <em>Applet</em><br />
680 <!-- JAL-2687 -->Concurrent modification exception when
681 closing alignment panel
684 <em>BioJSON</em><br />
687 <!-- JAL-2546 -->BioJSON export does not preserve
688 non-positional features
691 <em>New Known Issues</em>
694 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
695 sequence features correctly (for many previous versions of
699 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
700 using cursor in wrapped panel other than top
703 <!-- JAL-2791 -->Select columns containing feature ignores
704 graduated colour threshold
707 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
708 always preserve numbering and sequence features
711 <em>Known Java 9 Issues</em>
714 <!-- JAL-2902 -->Groovy Console very slow to open and is
715 not responsive when entering characters (Webstart, Java
722 <td width="60" nowrap>
724 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
725 <em>2/10/2017</em></strong>
728 <td><div align="left">
729 <em>New features in Jalview Desktop</em>
732 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
734 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
738 <td><div align="left">
742 <td width="60" nowrap>
744 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
745 <em>7/9/2017</em></strong>
748 <td><div align="left">
752 <!-- JAL-2588 -->Show gaps in overview window by colouring
753 in grey (sequences used to be coloured grey, and gaps were
757 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
761 <!-- JAL-2587 -->Overview updates immediately on increase
762 in size and progress bar shown as higher resolution
763 overview is recalculated
768 <td><div align="left">
772 <!-- JAL-2664 -->Overview window redraws every hidden
773 column region row by row
776 <!-- JAL-2681 -->duplicate protein sequences shown after
777 retrieving Ensembl crossrefs for sequences from Uniprot
780 <!-- JAL-2603 -->Overview window throws NPE if show boxes
781 format setting is unticked
784 <!-- JAL-2610 -->Groups are coloured wrongly in overview
785 if group has show boxes format setting unticked
788 <!-- JAL-2672,JAL-2665 -->Redraw problems when
789 autoscrolling whilst dragging current selection group to
790 include sequences and columns not currently displayed
793 <!-- JAL-2691 -->Not all chains are mapped when multimeric
794 assemblies are imported via CIF file
797 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
798 displayed when threshold or conservation colouring is also
802 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
806 <!-- JAL-2673 -->Jalview continues to scroll after
807 dragging a selected region off the visible region of the
811 <!-- JAL-2724 -->Cannot apply annotation based
812 colourscheme to all groups in a view
815 <!-- JAL-2511 -->IDs don't line up with sequences
816 initially after font size change using the Font chooser or
823 <td width="60" nowrap>
825 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
828 <td><div align="left">
829 <em>Calculations</em>
833 <!-- JAL-1933 -->Occupancy annotation row shows number of
834 ungapped positions in each column of the alignment.
837 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
838 a calculation dialog box
841 <!-- JAL-2379 -->Revised implementation of PCA for speed
842 and memory efficiency (~30x faster)
845 <!-- JAL-2403 -->Revised implementation of sequence
846 similarity scores as used by Tree, PCA, Shading Consensus
847 and other calculations
850 <!-- JAL-2416 -->Score matrices are stored as resource
851 files within the Jalview codebase
854 <!-- JAL-2500 -->Trees computed on Sequence Feature
855 Similarity may have different topology due to increased
862 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
863 model for alignments and groups
866 <!-- JAL-384 -->Custom shading schemes created via groovy
873 <!-- JAL-2526 -->Efficiency improvements for interacting
874 with alignment and overview windows
877 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
881 <!-- JAL-2388 -->Hidden columns and sequences can be
885 <!-- JAL-2611 -->Click-drag in visible area allows fine
886 adjustment of visible position
890 <em>Data import/export</em>
893 <!-- JAL-2535 -->Posterior probability annotation from
894 Stockholm files imported as sequence associated annotation
897 <!-- JAL-2507 -->More robust per-sequence positional
898 annotation input/output via stockholm flatfile
901 <!-- JAL-2533 -->Sequence names don't include file
902 extension when importing structure files without embedded
903 names or PDB accessions
906 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
907 format sequence substitution matrices
910 <em>User Interface</em>
913 <!-- JAL-2447 --> Experimental Features Checkbox in
914 Desktop's Tools menu to hide or show untested features in
918 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
919 via Overview or sequence motif search operations
922 <!-- JAL-2547 -->Amend sequence features dialog box can be
923 opened by double clicking gaps within sequence feature
927 <!-- JAL-1476 -->Status bar message shown when not enough
928 aligned positions were available to create a 3D structure
932 <em>3D Structure</em>
935 <!-- JAL-2430 -->Hidden regions in alignment views are not
936 coloured in linked structure views
939 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
940 file-based command exchange
943 <!-- JAL-2375 -->Structure chooser automatically shows
944 Cached Structures rather than querying the PDBe if
945 structures are already available for sequences
948 <!-- JAL-2520 -->Structures imported via URL are cached in
949 the Jalview project rather than downloaded again when the
953 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
954 to transfer Chimera's structure attributes as Jalview
955 features, and vice-versa (<strong>Experimental
959 <em>Web Services</em>
962 <!-- JAL-2549 -->Updated JABAWS client to v2.2
965 <!-- JAL-2335 -->Filter non-standard amino acids and
966 nucleotides when submitting to AACon and other MSA
970 <!-- JAL-2316, -->URLs for viewing database
971 cross-references provided by identifiers.org and the
979 <!-- JAL-2344 -->FileFormatI interface for describing and
980 identifying file formats (instead of String constants)
983 <!-- JAL-2228 -->FeatureCounter script refactored for
984 efficiency when counting all displayed features (not
985 backwards compatible with 2.10.1)
988 <em>Example files</em>
991 <!-- JAL-2631 -->Graduated feature colour style example
992 included in the example feature file
995 <em>Documentation</em>
998 <!-- JAL-2339 -->Release notes reformatted for readability
999 with the built-in Java help viewer
1002 <!-- JAL-1644 -->Find documentation updated with 'search
1003 sequence description' option
1009 <!-- JAL-2485, -->External service integration tests for
1010 Uniprot REST Free Text Search Client
1013 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1016 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1021 <td><div align="left">
1022 <em>Calculations</em>
1025 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1026 matrix - C->R should be '-3'<br />Old matrix restored
1027 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1029 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1030 Jalview's treatment of gaps in PCA and substitution matrix
1031 based Tree calculations.<br /> <br />In earlier versions
1032 of Jalview, gaps matching gaps were penalised, and gaps
1033 matching non-gaps penalised even more. In the PCA
1034 calculation, gaps were actually treated as non-gaps - so
1035 different costs were applied, which meant Jalview's PCAs
1036 were different to those produced by SeqSpace.<br />Jalview
1037 now treats gaps in the same way as SeqSpace (ie it scores
1038 them as 0). <br /> <br />Enter the following in the
1039 Groovy console to restore pre-2.10.2 behaviour:<br />
1040 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1041 // for 2.10.1 mode <br />
1042 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1043 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1044 these settings will affect all subsequent tree and PCA
1045 calculations (not recommended)</em></li>
1047 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1048 scaling of branch lengths for trees computed using
1049 Sequence Feature Similarity.
1052 <!-- JAL-2377 -->PCA calculation could hang when
1053 generating output report when working with highly
1054 redundant alignments
1057 <!-- JAL-2544 --> Sort by features includes features to
1058 right of selected region when gaps present on right-hand
1062 <em>User Interface</em>
1065 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1066 doesn't reselect a specific sequence's associated
1067 annotation after it was used for colouring a view
1070 <!-- JAL-2419 -->Current selection lost if popup menu
1071 opened on a region of alignment without groups
1074 <!-- JAL-2374 -->Popup menu not always shown for regions
1075 of an alignment with overlapping groups
1078 <!-- JAL-2310 -->Finder double counts if both a sequence's
1079 name and description match
1082 <!-- JAL-2370 -->Hiding column selection containing two
1083 hidden regions results in incorrect hidden regions
1086 <!-- JAL-2386 -->'Apply to all groups' setting when
1087 changing colour does not apply Conservation slider value
1091 <!-- JAL-2373 -->Percentage identity and conservation menu
1092 items do not show a tick or allow shading to be disabled
1095 <!-- JAL-2385 -->Conservation shading or PID threshold
1096 lost when base colourscheme changed if slider not visible
1099 <!-- JAL-2547 -->Sequence features shown in tooltip for
1100 gaps before start of features
1103 <!-- JAL-2623 -->Graduated feature colour threshold not
1104 restored to UI when feature colour is edited
1107 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1108 a time when scrolling vertically in wrapped mode.
1111 <!-- JAL-2630 -->Structure and alignment overview update
1112 as graduate feature colour settings are modified via the
1116 <!-- JAL-2034 -->Overview window doesn't always update
1117 when a group defined on the alignment is resized
1120 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1121 wrapped view result in positional status updates
1125 <!-- JAL-2563 -->Status bar doesn't show position for
1126 ambiguous amino acid and nucleotide symbols
1129 <!-- JAL-2602 -->Copy consensus sequence failed if
1130 alignment included gapped columns
1133 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1134 widgets don't permanently disappear
1137 <!-- JAL-2503 -->Cannot select or filter quantitative
1138 annotation that are shown only as column labels (e.g.
1139 T-Coffee column reliability scores)
1142 <!-- JAL-2594 -->Exception thrown if trying to create a
1143 sequence feature on gaps only
1146 <!-- JAL-2504 -->Features created with 'New feature'
1147 button from a Find inherit previously defined feature type
1148 rather than the Find query string
1151 <!-- JAL-2423 -->incorrect title in output window when
1152 exporting tree calculated in Jalview
1155 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1156 and then revealing them reorders sequences on the
1160 <!-- JAL-964 -->Group panel in sequence feature settings
1161 doesn't update to reflect available set of groups after
1162 interactively adding or modifying features
1165 <!-- JAL-2225 -->Sequence Database chooser unusable on
1169 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1170 only excluded gaps in current sequence and ignored
1177 <!-- JAL-2421 -->Overview window visible region moves
1178 erratically when hidden rows or columns are present
1181 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1182 Structure Viewer's colour menu don't correspond to
1186 <!-- JAL-2405 -->Protein specific colours only offered in
1187 colour and group colour menu for protein alignments
1190 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1191 reflect currently selected view or group's shading
1195 <!-- JAL-2624 -->Feature colour thresholds not respected
1196 when rendered on overview and structures when opacity at
1200 <!-- JAL-2589 -->User defined gap colour not shown in
1201 overview when features overlaid on alignment
1204 <em>Data import/export</em>
1207 <!-- JAL-2576 -->Very large alignments take a long time to
1211 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1212 added after a sequence was imported are not written to
1216 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1217 when importing RNA secondary structure via Stockholm
1220 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1221 not shown in correct direction for simple pseudoknots
1224 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1225 with lightGray or darkGray via features file (but can
1229 <!-- JAL-2383 -->Above PID colour threshold not recovered
1230 when alignment view imported from project
1233 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1234 structure and sequences extracted from structure files
1235 imported via URL and viewed in Jmol
1238 <!-- JAL-2520 -->Structures loaded via URL are saved in
1239 Jalview Projects rather than fetched via URL again when
1240 the project is loaded and the structure viewed
1243 <em>Web Services</em>
1246 <!-- JAL-2519 -->EnsemblGenomes example failing after
1247 release of Ensembl v.88
1250 <!-- JAL-2366 -->Proxy server address and port always
1251 appear enabled in Preferences->Connections
1254 <!-- JAL-2461 -->DAS registry not found exceptions
1255 removed from console output
1258 <!-- JAL-2582 -->Cannot retrieve protein products from
1259 Ensembl by Peptide ID
1262 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1263 created from SIFTs, and spurious 'Couldn't open structure
1264 in Chimera' errors raised after April 2017 update (problem
1265 due to 'null' string rather than empty string used for
1266 residues with no corresponding PDB mapping).
1269 <em>Application UI</em>
1272 <!-- JAL-2361 -->User Defined Colours not added to Colour
1276 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1277 case' residues (button in colourscheme editor debugged and
1278 new documentation and tooltips added)
1281 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1282 doesn't restore group-specific text colour thresholds
1285 <!-- JAL-2243 -->Feature settings panel does not update as
1286 new features are added to alignment
1289 <!-- JAL-2532 -->Cancel in feature settings reverts
1290 changes to feature colours via the Amend features dialog
1293 <!-- JAL-2506 -->Null pointer exception when attempting to
1294 edit graduated feature colour via amend features dialog
1298 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1299 selection menu changes colours of alignment views
1302 <!-- JAL-2426 -->Spurious exceptions in console raised
1303 from alignment calculation workers after alignment has
1307 <!-- JAL-1608 -->Typo in selection popup menu - Create
1308 groups now 'Create Group'
1311 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1312 Create/Undefine group doesn't always work
1315 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1316 shown again after pressing 'Cancel'
1319 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1320 adjusts start position in wrap mode
1323 <!-- JAL-2563 -->Status bar doesn't show positions for
1324 ambiguous amino acids
1327 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1328 CDS/Protein view after CDS sequences added for aligned
1332 <!-- JAL-2592 -->User defined colourschemes called 'User
1333 Defined' don't appear in Colours menu
1339 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1340 score models doesn't always result in an updated PCA plot
1343 <!-- JAL-2442 -->Features not rendered as transparent on
1344 overview or linked structure view
1347 <!-- JAL-2372 -->Colour group by conservation doesn't
1351 <!-- JAL-2517 -->Hitting Cancel after applying
1352 user-defined colourscheme doesn't restore original
1359 <!-- JAL-2314 -->Unit test failure:
1360 jalview.ws.jabaws.RNAStructExportImport setup fails
1363 <!-- JAL-2307 -->Unit test failure:
1364 jalview.ws.sifts.SiftsClientTest due to compatibility
1365 problems with deep array comparison equality asserts in
1366 successive versions of TestNG
1369 <!-- JAL-2479 -->Relocated StructureChooserTest and
1370 ParameterUtilsTest Unit tests to Network suite
1373 <em>New Known Issues</em>
1376 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1377 phase after a sequence motif find operation
1380 <!-- JAL-2550 -->Importing annotation file with rows
1381 containing just upper and lower case letters are
1382 interpreted as WUSS RNA secondary structure symbols
1385 <!-- JAL-2590 -->Cannot load and display Newick trees
1386 reliably from eggnog Ortholog database
1389 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1390 containing features of type Highlight' when 'B' is pressed
1391 to mark columns containing highlighted regions.
1394 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1395 doesn't always add secondary structure annotation.
1400 <td width="60" nowrap>
1401 <div align="center">
1402 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1405 <td><div align="left">
1409 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1410 for all consensus calculations
1413 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1416 <li>Updated Jalview's Certum code signing certificate
1419 <em>Application</em>
1422 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1423 set of database cross-references, sorted alphabetically
1426 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1427 from database cross references. Users with custom links
1428 will receive a <a href="webServices/urllinks.html#warning">warning
1429 dialog</a> asking them to update their preferences.
1432 <!-- JAL-2287-->Cancel button and escape listener on
1433 dialog warning user about disconnecting Jalview from a
1437 <!-- JAL-2320-->Jalview's Chimera control window closes if
1438 the Chimera it is connected to is shut down
1441 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1442 columns menu item to mark columns containing highlighted
1443 regions (e.g. from structure selections or results of a
1447 <!-- JAL-2284-->Command line option for batch-generation
1448 of HTML pages rendering alignment data with the BioJS
1458 <!-- JAL-2286 -->Columns with more than one modal residue
1459 are not coloured or thresholded according to percent
1460 identity (first observed in Jalview 2.8.2)
1463 <!-- JAL-2301 -->Threonine incorrectly reported as not
1467 <!-- JAL-2318 -->Updates to documentation pages (above PID
1468 threshold, amino acid properties)
1471 <!-- JAL-2292 -->Lower case residues in sequences are not
1472 reported as mapped to residues in a structure file in the
1476 <!--JAL-2324 -->Identical features with non-numeric scores
1477 could be added multiple times to a sequence
1480 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1481 bond features shown as two highlighted residues rather
1482 than a range in linked structure views, and treated
1483 correctly when selecting and computing trees from features
1486 <!-- JAL-2281-->Custom URL links for database
1487 cross-references are matched to database name regardless
1492 <em>Application</em>
1495 <!-- JAL-2282-->Custom URL links for specific database
1496 names without regular expressions also offer links from
1500 <!-- JAL-2315-->Removing a single configured link in the
1501 URL links pane in Connections preferences doesn't actually
1502 update Jalview configuration
1505 <!-- JAL-2272-->CTRL-Click on a selected region to open
1506 the alignment area popup menu doesn't work on El-Capitan
1509 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1510 files with similarly named sequences if dropped onto the
1514 <!-- JAL-2312 -->Additional mappings are shown for PDB
1515 entries where more chains exist in the PDB accession than
1516 are reported in the SIFTS file
1519 <!-- JAL-2317-->Certain structures do not get mapped to
1520 the structure view when displayed with Chimera
1523 <!-- JAL-2317-->No chains shown in the Chimera view
1524 panel's View->Show Chains submenu
1527 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1528 work for wrapped alignment views
1531 <!--JAL-2197 -->Rename UI components for running JPred
1532 predictions from 'JNet' to 'JPred'
1535 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1536 corrupted when annotation panel vertical scroll is not at
1537 first annotation row
1540 <!--JAL-2332 -->Attempting to view structure for Hen
1541 lysozyme results in a PDB Client error dialog box
1544 <!-- JAL-2319 -->Structure View's mapping report switched
1545 ranges for PDB and sequence for SIFTS
1548 SIFTS 'Not_Observed' residues mapped to non-existant
1552 <!-- <em>New Known Issues</em>
1559 <td width="60" nowrap>
1560 <div align="center">
1561 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1562 <em>25/10/2016</em></strong>
1565 <td><em>Application</em>
1567 <li>3D Structure chooser opens with 'Cached structures'
1568 view if structures already loaded</li>
1569 <li>Progress bar reports models as they are loaded to
1570 structure views</li>
1576 <li>Colour by conservation always enabled and no tick
1577 shown in menu when BLOSUM or PID shading applied</li>
1578 <li>FER1_ARATH and FER2_ARATH labels were switched in
1579 example sequences/projects/trees</li>
1581 <em>Application</em>
1583 <li>Jalview projects with views of local PDB structure
1584 files saved on Windows cannot be opened on OSX</li>
1585 <li>Multiple structure views can be opened and superposed
1586 without timeout for structures with multiple models or
1587 multiple sequences in alignment</li>
1588 <li>Cannot import or associated local PDB files without a
1589 PDB ID HEADER line</li>
1590 <li>RMSD is not output in Jmol console when superposition
1592 <li>Drag and drop of URL from Browser fails for Linux and
1593 OSX versions earlier than El Capitan</li>
1594 <li>ENA client ignores invalid content from ENA server</li>
1595 <li>Exceptions are not raised in console when ENA client
1596 attempts to fetch non-existent IDs via Fetch DB Refs UI
1598 <li>Exceptions are not raised in console when a new view
1599 is created on the alignment</li>
1600 <li>OSX right-click fixed for group selections: CMD-click
1601 to insert/remove gaps in groups and CTRL-click to open group
1604 <em>Build and deployment</em>
1606 <li>URL link checker now copes with multi-line anchor
1609 <em>New Known Issues</em>
1611 <li>Drag and drop from URL links in browsers do not work
1618 <td width="60" nowrap>
1619 <div align="center">
1620 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1623 <td><em>General</em>
1626 <!-- JAL-2124 -->Updated Spanish translations.
1629 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1630 for importing structure data to Jalview. Enables mmCIF and
1634 <!-- JAL-192 --->Alignment ruler shows positions relative to
1638 <!-- JAL-2202 -->Position/residue shown in status bar when
1639 mousing over sequence associated annotation
1642 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1646 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1647 '()', canonical '[]' and invalid '{}' base pair populations
1651 <!-- JAL-2092 -->Feature settings popup menu options for
1652 showing or hiding columns containing a feature
1655 <!-- JAL-1557 -->Edit selected group by double clicking on
1656 group and sequence associated annotation labels
1659 <!-- JAL-2236 -->Sequence name added to annotation label in
1660 select/hide columns by annotation and colour by annotation
1664 </ul> <em>Application</em>
1667 <!-- JAL-2050-->Automatically hide introns when opening a
1668 gene/transcript view
1671 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1675 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1676 structure mappings with the EMBL-EBI PDBe SIFTS database
1679 <!-- JAL-2079 -->Updated download sites used for Rfam and
1680 Pfam sources to xfam.org
1683 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1686 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1687 over sequences in Jalview
1690 <!-- JAL-2027-->Support for reverse-complement coding
1691 regions in ENA and EMBL
1694 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1695 for record retrieval via ENA rest API
1698 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1702 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1703 groovy script execution
1706 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1707 alignment window's Calculate menu
1710 <!-- JAL-1812 -->Allow groovy scripts that call
1711 Jalview.getAlignFrames() to run in headless mode
1714 <!-- JAL-2068 -->Support for creating new alignment
1715 calculation workers from groovy scripts
1718 <!-- JAL-1369 --->Store/restore reference sequence in
1722 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1723 associations are now saved/restored from project
1726 <!-- JAL-1993 -->Database selection dialog always shown
1727 before sequence fetcher is opened
1730 <!-- JAL-2183 -->Double click on an entry in Jalview's
1731 database chooser opens a sequence fetcher
1734 <!-- JAL-1563 -->Free-text search client for UniProt using
1735 the UniProt REST API
1738 <!-- JAL-2168 -->-nonews command line parameter to prevent
1739 the news reader opening
1742 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1743 querying stored in preferences
1746 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1750 <!-- JAL-1977-->Tooltips shown on database chooser
1753 <!-- JAL-391 -->Reverse complement function in calculate
1754 menu for nucleotide sequences
1757 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1758 and feature counts preserves alignment ordering (and
1759 debugged for complex feature sets).
1762 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1763 viewing structures with Jalview 2.10
1766 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1767 genome, transcript CCDS and gene ids via the Ensembl and
1768 Ensembl Genomes REST API
1771 <!-- JAL-2049 -->Protein sequence variant annotation
1772 computed for 'sequence_variant' annotation on CDS regions
1776 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1780 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1781 Ref Fetcher fails to match, or otherwise updates sequence
1782 data from external database records.
1785 <!-- JAL-2154 -->Revised Jalview Project format for
1786 efficient recovery of sequence coding and alignment
1787 annotation relationships.
1789 </ul> <!-- <em>Applet</em>
1800 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1804 <!-- JAL-2018-->Export features in Jalview format (again)
1805 includes graduated colourschemes
1808 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1809 working with big alignments and lots of hidden columns
1812 <!-- JAL-2053-->Hidden column markers not always rendered
1813 at right of alignment window
1816 <!-- JAL-2067 -->Tidied up links in help file table of
1820 <!-- JAL-2072 -->Feature based tree calculation not shown
1824 <!-- JAL-2075 -->Hidden columns ignored during feature
1825 based tree calculation
1828 <!-- JAL-2065 -->Alignment view stops updating when show
1829 unconserved enabled for group on alignment
1832 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1836 <!-- JAL-2146 -->Alignment column in status incorrectly
1837 shown as "Sequence position" when mousing over
1841 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1842 hidden columns present
1845 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1846 user created annotation added to alignment
1849 <!-- JAL-1841 -->RNA Structure consensus only computed for
1850 '()' base pair annotation
1853 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1854 in zero scores for all base pairs in RNA Structure
1858 <!-- JAL-2174-->Extend selection with columns containing
1862 <!-- JAL-2275 -->Pfam format writer puts extra space at
1863 beginning of sequence
1866 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1870 <!-- JAL-2238 -->Cannot create groups on an alignment from
1871 from a tree when t-coffee scores are shown
1874 <!-- JAL-1836,1967 -->Cannot import and view PDB
1875 structures with chains containing negative resnums (4q4h)
1878 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1882 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1883 to Clustal, PIR and PileUp output
1886 <!-- JAL-2008 -->Reordering sequence features that are
1887 not visible causes alignment window to repaint
1890 <!-- JAL-2006 -->Threshold sliders don't work in
1891 graduated colour and colour by annotation row for e-value
1892 scores associated with features and annotation rows
1895 <!-- JAL-1797 -->amino acid physicochemical conservation
1896 calculation should be case independent
1899 <!-- JAL-2173 -->Remove annotation also updates hidden
1903 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1904 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1905 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1908 <!-- JAL-2065 -->Null pointer exceptions and redraw
1909 problems when reference sequence defined and 'show
1910 non-conserved' enabled
1913 <!-- JAL-1306 -->Quality and Conservation are now shown on
1914 load even when Consensus calculation is disabled
1917 <!-- JAL-1932 -->Remove right on penultimate column of
1918 alignment does nothing
1921 <em>Application</em>
1924 <!-- JAL-1552-->URLs and links can't be imported by
1925 drag'n'drop on OSX when launched via webstart (note - not
1926 yet fixed for El Capitan)
1929 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1930 output when running on non-gb/us i18n platforms
1933 <!-- JAL-1944 -->Error thrown when exporting a view with
1934 hidden sequences as flat-file alignment
1937 <!-- JAL-2030-->InstallAnywhere distribution fails when
1941 <!-- JAL-2080-->Jalview very slow to launch via webstart
1942 (also hotfix for 2.9.0b2)
1945 <!-- JAL-2085 -->Cannot save project when view has a
1946 reference sequence defined
1949 <!-- JAL-1011 -->Columns are suddenly selected in other
1950 alignments and views when revealing hidden columns
1953 <!-- JAL-1989 -->Hide columns not mirrored in complement
1954 view in a cDNA/Protein splitframe
1957 <!-- JAL-1369 -->Cannot save/restore representative
1958 sequence from project when only one sequence is
1962 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1963 in Structure Chooser
1966 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1967 structure consensus didn't refresh annotation panel
1970 <!-- JAL-1962 -->View mapping in structure view shows
1971 mappings between sequence and all chains in a PDB file
1974 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1975 dialogs format columns correctly, don't display array
1976 data, sort columns according to type
1979 <!-- JAL-1975 -->Export complete shown after destination
1980 file chooser is cancelled during an image export
1983 <!-- JAL-2025 -->Error when querying PDB Service with
1984 sequence name containing special characters
1987 <!-- JAL-2024 -->Manual PDB structure querying should be
1991 <!-- JAL-2104 -->Large tooltips with broken HTML
1992 formatting don't wrap
1995 <!-- JAL-1128 -->Figures exported from wrapped view are
1996 truncated so L looks like I in consensus annotation
1999 <!-- JAL-2003 -->Export features should only export the
2000 currently displayed features for the current selection or
2004 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
2005 after fetching cross-references, and restoring from
2009 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2010 followed in the structure viewer
2013 <!-- JAL-2163 -->Titles for individual alignments in
2014 splitframe not restored from project
2017 <!-- JAL-2145 -->missing autocalculated annotation at
2018 trailing end of protein alignment in transcript/product
2019 splitview when pad-gaps not enabled by default
2022 <!-- JAL-1797 -->amino acid physicochemical conservation
2026 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2027 article has been read (reopened issue due to
2028 internationalisation problems)
2031 <!-- JAL-1960 -->Only offer PDB structures in structure
2032 viewer based on sequence name, PDB and UniProt
2037 <!-- JAL-1976 -->No progress bar shown during export of
2041 <!-- JAL-2213 -->Structures not always superimposed after
2042 multiple structures are shown for one or more sequences.
2045 <!-- JAL-1370 -->Reference sequence characters should not
2046 be replaced with '.' when 'Show unconserved' format option
2050 <!-- JAL-1823 -->Cannot specify chain code when entering
2051 specific PDB id for sequence
2054 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2055 'Export hidden sequences' is enabled, but 'export hidden
2056 columns' is disabled.
2059 <!--JAL-2026-->Best Quality option in structure chooser
2060 selects lowest rather than highest resolution structures
2064 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2065 to sequence mapping in 'View Mappings' report
2068 <!-- JAL-2284 -->Unable to read old Jalview projects that
2069 contain non-XML data added after Jalvew wrote project.
2072 <!-- JAL-2118 -->Newly created annotation row reorders
2073 after clicking on it to create new annotation for a
2077 <!-- JAL-1980 -->Null Pointer Exception raised when
2078 pressing Add on an orphaned cut'n'paste window.
2080 <!-- may exclude, this is an external service stability issue JAL-1941
2081 -- > RNA 3D structure not added via DSSR service</li> -->
2086 <!-- JAL-2151 -->Incorrect columns are selected when
2087 hidden columns present before start of sequence
2090 <!-- JAL-1986 -->Missing dependencies on applet pages
2094 <!-- JAL-1947 -->Overview pixel size changes when
2095 sequences are hidden in applet
2098 <!-- JAL-1996 -->Updated instructions for applet
2099 deployment on examples pages.
2106 <td width="60" nowrap>
2107 <div align="center">
2108 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2109 <em>16/10/2015</em></strong>
2112 <td><em>General</em>
2114 <li>Time stamps for signed Jalview application and applet
2119 <em>Application</em>
2121 <li>Duplicate group consensus and conservation rows
2122 shown when tree is partitioned</li>
2123 <li>Erratic behaviour when tree partitions made with
2124 multiple cDNA/Protein split views</li>
2130 <td width="60" nowrap>
2131 <div align="center">
2132 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2133 <em>8/10/2015</em></strong>
2136 <td><em>General</em>
2138 <li>Updated Spanish translations of localized text for
2140 </ul> <em>Application</em>
2142 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2143 <li>Signed OSX InstallAnywhere installer<br></li>
2144 <li>Support for per-sequence based annotations in BioJSON</li>
2145 </ul> <em>Applet</em>
2147 <li>Split frame example added to applet examples page</li>
2148 </ul> <em>Build and Deployment</em>
2151 <!-- JAL-1888 -->New ant target for running Jalview's test
2159 <li>Mapping of cDNA to protein in split frames
2160 incorrect when sequence start > 1</li>
2161 <li>Broken images in filter column by annotation dialog
2163 <li>Feature colours not parsed from features file</li>
2164 <li>Exceptions and incomplete link URLs recovered when
2165 loading a features file containing HTML tags in feature
2169 <em>Application</em>
2171 <li>Annotations corrupted after BioJS export and
2173 <li>Incorrect sequence limits after Fetch DB References
2174 with 'trim retrieved sequences'</li>
2175 <li>Incorrect warning about deleting all data when
2176 deleting selected columns</li>
2177 <li>Patch to build system for shipping properly signed
2178 JNLP templates for webstart launch</li>
2179 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2180 unreleased structures for download or viewing</li>
2181 <li>Tab/space/return keystroke operation of EMBL-PDBe
2182 fetcher/viewer dialogs works correctly</li>
2183 <li>Disabled 'minimise' button on Jalview windows
2184 running on OSX to workaround redraw hang bug</li>
2185 <li>Split cDNA/Protein view position and geometry not
2186 recovered from jalview project</li>
2187 <li>Initial enabled/disabled state of annotation menu
2188 sorter 'show autocalculated first/last' corresponds to
2190 <li>Restoring of Clustal, RNA Helices and T-Coffee
2191 color schemes from BioJSON</li>
2195 <li>Reorder sequences mirrored in cDNA/Protein split
2197 <li>Applet with Jmol examples not loading correctly</li>
2203 <td><div align="center">
2204 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2206 <td><em>General</em>
2208 <li>Linked visualisation and analysis of DNA and Protein
2211 <li>Translated cDNA alignments shown as split protein
2212 and DNA alignment views</li>
2213 <li>Codon consensus annotation for linked protein and
2214 cDNA alignment views</li>
2215 <li>Link cDNA or Protein product sequences by loading
2216 them onto Protein or cDNA alignments</li>
2217 <li>Reconstruct linked cDNA alignment from aligned
2218 protein sequences</li>
2221 <li>Jmol integration updated to Jmol v14.2.14</li>
2222 <li>Import and export of Jalview alignment views as <a
2223 href="features/bioJsonFormat.html">BioJSON</a></li>
2224 <li>New alignment annotation file statements for
2225 reference sequences and marking hidden columns</li>
2226 <li>Reference sequence based alignment shading to
2227 highlight variation</li>
2228 <li>Select or hide columns according to alignment
2230 <li>Find option for locating sequences by description</li>
2231 <li>Conserved physicochemical properties shown in amino
2232 acid conservation row</li>
2233 <li>Alignments can be sorted by number of RNA helices</li>
2234 </ul> <em>Application</em>
2236 <li>New cDNA/Protein analysis capabilities
2238 <li>Get Cross-References should open a Split Frame
2239 view with cDNA/Protein</li>
2240 <li>Detect when nucleotide sequences and protein
2241 sequences are placed in the same alignment</li>
2242 <li>Split cDNA/Protein views are saved in Jalview
2247 <li>Use REST API to talk to Chimera</li>
2248 <li>Selected regions in Chimera are highlighted in linked
2249 Jalview windows</li>
2251 <li>VARNA RNA viewer updated to v3.93</li>
2252 <li>VARNA views are saved in Jalview Projects</li>
2253 <li>Pseudoknots displayed as Jalview RNA annotation can
2254 be shown in VARNA</li>
2256 <li>Make groups for selection uses marked columns as well
2257 as the active selected region</li>
2259 <li>Calculate UPGMA and NJ trees using sequence feature
2261 <li>New Export options
2263 <li>New Export Settings dialog to control hidden
2264 region export in flat file generation</li>
2266 <li>Export alignment views for display with the <a
2267 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2269 <li>Export scrollable SVG in HTML page</li>
2270 <li>Optional embedding of BioJSON data when exporting
2271 alignment figures to HTML</li>
2273 <li>3D structure retrieval and display
2275 <li>Free text and structured queries with the PDBe
2277 <li>PDBe Search API based discovery and selection of
2278 PDB structures for a sequence set</li>
2282 <li>JPred4 employed for protein secondary structure
2284 <li>Hide Insertions menu option to hide unaligned columns
2285 for one or a group of sequences</li>
2286 <li>Automatically hide insertions in alignments imported
2287 from the JPred4 web server</li>
2288 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2289 system on OSX<br />LGPL libraries courtesy of <a
2290 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2292 <li>changed 'View nucleotide structure' submenu to 'View
2293 VARNA 2D Structure'</li>
2294 <li>change "View protein structure" menu option to "3D
2297 </ul> <em>Applet</em>
2299 <li>New layout for applet example pages</li>
2300 <li>New parameters to enable SplitFrame view
2301 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2302 <li>New example demonstrating linked viewing of cDNA and
2303 Protein alignments</li>
2304 </ul> <em>Development and deployment</em>
2306 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2307 <li>Include installation type and git revision in build
2308 properties and console log output</li>
2309 <li>Jalview Github organisation, and new github site for
2310 storing BioJsMSA Templates</li>
2311 <li>Jalview's unit tests now managed with TestNG</li>
2314 <!-- <em>General</em>
2316 </ul> --> <!-- issues resolved --> <em>Application</em>
2318 <li>Escape should close any open find dialogs</li>
2319 <li>Typo in select-by-features status report</li>
2320 <li>Consensus RNA secondary secondary structure
2321 predictions are not highlighted in amber</li>
2322 <li>Missing gap character in v2.7 example file means
2323 alignment appears unaligned when pad-gaps is not enabled</li>
2324 <li>First switch to RNA Helices colouring doesn't colour
2325 associated structure views</li>
2326 <li>ID width preference option is greyed out when auto
2327 width checkbox not enabled</li>
2328 <li>Stopped a warning dialog from being shown when
2329 creating user defined colours</li>
2330 <li>'View Mapping' in structure viewer shows sequence
2331 mappings for just that viewer's sequences</li>
2332 <li>Workaround for superposing PDB files containing
2333 multiple models in Chimera</li>
2334 <li>Report sequence position in status bar when hovering
2335 over Jmol structure</li>
2336 <li>Cannot output gaps as '.' symbols with Selection ->
2337 output to text box</li>
2338 <li>Flat file exports of alignments with hidden columns
2339 have incorrect sequence start/end</li>
2340 <li>'Aligning' a second chain to a Chimera structure from
2342 <li>Colour schemes applied to structure viewers don't
2343 work for nucleotide</li>
2344 <li>Loading/cut'n'pasting an empty or invalid file leads
2345 to a grey/invisible alignment window</li>
2346 <li>Exported Jpred annotation from a sequence region
2347 imports to different position</li>
2348 <li>Space at beginning of sequence feature tooltips shown
2349 on some platforms</li>
2350 <li>Chimera viewer 'View | Show Chain' menu is not
2352 <li>'New View' fails with a Null Pointer Exception in
2353 console if Chimera has been opened</li>
2354 <li>Mouseover to Chimera not working</li>
2355 <li>Miscellaneous ENA XML feature qualifiers not
2357 <li>NPE in annotation renderer after 'Extract Scores'</li>
2358 <li>If two structures in one Chimera window, mouseover of
2359 either sequence shows on first structure</li>
2360 <li>'Show annotations' options should not make
2361 non-positional annotations visible</li>
2362 <li>Subsequence secondary structure annotation not shown
2363 in right place after 'view flanking regions'</li>
2364 <li>File Save As type unset when current file format is
2366 <li>Save as '.jar' option removed for saving Jalview
2368 <li>Colour by Sequence colouring in Chimera more
2370 <li>Cannot 'add reference annotation' for a sequence in
2371 several views on same alignment</li>
2372 <li>Cannot show linked products for EMBL / ENA records</li>
2373 <li>Jalview's tooltip wraps long texts containing no
2375 </ul> <em>Applet</em>
2377 <li>Jmol to JalviewLite mouseover/link not working</li>
2378 <li>JalviewLite can't import sequences with ID
2379 descriptions containing angle brackets</li>
2380 </ul> <em>General</em>
2382 <li>Cannot export and reimport RNA secondary structure
2383 via jalview annotation file</li>
2384 <li>Random helix colour palette for colour by annotation
2385 with RNA secondary structure</li>
2386 <li>Mouseover to cDNA from STOP residue in protein
2387 translation doesn't work.</li>
2388 <li>hints when using the select by annotation dialog box</li>
2389 <li>Jmol alignment incorrect if PDB file has alternate CA
2391 <li>FontChooser message dialog appears to hang after
2392 choosing 1pt font</li>
2393 <li>Peptide secondary structure incorrectly imported from
2394 annotation file when annotation display text includes 'e' or
2396 <li>Cannot set colour of new feature type whilst creating
2398 <li>cDNA translation alignment should not be sequence
2399 order dependent</li>
2400 <li>'Show unconserved' doesn't work for lower case
2402 <li>Nucleotide ambiguity codes involving R not recognised</li>
2403 </ul> <em>Deployment and Documentation</em>
2405 <li>Applet example pages appear different to the rest of
2406 www.jalview.org</li>
2407 </ul> <em>Application Known issues</em>
2409 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2410 <li>Misleading message appears after trying to delete
2412 <li>Jalview icon not shown in dock after InstallAnywhere
2413 version launches</li>
2414 <li>Fetching EMBL reference for an RNA sequence results
2415 fails with a sequence mismatch</li>
2416 <li>Corrupted or unreadable alignment display when
2417 scrolling alignment to right</li>
2418 <li>ArrayIndexOutOfBoundsException thrown when remove
2419 empty columns called on alignment with ragged gapped ends</li>
2420 <li>auto calculated alignment annotation rows do not get
2421 placed above or below non-autocalculated rows</li>
2422 <li>Jalview dekstop becomes sluggish at full screen in
2423 ultra-high resolution</li>
2424 <li>Cannot disable consensus calculation independently of
2425 quality and conservation</li>
2426 <li>Mouseover highlighting between cDNA and protein can
2427 become sluggish with more than one splitframe shown</li>
2428 </ul> <em>Applet Known Issues</em>
2430 <li>Core PDB parsing code requires Jmol</li>
2431 <li>Sequence canvas panel goes white when alignment
2432 window is being resized</li>
2438 <td><div align="center">
2439 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2441 <td><em>General</em>
2443 <li>Updated Java code signing certificate donated by
2445 <li>Features and annotation preserved when performing
2446 pairwise alignment</li>
2447 <li>RNA pseudoknot annotation can be
2448 imported/exported/displayed</li>
2449 <li>'colour by annotation' can colour by RNA and
2450 protein secondary structure</li>
2451 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2452 post-hoc with 2.9 release</em>)
2455 </ul> <em>Application</em>
2457 <li>Extract and display secondary structure for sequences
2458 with 3D structures</li>
2459 <li>Support for parsing RNAML</li>
2460 <li>Annotations menu for layout
2462 <li>sort sequence annotation rows by alignment</li>
2463 <li>place sequence annotation above/below alignment
2466 <li>Output in Stockholm format</li>
2467 <li>Internationalisation: improved Spanish (es)
2469 <li>Structure viewer preferences tab</li>
2470 <li>Disorder and Secondary Structure annotation tracks
2471 shared between alignments</li>
2472 <li>UCSF Chimera launch and linked highlighting from
2474 <li>Show/hide all sequence associated annotation rows for
2475 all or current selection</li>
2476 <li>disorder and secondary structure predictions
2477 available as dataset annotation</li>
2478 <li>Per-sequence rna helices colouring</li>
2481 <li>Sequence database accessions imported when fetching
2482 alignments from Rfam</li>
2483 <li>update VARNA version to 3.91</li>
2485 <li>New groovy scripts for exporting aligned positions,
2486 conservation values, and calculating sum of pairs scores.</li>
2487 <li>Command line argument to set default JABAWS server</li>
2488 <li>include installation type in build properties and
2489 console log output</li>
2490 <li>Updated Jalview project format to preserve dataset
2494 <!-- issues resolved --> <em>Application</em>
2496 <li>Distinguish alignment and sequence associated RNA
2497 structure in structure->view->VARNA</li>
2498 <li>Raise dialog box if user deletes all sequences in an
2500 <li>Pressing F1 results in documentation opening twice</li>
2501 <li>Sequence feature tooltip is wrapped</li>
2502 <li>Double click on sequence associated annotation
2503 selects only first column</li>
2504 <li>Redundancy removal doesn't result in unlinked
2505 leaves shown in tree</li>
2506 <li>Undos after several redundancy removals don't undo
2508 <li>Hide sequence doesn't hide associated annotation</li>
2509 <li>User defined colours dialog box too big to fit on
2510 screen and buttons not visible</li>
2511 <li>author list isn't updated if already written to
2512 Jalview properties</li>
2513 <li>Popup menu won't open after retrieving sequence
2515 <li>File open window for associate PDB doesn't open</li>
2516 <li>Left-then-right click on a sequence id opens a
2517 browser search window</li>
2518 <li>Cannot open sequence feature shading/sort popup menu
2519 in feature settings dialog</li>
2520 <li>better tooltip placement for some areas of Jalview
2522 <li>Allow addition of JABAWS Server which doesn't
2523 pass validation</li>
2524 <li>Web services parameters dialog box is too large to
2526 <li>Muscle nucleotide alignment preset obscured by
2528 <li>JABAWS preset submenus don't contain newly
2529 defined user preset</li>
2530 <li>MSA web services warns user if they were launched
2531 with invalid input</li>
2532 <li>Jalview cannot contact DAS Registy when running on
2535 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2536 'Superpose with' submenu not shown when new view
2540 </ul> <!-- <em>Applet</em>
2542 </ul> <em>General</em>
2544 </ul>--> <em>Deployment and Documentation</em>
2546 <li>2G and 1G options in launchApp have no effect on
2547 memory allocation</li>
2548 <li>launchApp service doesn't automatically open
2549 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2551 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2552 InstallAnywhere reports cannot find valid JVM when Java
2553 1.7_055 is available
2555 </ul> <em>Application Known issues</em>
2558 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2559 corrupted or unreadable alignment display when scrolling
2563 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2564 retrieval fails but progress bar continues for DAS retrieval
2565 with large number of ID
2568 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2569 flatfile output of visible region has incorrect sequence
2573 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2574 rna structure consensus doesn't update when secondary
2575 structure tracks are rearranged
2578 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2579 invalid rna structure positional highlighting does not
2580 highlight position of invalid base pairs
2583 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2584 out of memory errors are not raised when saving Jalview
2585 project from alignment window file menu
2588 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2589 Switching to RNA Helices colouring doesn't propagate to
2593 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2594 colour by RNA Helices not enabled when user created
2595 annotation added to alignment
2598 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2599 Jalview icon not shown on dock in Mountain Lion/Webstart
2601 </ul> <em>Applet Known Issues</em>
2604 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2605 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2608 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2609 Jalview and Jmol example not compatible with IE9
2612 <li>Sort by annotation score doesn't reverse order
2618 <td><div align="center">
2619 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2622 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2625 <li>Internationalisation of user interface (usually
2626 called i18n support) and translation for Spanish locale</li>
2627 <li>Define/Undefine group on current selection with
2628 Ctrl-G/Shift Ctrl-G</li>
2629 <li>Improved group creation/removal options in
2630 alignment/sequence Popup menu</li>
2631 <li>Sensible precision for symbol distribution
2632 percentages shown in logo tooltip.</li>
2633 <li>Annotation panel height set according to amount of
2634 annotation when alignment first opened</li>
2635 </ul> <em>Application</em>
2637 <li>Interactive consensus RNA secondary structure
2638 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2639 <li>Select columns containing particular features from
2640 Feature Settings dialog</li>
2641 <li>View all 'representative' PDB structures for selected
2643 <li>Update Jalview project format:
2645 <li>New file extension for Jalview projects '.jvp'</li>
2646 <li>Preserve sequence and annotation dataset (to
2647 store secondary structure annotation,etc)</li>
2648 <li>Per group and alignment annotation and RNA helix
2652 <li>New similarity measures for PCA and Tree calculation
2654 <li>Experimental support for retrieval and viewing of
2655 flanking regions for an alignment</li>
2659 <!-- issues resolved --> <em>Application</em>
2661 <li>logo keeps spinning and status remains at queued or
2662 running after job is cancelled</li>
2663 <li>cannot export features from alignments imported from
2664 Jalview/VAMSAS projects</li>
2665 <li>Buggy slider for web service parameters that take
2667 <li>Newly created RNA secondary structure line doesn't
2668 have 'display all symbols' flag set</li>
2669 <li>T-COFFEE alignment score shading scheme and other
2670 annotation shading not saved in Jalview project</li>
2671 <li>Local file cannot be loaded in freshly downloaded
2673 <li>Jalview icon not shown on dock in Mountain
2675 <li>Load file from desktop file browser fails</li>
2676 <li>Occasional NPE thrown when calculating large trees</li>
2677 <li>Cannot reorder or slide sequences after dragging an
2678 alignment onto desktop</li>
2679 <li>Colour by annotation dialog throws NPE after using
2680 'extract scores' function</li>
2681 <li>Loading/cut'n'pasting an empty file leads to a grey
2682 alignment window</li>
2683 <li>Disorder thresholds rendered incorrectly after
2684 performing IUPred disorder prediction</li>
2685 <li>Multiple group annotated consensus rows shown when
2686 changing 'normalise logo' display setting</li>
2687 <li>Find shows blank dialog after 'finished searching' if
2688 nothing matches query</li>
2689 <li>Null Pointer Exceptions raised when sorting by
2690 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2692 <li>Errors in Jmol console when structures in alignment
2693 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2695 <li>Not all working JABAWS services are shown in
2697 <li>JAVAWS version of Jalview fails to launch with
2698 'invalid literal/length code'</li>
2699 <li>Annotation/RNA Helix colourschemes cannot be applied
2700 to alignment with groups (actually fixed in 2.8.0b1)</li>
2701 <li>RNA Helices and T-Coffee Scores available as default
2704 </ul> <em>Applet</em>
2706 <li>Remove group option is shown even when selection is
2708 <li>Apply to all groups ticked but colourscheme changes
2709 don't affect groups</li>
2710 <li>Documented RNA Helices and T-Coffee Scores as valid
2711 colourscheme name</li>
2712 <li>Annotation labels drawn on sequence IDs when
2713 Annotation panel is not displayed</li>
2714 <li>Increased font size for dropdown menus on OSX and
2715 embedded windows</li>
2716 </ul> <em>Other</em>
2718 <li>Consensus sequence for alignments/groups with a
2719 single sequence were not calculated</li>
2720 <li>annotation files that contain only groups imported as
2721 annotation and junk sequences</li>
2722 <li>Fasta files with sequences containing '*' incorrectly
2723 recognised as PFAM or BLC</li>
2724 <li>conservation/PID slider apply all groups option
2725 doesn't affect background (2.8.0b1)
2727 <li>redundancy highlighting is erratic at 0% and 100%</li>
2728 <li>Remove gapped columns fails for sequences with ragged
2730 <li>AMSA annotation row with leading spaces is not
2731 registered correctly on import</li>
2732 <li>Jalview crashes when selecting PCA analysis for
2733 certain alignments</li>
2734 <li>Opening the colour by annotation dialog for an
2735 existing annotation based 'use original colours'
2736 colourscheme loses original colours setting</li>
2741 <td><div align="center">
2742 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2743 <em>30/1/2014</em></strong>
2747 <li>Trusted certificates for JalviewLite applet and
2748 Jalview Desktop application<br />Certificate was donated by
2749 <a href="https://www.certum.eu">Certum</a> to the Jalview
2750 open source project).
2752 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2753 <li>Output in Stockholm format</li>
2754 <li>Allow import of data from gzipped files</li>
2755 <li>Export/import group and sequence associated line
2756 graph thresholds</li>
2757 <li>Nucleotide substitution matrix that supports RNA and
2758 ambiguity codes</li>
2759 <li>Allow disorder predictions to be made on the current
2760 selection (or visible selection) in the same way that JPred
2762 <li>Groovy scripting for headless Jalview operation</li>
2763 </ul> <em>Other improvements</em>
2765 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2766 <li>COMBINE statement uses current SEQUENCE_REF and
2767 GROUP_REF scope to group annotation rows</li>
2768 <li>Support '' style escaping of quotes in Newick
2770 <li>Group options for JABAWS service by command line name</li>
2771 <li>Empty tooltip shown for JABA service options with a
2772 link but no description</li>
2773 <li>Select primary source when selecting authority in
2774 database fetcher GUI</li>
2775 <li>Add .mfa to FASTA file extensions recognised by
2777 <li>Annotation label tooltip text wrap</li>
2782 <li>Slow scrolling when lots of annotation rows are
2784 <li>Lots of NPE (and slowness) after creating RNA
2785 secondary structure annotation line</li>
2786 <li>Sequence database accessions not imported when
2787 fetching alignments from Rfam</li>
2788 <li>Incorrect SHMR submission for sequences with
2790 <li>View all structures does not always superpose
2792 <li>Option widgets in service parameters not updated to
2793 reflect user or preset settings</li>
2794 <li>Null pointer exceptions for some services without
2795 presets or adjustable parameters</li>
2796 <li>Discover PDB IDs entry in structure menu doesn't
2797 discover PDB xRefs</li>
2798 <li>Exception encountered while trying to retrieve
2799 features with DAS</li>
2800 <li>Lowest value in annotation row isn't coloured
2801 when colour by annotation (per sequence) is coloured</li>
2802 <li>Keyboard mode P jumps to start of gapped region when
2803 residue follows a gap</li>
2804 <li>Jalview appears to hang importing an alignment with
2805 Wrap as default or after enabling Wrap</li>
2806 <li>'Right click to add annotations' message
2807 shown in wrap mode when no annotations present</li>
2808 <li>Disorder predictions fail with NPE if no automatic
2809 annotation already exists on alignment</li>
2810 <li>oninit javascript function should be called after
2811 initialisation completes</li>
2812 <li>Remove redundancy after disorder prediction corrupts
2813 alignment window display</li>
2814 <li>Example annotation file in documentation is invalid</li>
2815 <li>Grouped line graph annotation rows are not exported
2816 to annotation file</li>
2817 <li>Multi-harmony analysis cannot be run when only two
2819 <li>Cannot create multiple groups of line graphs with
2820 several 'combine' statements in annotation file</li>
2821 <li>Pressing return several times causes Number Format
2822 exceptions in keyboard mode</li>
2823 <li>Multi-harmony (SHMMR) method doesn't submit
2824 correct partitions for input data</li>
2825 <li>Translation from DNA to Amino Acids fails</li>
2826 <li>Jalview fail to load newick tree with quoted label</li>
2827 <li>--headless flag isn't understood</li>
2828 <li>ClassCastException when generating EPS in headless
2830 <li>Adjusting sequence-associated shading threshold only
2831 changes one row's threshold</li>
2832 <li>Preferences and Feature settings panel panel
2833 doesn't open</li>
2834 <li>hide consensus histogram also hides conservation and
2835 quality histograms</li>
2840 <td><div align="center">
2841 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2843 <td><em>Application</em>
2845 <li>Support for JABAWS 2.0 Services (AACon alignment
2846 conservation, protein disorder and Clustal Omega)</li>
2847 <li>JABAWS server status indicator in Web Services
2849 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2850 in Jalview alignment window</li>
2851 <li>Updated Jalview build and deploy framework for OSX
2852 mountain lion, windows 7, and 8</li>
2853 <li>Nucleotide substitution matrix for PCA that supports
2854 RNA and ambiguity codes</li>
2856 <li>Improved sequence database retrieval GUI</li>
2857 <li>Support fetching and database reference look up
2858 against multiple DAS sources (Fetch all from in 'fetch db
2860 <li>Jalview project improvements
2862 <li>Store and retrieve the 'belowAlignment'
2863 flag for annotation</li>
2864 <li>calcId attribute to group annotation rows on the
2866 <li>Store AACon calculation settings for a view in
2867 Jalview project</li>
2871 <li>horizontal scrolling gesture support</li>
2872 <li>Visual progress indicator when PCA calculation is
2874 <li>Simpler JABA web services menus</li>
2875 <li>visual indication that web service results are still
2876 being retrieved from server</li>
2877 <li>Serialise the dialogs that are shown when Jalview
2878 starts up for first time</li>
2879 <li>Jalview user agent string for interacting with HTTP
2881 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2883 <li>Examples directory and Groovy library included in
2884 InstallAnywhere distribution</li>
2885 </ul> <em>Applet</em>
2887 <li>RNA alignment and secondary structure annotation
2888 visualization applet example</li>
2889 </ul> <em>General</em>
2891 <li>Normalise option for consensus sequence logo</li>
2892 <li>Reset button in PCA window to return dimensions to
2894 <li>Allow seqspace or Jalview variant of alignment PCA
2896 <li>PCA with either nucleic acid and protein substitution
2898 <li>Allow windows containing HTML reports to be exported
2900 <li>Interactive display and editing of RNA secondary
2901 structure contacts</li>
2902 <li>RNA Helix Alignment Colouring</li>
2903 <li>RNA base pair logo consensus</li>
2904 <li>Parse sequence associated secondary structure
2905 information in Stockholm files</li>
2906 <li>HTML Export database accessions and annotation
2907 information presented in tooltip for sequences</li>
2908 <li>Import secondary structure from LOCARNA clustalw
2909 style RNA alignment files</li>
2910 <li>import and visualise T-COFFEE quality scores for an
2912 <li>'colour by annotation' per sequence option to
2913 shade each sequence according to its associated alignment
2915 <li>New Jalview Logo</li>
2916 </ul> <em>Documentation and Development</em>
2918 <li>documentation for score matrices used in Jalview</li>
2919 <li>New Website!</li>
2921 <td><em>Application</em>
2923 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2924 wsdbfetch REST service</li>
2925 <li>Stop windows being moved outside desktop on OSX</li>
2926 <li>Filetype associations not installed for webstart
2928 <li>Jalview does not always retrieve progress of a JABAWS
2929 job execution in full once it is complete</li>
2930 <li>revise SHMR RSBS definition to ensure alignment is
2931 uploaded via ali_file parameter</li>
2932 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2933 <li>View all structures superposed fails with exception</li>
2934 <li>Jnet job queues forever if a very short sequence is
2935 submitted for prediction</li>
2936 <li>Cut and paste menu not opened when mouse clicked on
2938 <li>Putting fractional value into integer text box in
2939 alignment parameter dialog causes Jalview to hang</li>
2940 <li>Structure view highlighting doesn't work on
2942 <li>View all structures fails with exception shown in
2944 <li>Characters in filename associated with PDBEntry not
2945 escaped in a platform independent way</li>
2946 <li>Jalview desktop fails to launch with exception when
2948 <li>Tree calculation reports 'you must have 2 or more
2949 sequences selected' when selection is empty</li>
2950 <li>Jalview desktop fails to launch with jar signature
2951 failure when java web start temporary file caching is
2953 <li>DAS Sequence retrieval with range qualification
2954 results in sequence xref which includes range qualification</li>
2955 <li>Errors during processing of command line arguments
2956 cause progress bar (JAL-898) to be removed</li>
2957 <li>Replace comma for semi-colon option not disabled for
2958 DAS sources in sequence fetcher</li>
2959 <li>Cannot close news reader when JABAWS server warning
2960 dialog is shown</li>
2961 <li>Option widgets not updated to reflect user settings</li>
2962 <li>Edited sequence not submitted to web service</li>
2963 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2964 <li>InstallAnywhere installer doesn't unpack and run
2965 on OSX Mountain Lion</li>
2966 <li>Annotation panel not given a scroll bar when
2967 sequences with alignment annotation are pasted into the
2969 <li>Sequence associated annotation rows not associated
2970 when loaded from Jalview project</li>
2971 <li>Browser launch fails with NPE on java 1.7</li>
2972 <li>JABAWS alignment marked as finished when job was
2973 cancelled or job failed due to invalid input</li>
2974 <li>NPE with v2.7 example when clicking on Tree
2975 associated with all views</li>
2976 <li>Exceptions when copy/paste sequences with grouped
2977 annotation rows to new window</li>
2978 </ul> <em>Applet</em>
2980 <li>Sequence features are momentarily displayed before
2981 they are hidden using hidefeaturegroups applet parameter</li>
2982 <li>loading features via javascript API automatically
2983 enables feature display</li>
2984 <li>scrollToColumnIn javascript API method doesn't
2986 </ul> <em>General</em>
2988 <li>Redundancy removal fails for rna alignment</li>
2989 <li>PCA calculation fails when sequence has been selected
2990 and then deselected</li>
2991 <li>PCA window shows grey box when first opened on OSX</li>
2992 <li>Letters coloured pink in sequence logo when alignment
2993 coloured with clustalx</li>
2994 <li>Choosing fonts without letter symbols defined causes
2995 exceptions and redraw errors</li>
2996 <li>Initial PCA plot view is not same as manually
2997 reconfigured view</li>
2998 <li>Grouped annotation graph label has incorrect line
3000 <li>Grouped annotation graph label display is corrupted
3001 for lots of labels</li>
3006 <div align="center">
3007 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3010 <td><em>Application</em>
3012 <li>Jalview Desktop News Reader</li>
3013 <li>Tweaked default layout of web services menu</li>
3014 <li>View/alignment association menu to enable user to
3015 easily specify which alignment a multi-structure view takes
3016 its colours/correspondences from</li>
3017 <li>Allow properties file location to be specified as URL</li>
3018 <li>Extend Jalview project to preserve associations
3019 between many alignment views and a single Jmol display</li>
3020 <li>Store annotation row height in Jalview project file</li>
3021 <li>Annotation row column label formatting attributes
3022 stored in project file</li>
3023 <li>Annotation row order for auto-calculated annotation
3024 rows preserved in Jalview project file</li>
3025 <li>Visual progress indication when Jalview state is
3026 saved using Desktop window menu</li>
3027 <li>Visual indication that command line arguments are
3028 still being processed</li>
3029 <li>Groovy script execution from URL</li>
3030 <li>Colour by annotation default min and max colours in
3032 <li>Automatically associate PDB files dragged onto an
3033 alignment with sequences that have high similarity and
3035 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3036 <li>'view structures' option to open many
3037 structures in same window</li>
3038 <li>Sort associated views menu option for tree panel</li>
3039 <li>Group all JABA and non-JABA services for a particular
3040 analysis function in its own submenu</li>
3041 </ul> <em>Applet</em>
3043 <li>Userdefined and autogenerated annotation rows for
3045 <li>Adjustment of alignment annotation pane height</li>
3046 <li>Annotation scrollbar for annotation panel</li>
3047 <li>Drag to reorder annotation rows in annotation panel</li>
3048 <li>'automaticScrolling' parameter</li>
3049 <li>Allow sequences with partial ID string matches to be
3050 annotated from GFF/Jalview features files</li>
3051 <li>Sequence logo annotation row in applet</li>
3052 <li>Absolute paths relative to host server in applet
3053 parameters are treated as such</li>
3054 <li>New in the JalviewLite javascript API:
3056 <li>JalviewLite.js javascript library</li>
3057 <li>Javascript callbacks for
3059 <li>Applet initialisation</li>
3060 <li>Sequence/alignment mouse-overs and selections</li>
3063 <li>scrollTo row and column alignment scrolling
3065 <li>Select sequence/alignment regions from javascript</li>
3066 <li>javascript structure viewer harness to pass
3067 messages between Jmol and Jalview when running as
3068 distinct applets</li>
3069 <li>sortBy method</li>
3070 <li>Set of applet and application examples shipped
3071 with documentation</li>
3072 <li>New example to demonstrate JalviewLite and Jmol
3073 javascript message exchange</li>
3075 </ul> <em>General</em>
3077 <li>Enable Jmol displays to be associated with multiple
3078 multiple alignments</li>
3079 <li>Option to automatically sort alignment with new tree</li>
3080 <li>User configurable link to enable redirects to a
3081 www.Jalview.org mirror</li>
3082 <li>Jmol colours option for Jmol displays</li>
3083 <li>Configurable newline string when writing alignment
3084 and other flat files</li>
3085 <li>Allow alignment annotation description lines to
3086 contain html tags</li>
3087 </ul> <em>Documentation and Development</em>
3089 <li>Add groovy test harness for bulk load testing to
3091 <li>Groovy script to load and align a set of sequences
3092 using a web service before displaying the result in the
3093 Jalview desktop</li>
3094 <li>Restructured javascript and applet api documentation</li>
3095 <li>Ant target to publish example html files with applet
3097 <li>Netbeans project for building Jalview from source</li>
3098 <li>ant task to create online javadoc for Jalview source</li>
3100 <td><em>Application</em>
3102 <li>User defined colourscheme throws exception when
3103 current built in colourscheme is saved as new scheme</li>
3104 <li>AlignFrame->Save in application pops up save
3105 dialog for valid filename/format</li>
3106 <li>Cannot view associated structure for UniProt sequence</li>
3107 <li>PDB file association breaks for UniProt sequence
3109 <li>Associate PDB from file dialog does not tell you
3110 which sequence is to be associated with the file</li>
3111 <li>Find All raises null pointer exception when query
3112 only matches sequence IDs</li>
3113 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3114 <li>Jalview project with Jmol views created with Jalview
3115 2.4 cannot be loaded</li>
3116 <li>Filetype associations not installed for webstart
3118 <li>Two or more chains in a single PDB file associated
3119 with sequences in different alignments do not get coloured
3120 by their associated sequence</li>
3121 <li>Visibility status of autocalculated annotation row
3122 not preserved when project is loaded</li>
3123 <li>Annotation row height and visibility attributes not
3124 stored in Jalview project</li>
3125 <li>Tree bootstraps are not preserved when saved as a
3126 Jalview project</li>
3127 <li>Envision2 workflow tooltips are corrupted</li>
3128 <li>Enabling show group conservation also enables colour
3129 by conservation</li>
3130 <li>Duplicate group associated conservation or consensus
3131 created on new view</li>
3132 <li>Annotation scrollbar not displayed after 'show
3133 all hidden annotation rows' option selected</li>
3134 <li>Alignment quality not updated after alignment
3135 annotation row is hidden then shown</li>
3136 <li>Preserve colouring of structures coloured by
3137 sequences in pre Jalview 2.7 projects</li>
3138 <li>Web service job parameter dialog is not laid out
3140 <li>Web services menu not refreshed after 'reset
3141 services' button is pressed in preferences</li>
3142 <li>Annotation off by one in Jalview v2_3 example project</li>
3143 <li>Structures imported from file and saved in project
3144 get name like jalview_pdb1234.txt when reloaded</li>
3145 <li>Jalview does not always retrieve progress of a JABAWS
3146 job execution in full once it is complete</li>
3147 </ul> <em>Applet</em>
3149 <li>Alignment height set incorrectly when lots of
3150 annotation rows are displayed</li>
3151 <li>Relative URLs in feature HTML text not resolved to
3153 <li>View follows highlighting does not work for positions
3155 <li><= shown as = in tooltip</li>
3156 <li>Export features raises exception when no features
3158 <li>Separator string used for serialising lists of IDs
3159 for javascript api is modified when separator string
3160 provided as parameter</li>
3161 <li>Null pointer exception when selecting tree leaves for
3162 alignment with no existing selection</li>
3163 <li>Relative URLs for datasources assumed to be relative
3164 to applet's codebase</li>
3165 <li>Status bar not updated after finished searching and
3166 search wraps around to first result</li>
3167 <li>StructureSelectionManager instance shared between
3168 several Jalview applets causes race conditions and memory
3170 <li>Hover tooltip and mouseover of position on structure
3171 not sent from Jmol in applet</li>
3172 <li>Certain sequences of javascript method calls to
3173 applet API fatally hang browser</li>
3174 </ul> <em>General</em>
3176 <li>View follows structure mouseover scrolls beyond
3177 position with wrapped view and hidden regions</li>
3178 <li>Find sequence position moves to wrong residue
3179 with/without hidden columns</li>
3180 <li>Sequence length given in alignment properties window
3182 <li>InvalidNumberFormat exceptions thrown when trying to
3183 import PDB like structure files</li>
3184 <li>Positional search results are only highlighted
3185 between user-supplied sequence start/end bounds</li>
3186 <li>End attribute of sequence is not validated</li>
3187 <li>Find dialog only finds first sequence containing a
3188 given sequence position</li>
3189 <li>Sequence numbering not preserved in MSF alignment
3191 <li>Jalview PDB file reader does not extract sequence
3192 from nucleotide chains correctly</li>
3193 <li>Structure colours not updated when tree partition
3194 changed in alignment</li>
3195 <li>Sequence associated secondary structure not correctly
3196 parsed in interleaved stockholm</li>
3197 <li>Colour by annotation dialog does not restore current
3199 <li>Hiding (nearly) all sequences doesn't work
3201 <li>Sequences containing lowercase letters are not
3202 properly associated with their pdb files</li>
3203 </ul> <em>Documentation and Development</em>
3205 <li>schemas/JalviewWsParamSet.xsd corrupted by
3206 ApplyCopyright tool</li>
3211 <div align="center">
3212 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3215 <td><em>Application</em>
3217 <li>New warning dialog when the Jalview Desktop cannot
3218 contact web services</li>
3219 <li>JABA service parameters for a preset are shown in
3220 service job window</li>
3221 <li>JABA Service menu entries reworded</li>
3225 <li>Modeller PIR IO broken - cannot correctly import a
3226 pir file emitted by Jalview</li>
3227 <li>Existing feature settings transferred to new
3228 alignment view created from cut'n'paste</li>
3229 <li>Improved test for mixed amino/nucleotide chains when
3230 parsing PDB files</li>
3231 <li>Consensus and conservation annotation rows
3232 occasionally become blank for all new windows</li>
3233 <li>Exception raised when right clicking above sequences
3234 in wrapped view mode</li>
3235 </ul> <em>Application</em>
3237 <li>multiple multiply aligned structure views cause cpu
3238 usage to hit 100% and computer to hang</li>
3239 <li>Web Service parameter layout breaks for long user
3240 parameter names</li>
3241 <li>Jaba service discovery hangs desktop if Jaba server
3248 <div align="center">
3249 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3252 <td><em>Application</em>
3254 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3255 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3258 <li>Web Services preference tab</li>
3259 <li>Analysis parameters dialog box and user defined
3261 <li>Improved speed and layout of Envision2 service menu</li>
3262 <li>Superpose structures using associated sequence
3264 <li>Export coordinates and projection as CSV from PCA
3266 </ul> <em>Applet</em>
3268 <li>enable javascript: execution by the applet via the
3269 link out mechanism</li>
3270 </ul> <em>Other</em>
3272 <li>Updated the Jmol Jalview interface to work with Jmol
3274 <li>The Jalview Desktop and JalviewLite applet now
3275 require Java 1.5</li>
3276 <li>Allow Jalview feature colour specification for GFF
3277 sequence annotation files</li>
3278 <li>New 'colour by label' keword in Jalview feature file
3279 type colour specification</li>
3280 <li>New Jalview Desktop Groovy API method that allows a
3281 script to check if it being run in an interactive session or
3282 in a batch operation from the Jalview command line</li>
3286 <li>clustalx colourscheme colours Ds preferentially when
3287 both D+E are present in over 50% of the column</li>
3288 </ul> <em>Application</em>
3290 <li>typo in AlignmentFrame->View->Hide->all but
3291 selected Regions menu item</li>
3292 <li>sequence fetcher replaces ',' for ';' when the ',' is
3293 part of a valid accession ID</li>
3294 <li>fatal OOM if object retrieved by sequence fetcher
3295 runs out of memory</li>
3296 <li>unhandled Out of Memory Error when viewing pca
3297 analysis results</li>
3298 <li>InstallAnywhere builds fail to launch on OS X java
3299 10.5 update 4 (due to apple Java 1.6 update)</li>
3300 <li>Installanywhere Jalview silently fails to launch</li>
3301 </ul> <em>Applet</em>
3303 <li>Jalview.getFeatureGroups() raises an
3304 ArrayIndexOutOfBoundsException if no feature groups are
3311 <div align="center">
3312 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3318 <li>Alignment prettyprinter doesn't cope with long
3320 <li>clustalx colourscheme colours Ds preferentially when
3321 both D+E are present in over 50% of the column</li>
3322 <li>nucleic acid structures retrieved from PDB do not
3323 import correctly</li>
3324 <li>More columns get selected than were clicked on when a
3325 number of columns are hidden</li>
3326 <li>annotation label popup menu not providing correct
3327 add/hide/show options when rows are hidden or none are
3329 <li>Stockholm format shown in list of readable formats,
3330 and parser copes better with alignments from RFAM.</li>
3331 <li>CSV output of consensus only includes the percentage
3332 of all symbols if sequence logo display is enabled</li>
3334 </ul> <em>Applet</em>
3336 <li>annotation panel disappears when annotation is
3338 </ul> <em>Application</em>
3340 <li>Alignment view not redrawn properly when new
3341 alignment opened where annotation panel is visible but no
3342 annotations are present on alignment</li>
3343 <li>pasted region containing hidden columns is
3344 incorrectly displayed in new alignment window</li>
3345 <li>Jalview slow to complete operations when stdout is
3346 flooded (fix is to close the Jalview console)</li>
3347 <li>typo in AlignmentFrame->View->Hide->all but
3348 selected Rregions menu item.</li>
3349 <li>inconsistent group submenu and Format submenu entry
3350 'Un' or 'Non'conserved</li>
3351 <li>Sequence feature settings are being shared by
3352 multiple distinct alignments</li>
3353 <li>group annotation not recreated when tree partition is
3355 <li>double click on group annotation to select sequences
3356 does not propagate to associated trees</li>
3357 <li>Mac OSX specific issues:
3359 <li>exception raised when mouse clicked on desktop
3360 window background</li>
3361 <li>Desktop menu placed on menu bar and application
3362 name set correctly</li>
3363 <li>sequence feature settings not wide enough for the
3364 save feature colourscheme button</li>
3373 <div align="center">
3374 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3377 <td><em>New Capabilities</em>
3379 <li>URL links generated from description line for
3380 regular-expression based URL links (applet and application)
3382 <li>Non-positional feature URL links are shown in link
3384 <li>Linked viewing of nucleic acid sequences and
3386 <li>Automatic Scrolling option in View menu to display
3387 the currently highlighted region of an alignment.</li>
3388 <li>Order an alignment by sequence length, or using the
3389 average score or total feature count for each sequence.</li>
3390 <li>Shading features by score or associated description</li>
3391 <li>Subdivide alignment and groups based on identity of
3392 selected subsequence (Make Groups from Selection).</li>
3393 <li>New hide/show options including Shift+Control+H to
3394 hide everything but the currently selected region.</li>
3395 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3396 </ul> <em>Application</em>
3398 <li>Fetch DB References capabilities and UI expanded to
3399 support retrieval from DAS sequence sources</li>
3400 <li>Local DAS Sequence sources can be added via the
3401 command line or via the Add local source dialog box.</li>
3402 <li>DAS Dbref and DbxRef feature types are parsed as
3403 database references and protein_name is parsed as
3404 description line (BioSapiens terms).</li>
3405 <li>Enable or disable non-positional feature and database
3406 references in sequence ID tooltip from View menu in
3408 <!-- <li>New hidden columns and rows and representatives capabilities
3409 in annotations file (in progress - not yet fully implemented)</li> -->
3410 <li>Group-associated consensus, sequence logos and
3411 conservation plots</li>
3412 <li>Symbol distributions for each column can be exported
3413 and visualized as sequence logos</li>
3414 <li>Optionally scale multi-character column labels to fit
3415 within each column of annotation row<!-- todo for applet -->
3417 <li>Optional automatic sort of associated alignment view
3418 when a new tree is opened.</li>
3419 <li>Jalview Java Console</li>
3420 <li>Better placement of desktop window when moving
3421 between different screens.</li>
3422 <li>New preference items for sequence ID tooltip and
3423 consensus annotation</li>
3424 <li>Client to submit sequences and IDs to Envision2
3426 <li><em>Vamsas Capabilities</em>
3428 <li>Improved VAMSAS synchronization (Jalview archive
3429 used to preserve views, structures, and tree display
3431 <li>Import of vamsas documents from disk or URL via
3433 <li>Sharing of selected regions between views and
3434 with other VAMSAS applications (Experimental feature!)</li>
3435 <li>Updated API to VAMSAS version 0.2</li>
3437 </ul> <em>Applet</em>
3439 <li>Middle button resizes annotation row height</li>
3442 <li>sortByTree (true/false) - automatically sort the
3443 associated alignment view by the tree when a new tree is
3445 <li>showTreeBootstraps (true/false) - show or hide
3446 branch bootstraps (default is to show them if available)</li>
3447 <li>showTreeDistances (true/false) - show or hide
3448 branch lengths (default is to show them if available)</li>
3449 <li>showUnlinkedTreeNodes (true/false) - indicate if
3450 unassociated nodes should be highlighted in the tree
3452 <li>heightScale and widthScale (1.0 or more) -
3453 increase the height or width of a cell in the alignment
3454 grid relative to the current font size.</li>
3457 <li>Non-positional features displayed in sequence ID
3459 </ul> <em>Other</em>
3461 <li>Features format: graduated colour definitions and
3462 specification of feature scores</li>
3463 <li>Alignment Annotations format: new keywords for group
3464 associated annotation (GROUP_REF) and annotation row display
3465 properties (ROW_PROPERTIES)</li>
3466 <li>XML formats extended to support graduated feature
3467 colourschemes, group associated annotation, and profile
3468 visualization settings.</li></td>
3471 <li>Source field in GFF files parsed as feature source
3472 rather than description</li>
3473 <li>Non-positional features are now included in sequence
3474 feature and gff files (controlled via non-positional feature
3475 visibility in tooltip).</li>
3476 <li>URL links generated for all feature links (bugfix)</li>
3477 <li>Added URL embedding instructions to features file
3479 <li>Codons containing ambiguous nucleotides translated as
3480 'X' in peptide product</li>
3481 <li>Match case switch in find dialog box works for both
3482 sequence ID and sequence string and query strings do not
3483 have to be in upper case to match case-insensitively.</li>
3484 <li>AMSA files only contain first column of
3485 multi-character column annotation labels</li>
3486 <li>Jalview Annotation File generation/parsing consistent
3487 with documentation (e.g. Stockholm annotation can be
3488 exported and re-imported)</li>
3489 <li>PDB files without embedded PDB IDs given a friendly
3491 <li>Find incrementally searches ID string matches as well
3492 as subsequence matches, and correctly reports total number
3496 <li>Better handling of exceptions during sequence
3498 <li>Dasobert generated non-positional feature URL
3499 link text excludes the start_end suffix</li>
3500 <li>DAS feature and source retrieval buttons disabled
3501 when fetch or registry operations in progress.</li>
3502 <li>PDB files retrieved from URLs are cached properly</li>
3503 <li>Sequence description lines properly shared via
3505 <li>Sequence fetcher fetches multiple records for all
3507 <li>Ensured that command line das feature retrieval
3508 completes before alignment figures are generated.</li>
3509 <li>Reduced time taken when opening file browser for
3511 <li>isAligned check prior to calculating tree, PCA or
3512 submitting an MSA to JNet now excludes hidden sequences.</li>
3513 <li>User defined group colours properly recovered
3514 from Jalview projects.</li>
3523 <div align="center">
3524 <strong>2.4.0.b2</strong><br> 28/10/2009
3529 <li>Experimental support for google analytics usage
3531 <li>Jalview privacy settings (user preferences and docs).</li>
3536 <li>Race condition in applet preventing startup in
3538 <li>Exception when feature created from selection beyond
3539 length of sequence.</li>
3540 <li>Allow synthetic PDB files to be imported gracefully</li>
3541 <li>Sequence associated annotation rows associate with
3542 all sequences with a given id</li>
3543 <li>Find function matches case-insensitively for sequence
3544 ID string searches</li>
3545 <li>Non-standard characters do not cause pairwise
3546 alignment to fail with exception</li>
3547 </ul> <em>Application Issues</em>
3549 <li>Sequences are now validated against EMBL database</li>
3550 <li>Sequence fetcher fetches multiple records for all
3552 </ul> <em>InstallAnywhere Issues</em>
3554 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3555 issue with installAnywhere mechanism)</li>
3556 <li>Command line launching of JARs from InstallAnywhere
3557 version (java class versioning error fixed)</li>
3564 <div align="center">
3565 <strong>2.4</strong><br> 27/8/2008
3568 <td><em>User Interface</em>
3570 <li>Linked highlighting of codon and amino acid from
3571 translation and protein products</li>
3572 <li>Linked highlighting of structure associated with
3573 residue mapping to codon position</li>
3574 <li>Sequence Fetcher provides example accession numbers
3575 and 'clear' button</li>
3576 <li>MemoryMonitor added as an option under Desktop's
3578 <li>Extract score function to parse whitespace separated
3579 numeric data in description line</li>
3580 <li>Column labels in alignment annotation can be centred.</li>
3581 <li>Tooltip for sequence associated annotation give name
3583 </ul> <em>Web Services and URL fetching</em>
3585 <li>JPred3 web service</li>
3586 <li>Prototype sequence search client (no public services
3588 <li>Fetch either seed alignment or full alignment from
3590 <li>URL Links created for matching database cross
3591 references as well as sequence ID</li>
3592 <li>URL Links can be created using regular-expressions</li>
3593 </ul> <em>Sequence Database Connectivity</em>
3595 <li>Retrieval of cross-referenced sequences from other
3597 <li>Generalised database reference retrieval and
3598 validation to all fetchable databases</li>
3599 <li>Fetch sequences from DAS sources supporting the
3600 sequence command</li>
3601 </ul> <em>Import and Export</em>
3602 <li>export annotation rows as CSV for spreadsheet import</li>
3603 <li>Jalview projects record alignment dataset associations,
3604 EMBL products, and cDNA sequence mappings</li>
3605 <li>Sequence Group colour can be specified in Annotation
3607 <li>Ad-hoc colouring of group in Annotation File using RGB
3608 triplet as name of colourscheme</li>
3609 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3611 <li>treenode binding for VAMSAS tree exchange</li>
3612 <li>local editing and update of sequences in VAMSAS
3613 alignments (experimental)</li>
3614 <li>Create new or select existing session to join</li>
3615 <li>load and save of vamsas documents</li>
3616 </ul> <em>Application command line</em>
3618 <li>-tree parameter to open trees (introduced for passing
3620 <li>-fetchfrom command line argument to specify nicknames
3621 of DAS servers to query for alignment features</li>
3622 <li>-dasserver command line argument to add new servers
3623 that are also automatically queried for features</li>
3624 <li>-groovy command line argument executes a given groovy
3625 script after all input data has been loaded and parsed</li>
3626 </ul> <em>Applet-Application data exchange</em>
3628 <li>Trees passed as applet parameters can be passed to
3629 application (when using "View in full
3630 application")</li>
3631 </ul> <em>Applet Parameters</em>
3633 <li>feature group display control parameter</li>
3634 <li>debug parameter</li>
3635 <li>showbutton parameter</li>
3636 </ul> <em>Applet API methods</em>
3638 <li>newView public method</li>
3639 <li>Window (current view) specific get/set public methods</li>
3640 <li>Feature display control methods</li>
3641 <li>get list of currently selected sequences</li>
3642 </ul> <em>New Jalview distribution features</em>
3644 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3645 <li>RELEASE file gives build properties for the latest
3646 Jalview release.</li>
3647 <li>Java 1.1 Applet build made easier and donotobfuscate
3648 property controls execution of obfuscator</li>
3649 <li>Build target for generating source distribution</li>
3650 <li>Debug flag for javacc</li>
3651 <li>.jalview_properties file is documented (slightly) in
3652 jalview.bin.Cache</li>
3653 <li>Continuous Build Integration for stable and
3654 development version of Application, Applet and source
3659 <li>selected region output includes visible annotations
3660 (for certain formats)</li>
3661 <li>edit label/displaychar contains existing label/char
3663 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3664 <li>shorter peptide product names from EMBL records</li>
3665 <li>Newick string generator makes compact representations</li>
3666 <li>bootstrap values parsed correctly for tree files with
3668 <li>pathological filechooser bug avoided by not allowing
3669 filenames containing a ':'</li>
3670 <li>Fixed exception when parsing GFF files containing
3671 global sequence features</li>
3672 <li>Alignment datasets are finalized only when number of
3673 references from alignment sequences goes to zero</li>
3674 <li>Close of tree branch colour box without colour
3675 selection causes cascading exceptions</li>
3676 <li>occasional negative imgwidth exceptions</li>
3677 <li>better reporting of non-fatal warnings to user when
3678 file parsing fails.</li>
3679 <li>Save works when Jalview project is default format</li>
3680 <li>Save as dialog opened if current alignment format is
3681 not a valid output format</li>
3682 <li>UniProt canonical names introduced for both das and
3684 <li>Histidine should be midblue (not pink!) in Zappo</li>
3685 <li>error messages passed up and output when data read
3687 <li>edit undo recovers previous dataset sequence when
3688 sequence is edited</li>
3689 <li>allow PDB files without pdb ID HEADER lines (like
3690 those generated by MODELLER) to be read in properly</li>
3691 <li>allow reading of JPred concise files as a normal
3693 <li>Stockholm annotation parsing and alignment properties
3694 import fixed for PFAM records</li>
3695 <li>Structure view windows have correct name in Desktop
3697 <li>annotation consisting of sequence associated scores
3698 can be read and written correctly to annotation file</li>
3699 <li>Aligned cDNA translation to aligned peptide works
3701 <li>Fixed display of hidden sequence markers and
3702 non-italic font for representatives in Applet</li>
3703 <li>Applet Menus are always embedded in applet window on
3705 <li>Newly shown features appear at top of stack (in
3707 <li>Annotations added via parameter not drawn properly
3708 due to null pointer exceptions</li>
3709 <li>Secondary structure lines are drawn starting from
3710 first column of alignment</li>
3711 <li>UniProt XML import updated for new schema release in
3713 <li>Sequence feature to sequence ID match for Features
3714 file is case-insensitive</li>
3715 <li>Sequence features read from Features file appended to
3716 all sequences with matching IDs</li>
3717 <li>PDB structure coloured correctly for associated views
3718 containing a sub-sequence</li>
3719 <li>PDB files can be retrieved by applet from Jar files</li>
3720 <li>feature and annotation file applet parameters
3721 referring to different directories are retrieved correctly</li>
3722 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3723 <li>Fixed application hang whilst waiting for
3724 splash-screen version check to complete</li>
3725 <li>Applet properly URLencodes input parameter values
3726 when passing them to the launchApp service</li>
3727 <li>display name and local features preserved in results
3728 retrieved from web service</li>
3729 <li>Visual delay indication for sequence retrieval and
3730 sequence fetcher initialisation</li>
3731 <li>updated Application to use DAS 1.53e version of
3732 dasobert DAS client</li>
3733 <li>Re-instated Full AMSA support and .amsa file
3735 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3743 <div align="center">
3744 <strong>2.3</strong><br> 9/5/07
3749 <li>Jmol 11.0.2 integration</li>
3750 <li>PDB views stored in Jalview XML files</li>
3751 <li>Slide sequences</li>
3752 <li>Edit sequence in place</li>
3753 <li>EMBL CDS features</li>
3754 <li>DAS Feature mapping</li>
3755 <li>Feature ordering</li>
3756 <li>Alignment Properties</li>
3757 <li>Annotation Scores</li>
3758 <li>Sort by scores</li>
3759 <li>Feature/annotation editing in applet</li>
3764 <li>Headless state operation in 2.2.1</li>
3765 <li>Incorrect and unstable DNA pairwise alignment</li>
3766 <li>Cut and paste of sequences with annotation</li>
3767 <li>Feature group display state in XML</li>
3768 <li>Feature ordering in XML</li>
3769 <li>blc file iteration selection using filename # suffix</li>
3770 <li>Stockholm alignment properties</li>
3771 <li>Stockhom alignment secondary structure annotation</li>
3772 <li>2.2.1 applet had no feature transparency</li>
3773 <li>Number pad keys can be used in cursor mode</li>
3774 <li>Structure Viewer mirror image resolved</li>
3781 <div align="center">
3782 <strong>2.2.1</strong><br> 12/2/07
3787 <li>Non standard characters can be read and displayed
3788 <li>Annotations/Features can be imported/exported to the
3790 <li>Applet allows editing of sequence/annotation/group
3791 name & description
3792 <li>Preference setting to display sequence name in
3794 <li>Annotation file format extended to allow
3795 Sequence_groups to be defined
3796 <li>Default opening of alignment overview panel can be
3797 specified in preferences
3798 <li>PDB residue numbering annotation added to associated
3804 <li>Applet crash under certain Linux OS with Java 1.6
3806 <li>Annotation file export / import bugs fixed
3807 <li>PNG / EPS image output bugs fixed
3813 <div align="center">
3814 <strong>2.2</strong><br> 27/11/06
3819 <li>Multiple views on alignment
3820 <li>Sequence feature editing
3821 <li>"Reload" alignment
3822 <li>"Save" to current filename
3823 <li>Background dependent text colour
3824 <li>Right align sequence ids
3825 <li>User-defined lower case residue colours
3828 <li>Menu item accelerator keys
3829 <li>Control-V pastes to current alignment
3830 <li>Cancel button for DAS Feature Fetching
3831 <li>PCA and PDB Viewers zoom via mouse roller
3832 <li>User-defined sub-tree colours and sub-tree selection
3834 <li>'New Window' button on the 'Output to Text box'
3839 <li>New memory efficient Undo/Redo System
3840 <li>Optimised symbol lookups and conservation/consensus
3842 <li>Region Conservation/Consensus recalculated after
3844 <li>Fixed Remove Empty Columns Bug (empty columns at end
3846 <li>Slowed DAS Feature Fetching for increased robustness.
3848 <li>Made angle brackets in ASCII feature descriptions
3850 <li>Re-instated Zoom function for PCA
3851 <li>Sequence descriptions conserved in web service
3853 <li>UniProt ID discoverer uses any word separated by
3855 <li>WsDbFetch query/result association resolved
3856 <li>Tree leaf to sequence mapping improved
3857 <li>Smooth fonts switch moved to FontChooser dialog box.
3864 <div align="center">
3865 <strong>2.1.1</strong><br> 12/9/06
3870 <li>Copy consensus sequence to clipboard</li>
3875 <li>Image output - rightmost residues are rendered if
3876 sequence id panel has been resized</li>
3877 <li>Image output - all offscreen group boundaries are
3879 <li>Annotation files with sequence references - all
3880 elements in file are relative to sequence position</li>
3881 <li>Mac Applet users can use Alt key for group editing</li>
3887 <div align="center">
3888 <strong>2.1</strong><br> 22/8/06
3893 <li>MAFFT Multiple Alignment in default Web Service list</li>
3894 <li>DAS Feature fetching</li>
3895 <li>Hide sequences and columns</li>
3896 <li>Export Annotations and Features</li>
3897 <li>GFF file reading / writing</li>
3898 <li>Associate structures with sequences from local PDB
3900 <li>Add sequences to exisiting alignment</li>
3901 <li>Recently opened files / URL lists</li>
3902 <li>Applet can launch the full application</li>
3903 <li>Applet has transparency for features (Java 1.2
3905 <li>Applet has user defined colours parameter</li>
3906 <li>Applet can load sequences from parameter
3907 "sequence<em>x</em>"
3913 <li>Redundancy Panel reinstalled in the Applet</li>
3914 <li>Monospaced font - EPS / rescaling bug fixed</li>
3915 <li>Annotation files with sequence references bug fixed</li>
3921 <div align="center">
3922 <strong>2.08.1</strong><br> 2/5/06
3927 <li>Change case of selected region from Popup menu</li>
3928 <li>Choose to match case when searching</li>
3929 <li>Middle mouse button and mouse movement can compress /
3930 expand the visible width and height of the alignment</li>
3935 <li>Annotation Panel displays complete JNet results</li>
3941 <div align="center">
3942 <strong>2.08b</strong><br> 18/4/06
3948 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3949 <li>Righthand label on wrapped alignments shows correct
3956 <div align="center">
3957 <strong>2.08</strong><br> 10/4/06
3962 <li>Editing can be locked to the selection area</li>
3963 <li>Keyboard editing</li>
3964 <li>Create sequence features from searches</li>
3965 <li>Precalculated annotations can be loaded onto
3967 <li>Features file allows grouping of features</li>
3968 <li>Annotation Colouring scheme added</li>
3969 <li>Smooth fonts off by default - Faster rendering</li>
3970 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3975 <li>Drag & Drop fixed on Linux</li>
3976 <li>Jalview Archive file faster to load/save, sequence
3977 descriptions saved.</li>
3983 <div align="center">
3984 <strong>2.07</strong><br> 12/12/05
3989 <li>PDB Structure Viewer enhanced</li>
3990 <li>Sequence Feature retrieval and display enhanced</li>
3991 <li>Choose to output sequence start-end after sequence
3992 name for file output</li>
3993 <li>Sequence Fetcher WSDBFetch@EBI</li>
3994 <li>Applet can read feature files, PDB files and can be
3995 used for HTML form input</li>
4000 <li>HTML output writes groups and features</li>
4001 <li>Group editing is Control and mouse click</li>
4002 <li>File IO bugs</li>
4008 <div align="center">
4009 <strong>2.06</strong><br> 28/9/05
4014 <li>View annotations in wrapped mode</li>
4015 <li>More options for PCA viewer</li>
4020 <li>GUI bugs resolved</li>
4021 <li>Runs with -nodisplay from command line</li>
4027 <div align="center">
4028 <strong>2.05b</strong><br> 15/9/05
4033 <li>Choose EPS export as lineart or text</li>
4034 <li>Jar files are executable</li>
4035 <li>Can read in Uracil - maps to unknown residue</li>
4040 <li>Known OutOfMemory errors give warning message</li>
4041 <li>Overview window calculated more efficiently</li>
4042 <li>Several GUI bugs resolved</li>
4048 <div align="center">
4049 <strong>2.05</strong><br> 30/8/05
4054 <li>Edit and annotate in "Wrapped" view</li>
4059 <li>Several GUI bugs resolved</li>
4065 <div align="center">
4066 <strong>2.04</strong><br> 24/8/05
4071 <li>Hold down mouse wheel & scroll to change font
4077 <li>Improved JPred client reliability</li>
4078 <li>Improved loading of Jalview files</li>
4084 <div align="center">
4085 <strong>2.03</strong><br> 18/8/05
4090 <li>Set Proxy server name and port in preferences</li>
4091 <li>Multiple URL links from sequence ids</li>
4092 <li>User Defined Colours can have a scheme name and added
4094 <li>Choose to ignore gaps in consensus calculation</li>
4095 <li>Unix users can set default web browser</li>
4096 <li>Runs without GUI for batch processing</li>
4097 <li>Dynamically generated Web Service Menus</li>
4102 <li>InstallAnywhere download for Sparc Solaris</li>
4108 <div align="center">
4109 <strong>2.02</strong><br> 18/7/05
4115 <li>Copy & Paste order of sequences maintains
4116 alignment order.</li>
4122 <div align="center">
4123 <strong>2.01</strong><br> 12/7/05
4128 <li>Use delete key for deleting selection.</li>
4129 <li>Use Mouse wheel to scroll sequences.</li>
4130 <li>Help file updated to describe how to add alignment
4132 <li>Version and build date written to build properties
4134 <li>InstallAnywhere installation will check for updates
4135 at launch of Jalview.</li>
4140 <li>Delete gaps bug fixed.</li>
4141 <li>FileChooser sorts columns.</li>
4142 <li>Can remove groups one by one.</li>
4143 <li>Filechooser icons installed.</li>
4144 <li>Finder ignores return character when searching.
4145 Return key will initiate a search.<br>
4152 <div align="center">
4153 <strong>2.0</strong><br> 20/6/05
4158 <li>New codebase</li>