3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
74 <em>29/01/2019</em></strong>
77 <td><div align="left">
81 <!-- JAL-2865 -->Jalview hangs when closing windows
82 or the overview updates with large alignments.
85 <!-- JAL-2865 -->Tree and PCA calculation fails for selected
86 region if columns were selected by dragging right-to-left
87 and the mouse moved to the left of the first column.
91 <td><div align="left">
95 <!-- JAL-3035 -->DAS sequence retrieval and annotation
96 capabilities removed from the Jalview Desktop
102 <!-- JAL-2822 -->Start and End should be updated when
103 sequence data at beginning or end of alignment added/removed
107 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
108 sequence features correctly when start of sequence is
109 removed (Known defect since 2.10)
118 <td width="60" nowrap>
120 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
123 <td><div align="left">
127 <!-- JAL-3101 -->Default memory for Jalview webstart and
128 InstallAnywhere increased to 1G.
131 <!-- JAL-247 -->Hidden sequence markers and representative
132 sequence bolding included when exporting alignment as EPS,
133 SVG, PNG or HTML. <em>Display is configured via the
134 Format menu, or for command-line use via a jalview
135 properties file.</em>
138 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
139 API and sequence data now imported as JSON.
142 <!-- JAL-3065 -->Change in recommended way of starting
143 Jalview via a Java command line: add jars in lib directory
144 to CLASSPATH, rather than via the deprecated java.ext.dirs
151 <!-- JAL-3047 -->Support added to execute test suite
152 instrumented with <a href="http://openclover.org/">Open
157 <td><div align="left">
161 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
162 row shown in Feredoxin Structure alignment view of example
166 <!-- JAL-2854 -->Annotation obscures sequences if lots of
167 annotation displayed.
170 <!-- JAL-3107 -->Group conservation/consensus not shown
171 for newly created group when 'Apply to all groups'
175 <!-- JAL-3087 -->Corrupted display when switching to
176 wrapped mode when sequence panel's vertical scrollbar is
180 <!-- JAL-3003 -->Alignment is black in exported EPS file
181 when sequences are selected in exported view.</em>
184 <!-- JAL-3059 -->Groups with different coloured borders
185 aren't rendered with correct colour.
188 <!-- JAL-3092 -->Jalview could hang when importing certain
189 types of knotted RNA secondary structure.
192 <!-- JAL-3095 -->Sequence highlight and selection in
193 trimmed VARNA 2D structure is incorrect for sequences that
197 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
198 annotation when columns are inserted into an alignment,
199 and when exporting as Stockholm flatfile.
202 <!-- JAL-3053 -->Jalview annotation rows containing upper
203 and lower-case 'E' and 'H' do not automatically get
204 treated as RNA secondary structure.
207 <!-- JAL-3106 -->.jvp should be used as default extension
208 (not .jar) when saving a jalview project file.
211 <!-- JAL-3105 -->Mac Users: closing a window correctly
212 transfers focus to previous window on OSX
215 <em>Java 10 Issues Resolved</em>
218 <!-- JAL-2988 -->OSX - Can't save new files via the File
219 or export menus by typing in a name into the Save dialog
223 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
224 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
225 'look and feel' which has improved compatibility with the
226 latest version of OSX.
233 <td width="60" nowrap>
235 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
236 <em>7/06/2018</em></strong>
239 <td><div align="left">
243 <!-- JAL-2920 -->Use HGVS nomenclature for variant
244 annotation retrieved from Uniprot
247 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
248 onto the Jalview Desktop
252 <td><div align="left">
256 <!-- JAL-3017 -->Cannot import features with multiple
257 variant elements (blocks import of some Uniprot records)
260 <!-- JAL-2997 -->Clustal files with sequence positions in
261 right-hand column parsed correctly
264 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
265 not alignment area in exported graphic
268 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
269 window has input focus
272 <!-- JAL-2992 -->Annotation panel set too high when
273 annotation added to view (Windows)
276 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
277 network connectivity is poor
280 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
281 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
282 the currently open URL and links from a page viewed in
283 Firefox or Chrome on Windows is now fully supported. If
284 you are using Edge, only links in the page can be
285 dragged, and with Internet Explorer, only the currently
286 open URL in the browser can be dropped onto Jalview.</em>
292 <td width="60" nowrap>
294 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
297 <td><div align="left">
301 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
302 for disabling automatic superposition of multiple
303 structures and open structures in existing views
306 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
307 ID and annotation area margins can be click-dragged to
311 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
315 <!-- JAL-2759 -->Improved performance for large alignments
316 and lots of hidden columns
319 <!-- JAL-2593 -->Improved performance when rendering lots
320 of features (particularly when transparency is disabled)
325 <td><div align="left">
328 <!-- JAL-2899 -->Structure and Overview aren't updated
329 when Colour By Annotation threshold slider is adjusted
332 <!-- JAL-2778 -->Slow redraw when Overview panel shown
333 overlapping alignment panel
336 <!-- JAL-2929 -->Overview doesn't show end of unpadded
340 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
341 improved: CDS not handled correctly if transcript has no
345 <!-- JAL-2321 -->Secondary structure and temperature
346 factor annotation not added to sequence when local PDB
347 file associated with it by drag'n'drop or structure
351 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
352 dialog doesn't import PDB files dropped on an alignment
355 <!-- JAL-2666 -->Linked scrolling via protein horizontal
356 scroll bar doesn't work for some CDS/Protein views
359 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
360 Java 1.8u153 onwards and Java 1.9u4+.
363 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
364 columns in annotation row
367 <!-- JAL-2913 -->Preferences panel's ID Width control is not
368 honored in batch mode
371 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
372 for structures added to existing Jmol view
375 <!-- JAL-2223 -->'View Mappings' includes duplicate
376 entries after importing project with multiple views
379 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
380 protein sequences via SIFTS from associated PDB entries
381 with negative residue numbers or missing residues fails
384 <!-- JAL-2952 -->Exception when shading sequence with negative
385 Temperature Factor values from annotated PDB files (e.g.
386 as generated by CONSURF)
389 <!-- JAL-2920 -->Uniprot 'sequence variant' features
390 tooltip doesn't include a text description of mutation
393 <!-- JAL-2922 -->Invert displayed features very slow when
394 structure and/or overview windows are also shown
397 <!-- JAL-2954 -->Selecting columns from highlighted regions
398 very slow for alignments with large numbers of sequences
401 <!-- JAL-2925 -->Copy Consensus fails for group consensus
402 with 'StringIndexOutOfBounds'
405 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
406 platforms running Java 10
409 <!-- JAL-2960 -->Adding a structure to existing structure
410 view appears to do nothing because the view is hidden behind the alignment view
416 <!-- JAL-2926 -->Copy consensus sequence option in applet
417 should copy the group consensus when popup is opened on it
423 <!-- JAL-2913 -->Fixed ID width preference is not respected
426 <em>New Known Defects</em>
429 <!-- JAL-2973 --> Exceptions occasionally raised when
430 editing a large alignment and overview is displayed
433 <!-- JAL-2974 -->'Overview updating' progress bar is shown
434 repeatedly after a series of edits even when the overview
435 is no longer reflecting updates
438 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
439 structures for protein subsequence (if 'Trim Retrieved
440 Sequences' enabled) or Ensembl isoforms (Workaround in
441 2.10.4 is to fail back to N&W mapping)
448 <td width="60" nowrap>
450 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
453 <td><div align="left">
454 <ul><li>Updated Certum Codesigning Certificate
455 (Valid till 30th November 2018)</li></ul></div></td>
456 <td><div align="left">
459 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
460 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
461 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
462 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
463 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
464 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
465 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
471 <td width="60" nowrap>
473 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
476 <td><div align="left">
480 <!-- JAL-2446 -->Faster and more efficient management and
481 rendering of sequence features
484 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
485 429 rate limit request hander
488 <!-- JAL-2773 -->Structure views don't get updated unless
489 their colours have changed
492 <!-- JAL-2495 -->All linked sequences are highlighted for
493 a structure mousover (Jmol) or selection (Chimera)
496 <!-- JAL-2790 -->'Cancel' button in progress bar for
497 JABAWS AACon, RNAAliFold and Disorder prediction jobs
500 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
501 view from Ensembl locus cross-references
504 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
508 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
509 feature can be disabled
512 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
513 PDB easier retrieval of sequences for lists of IDs
516 <!-- JAL-2758 -->Short names for sequences retrieved from
522 <li>Groovy interpreter updated to 2.4.12</li>
523 <li>Example groovy script for generating a matrix of
524 percent identity scores for current alignment.</li>
526 <em>Testing and Deployment</em>
529 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
533 <td><div align="left">
537 <!-- JAL-2643 -->Pressing tab after updating the colour
538 threshold text field doesn't trigger an update to the
542 <!-- JAL-2682 -->Race condition when parsing sequence ID
546 <!-- JAL-2608 -->Overview windows are also closed when
547 alignment window is closed
550 <!-- JAL-2548 -->Export of features doesn't always respect
554 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
555 takes a long time in Cursor mode
561 <!-- JAL-2777 -->Structures with whitespace chainCode
562 cannot be viewed in Chimera
565 <!-- JAL-2728 -->Protein annotation panel too high in
569 <!-- JAL-2757 -->Can't edit the query after the server
570 error warning icon is shown in Uniprot and PDB Free Text
574 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
577 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
580 <!-- JAL-2739 -->Hidden column marker in last column not
581 rendered when switching back from Wrapped to normal view
584 <!-- JAL-2768 -->Annotation display corrupted when
585 scrolling right in unwapped alignment view
588 <!-- JAL-2542 -->Existing features on subsequence
589 incorrectly relocated when full sequence retrieved from
593 <!-- JAL-2733 -->Last reported memory still shown when
594 Desktop->Show Memory is unticked (OSX only)
597 <!-- JAL-2658 -->Amend Features dialog doesn't allow
598 features of same type and group to be selected for
602 <!-- JAL-2524 -->Jalview becomes sluggish in wide
603 alignments when hidden columns are present
606 <!-- JAL-2392 -->Jalview freezes when loading and
607 displaying several structures
610 <!-- JAL-2732 -->Black outlines left after resizing or
614 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
615 within the Jalview desktop on OSX
618 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
619 when in wrapped alignment mode
622 <!-- JAL-2636 -->Scale mark not shown when close to right
623 hand end of alignment
626 <!-- JAL-2684 -->Pairwise alignment of selected regions of
627 each selected sequence do not have correct start/end
631 <!-- JAL-2793 -->Alignment ruler height set incorrectly
632 after canceling the Alignment Window's Font dialog
635 <!-- JAL-2036 -->Show cross-references not enabled after
636 restoring project until a new view is created
639 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
640 URL links appears when only default EMBL-EBI link is
641 configured (since 2.10.2b2)
644 <!-- JAL-2775 -->Overview redraws whole window when box
648 <!-- JAL-2225 -->Structure viewer doesn't map all chains
649 in a multi-chain structure when viewing alignment
650 involving more than one chain (since 2.10)
653 <!-- JAL-2811 -->Double residue highlights in cursor mode
654 if new selection moves alignment window
657 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
658 arrow key in cursor mode to pass hidden column marker
661 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
662 that produces correctly annotated transcripts and products
665 <!-- JAL-2776 -->Toggling a feature group after first time
666 doesn't update associated structure view
669 <em>Applet</em><br />
672 <!-- JAL-2687 -->Concurrent modification exception when
673 closing alignment panel
676 <em>BioJSON</em><br />
679 <!-- JAL-2546 -->BioJSON export does not preserve
680 non-positional features
683 <em>New Known Issues</em>
686 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
687 sequence features correctly (for many previous versions of
691 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
692 using cursor in wrapped panel other than top
695 <!-- JAL-2791 -->Select columns containing feature ignores
696 graduated colour threshold
699 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
700 always preserve numbering and sequence features
703 <em>Known Java 9 Issues</em>
706 <!-- JAL-2902 -->Groovy Console very slow to open and is
707 not responsive when entering characters (Webstart, Java
714 <td width="60" nowrap>
716 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
717 <em>2/10/2017</em></strong>
720 <td><div align="left">
721 <em>New features in Jalview Desktop</em>
724 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
726 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
730 <td><div align="left">
734 <td width="60" nowrap>
736 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
737 <em>7/9/2017</em></strong>
740 <td><div align="left">
744 <!-- JAL-2588 -->Show gaps in overview window by colouring
745 in grey (sequences used to be coloured grey, and gaps were
749 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
753 <!-- JAL-2587 -->Overview updates immediately on increase
754 in size and progress bar shown as higher resolution
755 overview is recalculated
760 <td><div align="left">
764 <!-- JAL-2664 -->Overview window redraws every hidden
765 column region row by row
768 <!-- JAL-2681 -->duplicate protein sequences shown after
769 retrieving Ensembl crossrefs for sequences from Uniprot
772 <!-- JAL-2603 -->Overview window throws NPE if show boxes
773 format setting is unticked
776 <!-- JAL-2610 -->Groups are coloured wrongly in overview
777 if group has show boxes format setting unticked
780 <!-- JAL-2672,JAL-2665 -->Redraw problems when
781 autoscrolling whilst dragging current selection group to
782 include sequences and columns not currently displayed
785 <!-- JAL-2691 -->Not all chains are mapped when multimeric
786 assemblies are imported via CIF file
789 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
790 displayed when threshold or conservation colouring is also
794 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
798 <!-- JAL-2673 -->Jalview continues to scroll after
799 dragging a selected region off the visible region of the
803 <!-- JAL-2724 -->Cannot apply annotation based
804 colourscheme to all groups in a view
807 <!-- JAL-2511 -->IDs don't line up with sequences
808 initially after font size change using the Font chooser or
815 <td width="60" nowrap>
817 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
820 <td><div align="left">
821 <em>Calculations</em>
825 <!-- JAL-1933 -->Occupancy annotation row shows number of
826 ungapped positions in each column of the alignment.
829 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
830 a calculation dialog box
833 <!-- JAL-2379 -->Revised implementation of PCA for speed
834 and memory efficiency (~30x faster)
837 <!-- JAL-2403 -->Revised implementation of sequence
838 similarity scores as used by Tree, PCA, Shading Consensus
839 and other calculations
842 <!-- JAL-2416 -->Score matrices are stored as resource
843 files within the Jalview codebase
846 <!-- JAL-2500 -->Trees computed on Sequence Feature
847 Similarity may have different topology due to increased
854 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
855 model for alignments and groups
858 <!-- JAL-384 -->Custom shading schemes created via groovy
865 <!-- JAL-2526 -->Efficiency improvements for interacting
866 with alignment and overview windows
869 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
873 <!-- JAL-2388 -->Hidden columns and sequences can be
877 <!-- JAL-2611 -->Click-drag in visible area allows fine
878 adjustment of visible position
882 <em>Data import/export</em>
885 <!-- JAL-2535 -->Posterior probability annotation from
886 Stockholm files imported as sequence associated annotation
889 <!-- JAL-2507 -->More robust per-sequence positional
890 annotation input/output via stockholm flatfile
893 <!-- JAL-2533 -->Sequence names don't include file
894 extension when importing structure files without embedded
895 names or PDB accessions
898 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
899 format sequence substitution matrices
902 <em>User Interface</em>
905 <!-- JAL-2447 --> Experimental Features Checkbox in
906 Desktop's Tools menu to hide or show untested features in
910 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
911 via Overview or sequence motif search operations
914 <!-- JAL-2547 -->Amend sequence features dialog box can be
915 opened by double clicking gaps within sequence feature
919 <!-- JAL-1476 -->Status bar message shown when not enough
920 aligned positions were available to create a 3D structure
924 <em>3D Structure</em>
927 <!-- JAL-2430 -->Hidden regions in alignment views are not
928 coloured in linked structure views
931 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
932 file-based command exchange
935 <!-- JAL-2375 -->Structure chooser automatically shows
936 Cached Structures rather than querying the PDBe if
937 structures are already available for sequences
940 <!-- JAL-2520 -->Structures imported via URL are cached in
941 the Jalview project rather than downloaded again when the
945 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
946 to transfer Chimera's structure attributes as Jalview
947 features, and vice-versa (<strong>Experimental
951 <em>Web Services</em>
954 <!-- JAL-2549 -->Updated JABAWS client to v2.2
957 <!-- JAL-2335 -->Filter non-standard amino acids and
958 nucleotides when submitting to AACon and other MSA
962 <!-- JAL-2316, -->URLs for viewing database
963 cross-references provided by identifiers.org and the
971 <!-- JAL-2344 -->FileFormatI interface for describing and
972 identifying file formats (instead of String constants)
975 <!-- JAL-2228 -->FeatureCounter script refactored for
976 efficiency when counting all displayed features (not
977 backwards compatible with 2.10.1)
980 <em>Example files</em>
983 <!-- JAL-2631 -->Graduated feature colour style example
984 included in the example feature file
987 <em>Documentation</em>
990 <!-- JAL-2339 -->Release notes reformatted for readability
991 with the built-in Java help viewer
994 <!-- JAL-1644 -->Find documentation updated with 'search
995 sequence description' option
1001 <!-- JAL-2485, -->External service integration tests for
1002 Uniprot REST Free Text Search Client
1005 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
1008 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
1013 <td><div align="left">
1014 <em>Calculations</em>
1017 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
1018 matrix - C->R should be '-3'<br />Old matrix restored
1019 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
1021 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
1022 Jalview's treatment of gaps in PCA and substitution matrix
1023 based Tree calculations.<br /> <br />In earlier versions
1024 of Jalview, gaps matching gaps were penalised, and gaps
1025 matching non-gaps penalised even more. In the PCA
1026 calculation, gaps were actually treated as non-gaps - so
1027 different costs were applied, which meant Jalview's PCAs
1028 were different to those produced by SeqSpace.<br />Jalview
1029 now treats gaps in the same way as SeqSpace (ie it scores
1030 them as 0). <br /> <br />Enter the following in the
1031 Groovy console to restore pre-2.10.2 behaviour:<br />
1032 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
1033 // for 2.10.1 mode <br />
1034 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
1035 // to restore 2.10.2 mode <br /> <br /> <em>Note:
1036 these settings will affect all subsequent tree and PCA
1037 calculations (not recommended)</em></li>
1039 <!-- JAL-2424 -->Fixed off-by-one bug that affected
1040 scaling of branch lengths for trees computed using
1041 Sequence Feature Similarity.
1044 <!-- JAL-2377 -->PCA calculation could hang when
1045 generating output report when working with highly
1046 redundant alignments
1049 <!-- JAL-2544 --> Sort by features includes features to
1050 right of selected region when gaps present on right-hand
1054 <em>User Interface</em>
1057 <!-- JAL-2346 -->Reopening Colour by annotation dialog
1058 doesn't reselect a specific sequence's associated
1059 annotation after it was used for colouring a view
1062 <!-- JAL-2419 -->Current selection lost if popup menu
1063 opened on a region of alignment without groups
1066 <!-- JAL-2374 -->Popup menu not always shown for regions
1067 of an alignment with overlapping groups
1070 <!-- JAL-2310 -->Finder double counts if both a sequence's
1071 name and description match
1074 <!-- JAL-2370 -->Hiding column selection containing two
1075 hidden regions results in incorrect hidden regions
1078 <!-- JAL-2386 -->'Apply to all groups' setting when
1079 changing colour does not apply Conservation slider value
1083 <!-- JAL-2373 -->Percentage identity and conservation menu
1084 items do not show a tick or allow shading to be disabled
1087 <!-- JAL-2385 -->Conservation shading or PID threshold
1088 lost when base colourscheme changed if slider not visible
1091 <!-- JAL-2547 -->Sequence features shown in tooltip for
1092 gaps before start of features
1095 <!-- JAL-2623 -->Graduated feature colour threshold not
1096 restored to UI when feature colour is edited
1099 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1100 a time when scrolling vertically in wrapped mode.
1103 <!-- JAL-2630 -->Structure and alignment overview update
1104 as graduate feature colour settings are modified via the
1108 <!-- JAL-2034 -->Overview window doesn't always update
1109 when a group defined on the alignment is resized
1112 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1113 wrapped view result in positional status updates
1117 <!-- JAL-2563 -->Status bar doesn't show position for
1118 ambiguous amino acid and nucleotide symbols
1121 <!-- JAL-2602 -->Copy consensus sequence failed if
1122 alignment included gapped columns
1125 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1126 widgets don't permanently disappear
1129 <!-- JAL-2503 -->Cannot select or filter quantitative
1130 annotation that are shown only as column labels (e.g.
1131 T-Coffee column reliability scores)
1134 <!-- JAL-2594 -->Exception thrown if trying to create a
1135 sequence feature on gaps only
1138 <!-- JAL-2504 -->Features created with 'New feature'
1139 button from a Find inherit previously defined feature type
1140 rather than the Find query string
1143 <!-- JAL-2423 -->incorrect title in output window when
1144 exporting tree calculated in Jalview
1147 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1148 and then revealing them reorders sequences on the
1152 <!-- JAL-964 -->Group panel in sequence feature settings
1153 doesn't update to reflect available set of groups after
1154 interactively adding or modifying features
1157 <!-- JAL-2225 -->Sequence Database chooser unusable on
1161 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1162 only excluded gaps in current sequence and ignored
1169 <!-- JAL-2421 -->Overview window visible region moves
1170 erratically when hidden rows or columns are present
1173 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1174 Structure Viewer's colour menu don't correspond to
1178 <!-- JAL-2405 -->Protein specific colours only offered in
1179 colour and group colour menu for protein alignments
1182 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1183 reflect currently selected view or group's shading
1187 <!-- JAL-2624 -->Feature colour thresholds not respected
1188 when rendered on overview and structures when opacity at
1192 <!-- JAL-2589 -->User defined gap colour not shown in
1193 overview when features overlaid on alignment
1196 <em>Data import/export</em>
1199 <!-- JAL-2576 -->Very large alignments take a long time to
1203 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1204 added after a sequence was imported are not written to
1208 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1209 when importing RNA secondary structure via Stockholm
1212 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1213 not shown in correct direction for simple pseudoknots
1216 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1217 with lightGray or darkGray via features file (but can
1221 <!-- JAL-2383 -->Above PID colour threshold not recovered
1222 when alignment view imported from project
1225 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1226 structure and sequences extracted from structure files
1227 imported via URL and viewed in Jmol
1230 <!-- JAL-2520 -->Structures loaded via URL are saved in
1231 Jalview Projects rather than fetched via URL again when
1232 the project is loaded and the structure viewed
1235 <em>Web Services</em>
1238 <!-- JAL-2519 -->EnsemblGenomes example failing after
1239 release of Ensembl v.88
1242 <!-- JAL-2366 -->Proxy server address and port always
1243 appear enabled in Preferences->Connections
1246 <!-- JAL-2461 -->DAS registry not found exceptions
1247 removed from console output
1250 <!-- JAL-2582 -->Cannot retrieve protein products from
1251 Ensembl by Peptide ID
1254 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1255 created from SIFTs, and spurious 'Couldn't open structure
1256 in Chimera' errors raised after April 2017 update (problem
1257 due to 'null' string rather than empty string used for
1258 residues with no corresponding PDB mapping).
1261 <em>Application UI</em>
1264 <!-- JAL-2361 -->User Defined Colours not added to Colour
1268 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1269 case' residues (button in colourscheme editor debugged and
1270 new documentation and tooltips added)
1273 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1274 doesn't restore group-specific text colour thresholds
1277 <!-- JAL-2243 -->Feature settings panel does not update as
1278 new features are added to alignment
1281 <!-- JAL-2532 -->Cancel in feature settings reverts
1282 changes to feature colours via the Amend features dialog
1285 <!-- JAL-2506 -->Null pointer exception when attempting to
1286 edit graduated feature colour via amend features dialog
1290 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1291 selection menu changes colours of alignment views
1294 <!-- JAL-2426 -->Spurious exceptions in console raised
1295 from alignment calculation workers after alignment has
1299 <!-- JAL-1608 -->Typo in selection popup menu - Create
1300 groups now 'Create Group'
1303 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1304 Create/Undefine group doesn't always work
1307 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1308 shown again after pressing 'Cancel'
1311 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1312 adjusts start position in wrap mode
1315 <!-- JAL-2563 -->Status bar doesn't show positions for
1316 ambiguous amino acids
1319 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1320 CDS/Protein view after CDS sequences added for aligned
1324 <!-- JAL-2592 -->User defined colourschemes called 'User
1325 Defined' don't appear in Colours menu
1331 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1332 score models doesn't always result in an updated PCA plot
1335 <!-- JAL-2442 -->Features not rendered as transparent on
1336 overview or linked structure view
1339 <!-- JAL-2372 -->Colour group by conservation doesn't
1343 <!-- JAL-2517 -->Hitting Cancel after applying
1344 user-defined colourscheme doesn't restore original
1351 <!-- JAL-2314 -->Unit test failure:
1352 jalview.ws.jabaws.RNAStructExportImport setup fails
1355 <!-- JAL-2307 -->Unit test failure:
1356 jalview.ws.sifts.SiftsClientTest due to compatibility
1357 problems with deep array comparison equality asserts in
1358 successive versions of TestNG
1361 <!-- JAL-2479 -->Relocated StructureChooserTest and
1362 ParameterUtilsTest Unit tests to Network suite
1365 <em>New Known Issues</em>
1368 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1369 phase after a sequence motif find operation
1372 <!-- JAL-2550 -->Importing annotation file with rows
1373 containing just upper and lower case letters are
1374 interpreted as WUSS RNA secondary structure symbols
1377 <!-- JAL-2590 -->Cannot load and display Newick trees
1378 reliably from eggnog Ortholog database
1381 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1382 containing features of type Highlight' when 'B' is pressed
1383 to mark columns containing highlighted regions.
1386 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1387 doesn't always add secondary structure annotation.
1392 <td width="60" nowrap>
1393 <div align="center">
1394 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1397 <td><div align="left">
1401 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1402 for all consensus calculations
1405 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1408 <li>Updated Jalview's Certum code signing certificate
1411 <em>Application</em>
1414 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1415 set of database cross-references, sorted alphabetically
1418 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1419 from database cross references. Users with custom links
1420 will receive a <a href="webServices/urllinks.html#warning">warning
1421 dialog</a> asking them to update their preferences.
1424 <!-- JAL-2287-->Cancel button and escape listener on
1425 dialog warning user about disconnecting Jalview from a
1429 <!-- JAL-2320-->Jalview's Chimera control window closes if
1430 the Chimera it is connected to is shut down
1433 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1434 columns menu item to mark columns containing highlighted
1435 regions (e.g. from structure selections or results of a
1439 <!-- JAL-2284-->Command line option for batch-generation
1440 of HTML pages rendering alignment data with the BioJS
1450 <!-- JAL-2286 -->Columns with more than one modal residue
1451 are not coloured or thresholded according to percent
1452 identity (first observed in Jalview 2.8.2)
1455 <!-- JAL-2301 -->Threonine incorrectly reported as not
1459 <!-- JAL-2318 -->Updates to documentation pages (above PID
1460 threshold, amino acid properties)
1463 <!-- JAL-2292 -->Lower case residues in sequences are not
1464 reported as mapped to residues in a structure file in the
1468 <!--JAL-2324 -->Identical features with non-numeric scores
1469 could be added multiple times to a sequence
1472 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1473 bond features shown as two highlighted residues rather
1474 than a range in linked structure views, and treated
1475 correctly when selecting and computing trees from features
1478 <!-- JAL-2281-->Custom URL links for database
1479 cross-references are matched to database name regardless
1484 <em>Application</em>
1487 <!-- JAL-2282-->Custom URL links for specific database
1488 names without regular expressions also offer links from
1492 <!-- JAL-2315-->Removing a single configured link in the
1493 URL links pane in Connections preferences doesn't actually
1494 update Jalview configuration
1497 <!-- JAL-2272-->CTRL-Click on a selected region to open
1498 the alignment area popup menu doesn't work on El-Capitan
1501 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1502 files with similarly named sequences if dropped onto the
1506 <!-- JAL-2312 -->Additional mappings are shown for PDB
1507 entries where more chains exist in the PDB accession than
1508 are reported in the SIFTS file
1511 <!-- JAL-2317-->Certain structures do not get mapped to
1512 the structure view when displayed with Chimera
1515 <!-- JAL-2317-->No chains shown in the Chimera view
1516 panel's View->Show Chains submenu
1519 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1520 work for wrapped alignment views
1523 <!--JAL-2197 -->Rename UI components for running JPred
1524 predictions from 'JNet' to 'JPred'
1527 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1528 corrupted when annotation panel vertical scroll is not at
1529 first annotation row
1532 <!--JAL-2332 -->Attempting to view structure for Hen
1533 lysozyme results in a PDB Client error dialog box
1536 <!-- JAL-2319 -->Structure View's mapping report switched
1537 ranges for PDB and sequence for SIFTS
1540 SIFTS 'Not_Observed' residues mapped to non-existant
1544 <!-- <em>New Known Issues</em>
1551 <td width="60" nowrap>
1552 <div align="center">
1553 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1554 <em>25/10/2016</em></strong>
1557 <td><em>Application</em>
1559 <li>3D Structure chooser opens with 'Cached structures'
1560 view if structures already loaded</li>
1561 <li>Progress bar reports models as they are loaded to
1562 structure views</li>
1568 <li>Colour by conservation always enabled and no tick
1569 shown in menu when BLOSUM or PID shading applied</li>
1570 <li>FER1_ARATH and FER2_ARATH labels were switched in
1571 example sequences/projects/trees</li>
1573 <em>Application</em>
1575 <li>Jalview projects with views of local PDB structure
1576 files saved on Windows cannot be opened on OSX</li>
1577 <li>Multiple structure views can be opened and superposed
1578 without timeout for structures with multiple models or
1579 multiple sequences in alignment</li>
1580 <li>Cannot import or associated local PDB files without a
1581 PDB ID HEADER line</li>
1582 <li>RMSD is not output in Jmol console when superposition
1584 <li>Drag and drop of URL from Browser fails for Linux and
1585 OSX versions earlier than El Capitan</li>
1586 <li>ENA client ignores invalid content from ENA server</li>
1587 <li>Exceptions are not raised in console when ENA client
1588 attempts to fetch non-existent IDs via Fetch DB Refs UI
1590 <li>Exceptions are not raised in console when a new view
1591 is created on the alignment</li>
1592 <li>OSX right-click fixed for group selections: CMD-click
1593 to insert/remove gaps in groups and CTRL-click to open group
1596 <em>Build and deployment</em>
1598 <li>URL link checker now copes with multi-line anchor
1601 <em>New Known Issues</em>
1603 <li>Drag and drop from URL links in browsers do not work
1610 <td width="60" nowrap>
1611 <div align="center">
1612 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1615 <td><em>General</em>
1618 <!-- JAL-2124 -->Updated Spanish translations.
1621 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1622 for importing structure data to Jalview. Enables mmCIF and
1626 <!-- JAL-192 --->Alignment ruler shows positions relative to
1630 <!-- JAL-2202 -->Position/residue shown in status bar when
1631 mousing over sequence associated annotation
1634 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1638 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1639 '()', canonical '[]' and invalid '{}' base pair populations
1643 <!-- JAL-2092 -->Feature settings popup menu options for
1644 showing or hiding columns containing a feature
1647 <!-- JAL-1557 -->Edit selected group by double clicking on
1648 group and sequence associated annotation labels
1651 <!-- JAL-2236 -->Sequence name added to annotation label in
1652 select/hide columns by annotation and colour by annotation
1656 </ul> <em>Application</em>
1659 <!-- JAL-2050-->Automatically hide introns when opening a
1660 gene/transcript view
1663 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1667 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1668 structure mappings with the EMBL-EBI PDBe SIFTS database
1671 <!-- JAL-2079 -->Updated download sites used for Rfam and
1672 Pfam sources to xfam.org
1675 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1678 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1679 over sequences in Jalview
1682 <!-- JAL-2027-->Support for reverse-complement coding
1683 regions in ENA and EMBL
1686 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1687 for record retrieval via ENA rest API
1690 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1694 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1695 groovy script execution
1698 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1699 alignment window's Calculate menu
1702 <!-- JAL-1812 -->Allow groovy scripts that call
1703 Jalview.getAlignFrames() to run in headless mode
1706 <!-- JAL-2068 -->Support for creating new alignment
1707 calculation workers from groovy scripts
1710 <!-- JAL-1369 --->Store/restore reference sequence in
1714 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1715 associations are now saved/restored from project
1718 <!-- JAL-1993 -->Database selection dialog always shown
1719 before sequence fetcher is opened
1722 <!-- JAL-2183 -->Double click on an entry in Jalview's
1723 database chooser opens a sequence fetcher
1726 <!-- JAL-1563 -->Free-text search client for UniProt using
1727 the UniProt REST API
1730 <!-- JAL-2168 -->-nonews command line parameter to prevent
1731 the news reader opening
1734 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1735 querying stored in preferences
1738 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1742 <!-- JAL-1977-->Tooltips shown on database chooser
1745 <!-- JAL-391 -->Reverse complement function in calculate
1746 menu for nucleotide sequences
1749 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1750 and feature counts preserves alignment ordering (and
1751 debugged for complex feature sets).
1754 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1755 viewing structures with Jalview 2.10
1758 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1759 genome, transcript CCDS and gene ids via the Ensembl and
1760 Ensembl Genomes REST API
1763 <!-- JAL-2049 -->Protein sequence variant annotation
1764 computed for 'sequence_variant' annotation on CDS regions
1768 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1772 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1773 Ref Fetcher fails to match, or otherwise updates sequence
1774 data from external database records.
1777 <!-- JAL-2154 -->Revised Jalview Project format for
1778 efficient recovery of sequence coding and alignment
1779 annotation relationships.
1781 </ul> <!-- <em>Applet</em>
1792 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1796 <!-- JAL-2018-->Export features in Jalview format (again)
1797 includes graduated colourschemes
1800 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1801 working with big alignments and lots of hidden columns
1804 <!-- JAL-2053-->Hidden column markers not always rendered
1805 at right of alignment window
1808 <!-- JAL-2067 -->Tidied up links in help file table of
1812 <!-- JAL-2072 -->Feature based tree calculation not shown
1816 <!-- JAL-2075 -->Hidden columns ignored during feature
1817 based tree calculation
1820 <!-- JAL-2065 -->Alignment view stops updating when show
1821 unconserved enabled for group on alignment
1824 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1828 <!-- JAL-2146 -->Alignment column in status incorrectly
1829 shown as "Sequence position" when mousing over
1833 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1834 hidden columns present
1837 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1838 user created annotation added to alignment
1841 <!-- JAL-1841 -->RNA Structure consensus only computed for
1842 '()' base pair annotation
1845 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1846 in zero scores for all base pairs in RNA Structure
1850 <!-- JAL-2174-->Extend selection with columns containing
1854 <!-- JAL-2275 -->Pfam format writer puts extra space at
1855 beginning of sequence
1858 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1862 <!-- JAL-2238 -->Cannot create groups on an alignment from
1863 from a tree when t-coffee scores are shown
1866 <!-- JAL-1836,1967 -->Cannot import and view PDB
1867 structures with chains containing negative resnums (4q4h)
1870 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1874 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1875 to Clustal, PIR and PileUp output
1878 <!-- JAL-2008 -->Reordering sequence features that are
1879 not visible causes alignment window to repaint
1882 <!-- JAL-2006 -->Threshold sliders don't work in
1883 graduated colour and colour by annotation row for e-value
1884 scores associated with features and annotation rows
1887 <!-- JAL-1797 -->amino acid physicochemical conservation
1888 calculation should be case independent
1891 <!-- JAL-2173 -->Remove annotation also updates hidden
1895 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1896 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1897 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1900 <!-- JAL-2065 -->Null pointer exceptions and redraw
1901 problems when reference sequence defined and 'show
1902 non-conserved' enabled
1905 <!-- JAL-1306 -->Quality and Conservation are now shown on
1906 load even when Consensus calculation is disabled
1909 <!-- JAL-1932 -->Remove right on penultimate column of
1910 alignment does nothing
1913 <em>Application</em>
1916 <!-- JAL-1552-->URLs and links can't be imported by
1917 drag'n'drop on OSX when launched via webstart (note - not
1918 yet fixed for El Capitan)
1921 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1922 output when running on non-gb/us i18n platforms
1925 <!-- JAL-1944 -->Error thrown when exporting a view with
1926 hidden sequences as flat-file alignment
1929 <!-- JAL-2030-->InstallAnywhere distribution fails when
1933 <!-- JAL-2080-->Jalview very slow to launch via webstart
1934 (also hotfix for 2.9.0b2)
1937 <!-- JAL-2085 -->Cannot save project when view has a
1938 reference sequence defined
1941 <!-- JAL-1011 -->Columns are suddenly selected in other
1942 alignments and views when revealing hidden columns
1945 <!-- JAL-1989 -->Hide columns not mirrored in complement
1946 view in a cDNA/Protein splitframe
1949 <!-- JAL-1369 -->Cannot save/restore representative
1950 sequence from project when only one sequence is
1954 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1955 in Structure Chooser
1958 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1959 structure consensus didn't refresh annotation panel
1962 <!-- JAL-1962 -->View mapping in structure view shows
1963 mappings between sequence and all chains in a PDB file
1966 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1967 dialogs format columns correctly, don't display array
1968 data, sort columns according to type
1971 <!-- JAL-1975 -->Export complete shown after destination
1972 file chooser is cancelled during an image export
1975 <!-- JAL-2025 -->Error when querying PDB Service with
1976 sequence name containing special characters
1979 <!-- JAL-2024 -->Manual PDB structure querying should be
1983 <!-- JAL-2104 -->Large tooltips with broken HTML
1984 formatting don't wrap
1987 <!-- JAL-1128 -->Figures exported from wrapped view are
1988 truncated so L looks like I in consensus annotation
1991 <!-- JAL-2003 -->Export features should only export the
1992 currently displayed features for the current selection or
1996 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1997 after fetching cross-references, and restoring from
2001 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
2002 followed in the structure viewer
2005 <!-- JAL-2163 -->Titles for individual alignments in
2006 splitframe not restored from project
2009 <!-- JAL-2145 -->missing autocalculated annotation at
2010 trailing end of protein alignment in transcript/product
2011 splitview when pad-gaps not enabled by default
2014 <!-- JAL-1797 -->amino acid physicochemical conservation
2018 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
2019 article has been read (reopened issue due to
2020 internationalisation problems)
2023 <!-- JAL-1960 -->Only offer PDB structures in structure
2024 viewer based on sequence name, PDB and UniProt
2029 <!-- JAL-1976 -->No progress bar shown during export of
2033 <!-- JAL-2213 -->Structures not always superimposed after
2034 multiple structures are shown for one or more sequences.
2037 <!-- JAL-1370 -->Reference sequence characters should not
2038 be replaced with '.' when 'Show unconserved' format option
2042 <!-- JAL-1823 -->Cannot specify chain code when entering
2043 specific PDB id for sequence
2046 <!-- JAL-1944 -->File->Export->.. as doesn't work when
2047 'Export hidden sequences' is enabled, but 'export hidden
2048 columns' is disabled.
2051 <!--JAL-2026-->Best Quality option in structure chooser
2052 selects lowest rather than highest resolution structures
2056 <!-- JAL-1887 -->Incorrect start and end reported for PDB
2057 to sequence mapping in 'View Mappings' report
2060 <!-- JAL-2284 -->Unable to read old Jalview projects that
2061 contain non-XML data added after Jalvew wrote project.
2064 <!-- JAL-2118 -->Newly created annotation row reorders
2065 after clicking on it to create new annotation for a
2069 <!-- JAL-1980 -->Null Pointer Exception raised when
2070 pressing Add on an orphaned cut'n'paste window.
2072 <!-- may exclude, this is an external service stability issue JAL-1941
2073 -- > RNA 3D structure not added via DSSR service</li> -->
2078 <!-- JAL-2151 -->Incorrect columns are selected when
2079 hidden columns present before start of sequence
2082 <!-- JAL-1986 -->Missing dependencies on applet pages
2086 <!-- JAL-1947 -->Overview pixel size changes when
2087 sequences are hidden in applet
2090 <!-- JAL-1996 -->Updated instructions for applet
2091 deployment on examples pages.
2098 <td width="60" nowrap>
2099 <div align="center">
2100 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2101 <em>16/10/2015</em></strong>
2104 <td><em>General</em>
2106 <li>Time stamps for signed Jalview application and applet
2111 <em>Application</em>
2113 <li>Duplicate group consensus and conservation rows
2114 shown when tree is partitioned</li>
2115 <li>Erratic behaviour when tree partitions made with
2116 multiple cDNA/Protein split views</li>
2122 <td width="60" nowrap>
2123 <div align="center">
2124 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2125 <em>8/10/2015</em></strong>
2128 <td><em>General</em>
2130 <li>Updated Spanish translations of localized text for
2132 </ul> <em>Application</em>
2134 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2135 <li>Signed OSX InstallAnywhere installer<br></li>
2136 <li>Support for per-sequence based annotations in BioJSON</li>
2137 </ul> <em>Applet</em>
2139 <li>Split frame example added to applet examples page</li>
2140 </ul> <em>Build and Deployment</em>
2143 <!-- JAL-1888 -->New ant target for running Jalview's test
2151 <li>Mapping of cDNA to protein in split frames
2152 incorrect when sequence start > 1</li>
2153 <li>Broken images in filter column by annotation dialog
2155 <li>Feature colours not parsed from features file</li>
2156 <li>Exceptions and incomplete link URLs recovered when
2157 loading a features file containing HTML tags in feature
2161 <em>Application</em>
2163 <li>Annotations corrupted after BioJS export and
2165 <li>Incorrect sequence limits after Fetch DB References
2166 with 'trim retrieved sequences'</li>
2167 <li>Incorrect warning about deleting all data when
2168 deleting selected columns</li>
2169 <li>Patch to build system for shipping properly signed
2170 JNLP templates for webstart launch</li>
2171 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2172 unreleased structures for download or viewing</li>
2173 <li>Tab/space/return keystroke operation of EMBL-PDBe
2174 fetcher/viewer dialogs works correctly</li>
2175 <li>Disabled 'minimise' button on Jalview windows
2176 running on OSX to workaround redraw hang bug</li>
2177 <li>Split cDNA/Protein view position and geometry not
2178 recovered from jalview project</li>
2179 <li>Initial enabled/disabled state of annotation menu
2180 sorter 'show autocalculated first/last' corresponds to
2182 <li>Restoring of Clustal, RNA Helices and T-Coffee
2183 color schemes from BioJSON</li>
2187 <li>Reorder sequences mirrored in cDNA/Protein split
2189 <li>Applet with Jmol examples not loading correctly</li>
2195 <td><div align="center">
2196 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2198 <td><em>General</em>
2200 <li>Linked visualisation and analysis of DNA and Protein
2203 <li>Translated cDNA alignments shown as split protein
2204 and DNA alignment views</li>
2205 <li>Codon consensus annotation for linked protein and
2206 cDNA alignment views</li>
2207 <li>Link cDNA or Protein product sequences by loading
2208 them onto Protein or cDNA alignments</li>
2209 <li>Reconstruct linked cDNA alignment from aligned
2210 protein sequences</li>
2213 <li>Jmol integration updated to Jmol v14.2.14</li>
2214 <li>Import and export of Jalview alignment views as <a
2215 href="features/bioJsonFormat.html">BioJSON</a></li>
2216 <li>New alignment annotation file statements for
2217 reference sequences and marking hidden columns</li>
2218 <li>Reference sequence based alignment shading to
2219 highlight variation</li>
2220 <li>Select or hide columns according to alignment
2222 <li>Find option for locating sequences by description</li>
2223 <li>Conserved physicochemical properties shown in amino
2224 acid conservation row</li>
2225 <li>Alignments can be sorted by number of RNA helices</li>
2226 </ul> <em>Application</em>
2228 <li>New cDNA/Protein analysis capabilities
2230 <li>Get Cross-References should open a Split Frame
2231 view with cDNA/Protein</li>
2232 <li>Detect when nucleotide sequences and protein
2233 sequences are placed in the same alignment</li>
2234 <li>Split cDNA/Protein views are saved in Jalview
2239 <li>Use REST API to talk to Chimera</li>
2240 <li>Selected regions in Chimera are highlighted in linked
2241 Jalview windows</li>
2243 <li>VARNA RNA viewer updated to v3.93</li>
2244 <li>VARNA views are saved in Jalview Projects</li>
2245 <li>Pseudoknots displayed as Jalview RNA annotation can
2246 be shown in VARNA</li>
2248 <li>Make groups for selection uses marked columns as well
2249 as the active selected region</li>
2251 <li>Calculate UPGMA and NJ trees using sequence feature
2253 <li>New Export options
2255 <li>New Export Settings dialog to control hidden
2256 region export in flat file generation</li>
2258 <li>Export alignment views for display with the <a
2259 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2261 <li>Export scrollable SVG in HTML page</li>
2262 <li>Optional embedding of BioJSON data when exporting
2263 alignment figures to HTML</li>
2265 <li>3D structure retrieval and display
2267 <li>Free text and structured queries with the PDBe
2269 <li>PDBe Search API based discovery and selection of
2270 PDB structures for a sequence set</li>
2274 <li>JPred4 employed for protein secondary structure
2276 <li>Hide Insertions menu option to hide unaligned columns
2277 for one or a group of sequences</li>
2278 <li>Automatically hide insertions in alignments imported
2279 from the JPred4 web server</li>
2280 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2281 system on OSX<br />LGPL libraries courtesy of <a
2282 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2284 <li>changed 'View nucleotide structure' submenu to 'View
2285 VARNA 2D Structure'</li>
2286 <li>change "View protein structure" menu option to "3D
2289 </ul> <em>Applet</em>
2291 <li>New layout for applet example pages</li>
2292 <li>New parameters to enable SplitFrame view
2293 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2294 <li>New example demonstrating linked viewing of cDNA and
2295 Protein alignments</li>
2296 </ul> <em>Development and deployment</em>
2298 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2299 <li>Include installation type and git revision in build
2300 properties and console log output</li>
2301 <li>Jalview Github organisation, and new github site for
2302 storing BioJsMSA Templates</li>
2303 <li>Jalview's unit tests now managed with TestNG</li>
2306 <!-- <em>General</em>
2308 </ul> --> <!-- issues resolved --> <em>Application</em>
2310 <li>Escape should close any open find dialogs</li>
2311 <li>Typo in select-by-features status report</li>
2312 <li>Consensus RNA secondary secondary structure
2313 predictions are not highlighted in amber</li>
2314 <li>Missing gap character in v2.7 example file means
2315 alignment appears unaligned when pad-gaps is not enabled</li>
2316 <li>First switch to RNA Helices colouring doesn't colour
2317 associated structure views</li>
2318 <li>ID width preference option is greyed out when auto
2319 width checkbox not enabled</li>
2320 <li>Stopped a warning dialog from being shown when
2321 creating user defined colours</li>
2322 <li>'View Mapping' in structure viewer shows sequence
2323 mappings for just that viewer's sequences</li>
2324 <li>Workaround for superposing PDB files containing
2325 multiple models in Chimera</li>
2326 <li>Report sequence position in status bar when hovering
2327 over Jmol structure</li>
2328 <li>Cannot output gaps as '.' symbols with Selection ->
2329 output to text box</li>
2330 <li>Flat file exports of alignments with hidden columns
2331 have incorrect sequence start/end</li>
2332 <li>'Aligning' a second chain to a Chimera structure from
2334 <li>Colour schemes applied to structure viewers don't
2335 work for nucleotide</li>
2336 <li>Loading/cut'n'pasting an empty or invalid file leads
2337 to a grey/invisible alignment window</li>
2338 <li>Exported Jpred annotation from a sequence region
2339 imports to different position</li>
2340 <li>Space at beginning of sequence feature tooltips shown
2341 on some platforms</li>
2342 <li>Chimera viewer 'View | Show Chain' menu is not
2344 <li>'New View' fails with a Null Pointer Exception in
2345 console if Chimera has been opened</li>
2346 <li>Mouseover to Chimera not working</li>
2347 <li>Miscellaneous ENA XML feature qualifiers not
2349 <li>NPE in annotation renderer after 'Extract Scores'</li>
2350 <li>If two structures in one Chimera window, mouseover of
2351 either sequence shows on first structure</li>
2352 <li>'Show annotations' options should not make
2353 non-positional annotations visible</li>
2354 <li>Subsequence secondary structure annotation not shown
2355 in right place after 'view flanking regions'</li>
2356 <li>File Save As type unset when current file format is
2358 <li>Save as '.jar' option removed for saving Jalview
2360 <li>Colour by Sequence colouring in Chimera more
2362 <li>Cannot 'add reference annotation' for a sequence in
2363 several views on same alignment</li>
2364 <li>Cannot show linked products for EMBL / ENA records</li>
2365 <li>Jalview's tooltip wraps long texts containing no
2367 </ul> <em>Applet</em>
2369 <li>Jmol to JalviewLite mouseover/link not working</li>
2370 <li>JalviewLite can't import sequences with ID
2371 descriptions containing angle brackets</li>
2372 </ul> <em>General</em>
2374 <li>Cannot export and reimport RNA secondary structure
2375 via jalview annotation file</li>
2376 <li>Random helix colour palette for colour by annotation
2377 with RNA secondary structure</li>
2378 <li>Mouseover to cDNA from STOP residue in protein
2379 translation doesn't work.</li>
2380 <li>hints when using the select by annotation dialog box</li>
2381 <li>Jmol alignment incorrect if PDB file has alternate CA
2383 <li>FontChooser message dialog appears to hang after
2384 choosing 1pt font</li>
2385 <li>Peptide secondary structure incorrectly imported from
2386 annotation file when annotation display text includes 'e' or
2388 <li>Cannot set colour of new feature type whilst creating
2390 <li>cDNA translation alignment should not be sequence
2391 order dependent</li>
2392 <li>'Show unconserved' doesn't work for lower case
2394 <li>Nucleotide ambiguity codes involving R not recognised</li>
2395 </ul> <em>Deployment and Documentation</em>
2397 <li>Applet example pages appear different to the rest of
2398 www.jalview.org</li>
2399 </ul> <em>Application Known issues</em>
2401 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2402 <li>Misleading message appears after trying to delete
2404 <li>Jalview icon not shown in dock after InstallAnywhere
2405 version launches</li>
2406 <li>Fetching EMBL reference for an RNA sequence results
2407 fails with a sequence mismatch</li>
2408 <li>Corrupted or unreadable alignment display when
2409 scrolling alignment to right</li>
2410 <li>ArrayIndexOutOfBoundsException thrown when remove
2411 empty columns called on alignment with ragged gapped ends</li>
2412 <li>auto calculated alignment annotation rows do not get
2413 placed above or below non-autocalculated rows</li>
2414 <li>Jalview dekstop becomes sluggish at full screen in
2415 ultra-high resolution</li>
2416 <li>Cannot disable consensus calculation independently of
2417 quality and conservation</li>
2418 <li>Mouseover highlighting between cDNA and protein can
2419 become sluggish with more than one splitframe shown</li>
2420 </ul> <em>Applet Known Issues</em>
2422 <li>Core PDB parsing code requires Jmol</li>
2423 <li>Sequence canvas panel goes white when alignment
2424 window is being resized</li>
2430 <td><div align="center">
2431 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2433 <td><em>General</em>
2435 <li>Updated Java code signing certificate donated by
2437 <li>Features and annotation preserved when performing
2438 pairwise alignment</li>
2439 <li>RNA pseudoknot annotation can be
2440 imported/exported/displayed</li>
2441 <li>'colour by annotation' can colour by RNA and
2442 protein secondary structure</li>
2443 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2444 post-hoc with 2.9 release</em>)
2447 </ul> <em>Application</em>
2449 <li>Extract and display secondary structure for sequences
2450 with 3D structures</li>
2451 <li>Support for parsing RNAML</li>
2452 <li>Annotations menu for layout
2454 <li>sort sequence annotation rows by alignment</li>
2455 <li>place sequence annotation above/below alignment
2458 <li>Output in Stockholm format</li>
2459 <li>Internationalisation: improved Spanish (es)
2461 <li>Structure viewer preferences tab</li>
2462 <li>Disorder and Secondary Structure annotation tracks
2463 shared between alignments</li>
2464 <li>UCSF Chimera launch and linked highlighting from
2466 <li>Show/hide all sequence associated annotation rows for
2467 all or current selection</li>
2468 <li>disorder and secondary structure predictions
2469 available as dataset annotation</li>
2470 <li>Per-sequence rna helices colouring</li>
2473 <li>Sequence database accessions imported when fetching
2474 alignments from Rfam</li>
2475 <li>update VARNA version to 3.91</li>
2477 <li>New groovy scripts for exporting aligned positions,
2478 conservation values, and calculating sum of pairs scores.</li>
2479 <li>Command line argument to set default JABAWS server</li>
2480 <li>include installation type in build properties and
2481 console log output</li>
2482 <li>Updated Jalview project format to preserve dataset
2486 <!-- issues resolved --> <em>Application</em>
2488 <li>Distinguish alignment and sequence associated RNA
2489 structure in structure->view->VARNA</li>
2490 <li>Raise dialog box if user deletes all sequences in an
2492 <li>Pressing F1 results in documentation opening twice</li>
2493 <li>Sequence feature tooltip is wrapped</li>
2494 <li>Double click on sequence associated annotation
2495 selects only first column</li>
2496 <li>Redundancy removal doesn't result in unlinked
2497 leaves shown in tree</li>
2498 <li>Undos after several redundancy removals don't undo
2500 <li>Hide sequence doesn't hide associated annotation</li>
2501 <li>User defined colours dialog box too big to fit on
2502 screen and buttons not visible</li>
2503 <li>author list isn't updated if already written to
2504 Jalview properties</li>
2505 <li>Popup menu won't open after retrieving sequence
2507 <li>File open window for associate PDB doesn't open</li>
2508 <li>Left-then-right click on a sequence id opens a
2509 browser search window</li>
2510 <li>Cannot open sequence feature shading/sort popup menu
2511 in feature settings dialog</li>
2512 <li>better tooltip placement for some areas of Jalview
2514 <li>Allow addition of JABAWS Server which doesn't
2515 pass validation</li>
2516 <li>Web services parameters dialog box is too large to
2518 <li>Muscle nucleotide alignment preset obscured by
2520 <li>JABAWS preset submenus don't contain newly
2521 defined user preset</li>
2522 <li>MSA web services warns user if they were launched
2523 with invalid input</li>
2524 <li>Jalview cannot contact DAS Registy when running on
2527 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2528 'Superpose with' submenu not shown when new view
2532 </ul> <!-- <em>Applet</em>
2534 </ul> <em>General</em>
2536 </ul>--> <em>Deployment and Documentation</em>
2538 <li>2G and 1G options in launchApp have no effect on
2539 memory allocation</li>
2540 <li>launchApp service doesn't automatically open
2541 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2543 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2544 InstallAnywhere reports cannot find valid JVM when Java
2545 1.7_055 is available
2547 </ul> <em>Application Known issues</em>
2550 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2551 corrupted or unreadable alignment display when scrolling
2555 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2556 retrieval fails but progress bar continues for DAS retrieval
2557 with large number of ID
2560 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2561 flatfile output of visible region has incorrect sequence
2565 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2566 rna structure consensus doesn't update when secondary
2567 structure tracks are rearranged
2570 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2571 invalid rna structure positional highlighting does not
2572 highlight position of invalid base pairs
2575 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2576 out of memory errors are not raised when saving Jalview
2577 project from alignment window file menu
2580 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2581 Switching to RNA Helices colouring doesn't propagate to
2585 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2586 colour by RNA Helices not enabled when user created
2587 annotation added to alignment
2590 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2591 Jalview icon not shown on dock in Mountain Lion/Webstart
2593 </ul> <em>Applet Known Issues</em>
2596 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2597 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2600 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2601 Jalview and Jmol example not compatible with IE9
2604 <li>Sort by annotation score doesn't reverse order
2610 <td><div align="center">
2611 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2614 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2617 <li>Internationalisation of user interface (usually
2618 called i18n support) and translation for Spanish locale</li>
2619 <li>Define/Undefine group on current selection with
2620 Ctrl-G/Shift Ctrl-G</li>
2621 <li>Improved group creation/removal options in
2622 alignment/sequence Popup menu</li>
2623 <li>Sensible precision for symbol distribution
2624 percentages shown in logo tooltip.</li>
2625 <li>Annotation panel height set according to amount of
2626 annotation when alignment first opened</li>
2627 </ul> <em>Application</em>
2629 <li>Interactive consensus RNA secondary structure
2630 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2631 <li>Select columns containing particular features from
2632 Feature Settings dialog</li>
2633 <li>View all 'representative' PDB structures for selected
2635 <li>Update Jalview project format:
2637 <li>New file extension for Jalview projects '.jvp'</li>
2638 <li>Preserve sequence and annotation dataset (to
2639 store secondary structure annotation,etc)</li>
2640 <li>Per group and alignment annotation and RNA helix
2644 <li>New similarity measures for PCA and Tree calculation
2646 <li>Experimental support for retrieval and viewing of
2647 flanking regions for an alignment</li>
2651 <!-- issues resolved --> <em>Application</em>
2653 <li>logo keeps spinning and status remains at queued or
2654 running after job is cancelled</li>
2655 <li>cannot export features from alignments imported from
2656 Jalview/VAMSAS projects</li>
2657 <li>Buggy slider for web service parameters that take
2659 <li>Newly created RNA secondary structure line doesn't
2660 have 'display all symbols' flag set</li>
2661 <li>T-COFFEE alignment score shading scheme and other
2662 annotation shading not saved in Jalview project</li>
2663 <li>Local file cannot be loaded in freshly downloaded
2665 <li>Jalview icon not shown on dock in Mountain
2667 <li>Load file from desktop file browser fails</li>
2668 <li>Occasional NPE thrown when calculating large trees</li>
2669 <li>Cannot reorder or slide sequences after dragging an
2670 alignment onto desktop</li>
2671 <li>Colour by annotation dialog throws NPE after using
2672 'extract scores' function</li>
2673 <li>Loading/cut'n'pasting an empty file leads to a grey
2674 alignment window</li>
2675 <li>Disorder thresholds rendered incorrectly after
2676 performing IUPred disorder prediction</li>
2677 <li>Multiple group annotated consensus rows shown when
2678 changing 'normalise logo' display setting</li>
2679 <li>Find shows blank dialog after 'finished searching' if
2680 nothing matches query</li>
2681 <li>Null Pointer Exceptions raised when sorting by
2682 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2684 <li>Errors in Jmol console when structures in alignment
2685 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2687 <li>Not all working JABAWS services are shown in
2689 <li>JAVAWS version of Jalview fails to launch with
2690 'invalid literal/length code'</li>
2691 <li>Annotation/RNA Helix colourschemes cannot be applied
2692 to alignment with groups (actually fixed in 2.8.0b1)</li>
2693 <li>RNA Helices and T-Coffee Scores available as default
2696 </ul> <em>Applet</em>
2698 <li>Remove group option is shown even when selection is
2700 <li>Apply to all groups ticked but colourscheme changes
2701 don't affect groups</li>
2702 <li>Documented RNA Helices and T-Coffee Scores as valid
2703 colourscheme name</li>
2704 <li>Annotation labels drawn on sequence IDs when
2705 Annotation panel is not displayed</li>
2706 <li>Increased font size for dropdown menus on OSX and
2707 embedded windows</li>
2708 </ul> <em>Other</em>
2710 <li>Consensus sequence for alignments/groups with a
2711 single sequence were not calculated</li>
2712 <li>annotation files that contain only groups imported as
2713 annotation and junk sequences</li>
2714 <li>Fasta files with sequences containing '*' incorrectly
2715 recognised as PFAM or BLC</li>
2716 <li>conservation/PID slider apply all groups option
2717 doesn't affect background (2.8.0b1)
2719 <li>redundancy highlighting is erratic at 0% and 100%</li>
2720 <li>Remove gapped columns fails for sequences with ragged
2722 <li>AMSA annotation row with leading spaces is not
2723 registered correctly on import</li>
2724 <li>Jalview crashes when selecting PCA analysis for
2725 certain alignments</li>
2726 <li>Opening the colour by annotation dialog for an
2727 existing annotation based 'use original colours'
2728 colourscheme loses original colours setting</li>
2733 <td><div align="center">
2734 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2735 <em>30/1/2014</em></strong>
2739 <li>Trusted certificates for JalviewLite applet and
2740 Jalview Desktop application<br />Certificate was donated by
2741 <a href="https://www.certum.eu">Certum</a> to the Jalview
2742 open source project).
2744 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2745 <li>Output in Stockholm format</li>
2746 <li>Allow import of data from gzipped files</li>
2747 <li>Export/import group and sequence associated line
2748 graph thresholds</li>
2749 <li>Nucleotide substitution matrix that supports RNA and
2750 ambiguity codes</li>
2751 <li>Allow disorder predictions to be made on the current
2752 selection (or visible selection) in the same way that JPred
2754 <li>Groovy scripting for headless Jalview operation</li>
2755 </ul> <em>Other improvements</em>
2757 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2758 <li>COMBINE statement uses current SEQUENCE_REF and
2759 GROUP_REF scope to group annotation rows</li>
2760 <li>Support '' style escaping of quotes in Newick
2762 <li>Group options for JABAWS service by command line name</li>
2763 <li>Empty tooltip shown for JABA service options with a
2764 link but no description</li>
2765 <li>Select primary source when selecting authority in
2766 database fetcher GUI</li>
2767 <li>Add .mfa to FASTA file extensions recognised by
2769 <li>Annotation label tooltip text wrap</li>
2774 <li>Slow scrolling when lots of annotation rows are
2776 <li>Lots of NPE (and slowness) after creating RNA
2777 secondary structure annotation line</li>
2778 <li>Sequence database accessions not imported when
2779 fetching alignments from Rfam</li>
2780 <li>Incorrect SHMR submission for sequences with
2782 <li>View all structures does not always superpose
2784 <li>Option widgets in service parameters not updated to
2785 reflect user or preset settings</li>
2786 <li>Null pointer exceptions for some services without
2787 presets or adjustable parameters</li>
2788 <li>Discover PDB IDs entry in structure menu doesn't
2789 discover PDB xRefs</li>
2790 <li>Exception encountered while trying to retrieve
2791 features with DAS</li>
2792 <li>Lowest value in annotation row isn't coloured
2793 when colour by annotation (per sequence) is coloured</li>
2794 <li>Keyboard mode P jumps to start of gapped region when
2795 residue follows a gap</li>
2796 <li>Jalview appears to hang importing an alignment with
2797 Wrap as default or after enabling Wrap</li>
2798 <li>'Right click to add annotations' message
2799 shown in wrap mode when no annotations present</li>
2800 <li>Disorder predictions fail with NPE if no automatic
2801 annotation already exists on alignment</li>
2802 <li>oninit javascript function should be called after
2803 initialisation completes</li>
2804 <li>Remove redundancy after disorder prediction corrupts
2805 alignment window display</li>
2806 <li>Example annotation file in documentation is invalid</li>
2807 <li>Grouped line graph annotation rows are not exported
2808 to annotation file</li>
2809 <li>Multi-harmony analysis cannot be run when only two
2811 <li>Cannot create multiple groups of line graphs with
2812 several 'combine' statements in annotation file</li>
2813 <li>Pressing return several times causes Number Format
2814 exceptions in keyboard mode</li>
2815 <li>Multi-harmony (SHMMR) method doesn't submit
2816 correct partitions for input data</li>
2817 <li>Translation from DNA to Amino Acids fails</li>
2818 <li>Jalview fail to load newick tree with quoted label</li>
2819 <li>--headless flag isn't understood</li>
2820 <li>ClassCastException when generating EPS in headless
2822 <li>Adjusting sequence-associated shading threshold only
2823 changes one row's threshold</li>
2824 <li>Preferences and Feature settings panel panel
2825 doesn't open</li>
2826 <li>hide consensus histogram also hides conservation and
2827 quality histograms</li>
2832 <td><div align="center">
2833 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2835 <td><em>Application</em>
2837 <li>Support for JABAWS 2.0 Services (AACon alignment
2838 conservation, protein disorder and Clustal Omega)</li>
2839 <li>JABAWS server status indicator in Web Services
2841 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2842 in Jalview alignment window</li>
2843 <li>Updated Jalview build and deploy framework for OSX
2844 mountain lion, windows 7, and 8</li>
2845 <li>Nucleotide substitution matrix for PCA that supports
2846 RNA and ambiguity codes</li>
2848 <li>Improved sequence database retrieval GUI</li>
2849 <li>Support fetching and database reference look up
2850 against multiple DAS sources (Fetch all from in 'fetch db
2852 <li>Jalview project improvements
2854 <li>Store and retrieve the 'belowAlignment'
2855 flag for annotation</li>
2856 <li>calcId attribute to group annotation rows on the
2858 <li>Store AACon calculation settings for a view in
2859 Jalview project</li>
2863 <li>horizontal scrolling gesture support</li>
2864 <li>Visual progress indicator when PCA calculation is
2866 <li>Simpler JABA web services menus</li>
2867 <li>visual indication that web service results are still
2868 being retrieved from server</li>
2869 <li>Serialise the dialogs that are shown when Jalview
2870 starts up for first time</li>
2871 <li>Jalview user agent string for interacting with HTTP
2873 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2875 <li>Examples directory and Groovy library included in
2876 InstallAnywhere distribution</li>
2877 </ul> <em>Applet</em>
2879 <li>RNA alignment and secondary structure annotation
2880 visualization applet example</li>
2881 </ul> <em>General</em>
2883 <li>Normalise option for consensus sequence logo</li>
2884 <li>Reset button in PCA window to return dimensions to
2886 <li>Allow seqspace or Jalview variant of alignment PCA
2888 <li>PCA with either nucleic acid and protein substitution
2890 <li>Allow windows containing HTML reports to be exported
2892 <li>Interactive display and editing of RNA secondary
2893 structure contacts</li>
2894 <li>RNA Helix Alignment Colouring</li>
2895 <li>RNA base pair logo consensus</li>
2896 <li>Parse sequence associated secondary structure
2897 information in Stockholm files</li>
2898 <li>HTML Export database accessions and annotation
2899 information presented in tooltip for sequences</li>
2900 <li>Import secondary structure from LOCARNA clustalw
2901 style RNA alignment files</li>
2902 <li>import and visualise T-COFFEE quality scores for an
2904 <li>'colour by annotation' per sequence option to
2905 shade each sequence according to its associated alignment
2907 <li>New Jalview Logo</li>
2908 </ul> <em>Documentation and Development</em>
2910 <li>documentation for score matrices used in Jalview</li>
2911 <li>New Website!</li>
2913 <td><em>Application</em>
2915 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2916 wsdbfetch REST service</li>
2917 <li>Stop windows being moved outside desktop on OSX</li>
2918 <li>Filetype associations not installed for webstart
2920 <li>Jalview does not always retrieve progress of a JABAWS
2921 job execution in full once it is complete</li>
2922 <li>revise SHMR RSBS definition to ensure alignment is
2923 uploaded via ali_file parameter</li>
2924 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2925 <li>View all structures superposed fails with exception</li>
2926 <li>Jnet job queues forever if a very short sequence is
2927 submitted for prediction</li>
2928 <li>Cut and paste menu not opened when mouse clicked on
2930 <li>Putting fractional value into integer text box in
2931 alignment parameter dialog causes Jalview to hang</li>
2932 <li>Structure view highlighting doesn't work on
2934 <li>View all structures fails with exception shown in
2936 <li>Characters in filename associated with PDBEntry not
2937 escaped in a platform independent way</li>
2938 <li>Jalview desktop fails to launch with exception when
2940 <li>Tree calculation reports 'you must have 2 or more
2941 sequences selected' when selection is empty</li>
2942 <li>Jalview desktop fails to launch with jar signature
2943 failure when java web start temporary file caching is
2945 <li>DAS Sequence retrieval with range qualification
2946 results in sequence xref which includes range qualification</li>
2947 <li>Errors during processing of command line arguments
2948 cause progress bar (JAL-898) to be removed</li>
2949 <li>Replace comma for semi-colon option not disabled for
2950 DAS sources in sequence fetcher</li>
2951 <li>Cannot close news reader when JABAWS server warning
2952 dialog is shown</li>
2953 <li>Option widgets not updated to reflect user settings</li>
2954 <li>Edited sequence not submitted to web service</li>
2955 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2956 <li>InstallAnywhere installer doesn't unpack and run
2957 on OSX Mountain Lion</li>
2958 <li>Annotation panel not given a scroll bar when
2959 sequences with alignment annotation are pasted into the
2961 <li>Sequence associated annotation rows not associated
2962 when loaded from Jalview project</li>
2963 <li>Browser launch fails with NPE on java 1.7</li>
2964 <li>JABAWS alignment marked as finished when job was
2965 cancelled or job failed due to invalid input</li>
2966 <li>NPE with v2.7 example when clicking on Tree
2967 associated with all views</li>
2968 <li>Exceptions when copy/paste sequences with grouped
2969 annotation rows to new window</li>
2970 </ul> <em>Applet</em>
2972 <li>Sequence features are momentarily displayed before
2973 they are hidden using hidefeaturegroups applet parameter</li>
2974 <li>loading features via javascript API automatically
2975 enables feature display</li>
2976 <li>scrollToColumnIn javascript API method doesn't
2978 </ul> <em>General</em>
2980 <li>Redundancy removal fails for rna alignment</li>
2981 <li>PCA calculation fails when sequence has been selected
2982 and then deselected</li>
2983 <li>PCA window shows grey box when first opened on OSX</li>
2984 <li>Letters coloured pink in sequence logo when alignment
2985 coloured with clustalx</li>
2986 <li>Choosing fonts without letter symbols defined causes
2987 exceptions and redraw errors</li>
2988 <li>Initial PCA plot view is not same as manually
2989 reconfigured view</li>
2990 <li>Grouped annotation graph label has incorrect line
2992 <li>Grouped annotation graph label display is corrupted
2993 for lots of labels</li>
2998 <div align="center">
2999 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
3002 <td><em>Application</em>
3004 <li>Jalview Desktop News Reader</li>
3005 <li>Tweaked default layout of web services menu</li>
3006 <li>View/alignment association menu to enable user to
3007 easily specify which alignment a multi-structure view takes
3008 its colours/correspondences from</li>
3009 <li>Allow properties file location to be specified as URL</li>
3010 <li>Extend Jalview project to preserve associations
3011 between many alignment views and a single Jmol display</li>
3012 <li>Store annotation row height in Jalview project file</li>
3013 <li>Annotation row column label formatting attributes
3014 stored in project file</li>
3015 <li>Annotation row order for auto-calculated annotation
3016 rows preserved in Jalview project file</li>
3017 <li>Visual progress indication when Jalview state is
3018 saved using Desktop window menu</li>
3019 <li>Visual indication that command line arguments are
3020 still being processed</li>
3021 <li>Groovy script execution from URL</li>
3022 <li>Colour by annotation default min and max colours in
3024 <li>Automatically associate PDB files dragged onto an
3025 alignment with sequences that have high similarity and
3027 <li>Update JGoogleAnalytics to latest release (0.3)</li>
3028 <li>'view structures' option to open many
3029 structures in same window</li>
3030 <li>Sort associated views menu option for tree panel</li>
3031 <li>Group all JABA and non-JABA services for a particular
3032 analysis function in its own submenu</li>
3033 </ul> <em>Applet</em>
3035 <li>Userdefined and autogenerated annotation rows for
3037 <li>Adjustment of alignment annotation pane height</li>
3038 <li>Annotation scrollbar for annotation panel</li>
3039 <li>Drag to reorder annotation rows in annotation panel</li>
3040 <li>'automaticScrolling' parameter</li>
3041 <li>Allow sequences with partial ID string matches to be
3042 annotated from GFF/Jalview features files</li>
3043 <li>Sequence logo annotation row in applet</li>
3044 <li>Absolute paths relative to host server in applet
3045 parameters are treated as such</li>
3046 <li>New in the JalviewLite javascript API:
3048 <li>JalviewLite.js javascript library</li>
3049 <li>Javascript callbacks for
3051 <li>Applet initialisation</li>
3052 <li>Sequence/alignment mouse-overs and selections</li>
3055 <li>scrollTo row and column alignment scrolling
3057 <li>Select sequence/alignment regions from javascript</li>
3058 <li>javascript structure viewer harness to pass
3059 messages between Jmol and Jalview when running as
3060 distinct applets</li>
3061 <li>sortBy method</li>
3062 <li>Set of applet and application examples shipped
3063 with documentation</li>
3064 <li>New example to demonstrate JalviewLite and Jmol
3065 javascript message exchange</li>
3067 </ul> <em>General</em>
3069 <li>Enable Jmol displays to be associated with multiple
3070 multiple alignments</li>
3071 <li>Option to automatically sort alignment with new tree</li>
3072 <li>User configurable link to enable redirects to a
3073 www.Jalview.org mirror</li>
3074 <li>Jmol colours option for Jmol displays</li>
3075 <li>Configurable newline string when writing alignment
3076 and other flat files</li>
3077 <li>Allow alignment annotation description lines to
3078 contain html tags</li>
3079 </ul> <em>Documentation and Development</em>
3081 <li>Add groovy test harness for bulk load testing to
3083 <li>Groovy script to load and align a set of sequences
3084 using a web service before displaying the result in the
3085 Jalview desktop</li>
3086 <li>Restructured javascript and applet api documentation</li>
3087 <li>Ant target to publish example html files with applet
3089 <li>Netbeans project for building Jalview from source</li>
3090 <li>ant task to create online javadoc for Jalview source</li>
3092 <td><em>Application</em>
3094 <li>User defined colourscheme throws exception when
3095 current built in colourscheme is saved as new scheme</li>
3096 <li>AlignFrame->Save in application pops up save
3097 dialog for valid filename/format</li>
3098 <li>Cannot view associated structure for UniProt sequence</li>
3099 <li>PDB file association breaks for UniProt sequence
3101 <li>Associate PDB from file dialog does not tell you
3102 which sequence is to be associated with the file</li>
3103 <li>Find All raises null pointer exception when query
3104 only matches sequence IDs</li>
3105 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3106 <li>Jalview project with Jmol views created with Jalview
3107 2.4 cannot be loaded</li>
3108 <li>Filetype associations not installed for webstart
3110 <li>Two or more chains in a single PDB file associated
3111 with sequences in different alignments do not get coloured
3112 by their associated sequence</li>
3113 <li>Visibility status of autocalculated annotation row
3114 not preserved when project is loaded</li>
3115 <li>Annotation row height and visibility attributes not
3116 stored in Jalview project</li>
3117 <li>Tree bootstraps are not preserved when saved as a
3118 Jalview project</li>
3119 <li>Envision2 workflow tooltips are corrupted</li>
3120 <li>Enabling show group conservation also enables colour
3121 by conservation</li>
3122 <li>Duplicate group associated conservation or consensus
3123 created on new view</li>
3124 <li>Annotation scrollbar not displayed after 'show
3125 all hidden annotation rows' option selected</li>
3126 <li>Alignment quality not updated after alignment
3127 annotation row is hidden then shown</li>
3128 <li>Preserve colouring of structures coloured by
3129 sequences in pre Jalview 2.7 projects</li>
3130 <li>Web service job parameter dialog is not laid out
3132 <li>Web services menu not refreshed after 'reset
3133 services' button is pressed in preferences</li>
3134 <li>Annotation off by one in Jalview v2_3 example project</li>
3135 <li>Structures imported from file and saved in project
3136 get name like jalview_pdb1234.txt when reloaded</li>
3137 <li>Jalview does not always retrieve progress of a JABAWS
3138 job execution in full once it is complete</li>
3139 </ul> <em>Applet</em>
3141 <li>Alignment height set incorrectly when lots of
3142 annotation rows are displayed</li>
3143 <li>Relative URLs in feature HTML text not resolved to
3145 <li>View follows highlighting does not work for positions
3147 <li><= shown as = in tooltip</li>
3148 <li>Export features raises exception when no features
3150 <li>Separator string used for serialising lists of IDs
3151 for javascript api is modified when separator string
3152 provided as parameter</li>
3153 <li>Null pointer exception when selecting tree leaves for
3154 alignment with no existing selection</li>
3155 <li>Relative URLs for datasources assumed to be relative
3156 to applet's codebase</li>
3157 <li>Status bar not updated after finished searching and
3158 search wraps around to first result</li>
3159 <li>StructureSelectionManager instance shared between
3160 several Jalview applets causes race conditions and memory
3162 <li>Hover tooltip and mouseover of position on structure
3163 not sent from Jmol in applet</li>
3164 <li>Certain sequences of javascript method calls to
3165 applet API fatally hang browser</li>
3166 </ul> <em>General</em>
3168 <li>View follows structure mouseover scrolls beyond
3169 position with wrapped view and hidden regions</li>
3170 <li>Find sequence position moves to wrong residue
3171 with/without hidden columns</li>
3172 <li>Sequence length given in alignment properties window
3174 <li>InvalidNumberFormat exceptions thrown when trying to
3175 import PDB like structure files</li>
3176 <li>Positional search results are only highlighted
3177 between user-supplied sequence start/end bounds</li>
3178 <li>End attribute of sequence is not validated</li>
3179 <li>Find dialog only finds first sequence containing a
3180 given sequence position</li>
3181 <li>Sequence numbering not preserved in MSF alignment
3183 <li>Jalview PDB file reader does not extract sequence
3184 from nucleotide chains correctly</li>
3185 <li>Structure colours not updated when tree partition
3186 changed in alignment</li>
3187 <li>Sequence associated secondary structure not correctly
3188 parsed in interleaved stockholm</li>
3189 <li>Colour by annotation dialog does not restore current
3191 <li>Hiding (nearly) all sequences doesn't work
3193 <li>Sequences containing lowercase letters are not
3194 properly associated with their pdb files</li>
3195 </ul> <em>Documentation and Development</em>
3197 <li>schemas/JalviewWsParamSet.xsd corrupted by
3198 ApplyCopyright tool</li>
3203 <div align="center">
3204 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3207 <td><em>Application</em>
3209 <li>New warning dialog when the Jalview Desktop cannot
3210 contact web services</li>
3211 <li>JABA service parameters for a preset are shown in
3212 service job window</li>
3213 <li>JABA Service menu entries reworded</li>
3217 <li>Modeller PIR IO broken - cannot correctly import a
3218 pir file emitted by Jalview</li>
3219 <li>Existing feature settings transferred to new
3220 alignment view created from cut'n'paste</li>
3221 <li>Improved test for mixed amino/nucleotide chains when
3222 parsing PDB files</li>
3223 <li>Consensus and conservation annotation rows
3224 occasionally become blank for all new windows</li>
3225 <li>Exception raised when right clicking above sequences
3226 in wrapped view mode</li>
3227 </ul> <em>Application</em>
3229 <li>multiple multiply aligned structure views cause cpu
3230 usage to hit 100% and computer to hang</li>
3231 <li>Web Service parameter layout breaks for long user
3232 parameter names</li>
3233 <li>Jaba service discovery hangs desktop if Jaba server
3240 <div align="center">
3241 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3244 <td><em>Application</em>
3246 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3247 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3250 <li>Web Services preference tab</li>
3251 <li>Analysis parameters dialog box and user defined
3253 <li>Improved speed and layout of Envision2 service menu</li>
3254 <li>Superpose structures using associated sequence
3256 <li>Export coordinates and projection as CSV from PCA
3258 </ul> <em>Applet</em>
3260 <li>enable javascript: execution by the applet via the
3261 link out mechanism</li>
3262 </ul> <em>Other</em>
3264 <li>Updated the Jmol Jalview interface to work with Jmol
3266 <li>The Jalview Desktop and JalviewLite applet now
3267 require Java 1.5</li>
3268 <li>Allow Jalview feature colour specification for GFF
3269 sequence annotation files</li>
3270 <li>New 'colour by label' keword in Jalview feature file
3271 type colour specification</li>
3272 <li>New Jalview Desktop Groovy API method that allows a
3273 script to check if it being run in an interactive session or
3274 in a batch operation from the Jalview command line</li>
3278 <li>clustalx colourscheme colours Ds preferentially when
3279 both D+E are present in over 50% of the column</li>
3280 </ul> <em>Application</em>
3282 <li>typo in AlignmentFrame->View->Hide->all but
3283 selected Regions menu item</li>
3284 <li>sequence fetcher replaces ',' for ';' when the ',' is
3285 part of a valid accession ID</li>
3286 <li>fatal OOM if object retrieved by sequence fetcher
3287 runs out of memory</li>
3288 <li>unhandled Out of Memory Error when viewing pca
3289 analysis results</li>
3290 <li>InstallAnywhere builds fail to launch on OS X java
3291 10.5 update 4 (due to apple Java 1.6 update)</li>
3292 <li>Installanywhere Jalview silently fails to launch</li>
3293 </ul> <em>Applet</em>
3295 <li>Jalview.getFeatureGroups() raises an
3296 ArrayIndexOutOfBoundsException if no feature groups are
3303 <div align="center">
3304 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3310 <li>Alignment prettyprinter doesn't cope with long
3312 <li>clustalx colourscheme colours Ds preferentially when
3313 both D+E are present in over 50% of the column</li>
3314 <li>nucleic acid structures retrieved from PDB do not
3315 import correctly</li>
3316 <li>More columns get selected than were clicked on when a
3317 number of columns are hidden</li>
3318 <li>annotation label popup menu not providing correct
3319 add/hide/show options when rows are hidden or none are
3321 <li>Stockholm format shown in list of readable formats,
3322 and parser copes better with alignments from RFAM.</li>
3323 <li>CSV output of consensus only includes the percentage
3324 of all symbols if sequence logo display is enabled</li>
3326 </ul> <em>Applet</em>
3328 <li>annotation panel disappears when annotation is
3330 </ul> <em>Application</em>
3332 <li>Alignment view not redrawn properly when new
3333 alignment opened where annotation panel is visible but no
3334 annotations are present on alignment</li>
3335 <li>pasted region containing hidden columns is
3336 incorrectly displayed in new alignment window</li>
3337 <li>Jalview slow to complete operations when stdout is
3338 flooded (fix is to close the Jalview console)</li>
3339 <li>typo in AlignmentFrame->View->Hide->all but
3340 selected Rregions menu item.</li>
3341 <li>inconsistent group submenu and Format submenu entry
3342 'Un' or 'Non'conserved</li>
3343 <li>Sequence feature settings are being shared by
3344 multiple distinct alignments</li>
3345 <li>group annotation not recreated when tree partition is
3347 <li>double click on group annotation to select sequences
3348 does not propagate to associated trees</li>
3349 <li>Mac OSX specific issues:
3351 <li>exception raised when mouse clicked on desktop
3352 window background</li>
3353 <li>Desktop menu placed on menu bar and application
3354 name set correctly</li>
3355 <li>sequence feature settings not wide enough for the
3356 save feature colourscheme button</li>
3365 <div align="center">
3366 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3369 <td><em>New Capabilities</em>
3371 <li>URL links generated from description line for
3372 regular-expression based URL links (applet and application)
3374 <li>Non-positional feature URL links are shown in link
3376 <li>Linked viewing of nucleic acid sequences and
3378 <li>Automatic Scrolling option in View menu to display
3379 the currently highlighted region of an alignment.</li>
3380 <li>Order an alignment by sequence length, or using the
3381 average score or total feature count for each sequence.</li>
3382 <li>Shading features by score or associated description</li>
3383 <li>Subdivide alignment and groups based on identity of
3384 selected subsequence (Make Groups from Selection).</li>
3385 <li>New hide/show options including Shift+Control+H to
3386 hide everything but the currently selected region.</li>
3387 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3388 </ul> <em>Application</em>
3390 <li>Fetch DB References capabilities and UI expanded to
3391 support retrieval from DAS sequence sources</li>
3392 <li>Local DAS Sequence sources can be added via the
3393 command line or via the Add local source dialog box.</li>
3394 <li>DAS Dbref and DbxRef feature types are parsed as
3395 database references and protein_name is parsed as
3396 description line (BioSapiens terms).</li>
3397 <li>Enable or disable non-positional feature and database
3398 references in sequence ID tooltip from View menu in
3400 <!-- <li>New hidden columns and rows and representatives capabilities
3401 in annotations file (in progress - not yet fully implemented)</li> -->
3402 <li>Group-associated consensus, sequence logos and
3403 conservation plots</li>
3404 <li>Symbol distributions for each column can be exported
3405 and visualized as sequence logos</li>
3406 <li>Optionally scale multi-character column labels to fit
3407 within each column of annotation row<!-- todo for applet -->
3409 <li>Optional automatic sort of associated alignment view
3410 when a new tree is opened.</li>
3411 <li>Jalview Java Console</li>
3412 <li>Better placement of desktop window when moving
3413 between different screens.</li>
3414 <li>New preference items for sequence ID tooltip and
3415 consensus annotation</li>
3416 <li>Client to submit sequences and IDs to Envision2
3418 <li><em>Vamsas Capabilities</em>
3420 <li>Improved VAMSAS synchronization (Jalview archive
3421 used to preserve views, structures, and tree display
3423 <li>Import of vamsas documents from disk or URL via
3425 <li>Sharing of selected regions between views and
3426 with other VAMSAS applications (Experimental feature!)</li>
3427 <li>Updated API to VAMSAS version 0.2</li>
3429 </ul> <em>Applet</em>
3431 <li>Middle button resizes annotation row height</li>
3434 <li>sortByTree (true/false) - automatically sort the
3435 associated alignment view by the tree when a new tree is
3437 <li>showTreeBootstraps (true/false) - show or hide
3438 branch bootstraps (default is to show them if available)</li>
3439 <li>showTreeDistances (true/false) - show or hide
3440 branch lengths (default is to show them if available)</li>
3441 <li>showUnlinkedTreeNodes (true/false) - indicate if
3442 unassociated nodes should be highlighted in the tree
3444 <li>heightScale and widthScale (1.0 or more) -
3445 increase the height or width of a cell in the alignment
3446 grid relative to the current font size.</li>
3449 <li>Non-positional features displayed in sequence ID
3451 </ul> <em>Other</em>
3453 <li>Features format: graduated colour definitions and
3454 specification of feature scores</li>
3455 <li>Alignment Annotations format: new keywords for group
3456 associated annotation (GROUP_REF) and annotation row display
3457 properties (ROW_PROPERTIES)</li>
3458 <li>XML formats extended to support graduated feature
3459 colourschemes, group associated annotation, and profile
3460 visualization settings.</li></td>
3463 <li>Source field in GFF files parsed as feature source
3464 rather than description</li>
3465 <li>Non-positional features are now included in sequence
3466 feature and gff files (controlled via non-positional feature
3467 visibility in tooltip).</li>
3468 <li>URL links generated for all feature links (bugfix)</li>
3469 <li>Added URL embedding instructions to features file
3471 <li>Codons containing ambiguous nucleotides translated as
3472 'X' in peptide product</li>
3473 <li>Match case switch in find dialog box works for both
3474 sequence ID and sequence string and query strings do not
3475 have to be in upper case to match case-insensitively.</li>
3476 <li>AMSA files only contain first column of
3477 multi-character column annotation labels</li>
3478 <li>Jalview Annotation File generation/parsing consistent
3479 with documentation (e.g. Stockholm annotation can be
3480 exported and re-imported)</li>
3481 <li>PDB files without embedded PDB IDs given a friendly
3483 <li>Find incrementally searches ID string matches as well
3484 as subsequence matches, and correctly reports total number
3488 <li>Better handling of exceptions during sequence
3490 <li>Dasobert generated non-positional feature URL
3491 link text excludes the start_end suffix</li>
3492 <li>DAS feature and source retrieval buttons disabled
3493 when fetch or registry operations in progress.</li>
3494 <li>PDB files retrieved from URLs are cached properly</li>
3495 <li>Sequence description lines properly shared via
3497 <li>Sequence fetcher fetches multiple records for all
3499 <li>Ensured that command line das feature retrieval
3500 completes before alignment figures are generated.</li>
3501 <li>Reduced time taken when opening file browser for
3503 <li>isAligned check prior to calculating tree, PCA or
3504 submitting an MSA to JNet now excludes hidden sequences.</li>
3505 <li>User defined group colours properly recovered
3506 from Jalview projects.</li>
3515 <div align="center">
3516 <strong>2.4.0.b2</strong><br> 28/10/2009
3521 <li>Experimental support for google analytics usage
3523 <li>Jalview privacy settings (user preferences and docs).</li>
3528 <li>Race condition in applet preventing startup in
3530 <li>Exception when feature created from selection beyond
3531 length of sequence.</li>
3532 <li>Allow synthetic PDB files to be imported gracefully</li>
3533 <li>Sequence associated annotation rows associate with
3534 all sequences with a given id</li>
3535 <li>Find function matches case-insensitively for sequence
3536 ID string searches</li>
3537 <li>Non-standard characters do not cause pairwise
3538 alignment to fail with exception</li>
3539 </ul> <em>Application Issues</em>
3541 <li>Sequences are now validated against EMBL database</li>
3542 <li>Sequence fetcher fetches multiple records for all
3544 </ul> <em>InstallAnywhere Issues</em>
3546 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3547 issue with installAnywhere mechanism)</li>
3548 <li>Command line launching of JARs from InstallAnywhere
3549 version (java class versioning error fixed)</li>
3556 <div align="center">
3557 <strong>2.4</strong><br> 27/8/2008
3560 <td><em>User Interface</em>
3562 <li>Linked highlighting of codon and amino acid from
3563 translation and protein products</li>
3564 <li>Linked highlighting of structure associated with
3565 residue mapping to codon position</li>
3566 <li>Sequence Fetcher provides example accession numbers
3567 and 'clear' button</li>
3568 <li>MemoryMonitor added as an option under Desktop's
3570 <li>Extract score function to parse whitespace separated
3571 numeric data in description line</li>
3572 <li>Column labels in alignment annotation can be centred.</li>
3573 <li>Tooltip for sequence associated annotation give name
3575 </ul> <em>Web Services and URL fetching</em>
3577 <li>JPred3 web service</li>
3578 <li>Prototype sequence search client (no public services
3580 <li>Fetch either seed alignment or full alignment from
3582 <li>URL Links created for matching database cross
3583 references as well as sequence ID</li>
3584 <li>URL Links can be created using regular-expressions</li>
3585 </ul> <em>Sequence Database Connectivity</em>
3587 <li>Retrieval of cross-referenced sequences from other
3589 <li>Generalised database reference retrieval and
3590 validation to all fetchable databases</li>
3591 <li>Fetch sequences from DAS sources supporting the
3592 sequence command</li>
3593 </ul> <em>Import and Export</em>
3594 <li>export annotation rows as CSV for spreadsheet import</li>
3595 <li>Jalview projects record alignment dataset associations,
3596 EMBL products, and cDNA sequence mappings</li>
3597 <li>Sequence Group colour can be specified in Annotation
3599 <li>Ad-hoc colouring of group in Annotation File using RGB
3600 triplet as name of colourscheme</li>
3601 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3603 <li>treenode binding for VAMSAS tree exchange</li>
3604 <li>local editing and update of sequences in VAMSAS
3605 alignments (experimental)</li>
3606 <li>Create new or select existing session to join</li>
3607 <li>load and save of vamsas documents</li>
3608 </ul> <em>Application command line</em>
3610 <li>-tree parameter to open trees (introduced for passing
3612 <li>-fetchfrom command line argument to specify nicknames
3613 of DAS servers to query for alignment features</li>
3614 <li>-dasserver command line argument to add new servers
3615 that are also automatically queried for features</li>
3616 <li>-groovy command line argument executes a given groovy
3617 script after all input data has been loaded and parsed</li>
3618 </ul> <em>Applet-Application data exchange</em>
3620 <li>Trees passed as applet parameters can be passed to
3621 application (when using "View in full
3622 application")</li>
3623 </ul> <em>Applet Parameters</em>
3625 <li>feature group display control parameter</li>
3626 <li>debug parameter</li>
3627 <li>showbutton parameter</li>
3628 </ul> <em>Applet API methods</em>
3630 <li>newView public method</li>
3631 <li>Window (current view) specific get/set public methods</li>
3632 <li>Feature display control methods</li>
3633 <li>get list of currently selected sequences</li>
3634 </ul> <em>New Jalview distribution features</em>
3636 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3637 <li>RELEASE file gives build properties for the latest
3638 Jalview release.</li>
3639 <li>Java 1.1 Applet build made easier and donotobfuscate
3640 property controls execution of obfuscator</li>
3641 <li>Build target for generating source distribution</li>
3642 <li>Debug flag for javacc</li>
3643 <li>.jalview_properties file is documented (slightly) in
3644 jalview.bin.Cache</li>
3645 <li>Continuous Build Integration for stable and
3646 development version of Application, Applet and source
3651 <li>selected region output includes visible annotations
3652 (for certain formats)</li>
3653 <li>edit label/displaychar contains existing label/char
3655 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3656 <li>shorter peptide product names from EMBL records</li>
3657 <li>Newick string generator makes compact representations</li>
3658 <li>bootstrap values parsed correctly for tree files with
3660 <li>pathological filechooser bug avoided by not allowing
3661 filenames containing a ':'</li>
3662 <li>Fixed exception when parsing GFF files containing
3663 global sequence features</li>
3664 <li>Alignment datasets are finalized only when number of
3665 references from alignment sequences goes to zero</li>
3666 <li>Close of tree branch colour box without colour
3667 selection causes cascading exceptions</li>
3668 <li>occasional negative imgwidth exceptions</li>
3669 <li>better reporting of non-fatal warnings to user when
3670 file parsing fails.</li>
3671 <li>Save works when Jalview project is default format</li>
3672 <li>Save as dialog opened if current alignment format is
3673 not a valid output format</li>
3674 <li>UniProt canonical names introduced for both das and
3676 <li>Histidine should be midblue (not pink!) in Zappo</li>
3677 <li>error messages passed up and output when data read
3679 <li>edit undo recovers previous dataset sequence when
3680 sequence is edited</li>
3681 <li>allow PDB files without pdb ID HEADER lines (like
3682 those generated by MODELLER) to be read in properly</li>
3683 <li>allow reading of JPred concise files as a normal
3685 <li>Stockholm annotation parsing and alignment properties
3686 import fixed for PFAM records</li>
3687 <li>Structure view windows have correct name in Desktop
3689 <li>annotation consisting of sequence associated scores
3690 can be read and written correctly to annotation file</li>
3691 <li>Aligned cDNA translation to aligned peptide works
3693 <li>Fixed display of hidden sequence markers and
3694 non-italic font for representatives in Applet</li>
3695 <li>Applet Menus are always embedded in applet window on
3697 <li>Newly shown features appear at top of stack (in
3699 <li>Annotations added via parameter not drawn properly
3700 due to null pointer exceptions</li>
3701 <li>Secondary structure lines are drawn starting from
3702 first column of alignment</li>
3703 <li>UniProt XML import updated for new schema release in
3705 <li>Sequence feature to sequence ID match for Features
3706 file is case-insensitive</li>
3707 <li>Sequence features read from Features file appended to
3708 all sequences with matching IDs</li>
3709 <li>PDB structure coloured correctly for associated views
3710 containing a sub-sequence</li>
3711 <li>PDB files can be retrieved by applet from Jar files</li>
3712 <li>feature and annotation file applet parameters
3713 referring to different directories are retrieved correctly</li>
3714 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3715 <li>Fixed application hang whilst waiting for
3716 splash-screen version check to complete</li>
3717 <li>Applet properly URLencodes input parameter values
3718 when passing them to the launchApp service</li>
3719 <li>display name and local features preserved in results
3720 retrieved from web service</li>
3721 <li>Visual delay indication for sequence retrieval and
3722 sequence fetcher initialisation</li>
3723 <li>updated Application to use DAS 1.53e version of
3724 dasobert DAS client</li>
3725 <li>Re-instated Full AMSA support and .amsa file
3727 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3735 <div align="center">
3736 <strong>2.3</strong><br> 9/5/07
3741 <li>Jmol 11.0.2 integration</li>
3742 <li>PDB views stored in Jalview XML files</li>
3743 <li>Slide sequences</li>
3744 <li>Edit sequence in place</li>
3745 <li>EMBL CDS features</li>
3746 <li>DAS Feature mapping</li>
3747 <li>Feature ordering</li>
3748 <li>Alignment Properties</li>
3749 <li>Annotation Scores</li>
3750 <li>Sort by scores</li>
3751 <li>Feature/annotation editing in applet</li>
3756 <li>Headless state operation in 2.2.1</li>
3757 <li>Incorrect and unstable DNA pairwise alignment</li>
3758 <li>Cut and paste of sequences with annotation</li>
3759 <li>Feature group display state in XML</li>
3760 <li>Feature ordering in XML</li>
3761 <li>blc file iteration selection using filename # suffix</li>
3762 <li>Stockholm alignment properties</li>
3763 <li>Stockhom alignment secondary structure annotation</li>
3764 <li>2.2.1 applet had no feature transparency</li>
3765 <li>Number pad keys can be used in cursor mode</li>
3766 <li>Structure Viewer mirror image resolved</li>
3773 <div align="center">
3774 <strong>2.2.1</strong><br> 12/2/07
3779 <li>Non standard characters can be read and displayed
3780 <li>Annotations/Features can be imported/exported to the
3782 <li>Applet allows editing of sequence/annotation/group
3783 name & description
3784 <li>Preference setting to display sequence name in
3786 <li>Annotation file format extended to allow
3787 Sequence_groups to be defined
3788 <li>Default opening of alignment overview panel can be
3789 specified in preferences
3790 <li>PDB residue numbering annotation added to associated
3796 <li>Applet crash under certain Linux OS with Java 1.6
3798 <li>Annotation file export / import bugs fixed
3799 <li>PNG / EPS image output bugs fixed
3805 <div align="center">
3806 <strong>2.2</strong><br> 27/11/06
3811 <li>Multiple views on alignment
3812 <li>Sequence feature editing
3813 <li>"Reload" alignment
3814 <li>"Save" to current filename
3815 <li>Background dependent text colour
3816 <li>Right align sequence ids
3817 <li>User-defined lower case residue colours
3820 <li>Menu item accelerator keys
3821 <li>Control-V pastes to current alignment
3822 <li>Cancel button for DAS Feature Fetching
3823 <li>PCA and PDB Viewers zoom via mouse roller
3824 <li>User-defined sub-tree colours and sub-tree selection
3826 <li>'New Window' button on the 'Output to Text box'
3831 <li>New memory efficient Undo/Redo System
3832 <li>Optimised symbol lookups and conservation/consensus
3834 <li>Region Conservation/Consensus recalculated after
3836 <li>Fixed Remove Empty Columns Bug (empty columns at end
3838 <li>Slowed DAS Feature Fetching for increased robustness.
3840 <li>Made angle brackets in ASCII feature descriptions
3842 <li>Re-instated Zoom function for PCA
3843 <li>Sequence descriptions conserved in web service
3845 <li>UniProt ID discoverer uses any word separated by
3847 <li>WsDbFetch query/result association resolved
3848 <li>Tree leaf to sequence mapping improved
3849 <li>Smooth fonts switch moved to FontChooser dialog box.
3856 <div align="center">
3857 <strong>2.1.1</strong><br> 12/9/06
3862 <li>Copy consensus sequence to clipboard</li>
3867 <li>Image output - rightmost residues are rendered if
3868 sequence id panel has been resized</li>
3869 <li>Image output - all offscreen group boundaries are
3871 <li>Annotation files with sequence references - all
3872 elements in file are relative to sequence position</li>
3873 <li>Mac Applet users can use Alt key for group editing</li>
3879 <div align="center">
3880 <strong>2.1</strong><br> 22/8/06
3885 <li>MAFFT Multiple Alignment in default Web Service list</li>
3886 <li>DAS Feature fetching</li>
3887 <li>Hide sequences and columns</li>
3888 <li>Export Annotations and Features</li>
3889 <li>GFF file reading / writing</li>
3890 <li>Associate structures with sequences from local PDB
3892 <li>Add sequences to exisiting alignment</li>
3893 <li>Recently opened files / URL lists</li>
3894 <li>Applet can launch the full application</li>
3895 <li>Applet has transparency for features (Java 1.2
3897 <li>Applet has user defined colours parameter</li>
3898 <li>Applet can load sequences from parameter
3899 "sequence<em>x</em>"
3905 <li>Redundancy Panel reinstalled in the Applet</li>
3906 <li>Monospaced font - EPS / rescaling bug fixed</li>
3907 <li>Annotation files with sequence references bug fixed</li>
3913 <div align="center">
3914 <strong>2.08.1</strong><br> 2/5/06
3919 <li>Change case of selected region from Popup menu</li>
3920 <li>Choose to match case when searching</li>
3921 <li>Middle mouse button and mouse movement can compress /
3922 expand the visible width and height of the alignment</li>
3927 <li>Annotation Panel displays complete JNet results</li>
3933 <div align="center">
3934 <strong>2.08b</strong><br> 18/4/06
3940 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3941 <li>Righthand label on wrapped alignments shows correct
3948 <div align="center">
3949 <strong>2.08</strong><br> 10/4/06
3954 <li>Editing can be locked to the selection area</li>
3955 <li>Keyboard editing</li>
3956 <li>Create sequence features from searches</li>
3957 <li>Precalculated annotations can be loaded onto
3959 <li>Features file allows grouping of features</li>
3960 <li>Annotation Colouring scheme added</li>
3961 <li>Smooth fonts off by default - Faster rendering</li>
3962 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3967 <li>Drag & Drop fixed on Linux</li>
3968 <li>Jalview Archive file faster to load/save, sequence
3969 descriptions saved.</li>
3975 <div align="center">
3976 <strong>2.07</strong><br> 12/12/05
3981 <li>PDB Structure Viewer enhanced</li>
3982 <li>Sequence Feature retrieval and display enhanced</li>
3983 <li>Choose to output sequence start-end after sequence
3984 name for file output</li>
3985 <li>Sequence Fetcher WSDBFetch@EBI</li>
3986 <li>Applet can read feature files, PDB files and can be
3987 used for HTML form input</li>
3992 <li>HTML output writes groups and features</li>
3993 <li>Group editing is Control and mouse click</li>
3994 <li>File IO bugs</li>
4000 <div align="center">
4001 <strong>2.06</strong><br> 28/9/05
4006 <li>View annotations in wrapped mode</li>
4007 <li>More options for PCA viewer</li>
4012 <li>GUI bugs resolved</li>
4013 <li>Runs with -nodisplay from command line</li>
4019 <div align="center">
4020 <strong>2.05b</strong><br> 15/9/05
4025 <li>Choose EPS export as lineart or text</li>
4026 <li>Jar files are executable</li>
4027 <li>Can read in Uracil - maps to unknown residue</li>
4032 <li>Known OutOfMemory errors give warning message</li>
4033 <li>Overview window calculated more efficiently</li>
4034 <li>Several GUI bugs resolved</li>
4040 <div align="center">
4041 <strong>2.05</strong><br> 30/8/05
4046 <li>Edit and annotate in "Wrapped" view</li>
4051 <li>Several GUI bugs resolved</li>
4057 <div align="center">
4058 <strong>2.04</strong><br> 24/8/05
4063 <li>Hold down mouse wheel & scroll to change font
4069 <li>Improved JPred client reliability</li>
4070 <li>Improved loading of Jalview files</li>
4076 <div align="center">
4077 <strong>2.03</strong><br> 18/8/05
4082 <li>Set Proxy server name and port in preferences</li>
4083 <li>Multiple URL links from sequence ids</li>
4084 <li>User Defined Colours can have a scheme name and added
4086 <li>Choose to ignore gaps in consensus calculation</li>
4087 <li>Unix users can set default web browser</li>
4088 <li>Runs without GUI for batch processing</li>
4089 <li>Dynamically generated Web Service Menus</li>
4094 <li>InstallAnywhere download for Sparc Solaris</li>
4100 <div align="center">
4101 <strong>2.02</strong><br> 18/7/05
4107 <li>Copy & Paste order of sequences maintains
4108 alignment order.</li>
4114 <div align="center">
4115 <strong>2.01</strong><br> 12/7/05
4120 <li>Use delete key for deleting selection.</li>
4121 <li>Use Mouse wheel to scroll sequences.</li>
4122 <li>Help file updated to describe how to add alignment
4124 <li>Version and build date written to build properties
4126 <li>InstallAnywhere installation will check for updates
4127 at launch of Jalview.</li>
4132 <li>Delete gaps bug fixed.</li>
4133 <li>FileChooser sorts columns.</li>
4134 <li>Can remove groups one by one.</li>
4135 <li>Filechooser icons installed.</li>
4136 <li>Finder ignores return character when searching.
4137 Return key will initiate a search.<br>
4144 <div align="center">
4145 <strong>2.0</strong><br> 20/6/05
4150 <li>New codebase</li>