3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>4/09/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-3065 -->Change in recommended way of starting
81 Jalview via a Java command line: add jars in lib directory
82 to CLASSPATH, rather than via the deprecated java.ext.dirs
87 <td><div align="left">
91 <!-- JAL-247 -->Hidden sequence markers and representative
92 sequence bolding included when exporting alignment as EPS,
93 SVG, PNG or HTML. <em>Display of these can be
94 configured via the Format menu or in batch mode with a
95 jalview properties file.</em>
98 <!-- JAL-3087 -->Corrupted display when switching to
99 wrapped mode when sequence panel's vertical scrollbar is
103 <!-- JAL-3003 -->Alignment is black in exported EPS file
104 when sequences are selected in exported view.</em>
107 <!-- JAL-3059 -->Groups with different coloured borders
108 aren't rendered with correct colour.
111 <!-- JAL-3092 -->Jalview could hang when importing certain
112 types of knotted RNA secondary structure
115 <!-- JAL-3095 -->Sequence highlight and selection in
116 trimmed VARNA 2D structure is incorrect for sequences that
120 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
121 annotation when columns are inserted into an alignment
124 <!-- JAL-3061 -->'.' written into RNA secondary structure
125 annotation when writing out Stockholm format
128 <!-- JAL-3053 -->Jalview annotation rows containing upper
129 and lower-case 'E' and 'H' do not automatically get
130 treated as RNA secondary structure
137 <td width="60" nowrap>
139 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
140 <em>7/06/2018</em></strong>
143 <td><div align="left">
147 <!-- JAL-2920 -->Use HGVS nomenclature for variant
148 annotation retrieved from Uniprot
151 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
152 onto the Jalview Desktop
156 <td><div align="left">
160 <!-- JAL-3017 -->Cannot import features with multiple
161 variant elements (blocks import of some Uniprot records)
164 <!-- JAL-2997 -->Clustal files with sequence positions in
165 right-hand column parsed correctly
168 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
169 not alignment area in exported graphic
172 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
173 window has input focus
176 <!-- JAL-2992 -->Annotation panel set too high when
177 annotation added to view (Windows)
180 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
181 network connectivity is poor
184 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
185 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
186 the currently open URL and links from a page viewed in
187 Firefox or Chrome on Windows is now fully supported. If
188 you are using Edge, only links in the page can be
189 dragged, and with Internet Explorer, only the currently
190 open URL in the browser can be dropped onto Jalview.</em>
196 <td width="60" nowrap>
198 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
201 <td><div align="left">
205 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
206 for disabling automatic superposition of multiple
207 structures and open structures in existing views
210 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
211 ID and annotation area margins can be click-dragged to
215 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
219 <!-- JAL-2759 -->Improved performance for large alignments
220 and lots of hidden columns
223 <!-- JAL-2593 -->Improved performance when rendering lots
224 of features (particularly when transparency is disabled)
229 <td><div align="left">
232 <!-- JAL-2899 -->Structure and Overview aren't updated
233 when Colour By Annotation threshold slider is adjusted
236 <!-- JAL-2778 -->Slow redraw when Overview panel shown
237 overlapping alignment panel
240 <!-- JAL-2929 -->Overview doesn't show end of unpadded
244 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
245 improved: CDS not handled correctly if transcript has no
249 <!-- JAL-2321 -->Secondary structure and temperature
250 factor annotation not added to sequence when local PDB
251 file associated with it by drag'n'drop or structure
255 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
256 dialog doesn't import PDB files dropped on an alignment
259 <!-- JAL-2666 -->Linked scrolling via protein horizontal
260 scroll bar doesn't work for some CDS/Protein views
263 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
264 Java 1.8u153 onwards and Java 1.9u4+.
267 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
268 columns in annotation row
271 <!-- JAL-2913 -->Preferences panel's ID Width control is not
272 honored in batch mode
275 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
276 for structures added to existing Jmol view
279 <!-- JAL-2223 -->'View Mappings' includes duplicate
280 entries after importing project with multiple views
283 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
284 protein sequences via SIFTS from associated PDB entries
285 with negative residue numbers or missing residues fails
288 <!-- JAL-2952 -->Exception when shading sequence with negative
289 Temperature Factor values from annotated PDB files (e.g.
290 as generated by CONSURF)
293 <!-- JAL-2920 -->Uniprot 'sequence variant' features
294 tooltip doesn't include a text description of mutation
297 <!-- JAL-2922 -->Invert displayed features very slow when
298 structure and/or overview windows are also shown
301 <!-- JAL-2954 -->Selecting columns from highlighted regions
302 very slow for alignments with large numbers of sequences
305 <!-- JAL-2925 -->Copy Consensus fails for group consensus
306 with 'StringIndexOutOfBounds'
309 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
310 platforms running Java 10
313 <!-- JAL-2960 -->Adding a structure to existing structure
314 view appears to do nothing because the view is hidden behind the alignment view
320 <!-- JAL-2926 -->Copy consensus sequence option in applet
321 should copy the group consensus when popup is opened on it
327 <!-- JAL-2913 -->Fixed ID width preference is not respected
330 <em>New Known Defects</em>
333 <!-- JAL-2973 --> Exceptions occasionally raised when
334 editing a large alignment and overview is displayed
337 <!-- JAL-2974 -->'Overview updating' progress bar is shown
338 repeatedly after a series of edits even when the overview
339 is no longer reflecting updates
342 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
343 structures for protein subsequence (if 'Trim Retrieved
344 Sequences' enabled) or Ensembl isoforms (Workaround in
345 2.10.4 is to fail back to N&W mapping)
352 <td width="60" nowrap>
354 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
357 <td><div align="left">
358 <ul><li>Updated Certum Codesigning Certificate
359 (Valid till 30th November 2018)</li></ul></div></td>
360 <td><div align="left">
363 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
364 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
365 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
366 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
367 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
368 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
369 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
375 <td width="60" nowrap>
377 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
380 <td><div align="left">
384 <!-- JAL-2446 -->Faster and more efficient management and
385 rendering of sequence features
388 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
389 429 rate limit request hander
392 <!-- JAL-2773 -->Structure views don't get updated unless
393 their colours have changed
396 <!-- JAL-2495 -->All linked sequences are highlighted for
397 a structure mousover (Jmol) or selection (Chimera)
400 <!-- JAL-2790 -->'Cancel' button in progress bar for
401 JABAWS AACon, RNAAliFold and Disorder prediction jobs
404 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
405 view from Ensembl locus cross-references
408 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
412 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
413 feature can be disabled
416 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
417 PDB easier retrieval of sequences for lists of IDs
420 <!-- JAL-2758 -->Short names for sequences retrieved from
426 <li>Groovy interpreter updated to 2.4.12</li>
427 <li>Example groovy script for generating a matrix of
428 percent identity scores for current alignment.</li>
430 <em>Testing and Deployment</em>
433 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
437 <td><div align="left">
441 <!-- JAL-2643 -->Pressing tab after updating the colour
442 threshold text field doesn't trigger an update to the
446 <!-- JAL-2682 -->Race condition when parsing sequence ID
450 <!-- JAL-2608 -->Overview windows are also closed when
451 alignment window is closed
454 <!-- JAL-2548 -->Export of features doesn't always respect
458 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
459 takes a long time in Cursor mode
465 <!-- JAL-2777 -->Structures with whitespace chainCode
466 cannot be viewed in Chimera
469 <!-- JAL-2728 -->Protein annotation panel too high in
473 <!-- JAL-2757 -->Can't edit the query after the server
474 error warning icon is shown in Uniprot and PDB Free Text
478 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
481 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
484 <!-- JAL-2739 -->Hidden column marker in last column not
485 rendered when switching back from Wrapped to normal view
488 <!-- JAL-2768 -->Annotation display corrupted when
489 scrolling right in unwapped alignment view
492 <!-- JAL-2542 -->Existing features on subsequence
493 incorrectly relocated when full sequence retrieved from
497 <!-- JAL-2733 -->Last reported memory still shown when
498 Desktop->Show Memory is unticked (OSX only)
501 <!-- JAL-2658 -->Amend Features dialog doesn't allow
502 features of same type and group to be selected for
506 <!-- JAL-2524 -->Jalview becomes sluggish in wide
507 alignments when hidden columns are present
510 <!-- JAL-2392 -->Jalview freezes when loading and
511 displaying several structures
514 <!-- JAL-2732 -->Black outlines left after resizing or
518 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
519 within the Jalview desktop on OSX
522 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
523 when in wrapped alignment mode
526 <!-- JAL-2636 -->Scale mark not shown when close to right
527 hand end of alignment
530 <!-- JAL-2684 -->Pairwise alignment of selected regions of
531 each selected sequence do not have correct start/end
535 <!-- JAL-2793 -->Alignment ruler height set incorrectly
536 after canceling the Alignment Window's Font dialog
539 <!-- JAL-2036 -->Show cross-references not enabled after
540 restoring project until a new view is created
543 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
544 URL links appears when only default EMBL-EBI link is
545 configured (since 2.10.2b2)
548 <!-- JAL-2775 -->Overview redraws whole window when box
552 <!-- JAL-2225 -->Structure viewer doesn't map all chains
553 in a multi-chain structure when viewing alignment
554 involving more than one chain (since 2.10)
557 <!-- JAL-2811 -->Double residue highlights in cursor mode
558 if new selection moves alignment window
561 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
562 arrow key in cursor mode to pass hidden column marker
565 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
566 that produces correctly annotated transcripts and products
569 <!-- JAL-2776 -->Toggling a feature group after first time
570 doesn't update associated structure view
573 <em>Applet</em><br />
576 <!-- JAL-2687 -->Concurrent modification exception when
577 closing alignment panel
580 <em>BioJSON</em><br />
583 <!-- JAL-2546 -->BioJSON export does not preserve
584 non-positional features
587 <em>New Known Issues</em>
590 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
591 sequence features correctly (for many previous versions of
595 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
596 using cursor in wrapped panel other than top
599 <!-- JAL-2791 -->Select columns containing feature ignores
600 graduated colour threshold
603 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
604 always preserve numbering and sequence features
607 <em>Known Java 9 Issues</em>
610 <!-- JAL-2902 -->Groovy Console very slow to open and is
611 not responsive when entering characters (Webstart, Java
618 <td width="60" nowrap>
620 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
621 <em>2/10/2017</em></strong>
624 <td><div align="left">
625 <em>New features in Jalview Desktop</em>
628 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
630 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
634 <td><div align="left">
638 <td width="60" nowrap>
640 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
641 <em>7/9/2017</em></strong>
644 <td><div align="left">
648 <!-- JAL-2588 -->Show gaps in overview window by colouring
649 in grey (sequences used to be coloured grey, and gaps were
653 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
657 <!-- JAL-2587 -->Overview updates immediately on increase
658 in size and progress bar shown as higher resolution
659 overview is recalculated
664 <td><div align="left">
668 <!-- JAL-2664 -->Overview window redraws every hidden
669 column region row by row
672 <!-- JAL-2681 -->duplicate protein sequences shown after
673 retrieving Ensembl crossrefs for sequences from Uniprot
676 <!-- JAL-2603 -->Overview window throws NPE if show boxes
677 format setting is unticked
680 <!-- JAL-2610 -->Groups are coloured wrongly in overview
681 if group has show boxes format setting unticked
684 <!-- JAL-2672,JAL-2665 -->Redraw problems when
685 autoscrolling whilst dragging current selection group to
686 include sequences and columns not currently displayed
689 <!-- JAL-2691 -->Not all chains are mapped when multimeric
690 assemblies are imported via CIF file
693 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
694 displayed when threshold or conservation colouring is also
698 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
702 <!-- JAL-2673 -->Jalview continues to scroll after
703 dragging a selected region off the visible region of the
707 <!-- JAL-2724 -->Cannot apply annotation based
708 colourscheme to all groups in a view
711 <!-- JAL-2511 -->IDs don't line up with sequences
712 initially after font size change using the Font chooser or
719 <td width="60" nowrap>
721 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
724 <td><div align="left">
725 <em>Calculations</em>
729 <!-- JAL-1933 -->Occupancy annotation row shows number of
730 ungapped positions in each column of the alignment.
733 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
734 a calculation dialog box
737 <!-- JAL-2379 -->Revised implementation of PCA for speed
738 and memory efficiency (~30x faster)
741 <!-- JAL-2403 -->Revised implementation of sequence
742 similarity scores as used by Tree, PCA, Shading Consensus
743 and other calculations
746 <!-- JAL-2416 -->Score matrices are stored as resource
747 files within the Jalview codebase
750 <!-- JAL-2500 -->Trees computed on Sequence Feature
751 Similarity may have different topology due to increased
758 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
759 model for alignments and groups
762 <!-- JAL-384 -->Custom shading schemes created via groovy
769 <!-- JAL-2526 -->Efficiency improvements for interacting
770 with alignment and overview windows
773 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
777 <!-- JAL-2388 -->Hidden columns and sequences can be
781 <!-- JAL-2611 -->Click-drag in visible area allows fine
782 adjustment of visible position
786 <em>Data import/export</em>
789 <!-- JAL-2535 -->Posterior probability annotation from
790 Stockholm files imported as sequence associated annotation
793 <!-- JAL-2507 -->More robust per-sequence positional
794 annotation input/output via stockholm flatfile
797 <!-- JAL-2533 -->Sequence names don't include file
798 extension when importing structure files without embedded
799 names or PDB accessions
802 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
803 format sequence substitution matrices
806 <em>User Interface</em>
809 <!-- JAL-2447 --> Experimental Features Checkbox in
810 Desktop's Tools menu to hide or show untested features in
814 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
815 via Overview or sequence motif search operations
818 <!-- JAL-2547 -->Amend sequence features dialog box can be
819 opened by double clicking gaps within sequence feature
823 <!-- JAL-1476 -->Status bar message shown when not enough
824 aligned positions were available to create a 3D structure
828 <em>3D Structure</em>
831 <!-- JAL-2430 -->Hidden regions in alignment views are not
832 coloured in linked structure views
835 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
836 file-based command exchange
839 <!-- JAL-2375 -->Structure chooser automatically shows
840 Cached Structures rather than querying the PDBe if
841 structures are already available for sequences
844 <!-- JAL-2520 -->Structures imported via URL are cached in
845 the Jalview project rather than downloaded again when the
849 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
850 to transfer Chimera's structure attributes as Jalview
851 features, and vice-versa (<strong>Experimental
855 <em>Web Services</em>
858 <!-- JAL-2549 -->Updated JABAWS client to v2.2
861 <!-- JAL-2335 -->Filter non-standard amino acids and
862 nucleotides when submitting to AACon and other MSA
866 <!-- JAL-2316, -->URLs for viewing database
867 cross-references provided by identifiers.org and the
875 <!-- JAL-2344 -->FileFormatI interface for describing and
876 identifying file formats (instead of String constants)
879 <!-- JAL-2228 -->FeatureCounter script refactored for
880 efficiency when counting all displayed features (not
881 backwards compatible with 2.10.1)
884 <em>Example files</em>
887 <!-- JAL-2631 -->Graduated feature colour style example
888 included in the example feature file
891 <em>Documentation</em>
894 <!-- JAL-2339 -->Release notes reformatted for readability
895 with the built-in Java help viewer
898 <!-- JAL-1644 -->Find documentation updated with 'search
899 sequence description' option
905 <!-- JAL-2485, -->External service integration tests for
906 Uniprot REST Free Text Search Client
909 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
912 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
917 <td><div align="left">
918 <em>Calculations</em>
921 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
922 matrix - C->R should be '-3'<br />Old matrix restored
923 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
925 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
926 Jalview's treatment of gaps in PCA and substitution matrix
927 based Tree calculations.<br /> <br />In earlier versions
928 of Jalview, gaps matching gaps were penalised, and gaps
929 matching non-gaps penalised even more. In the PCA
930 calculation, gaps were actually treated as non-gaps - so
931 different costs were applied, which meant Jalview's PCAs
932 were different to those produced by SeqSpace.<br />Jalview
933 now treats gaps in the same way as SeqSpace (ie it scores
934 them as 0). <br /> <br />Enter the following in the
935 Groovy console to restore pre-2.10.2 behaviour:<br />
936 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
937 // for 2.10.1 mode <br />
938 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
939 // to restore 2.10.2 mode <br /> <br /> <em>Note:
940 these settings will affect all subsequent tree and PCA
941 calculations (not recommended)</em></li>
943 <!-- JAL-2424 -->Fixed off-by-one bug that affected
944 scaling of branch lengths for trees computed using
945 Sequence Feature Similarity.
948 <!-- JAL-2377 -->PCA calculation could hang when
949 generating output report when working with highly
953 <!-- JAL-2544 --> Sort by features includes features to
954 right of selected region when gaps present on right-hand
958 <em>User Interface</em>
961 <!-- JAL-2346 -->Reopening Colour by annotation dialog
962 doesn't reselect a specific sequence's associated
963 annotation after it was used for colouring a view
966 <!-- JAL-2419 -->Current selection lost if popup menu
967 opened on a region of alignment without groups
970 <!-- JAL-2374 -->Popup menu not always shown for regions
971 of an alignment with overlapping groups
974 <!-- JAL-2310 -->Finder double counts if both a sequence's
975 name and description match
978 <!-- JAL-2370 -->Hiding column selection containing two
979 hidden regions results in incorrect hidden regions
982 <!-- JAL-2386 -->'Apply to all groups' setting when
983 changing colour does not apply Conservation slider value
987 <!-- JAL-2373 -->Percentage identity and conservation menu
988 items do not show a tick or allow shading to be disabled
991 <!-- JAL-2385 -->Conservation shading or PID threshold
992 lost when base colourscheme changed if slider not visible
995 <!-- JAL-2547 -->Sequence features shown in tooltip for
996 gaps before start of features
999 <!-- JAL-2623 -->Graduated feature colour threshold not
1000 restored to UI when feature colour is edited
1003 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
1004 a time when scrolling vertically in wrapped mode.
1007 <!-- JAL-2630 -->Structure and alignment overview update
1008 as graduate feature colour settings are modified via the
1012 <!-- JAL-2034 -->Overview window doesn't always update
1013 when a group defined on the alignment is resized
1016 <!-- JAL-2605 -->Mouseovers on left/right scale region in
1017 wrapped view result in positional status updates
1021 <!-- JAL-2563 -->Status bar doesn't show position for
1022 ambiguous amino acid and nucleotide symbols
1025 <!-- JAL-2602 -->Copy consensus sequence failed if
1026 alignment included gapped columns
1029 <!-- JAL-2473 -->Minimum size set for Jalview windows so
1030 widgets don't permanently disappear
1033 <!-- JAL-2503 -->Cannot select or filter quantitative
1034 annotation that are shown only as column labels (e.g.
1035 T-Coffee column reliability scores)
1038 <!-- JAL-2594 -->Exception thrown if trying to create a
1039 sequence feature on gaps only
1042 <!-- JAL-2504 -->Features created with 'New feature'
1043 button from a Find inherit previously defined feature type
1044 rather than the Find query string
1047 <!-- JAL-2423 -->incorrect title in output window when
1048 exporting tree calculated in Jalview
1051 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
1052 and then revealing them reorders sequences on the
1056 <!-- JAL-964 -->Group panel in sequence feature settings
1057 doesn't update to reflect available set of groups after
1058 interactively adding or modifying features
1061 <!-- JAL-2225 -->Sequence Database chooser unusable on
1065 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
1066 only excluded gaps in current sequence and ignored
1073 <!-- JAL-2421 -->Overview window visible region moves
1074 erratically when hidden rows or columns are present
1077 <!-- JAL-2362 -->Per-residue colourschemes applied via the
1078 Structure Viewer's colour menu don't correspond to
1082 <!-- JAL-2405 -->Protein specific colours only offered in
1083 colour and group colour menu for protein alignments
1086 <!-- JAL-2385 -->Colour threshold slider doesn't update to
1087 reflect currently selected view or group's shading
1091 <!-- JAL-2624 -->Feature colour thresholds not respected
1092 when rendered on overview and structures when opacity at
1096 <!-- JAL-2589 -->User defined gap colour not shown in
1097 overview when features overlaid on alignment
1100 <em>Data import/export</em>
1103 <!-- JAL-2576 -->Very large alignments take a long time to
1107 <!-- JAL-2507 -->Per-sequence RNA secondary structures
1108 added after a sequence was imported are not written to
1112 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
1113 when importing RNA secondary structure via Stockholm
1116 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
1117 not shown in correct direction for simple pseudoknots
1120 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
1121 with lightGray or darkGray via features file (but can
1125 <!-- JAL-2383 -->Above PID colour threshold not recovered
1126 when alignment view imported from project
1129 <!-- JAL-2520,JAL-2465 -->No mappings generated between
1130 structure and sequences extracted from structure files
1131 imported via URL and viewed in Jmol
1134 <!-- JAL-2520 -->Structures loaded via URL are saved in
1135 Jalview Projects rather than fetched via URL again when
1136 the project is loaded and the structure viewed
1139 <em>Web Services</em>
1142 <!-- JAL-2519 -->EnsemblGenomes example failing after
1143 release of Ensembl v.88
1146 <!-- JAL-2366 -->Proxy server address and port always
1147 appear enabled in Preferences->Connections
1150 <!-- JAL-2461 -->DAS registry not found exceptions
1151 removed from console output
1154 <!-- JAL-2582 -->Cannot retrieve protein products from
1155 Ensembl by Peptide ID
1158 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1159 created from SIFTs, and spurious 'Couldn't open structure
1160 in Chimera' errors raised after April 2017 update (problem
1161 due to 'null' string rather than empty string used for
1162 residues with no corresponding PDB mapping).
1165 <em>Application UI</em>
1168 <!-- JAL-2361 -->User Defined Colours not added to Colour
1172 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1173 case' residues (button in colourscheme editor debugged and
1174 new documentation and tooltips added)
1177 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1178 doesn't restore group-specific text colour thresholds
1181 <!-- JAL-2243 -->Feature settings panel does not update as
1182 new features are added to alignment
1185 <!-- JAL-2532 -->Cancel in feature settings reverts
1186 changes to feature colours via the Amend features dialog
1189 <!-- JAL-2506 -->Null pointer exception when attempting to
1190 edit graduated feature colour via amend features dialog
1194 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1195 selection menu changes colours of alignment views
1198 <!-- JAL-2426 -->Spurious exceptions in console raised
1199 from alignment calculation workers after alignment has
1203 <!-- JAL-1608 -->Typo in selection popup menu - Create
1204 groups now 'Create Group'
1207 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1208 Create/Undefine group doesn't always work
1211 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1212 shown again after pressing 'Cancel'
1215 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1216 adjusts start position in wrap mode
1219 <!-- JAL-2563 -->Status bar doesn't show positions for
1220 ambiguous amino acids
1223 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1224 CDS/Protein view after CDS sequences added for aligned
1228 <!-- JAL-2592 -->User defined colourschemes called 'User
1229 Defined' don't appear in Colours menu
1235 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1236 score models doesn't always result in an updated PCA plot
1239 <!-- JAL-2442 -->Features not rendered as transparent on
1240 overview or linked structure view
1243 <!-- JAL-2372 -->Colour group by conservation doesn't
1247 <!-- JAL-2517 -->Hitting Cancel after applying
1248 user-defined colourscheme doesn't restore original
1255 <!-- JAL-2314 -->Unit test failure:
1256 jalview.ws.jabaws.RNAStructExportImport setup fails
1259 <!-- JAL-2307 -->Unit test failure:
1260 jalview.ws.sifts.SiftsClientTest due to compatibility
1261 problems with deep array comparison equality asserts in
1262 successive versions of TestNG
1265 <!-- JAL-2479 -->Relocated StructureChooserTest and
1266 ParameterUtilsTest Unit tests to Network suite
1269 <em>New Known Issues</em>
1272 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1273 phase after a sequence motif find operation
1276 <!-- JAL-2550 -->Importing annotation file with rows
1277 containing just upper and lower case letters are
1278 interpreted as WUSS RNA secondary structure symbols
1281 <!-- JAL-2590 -->Cannot load and display Newick trees
1282 reliably from eggnog Ortholog database
1285 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1286 containing features of type Highlight' when 'B' is pressed
1287 to mark columns containing highlighted regions.
1290 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1291 doesn't always add secondary structure annotation.
1296 <td width="60" nowrap>
1297 <div align="center">
1298 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1301 <td><div align="left">
1305 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1306 for all consensus calculations
1309 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1312 <li>Updated Jalview's Certum code signing certificate
1315 <em>Application</em>
1318 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1319 set of database cross-references, sorted alphabetically
1322 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1323 from database cross references. Users with custom links
1324 will receive a <a href="webServices/urllinks.html#warning">warning
1325 dialog</a> asking them to update their preferences.
1328 <!-- JAL-2287-->Cancel button and escape listener on
1329 dialog warning user about disconnecting Jalview from a
1333 <!-- JAL-2320-->Jalview's Chimera control window closes if
1334 the Chimera it is connected to is shut down
1337 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1338 columns menu item to mark columns containing highlighted
1339 regions (e.g. from structure selections or results of a
1343 <!-- JAL-2284-->Command line option for batch-generation
1344 of HTML pages rendering alignment data with the BioJS
1354 <!-- JAL-2286 -->Columns with more than one modal residue
1355 are not coloured or thresholded according to percent
1356 identity (first observed in Jalview 2.8.2)
1359 <!-- JAL-2301 -->Threonine incorrectly reported as not
1363 <!-- JAL-2318 -->Updates to documentation pages (above PID
1364 threshold, amino acid properties)
1367 <!-- JAL-2292 -->Lower case residues in sequences are not
1368 reported as mapped to residues in a structure file in the
1372 <!--JAL-2324 -->Identical features with non-numeric scores
1373 could be added multiple times to a sequence
1376 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1377 bond features shown as two highlighted residues rather
1378 than a range in linked structure views, and treated
1379 correctly when selecting and computing trees from features
1382 <!-- JAL-2281-->Custom URL links for database
1383 cross-references are matched to database name regardless
1388 <em>Application</em>
1391 <!-- JAL-2282-->Custom URL links for specific database
1392 names without regular expressions also offer links from
1396 <!-- JAL-2315-->Removing a single configured link in the
1397 URL links pane in Connections preferences doesn't actually
1398 update Jalview configuration
1401 <!-- JAL-2272-->CTRL-Click on a selected region to open
1402 the alignment area popup menu doesn't work on El-Capitan
1405 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1406 files with similarly named sequences if dropped onto the
1410 <!-- JAL-2312 -->Additional mappings are shown for PDB
1411 entries where more chains exist in the PDB accession than
1412 are reported in the SIFTS file
1415 <!-- JAL-2317-->Certain structures do not get mapped to
1416 the structure view when displayed with Chimera
1419 <!-- JAL-2317-->No chains shown in the Chimera view
1420 panel's View->Show Chains submenu
1423 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1424 work for wrapped alignment views
1427 <!--JAL-2197 -->Rename UI components for running JPred
1428 predictions from 'JNet' to 'JPred'
1431 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1432 corrupted when annotation panel vertical scroll is not at
1433 first annotation row
1436 <!--JAL-2332 -->Attempting to view structure for Hen
1437 lysozyme results in a PDB Client error dialog box
1440 <!-- JAL-2319 -->Structure View's mapping report switched
1441 ranges for PDB and sequence for SIFTS
1444 SIFTS 'Not_Observed' residues mapped to non-existant
1448 <!-- <em>New Known Issues</em>
1455 <td width="60" nowrap>
1456 <div align="center">
1457 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1458 <em>25/10/2016</em></strong>
1461 <td><em>Application</em>
1463 <li>3D Structure chooser opens with 'Cached structures'
1464 view if structures already loaded</li>
1465 <li>Progress bar reports models as they are loaded to
1466 structure views</li>
1472 <li>Colour by conservation always enabled and no tick
1473 shown in menu when BLOSUM or PID shading applied</li>
1474 <li>FER1_ARATH and FER2_ARATH labels were switched in
1475 example sequences/projects/trees</li>
1477 <em>Application</em>
1479 <li>Jalview projects with views of local PDB structure
1480 files saved on Windows cannot be opened on OSX</li>
1481 <li>Multiple structure views can be opened and superposed
1482 without timeout for structures with multiple models or
1483 multiple sequences in alignment</li>
1484 <li>Cannot import or associated local PDB files without a
1485 PDB ID HEADER line</li>
1486 <li>RMSD is not output in Jmol console when superposition
1488 <li>Drag and drop of URL from Browser fails for Linux and
1489 OSX versions earlier than El Capitan</li>
1490 <li>ENA client ignores invalid content from ENA server</li>
1491 <li>Exceptions are not raised in console when ENA client
1492 attempts to fetch non-existent IDs via Fetch DB Refs UI
1494 <li>Exceptions are not raised in console when a new view
1495 is created on the alignment</li>
1496 <li>OSX right-click fixed for group selections: CMD-click
1497 to insert/remove gaps in groups and CTRL-click to open group
1500 <em>Build and deployment</em>
1502 <li>URL link checker now copes with multi-line anchor
1505 <em>New Known Issues</em>
1507 <li>Drag and drop from URL links in browsers do not work
1514 <td width="60" nowrap>
1515 <div align="center">
1516 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1519 <td><em>General</em>
1522 <!-- JAL-2124 -->Updated Spanish translations.
1525 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1526 for importing structure data to Jalview. Enables mmCIF and
1530 <!-- JAL-192 --->Alignment ruler shows positions relative to
1534 <!-- JAL-2202 -->Position/residue shown in status bar when
1535 mousing over sequence associated annotation
1538 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1542 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1543 '()', canonical '[]' and invalid '{}' base pair populations
1547 <!-- JAL-2092 -->Feature settings popup menu options for
1548 showing or hiding columns containing a feature
1551 <!-- JAL-1557 -->Edit selected group by double clicking on
1552 group and sequence associated annotation labels
1555 <!-- JAL-2236 -->Sequence name added to annotation label in
1556 select/hide columns by annotation and colour by annotation
1560 </ul> <em>Application</em>
1563 <!-- JAL-2050-->Automatically hide introns when opening a
1564 gene/transcript view
1567 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1571 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1572 structure mappings with the EMBL-EBI PDBe SIFTS database
1575 <!-- JAL-2079 -->Updated download sites used for Rfam and
1576 Pfam sources to xfam.org
1579 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1582 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1583 over sequences in Jalview
1586 <!-- JAL-2027-->Support for reverse-complement coding
1587 regions in ENA and EMBL
1590 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1591 for record retrieval via ENA rest API
1594 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1598 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1599 groovy script execution
1602 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1603 alignment window's Calculate menu
1606 <!-- JAL-1812 -->Allow groovy scripts that call
1607 Jalview.getAlignFrames() to run in headless mode
1610 <!-- JAL-2068 -->Support for creating new alignment
1611 calculation workers from groovy scripts
1614 <!-- JAL-1369 --->Store/restore reference sequence in
1618 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1619 associations are now saved/restored from project
1622 <!-- JAL-1993 -->Database selection dialog always shown
1623 before sequence fetcher is opened
1626 <!-- JAL-2183 -->Double click on an entry in Jalview's
1627 database chooser opens a sequence fetcher
1630 <!-- JAL-1563 -->Free-text search client for UniProt using
1631 the UniProt REST API
1634 <!-- JAL-2168 -->-nonews command line parameter to prevent
1635 the news reader opening
1638 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1639 querying stored in preferences
1642 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1646 <!-- JAL-1977-->Tooltips shown on database chooser
1649 <!-- JAL-391 -->Reverse complement function in calculate
1650 menu for nucleotide sequences
1653 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1654 and feature counts preserves alignment ordering (and
1655 debugged for complex feature sets).
1658 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1659 viewing structures with Jalview 2.10
1662 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1663 genome, transcript CCDS and gene ids via the Ensembl and
1664 Ensembl Genomes REST API
1667 <!-- JAL-2049 -->Protein sequence variant annotation
1668 computed for 'sequence_variant' annotation on CDS regions
1672 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1676 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1677 Ref Fetcher fails to match, or otherwise updates sequence
1678 data from external database records.
1681 <!-- JAL-2154 -->Revised Jalview Project format for
1682 efficient recovery of sequence coding and alignment
1683 annotation relationships.
1685 </ul> <!-- <em>Applet</em>
1696 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1700 <!-- JAL-2018-->Export features in Jalview format (again)
1701 includes graduated colourschemes
1704 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1705 working with big alignments and lots of hidden columns
1708 <!-- JAL-2053-->Hidden column markers not always rendered
1709 at right of alignment window
1712 <!-- JAL-2067 -->Tidied up links in help file table of
1716 <!-- JAL-2072 -->Feature based tree calculation not shown
1720 <!-- JAL-2075 -->Hidden columns ignored during feature
1721 based tree calculation
1724 <!-- JAL-2065 -->Alignment view stops updating when show
1725 unconserved enabled for group on alignment
1728 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1732 <!-- JAL-2146 -->Alignment column in status incorrectly
1733 shown as "Sequence position" when mousing over
1737 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1738 hidden columns present
1741 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1742 user created annotation added to alignment
1745 <!-- JAL-1841 -->RNA Structure consensus only computed for
1746 '()' base pair annotation
1749 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1750 in zero scores for all base pairs in RNA Structure
1754 <!-- JAL-2174-->Extend selection with columns containing
1758 <!-- JAL-2275 -->Pfam format writer puts extra space at
1759 beginning of sequence
1762 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1766 <!-- JAL-2238 -->Cannot create groups on an alignment from
1767 from a tree when t-coffee scores are shown
1770 <!-- JAL-1836,1967 -->Cannot import and view PDB
1771 structures with chains containing negative resnums (4q4h)
1774 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1778 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1779 to Clustal, PIR and PileUp output
1782 <!-- JAL-2008 -->Reordering sequence features that are
1783 not visible causes alignment window to repaint
1786 <!-- JAL-2006 -->Threshold sliders don't work in
1787 graduated colour and colour by annotation row for e-value
1788 scores associated with features and annotation rows
1791 <!-- JAL-1797 -->amino acid physicochemical conservation
1792 calculation should be case independent
1795 <!-- JAL-2173 -->Remove annotation also updates hidden
1799 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1800 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1801 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1804 <!-- JAL-2065 -->Null pointer exceptions and redraw
1805 problems when reference sequence defined and 'show
1806 non-conserved' enabled
1809 <!-- JAL-1306 -->Quality and Conservation are now shown on
1810 load even when Consensus calculation is disabled
1813 <!-- JAL-1932 -->Remove right on penultimate column of
1814 alignment does nothing
1817 <em>Application</em>
1820 <!-- JAL-1552-->URLs and links can't be imported by
1821 drag'n'drop on OSX when launched via webstart (note - not
1822 yet fixed for El Capitan)
1825 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1826 output when running on non-gb/us i18n platforms
1829 <!-- JAL-1944 -->Error thrown when exporting a view with
1830 hidden sequences as flat-file alignment
1833 <!-- JAL-2030-->InstallAnywhere distribution fails when
1837 <!-- JAL-2080-->Jalview very slow to launch via webstart
1838 (also hotfix for 2.9.0b2)
1841 <!-- JAL-2085 -->Cannot save project when view has a
1842 reference sequence defined
1845 <!-- JAL-1011 -->Columns are suddenly selected in other
1846 alignments and views when revealing hidden columns
1849 <!-- JAL-1989 -->Hide columns not mirrored in complement
1850 view in a cDNA/Protein splitframe
1853 <!-- JAL-1369 -->Cannot save/restore representative
1854 sequence from project when only one sequence is
1858 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1859 in Structure Chooser
1862 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1863 structure consensus didn't refresh annotation panel
1866 <!-- JAL-1962 -->View mapping in structure view shows
1867 mappings between sequence and all chains in a PDB file
1870 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1871 dialogs format columns correctly, don't display array
1872 data, sort columns according to type
1875 <!-- JAL-1975 -->Export complete shown after destination
1876 file chooser is cancelled during an image export
1879 <!-- JAL-2025 -->Error when querying PDB Service with
1880 sequence name containing special characters
1883 <!-- JAL-2024 -->Manual PDB structure querying should be
1887 <!-- JAL-2104 -->Large tooltips with broken HTML
1888 formatting don't wrap
1891 <!-- JAL-1128 -->Figures exported from wrapped view are
1892 truncated so L looks like I in consensus annotation
1895 <!-- JAL-2003 -->Export features should only export the
1896 currently displayed features for the current selection or
1900 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1901 after fetching cross-references, and restoring from
1905 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1906 followed in the structure viewer
1909 <!-- JAL-2163 -->Titles for individual alignments in
1910 splitframe not restored from project
1913 <!-- JAL-2145 -->missing autocalculated annotation at
1914 trailing end of protein alignment in transcript/product
1915 splitview when pad-gaps not enabled by default
1918 <!-- JAL-1797 -->amino acid physicochemical conservation
1922 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1923 article has been read (reopened issue due to
1924 internationalisation problems)
1927 <!-- JAL-1960 -->Only offer PDB structures in structure
1928 viewer based on sequence name, PDB and UniProt
1933 <!-- JAL-1976 -->No progress bar shown during export of
1937 <!-- JAL-2213 -->Structures not always superimposed after
1938 multiple structures are shown for one or more sequences.
1941 <!-- JAL-1370 -->Reference sequence characters should not
1942 be replaced with '.' when 'Show unconserved' format option
1946 <!-- JAL-1823 -->Cannot specify chain code when entering
1947 specific PDB id for sequence
1950 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1951 'Export hidden sequences' is enabled, but 'export hidden
1952 columns' is disabled.
1955 <!--JAL-2026-->Best Quality option in structure chooser
1956 selects lowest rather than highest resolution structures
1960 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1961 to sequence mapping in 'View Mappings' report
1964 <!-- JAL-2284 -->Unable to read old Jalview projects that
1965 contain non-XML data added after Jalvew wrote project.
1968 <!-- JAL-2118 -->Newly created annotation row reorders
1969 after clicking on it to create new annotation for a
1973 <!-- JAL-1980 -->Null Pointer Exception raised when
1974 pressing Add on an orphaned cut'n'paste window.
1976 <!-- may exclude, this is an external service stability issue JAL-1941
1977 -- > RNA 3D structure not added via DSSR service</li> -->
1982 <!-- JAL-2151 -->Incorrect columns are selected when
1983 hidden columns present before start of sequence
1986 <!-- JAL-1986 -->Missing dependencies on applet pages
1990 <!-- JAL-1947 -->Overview pixel size changes when
1991 sequences are hidden in applet
1994 <!-- JAL-1996 -->Updated instructions for applet
1995 deployment on examples pages.
2002 <td width="60" nowrap>
2003 <div align="center">
2004 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
2005 <em>16/10/2015</em></strong>
2008 <td><em>General</em>
2010 <li>Time stamps for signed Jalview application and applet
2015 <em>Application</em>
2017 <li>Duplicate group consensus and conservation rows
2018 shown when tree is partitioned</li>
2019 <li>Erratic behaviour when tree partitions made with
2020 multiple cDNA/Protein split views</li>
2026 <td width="60" nowrap>
2027 <div align="center">
2028 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
2029 <em>8/10/2015</em></strong>
2032 <td><em>General</em>
2034 <li>Updated Spanish translations of localized text for
2036 </ul> <em>Application</em>
2038 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
2039 <li>Signed OSX InstallAnywhere installer<br></li>
2040 <li>Support for per-sequence based annotations in BioJSON</li>
2041 </ul> <em>Applet</em>
2043 <li>Split frame example added to applet examples page</li>
2044 </ul> <em>Build and Deployment</em>
2047 <!-- JAL-1888 -->New ant target for running Jalview's test
2055 <li>Mapping of cDNA to protein in split frames
2056 incorrect when sequence start > 1</li>
2057 <li>Broken images in filter column by annotation dialog
2059 <li>Feature colours not parsed from features file</li>
2060 <li>Exceptions and incomplete link URLs recovered when
2061 loading a features file containing HTML tags in feature
2065 <em>Application</em>
2067 <li>Annotations corrupted after BioJS export and
2069 <li>Incorrect sequence limits after Fetch DB References
2070 with 'trim retrieved sequences'</li>
2071 <li>Incorrect warning about deleting all data when
2072 deleting selected columns</li>
2073 <li>Patch to build system for shipping properly signed
2074 JNLP templates for webstart launch</li>
2075 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
2076 unreleased structures for download or viewing</li>
2077 <li>Tab/space/return keystroke operation of EMBL-PDBe
2078 fetcher/viewer dialogs works correctly</li>
2079 <li>Disabled 'minimise' button on Jalview windows
2080 running on OSX to workaround redraw hang bug</li>
2081 <li>Split cDNA/Protein view position and geometry not
2082 recovered from jalview project</li>
2083 <li>Initial enabled/disabled state of annotation menu
2084 sorter 'show autocalculated first/last' corresponds to
2086 <li>Restoring of Clustal, RNA Helices and T-Coffee
2087 color schemes from BioJSON</li>
2091 <li>Reorder sequences mirrored in cDNA/Protein split
2093 <li>Applet with Jmol examples not loading correctly</li>
2099 <td><div align="center">
2100 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
2102 <td><em>General</em>
2104 <li>Linked visualisation and analysis of DNA and Protein
2107 <li>Translated cDNA alignments shown as split protein
2108 and DNA alignment views</li>
2109 <li>Codon consensus annotation for linked protein and
2110 cDNA alignment views</li>
2111 <li>Link cDNA or Protein product sequences by loading
2112 them onto Protein or cDNA alignments</li>
2113 <li>Reconstruct linked cDNA alignment from aligned
2114 protein sequences</li>
2117 <li>Jmol integration updated to Jmol v14.2.14</li>
2118 <li>Import and export of Jalview alignment views as <a
2119 href="features/bioJsonFormat.html">BioJSON</a></li>
2120 <li>New alignment annotation file statements for
2121 reference sequences and marking hidden columns</li>
2122 <li>Reference sequence based alignment shading to
2123 highlight variation</li>
2124 <li>Select or hide columns according to alignment
2126 <li>Find option for locating sequences by description</li>
2127 <li>Conserved physicochemical properties shown in amino
2128 acid conservation row</li>
2129 <li>Alignments can be sorted by number of RNA helices</li>
2130 </ul> <em>Application</em>
2132 <li>New cDNA/Protein analysis capabilities
2134 <li>Get Cross-References should open a Split Frame
2135 view with cDNA/Protein</li>
2136 <li>Detect when nucleotide sequences and protein
2137 sequences are placed in the same alignment</li>
2138 <li>Split cDNA/Protein views are saved in Jalview
2143 <li>Use REST API to talk to Chimera</li>
2144 <li>Selected regions in Chimera are highlighted in linked
2145 Jalview windows</li>
2147 <li>VARNA RNA viewer updated to v3.93</li>
2148 <li>VARNA views are saved in Jalview Projects</li>
2149 <li>Pseudoknots displayed as Jalview RNA annotation can
2150 be shown in VARNA</li>
2152 <li>Make groups for selection uses marked columns as well
2153 as the active selected region</li>
2155 <li>Calculate UPGMA and NJ trees using sequence feature
2157 <li>New Export options
2159 <li>New Export Settings dialog to control hidden
2160 region export in flat file generation</li>
2162 <li>Export alignment views for display with the <a
2163 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2165 <li>Export scrollable SVG in HTML page</li>
2166 <li>Optional embedding of BioJSON data when exporting
2167 alignment figures to HTML</li>
2169 <li>3D structure retrieval and display
2171 <li>Free text and structured queries with the PDBe
2173 <li>PDBe Search API based discovery and selection of
2174 PDB structures for a sequence set</li>
2178 <li>JPred4 employed for protein secondary structure
2180 <li>Hide Insertions menu option to hide unaligned columns
2181 for one or a group of sequences</li>
2182 <li>Automatically hide insertions in alignments imported
2183 from the JPred4 web server</li>
2184 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2185 system on OSX<br />LGPL libraries courtesy of <a
2186 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2188 <li>changed 'View nucleotide structure' submenu to 'View
2189 VARNA 2D Structure'</li>
2190 <li>change "View protein structure" menu option to "3D
2193 </ul> <em>Applet</em>
2195 <li>New layout for applet example pages</li>
2196 <li>New parameters to enable SplitFrame view
2197 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2198 <li>New example demonstrating linked viewing of cDNA and
2199 Protein alignments</li>
2200 </ul> <em>Development and deployment</em>
2202 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2203 <li>Include installation type and git revision in build
2204 properties and console log output</li>
2205 <li>Jalview Github organisation, and new github site for
2206 storing BioJsMSA Templates</li>
2207 <li>Jalview's unit tests now managed with TestNG</li>
2210 <!-- <em>General</em>
2212 </ul> --> <!-- issues resolved --> <em>Application</em>
2214 <li>Escape should close any open find dialogs</li>
2215 <li>Typo in select-by-features status report</li>
2216 <li>Consensus RNA secondary secondary structure
2217 predictions are not highlighted in amber</li>
2218 <li>Missing gap character in v2.7 example file means
2219 alignment appears unaligned when pad-gaps is not enabled</li>
2220 <li>First switch to RNA Helices colouring doesn't colour
2221 associated structure views</li>
2222 <li>ID width preference option is greyed out when auto
2223 width checkbox not enabled</li>
2224 <li>Stopped a warning dialog from being shown when
2225 creating user defined colours</li>
2226 <li>'View Mapping' in structure viewer shows sequence
2227 mappings for just that viewer's sequences</li>
2228 <li>Workaround for superposing PDB files containing
2229 multiple models in Chimera</li>
2230 <li>Report sequence position in status bar when hovering
2231 over Jmol structure</li>
2232 <li>Cannot output gaps as '.' symbols with Selection ->
2233 output to text box</li>
2234 <li>Flat file exports of alignments with hidden columns
2235 have incorrect sequence start/end</li>
2236 <li>'Aligning' a second chain to a Chimera structure from
2238 <li>Colour schemes applied to structure viewers don't
2239 work for nucleotide</li>
2240 <li>Loading/cut'n'pasting an empty or invalid file leads
2241 to a grey/invisible alignment window</li>
2242 <li>Exported Jpred annotation from a sequence region
2243 imports to different position</li>
2244 <li>Space at beginning of sequence feature tooltips shown
2245 on some platforms</li>
2246 <li>Chimera viewer 'View | Show Chain' menu is not
2248 <li>'New View' fails with a Null Pointer Exception in
2249 console if Chimera has been opened</li>
2250 <li>Mouseover to Chimera not working</li>
2251 <li>Miscellaneous ENA XML feature qualifiers not
2253 <li>NPE in annotation renderer after 'Extract Scores'</li>
2254 <li>If two structures in one Chimera window, mouseover of
2255 either sequence shows on first structure</li>
2256 <li>'Show annotations' options should not make
2257 non-positional annotations visible</li>
2258 <li>Subsequence secondary structure annotation not shown
2259 in right place after 'view flanking regions'</li>
2260 <li>File Save As type unset when current file format is
2262 <li>Save as '.jar' option removed for saving Jalview
2264 <li>Colour by Sequence colouring in Chimera more
2266 <li>Cannot 'add reference annotation' for a sequence in
2267 several views on same alignment</li>
2268 <li>Cannot show linked products for EMBL / ENA records</li>
2269 <li>Jalview's tooltip wraps long texts containing no
2271 </ul> <em>Applet</em>
2273 <li>Jmol to JalviewLite mouseover/link not working</li>
2274 <li>JalviewLite can't import sequences with ID
2275 descriptions containing angle brackets</li>
2276 </ul> <em>General</em>
2278 <li>Cannot export and reimport RNA secondary structure
2279 via jalview annotation file</li>
2280 <li>Random helix colour palette for colour by annotation
2281 with RNA secondary structure</li>
2282 <li>Mouseover to cDNA from STOP residue in protein
2283 translation doesn't work.</li>
2284 <li>hints when using the select by annotation dialog box</li>
2285 <li>Jmol alignment incorrect if PDB file has alternate CA
2287 <li>FontChooser message dialog appears to hang after
2288 choosing 1pt font</li>
2289 <li>Peptide secondary structure incorrectly imported from
2290 annotation file when annotation display text includes 'e' or
2292 <li>Cannot set colour of new feature type whilst creating
2294 <li>cDNA translation alignment should not be sequence
2295 order dependent</li>
2296 <li>'Show unconserved' doesn't work for lower case
2298 <li>Nucleotide ambiguity codes involving R not recognised</li>
2299 </ul> <em>Deployment and Documentation</em>
2301 <li>Applet example pages appear different to the rest of
2302 www.jalview.org</li>
2303 </ul> <em>Application Known issues</em>
2305 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2306 <li>Misleading message appears after trying to delete
2308 <li>Jalview icon not shown in dock after InstallAnywhere
2309 version launches</li>
2310 <li>Fetching EMBL reference for an RNA sequence results
2311 fails with a sequence mismatch</li>
2312 <li>Corrupted or unreadable alignment display when
2313 scrolling alignment to right</li>
2314 <li>ArrayIndexOutOfBoundsException thrown when remove
2315 empty columns called on alignment with ragged gapped ends</li>
2316 <li>auto calculated alignment annotation rows do not get
2317 placed above or below non-autocalculated rows</li>
2318 <li>Jalview dekstop becomes sluggish at full screen in
2319 ultra-high resolution</li>
2320 <li>Cannot disable consensus calculation independently of
2321 quality and conservation</li>
2322 <li>Mouseover highlighting between cDNA and protein can
2323 become sluggish with more than one splitframe shown</li>
2324 </ul> <em>Applet Known Issues</em>
2326 <li>Core PDB parsing code requires Jmol</li>
2327 <li>Sequence canvas panel goes white when alignment
2328 window is being resized</li>
2334 <td><div align="center">
2335 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2337 <td><em>General</em>
2339 <li>Updated Java code signing certificate donated by
2341 <li>Features and annotation preserved when performing
2342 pairwise alignment</li>
2343 <li>RNA pseudoknot annotation can be
2344 imported/exported/displayed</li>
2345 <li>'colour by annotation' can colour by RNA and
2346 protein secondary structure</li>
2347 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2348 post-hoc with 2.9 release</em>)
2351 </ul> <em>Application</em>
2353 <li>Extract and display secondary structure for sequences
2354 with 3D structures</li>
2355 <li>Support for parsing RNAML</li>
2356 <li>Annotations menu for layout
2358 <li>sort sequence annotation rows by alignment</li>
2359 <li>place sequence annotation above/below alignment
2362 <li>Output in Stockholm format</li>
2363 <li>Internationalisation: improved Spanish (es)
2365 <li>Structure viewer preferences tab</li>
2366 <li>Disorder and Secondary Structure annotation tracks
2367 shared between alignments</li>
2368 <li>UCSF Chimera launch and linked highlighting from
2370 <li>Show/hide all sequence associated annotation rows for
2371 all or current selection</li>
2372 <li>disorder and secondary structure predictions
2373 available as dataset annotation</li>
2374 <li>Per-sequence rna helices colouring</li>
2377 <li>Sequence database accessions imported when fetching
2378 alignments from Rfam</li>
2379 <li>update VARNA version to 3.91</li>
2381 <li>New groovy scripts for exporting aligned positions,
2382 conservation values, and calculating sum of pairs scores.</li>
2383 <li>Command line argument to set default JABAWS server</li>
2384 <li>include installation type in build properties and
2385 console log output</li>
2386 <li>Updated Jalview project format to preserve dataset
2390 <!-- issues resolved --> <em>Application</em>
2392 <li>Distinguish alignment and sequence associated RNA
2393 structure in structure->view->VARNA</li>
2394 <li>Raise dialog box if user deletes all sequences in an
2396 <li>Pressing F1 results in documentation opening twice</li>
2397 <li>Sequence feature tooltip is wrapped</li>
2398 <li>Double click on sequence associated annotation
2399 selects only first column</li>
2400 <li>Redundancy removal doesn't result in unlinked
2401 leaves shown in tree</li>
2402 <li>Undos after several redundancy removals don't undo
2404 <li>Hide sequence doesn't hide associated annotation</li>
2405 <li>User defined colours dialog box too big to fit on
2406 screen and buttons not visible</li>
2407 <li>author list isn't updated if already written to
2408 Jalview properties</li>
2409 <li>Popup menu won't open after retrieving sequence
2411 <li>File open window for associate PDB doesn't open</li>
2412 <li>Left-then-right click on a sequence id opens a
2413 browser search window</li>
2414 <li>Cannot open sequence feature shading/sort popup menu
2415 in feature settings dialog</li>
2416 <li>better tooltip placement for some areas of Jalview
2418 <li>Allow addition of JABAWS Server which doesn't
2419 pass validation</li>
2420 <li>Web services parameters dialog box is too large to
2422 <li>Muscle nucleotide alignment preset obscured by
2424 <li>JABAWS preset submenus don't contain newly
2425 defined user preset</li>
2426 <li>MSA web services warns user if they were launched
2427 with invalid input</li>
2428 <li>Jalview cannot contact DAS Registy when running on
2431 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2432 'Superpose with' submenu not shown when new view
2436 </ul> <!-- <em>Applet</em>
2438 </ul> <em>General</em>
2440 </ul>--> <em>Deployment and Documentation</em>
2442 <li>2G and 1G options in launchApp have no effect on
2443 memory allocation</li>
2444 <li>launchApp service doesn't automatically open
2445 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2447 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2448 InstallAnywhere reports cannot find valid JVM when Java
2449 1.7_055 is available
2451 </ul> <em>Application Known issues</em>
2454 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2455 corrupted or unreadable alignment display when scrolling
2459 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2460 retrieval fails but progress bar continues for DAS retrieval
2461 with large number of ID
2464 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2465 flatfile output of visible region has incorrect sequence
2469 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2470 rna structure consensus doesn't update when secondary
2471 structure tracks are rearranged
2474 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2475 invalid rna structure positional highlighting does not
2476 highlight position of invalid base pairs
2479 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2480 out of memory errors are not raised when saving Jalview
2481 project from alignment window file menu
2484 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2485 Switching to RNA Helices colouring doesn't propagate to
2489 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2490 colour by RNA Helices not enabled when user created
2491 annotation added to alignment
2494 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2495 Jalview icon not shown on dock in Mountain Lion/Webstart
2497 </ul> <em>Applet Known Issues</em>
2500 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2501 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2504 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2505 Jalview and Jmol example not compatible with IE9
2508 <li>Sort by annotation score doesn't reverse order
2514 <td><div align="center">
2515 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2518 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2521 <li>Internationalisation of user interface (usually
2522 called i18n support) and translation for Spanish locale</li>
2523 <li>Define/Undefine group on current selection with
2524 Ctrl-G/Shift Ctrl-G</li>
2525 <li>Improved group creation/removal options in
2526 alignment/sequence Popup menu</li>
2527 <li>Sensible precision for symbol distribution
2528 percentages shown in logo tooltip.</li>
2529 <li>Annotation panel height set according to amount of
2530 annotation when alignment first opened</li>
2531 </ul> <em>Application</em>
2533 <li>Interactive consensus RNA secondary structure
2534 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2535 <li>Select columns containing particular features from
2536 Feature Settings dialog</li>
2537 <li>View all 'representative' PDB structures for selected
2539 <li>Update Jalview project format:
2541 <li>New file extension for Jalview projects '.jvp'</li>
2542 <li>Preserve sequence and annotation dataset (to
2543 store secondary structure annotation,etc)</li>
2544 <li>Per group and alignment annotation and RNA helix
2548 <li>New similarity measures for PCA and Tree calculation
2550 <li>Experimental support for retrieval and viewing of
2551 flanking regions for an alignment</li>
2555 <!-- issues resolved --> <em>Application</em>
2557 <li>logo keeps spinning and status remains at queued or
2558 running after job is cancelled</li>
2559 <li>cannot export features from alignments imported from
2560 Jalview/VAMSAS projects</li>
2561 <li>Buggy slider for web service parameters that take
2563 <li>Newly created RNA secondary structure line doesn't
2564 have 'display all symbols' flag set</li>
2565 <li>T-COFFEE alignment score shading scheme and other
2566 annotation shading not saved in Jalview project</li>
2567 <li>Local file cannot be loaded in freshly downloaded
2569 <li>Jalview icon not shown on dock in Mountain
2571 <li>Load file from desktop file browser fails</li>
2572 <li>Occasional NPE thrown when calculating large trees</li>
2573 <li>Cannot reorder or slide sequences after dragging an
2574 alignment onto desktop</li>
2575 <li>Colour by annotation dialog throws NPE after using
2576 'extract scores' function</li>
2577 <li>Loading/cut'n'pasting an empty file leads to a grey
2578 alignment window</li>
2579 <li>Disorder thresholds rendered incorrectly after
2580 performing IUPred disorder prediction</li>
2581 <li>Multiple group annotated consensus rows shown when
2582 changing 'normalise logo' display setting</li>
2583 <li>Find shows blank dialog after 'finished searching' if
2584 nothing matches query</li>
2585 <li>Null Pointer Exceptions raised when sorting by
2586 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2588 <li>Errors in Jmol console when structures in alignment
2589 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2591 <li>Not all working JABAWS services are shown in
2593 <li>JAVAWS version of Jalview fails to launch with
2594 'invalid literal/length code'</li>
2595 <li>Annotation/RNA Helix colourschemes cannot be applied
2596 to alignment with groups (actually fixed in 2.8.0b1)</li>
2597 <li>RNA Helices and T-Coffee Scores available as default
2600 </ul> <em>Applet</em>
2602 <li>Remove group option is shown even when selection is
2604 <li>Apply to all groups ticked but colourscheme changes
2605 don't affect groups</li>
2606 <li>Documented RNA Helices and T-Coffee Scores as valid
2607 colourscheme name</li>
2608 <li>Annotation labels drawn on sequence IDs when
2609 Annotation panel is not displayed</li>
2610 <li>Increased font size for dropdown menus on OSX and
2611 embedded windows</li>
2612 </ul> <em>Other</em>
2614 <li>Consensus sequence for alignments/groups with a
2615 single sequence were not calculated</li>
2616 <li>annotation files that contain only groups imported as
2617 annotation and junk sequences</li>
2618 <li>Fasta files with sequences containing '*' incorrectly
2619 recognised as PFAM or BLC</li>
2620 <li>conservation/PID slider apply all groups option
2621 doesn't affect background (2.8.0b1)
2623 <li>redundancy highlighting is erratic at 0% and 100%</li>
2624 <li>Remove gapped columns fails for sequences with ragged
2626 <li>AMSA annotation row with leading spaces is not
2627 registered correctly on import</li>
2628 <li>Jalview crashes when selecting PCA analysis for
2629 certain alignments</li>
2630 <li>Opening the colour by annotation dialog for an
2631 existing annotation based 'use original colours'
2632 colourscheme loses original colours setting</li>
2637 <td><div align="center">
2638 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2639 <em>30/1/2014</em></strong>
2643 <li>Trusted certificates for JalviewLite applet and
2644 Jalview Desktop application<br />Certificate was donated by
2645 <a href="https://www.certum.eu">Certum</a> to the Jalview
2646 open source project).
2648 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2649 <li>Output in Stockholm format</li>
2650 <li>Allow import of data from gzipped files</li>
2651 <li>Export/import group and sequence associated line
2652 graph thresholds</li>
2653 <li>Nucleotide substitution matrix that supports RNA and
2654 ambiguity codes</li>
2655 <li>Allow disorder predictions to be made on the current
2656 selection (or visible selection) in the same way that JPred
2658 <li>Groovy scripting for headless Jalview operation</li>
2659 </ul> <em>Other improvements</em>
2661 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2662 <li>COMBINE statement uses current SEQUENCE_REF and
2663 GROUP_REF scope to group annotation rows</li>
2664 <li>Support '' style escaping of quotes in Newick
2666 <li>Group options for JABAWS service by command line name</li>
2667 <li>Empty tooltip shown for JABA service options with a
2668 link but no description</li>
2669 <li>Select primary source when selecting authority in
2670 database fetcher GUI</li>
2671 <li>Add .mfa to FASTA file extensions recognised by
2673 <li>Annotation label tooltip text wrap</li>
2678 <li>Slow scrolling when lots of annotation rows are
2680 <li>Lots of NPE (and slowness) after creating RNA
2681 secondary structure annotation line</li>
2682 <li>Sequence database accessions not imported when
2683 fetching alignments from Rfam</li>
2684 <li>Incorrect SHMR submission for sequences with
2686 <li>View all structures does not always superpose
2688 <li>Option widgets in service parameters not updated to
2689 reflect user or preset settings</li>
2690 <li>Null pointer exceptions for some services without
2691 presets or adjustable parameters</li>
2692 <li>Discover PDB IDs entry in structure menu doesn't
2693 discover PDB xRefs</li>
2694 <li>Exception encountered while trying to retrieve
2695 features with DAS</li>
2696 <li>Lowest value in annotation row isn't coloured
2697 when colour by annotation (per sequence) is coloured</li>
2698 <li>Keyboard mode P jumps to start of gapped region when
2699 residue follows a gap</li>
2700 <li>Jalview appears to hang importing an alignment with
2701 Wrap as default or after enabling Wrap</li>
2702 <li>'Right click to add annotations' message
2703 shown in wrap mode when no annotations present</li>
2704 <li>Disorder predictions fail with NPE if no automatic
2705 annotation already exists on alignment</li>
2706 <li>oninit javascript function should be called after
2707 initialisation completes</li>
2708 <li>Remove redundancy after disorder prediction corrupts
2709 alignment window display</li>
2710 <li>Example annotation file in documentation is invalid</li>
2711 <li>Grouped line graph annotation rows are not exported
2712 to annotation file</li>
2713 <li>Multi-harmony analysis cannot be run when only two
2715 <li>Cannot create multiple groups of line graphs with
2716 several 'combine' statements in annotation file</li>
2717 <li>Pressing return several times causes Number Format
2718 exceptions in keyboard mode</li>
2719 <li>Multi-harmony (SHMMR) method doesn't submit
2720 correct partitions for input data</li>
2721 <li>Translation from DNA to Amino Acids fails</li>
2722 <li>Jalview fail to load newick tree with quoted label</li>
2723 <li>--headless flag isn't understood</li>
2724 <li>ClassCastException when generating EPS in headless
2726 <li>Adjusting sequence-associated shading threshold only
2727 changes one row's threshold</li>
2728 <li>Preferences and Feature settings panel panel
2729 doesn't open</li>
2730 <li>hide consensus histogram also hides conservation and
2731 quality histograms</li>
2736 <td><div align="center">
2737 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2739 <td><em>Application</em>
2741 <li>Support for JABAWS 2.0 Services (AACon alignment
2742 conservation, protein disorder and Clustal Omega)</li>
2743 <li>JABAWS server status indicator in Web Services
2745 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2746 in Jalview alignment window</li>
2747 <li>Updated Jalview build and deploy framework for OSX
2748 mountain lion, windows 7, and 8</li>
2749 <li>Nucleotide substitution matrix for PCA that supports
2750 RNA and ambiguity codes</li>
2752 <li>Improved sequence database retrieval GUI</li>
2753 <li>Support fetching and database reference look up
2754 against multiple DAS sources (Fetch all from in 'fetch db
2756 <li>Jalview project improvements
2758 <li>Store and retrieve the 'belowAlignment'
2759 flag for annotation</li>
2760 <li>calcId attribute to group annotation rows on the
2762 <li>Store AACon calculation settings for a view in
2763 Jalview project</li>
2767 <li>horizontal scrolling gesture support</li>
2768 <li>Visual progress indicator when PCA calculation is
2770 <li>Simpler JABA web services menus</li>
2771 <li>visual indication that web service results are still
2772 being retrieved from server</li>
2773 <li>Serialise the dialogs that are shown when Jalview
2774 starts up for first time</li>
2775 <li>Jalview user agent string for interacting with HTTP
2777 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2779 <li>Examples directory and Groovy library included in
2780 InstallAnywhere distribution</li>
2781 </ul> <em>Applet</em>
2783 <li>RNA alignment and secondary structure annotation
2784 visualization applet example</li>
2785 </ul> <em>General</em>
2787 <li>Normalise option for consensus sequence logo</li>
2788 <li>Reset button in PCA window to return dimensions to
2790 <li>Allow seqspace or Jalview variant of alignment PCA
2792 <li>PCA with either nucleic acid and protein substitution
2794 <li>Allow windows containing HTML reports to be exported
2796 <li>Interactive display and editing of RNA secondary
2797 structure contacts</li>
2798 <li>RNA Helix Alignment Colouring</li>
2799 <li>RNA base pair logo consensus</li>
2800 <li>Parse sequence associated secondary structure
2801 information in Stockholm files</li>
2802 <li>HTML Export database accessions and annotation
2803 information presented in tooltip for sequences</li>
2804 <li>Import secondary structure from LOCARNA clustalw
2805 style RNA alignment files</li>
2806 <li>import and visualise T-COFFEE quality scores for an
2808 <li>'colour by annotation' per sequence option to
2809 shade each sequence according to its associated alignment
2811 <li>New Jalview Logo</li>
2812 </ul> <em>Documentation and Development</em>
2814 <li>documentation for score matrices used in Jalview</li>
2815 <li>New Website!</li>
2817 <td><em>Application</em>
2819 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2820 wsdbfetch REST service</li>
2821 <li>Stop windows being moved outside desktop on OSX</li>
2822 <li>Filetype associations not installed for webstart
2824 <li>Jalview does not always retrieve progress of a JABAWS
2825 job execution in full once it is complete</li>
2826 <li>revise SHMR RSBS definition to ensure alignment is
2827 uploaded via ali_file parameter</li>
2828 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2829 <li>View all structures superposed fails with exception</li>
2830 <li>Jnet job queues forever if a very short sequence is
2831 submitted for prediction</li>
2832 <li>Cut and paste menu not opened when mouse clicked on
2834 <li>Putting fractional value into integer text box in
2835 alignment parameter dialog causes Jalview to hang</li>
2836 <li>Structure view highlighting doesn't work on
2838 <li>View all structures fails with exception shown in
2840 <li>Characters in filename associated with PDBEntry not
2841 escaped in a platform independent way</li>
2842 <li>Jalview desktop fails to launch with exception when
2844 <li>Tree calculation reports 'you must have 2 or more
2845 sequences selected' when selection is empty</li>
2846 <li>Jalview desktop fails to launch with jar signature
2847 failure when java web start temporary file caching is
2849 <li>DAS Sequence retrieval with range qualification
2850 results in sequence xref which includes range qualification</li>
2851 <li>Errors during processing of command line arguments
2852 cause progress bar (JAL-898) to be removed</li>
2853 <li>Replace comma for semi-colon option not disabled for
2854 DAS sources in sequence fetcher</li>
2855 <li>Cannot close news reader when JABAWS server warning
2856 dialog is shown</li>
2857 <li>Option widgets not updated to reflect user settings</li>
2858 <li>Edited sequence not submitted to web service</li>
2859 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2860 <li>InstallAnywhere installer doesn't unpack and run
2861 on OSX Mountain Lion</li>
2862 <li>Annotation panel not given a scroll bar when
2863 sequences with alignment annotation are pasted into the
2865 <li>Sequence associated annotation rows not associated
2866 when loaded from Jalview project</li>
2867 <li>Browser launch fails with NPE on java 1.7</li>
2868 <li>JABAWS alignment marked as finished when job was
2869 cancelled or job failed due to invalid input</li>
2870 <li>NPE with v2.7 example when clicking on Tree
2871 associated with all views</li>
2872 <li>Exceptions when copy/paste sequences with grouped
2873 annotation rows to new window</li>
2874 </ul> <em>Applet</em>
2876 <li>Sequence features are momentarily displayed before
2877 they are hidden using hidefeaturegroups applet parameter</li>
2878 <li>loading features via javascript API automatically
2879 enables feature display</li>
2880 <li>scrollToColumnIn javascript API method doesn't
2882 </ul> <em>General</em>
2884 <li>Redundancy removal fails for rna alignment</li>
2885 <li>PCA calculation fails when sequence has been selected
2886 and then deselected</li>
2887 <li>PCA window shows grey box when first opened on OSX</li>
2888 <li>Letters coloured pink in sequence logo when alignment
2889 coloured with clustalx</li>
2890 <li>Choosing fonts without letter symbols defined causes
2891 exceptions and redraw errors</li>
2892 <li>Initial PCA plot view is not same as manually
2893 reconfigured view</li>
2894 <li>Grouped annotation graph label has incorrect line
2896 <li>Grouped annotation graph label display is corrupted
2897 for lots of labels</li>
2902 <div align="center">
2903 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2906 <td><em>Application</em>
2908 <li>Jalview Desktop News Reader</li>
2909 <li>Tweaked default layout of web services menu</li>
2910 <li>View/alignment association menu to enable user to
2911 easily specify which alignment a multi-structure view takes
2912 its colours/correspondences from</li>
2913 <li>Allow properties file location to be specified as URL</li>
2914 <li>Extend Jalview project to preserve associations
2915 between many alignment views and a single Jmol display</li>
2916 <li>Store annotation row height in Jalview project file</li>
2917 <li>Annotation row column label formatting attributes
2918 stored in project file</li>
2919 <li>Annotation row order for auto-calculated annotation
2920 rows preserved in Jalview project file</li>
2921 <li>Visual progress indication when Jalview state is
2922 saved using Desktop window menu</li>
2923 <li>Visual indication that command line arguments are
2924 still being processed</li>
2925 <li>Groovy script execution from URL</li>
2926 <li>Colour by annotation default min and max colours in
2928 <li>Automatically associate PDB files dragged onto an
2929 alignment with sequences that have high similarity and
2931 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2932 <li>'view structures' option to open many
2933 structures in same window</li>
2934 <li>Sort associated views menu option for tree panel</li>
2935 <li>Group all JABA and non-JABA services for a particular
2936 analysis function in its own submenu</li>
2937 </ul> <em>Applet</em>
2939 <li>Userdefined and autogenerated annotation rows for
2941 <li>Adjustment of alignment annotation pane height</li>
2942 <li>Annotation scrollbar for annotation panel</li>
2943 <li>Drag to reorder annotation rows in annotation panel</li>
2944 <li>'automaticScrolling' parameter</li>
2945 <li>Allow sequences with partial ID string matches to be
2946 annotated from GFF/Jalview features files</li>
2947 <li>Sequence logo annotation row in applet</li>
2948 <li>Absolute paths relative to host server in applet
2949 parameters are treated as such</li>
2950 <li>New in the JalviewLite javascript API:
2952 <li>JalviewLite.js javascript library</li>
2953 <li>Javascript callbacks for
2955 <li>Applet initialisation</li>
2956 <li>Sequence/alignment mouse-overs and selections</li>
2959 <li>scrollTo row and column alignment scrolling
2961 <li>Select sequence/alignment regions from javascript</li>
2962 <li>javascript structure viewer harness to pass
2963 messages between Jmol and Jalview when running as
2964 distinct applets</li>
2965 <li>sortBy method</li>
2966 <li>Set of applet and application examples shipped
2967 with documentation</li>
2968 <li>New example to demonstrate JalviewLite and Jmol
2969 javascript message exchange</li>
2971 </ul> <em>General</em>
2973 <li>Enable Jmol displays to be associated with multiple
2974 multiple alignments</li>
2975 <li>Option to automatically sort alignment with new tree</li>
2976 <li>User configurable link to enable redirects to a
2977 www.Jalview.org mirror</li>
2978 <li>Jmol colours option for Jmol displays</li>
2979 <li>Configurable newline string when writing alignment
2980 and other flat files</li>
2981 <li>Allow alignment annotation description lines to
2982 contain html tags</li>
2983 </ul> <em>Documentation and Development</em>
2985 <li>Add groovy test harness for bulk load testing to
2987 <li>Groovy script to load and align a set of sequences
2988 using a web service before displaying the result in the
2989 Jalview desktop</li>
2990 <li>Restructured javascript and applet api documentation</li>
2991 <li>Ant target to publish example html files with applet
2993 <li>Netbeans project for building Jalview from source</li>
2994 <li>ant task to create online javadoc for Jalview source</li>
2996 <td><em>Application</em>
2998 <li>User defined colourscheme throws exception when
2999 current built in colourscheme is saved as new scheme</li>
3000 <li>AlignFrame->Save in application pops up save
3001 dialog for valid filename/format</li>
3002 <li>Cannot view associated structure for UniProt sequence</li>
3003 <li>PDB file association breaks for UniProt sequence
3005 <li>Associate PDB from file dialog does not tell you
3006 which sequence is to be associated with the file</li>
3007 <li>Find All raises null pointer exception when query
3008 only matches sequence IDs</li>
3009 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
3010 <li>Jalview project with Jmol views created with Jalview
3011 2.4 cannot be loaded</li>
3012 <li>Filetype associations not installed for webstart
3014 <li>Two or more chains in a single PDB file associated
3015 with sequences in different alignments do not get coloured
3016 by their associated sequence</li>
3017 <li>Visibility status of autocalculated annotation row
3018 not preserved when project is loaded</li>
3019 <li>Annotation row height and visibility attributes not
3020 stored in Jalview project</li>
3021 <li>Tree bootstraps are not preserved when saved as a
3022 Jalview project</li>
3023 <li>Envision2 workflow tooltips are corrupted</li>
3024 <li>Enabling show group conservation also enables colour
3025 by conservation</li>
3026 <li>Duplicate group associated conservation or consensus
3027 created on new view</li>
3028 <li>Annotation scrollbar not displayed after 'show
3029 all hidden annotation rows' option selected</li>
3030 <li>Alignment quality not updated after alignment
3031 annotation row is hidden then shown</li>
3032 <li>Preserve colouring of structures coloured by
3033 sequences in pre Jalview 2.7 projects</li>
3034 <li>Web service job parameter dialog is not laid out
3036 <li>Web services menu not refreshed after 'reset
3037 services' button is pressed in preferences</li>
3038 <li>Annotation off by one in Jalview v2_3 example project</li>
3039 <li>Structures imported from file and saved in project
3040 get name like jalview_pdb1234.txt when reloaded</li>
3041 <li>Jalview does not always retrieve progress of a JABAWS
3042 job execution in full once it is complete</li>
3043 </ul> <em>Applet</em>
3045 <li>Alignment height set incorrectly when lots of
3046 annotation rows are displayed</li>
3047 <li>Relative URLs in feature HTML text not resolved to
3049 <li>View follows highlighting does not work for positions
3051 <li><= shown as = in tooltip</li>
3052 <li>Export features raises exception when no features
3054 <li>Separator string used for serialising lists of IDs
3055 for javascript api is modified when separator string
3056 provided as parameter</li>
3057 <li>Null pointer exception when selecting tree leaves for
3058 alignment with no existing selection</li>
3059 <li>Relative URLs for datasources assumed to be relative
3060 to applet's codebase</li>
3061 <li>Status bar not updated after finished searching and
3062 search wraps around to first result</li>
3063 <li>StructureSelectionManager instance shared between
3064 several Jalview applets causes race conditions and memory
3066 <li>Hover tooltip and mouseover of position on structure
3067 not sent from Jmol in applet</li>
3068 <li>Certain sequences of javascript method calls to
3069 applet API fatally hang browser</li>
3070 </ul> <em>General</em>
3072 <li>View follows structure mouseover scrolls beyond
3073 position with wrapped view and hidden regions</li>
3074 <li>Find sequence position moves to wrong residue
3075 with/without hidden columns</li>
3076 <li>Sequence length given in alignment properties window
3078 <li>InvalidNumberFormat exceptions thrown when trying to
3079 import PDB like structure files</li>
3080 <li>Positional search results are only highlighted
3081 between user-supplied sequence start/end bounds</li>
3082 <li>End attribute of sequence is not validated</li>
3083 <li>Find dialog only finds first sequence containing a
3084 given sequence position</li>
3085 <li>Sequence numbering not preserved in MSF alignment
3087 <li>Jalview PDB file reader does not extract sequence
3088 from nucleotide chains correctly</li>
3089 <li>Structure colours not updated when tree partition
3090 changed in alignment</li>
3091 <li>Sequence associated secondary structure not correctly
3092 parsed in interleaved stockholm</li>
3093 <li>Colour by annotation dialog does not restore current
3095 <li>Hiding (nearly) all sequences doesn't work
3097 <li>Sequences containing lowercase letters are not
3098 properly associated with their pdb files</li>
3099 </ul> <em>Documentation and Development</em>
3101 <li>schemas/JalviewWsParamSet.xsd corrupted by
3102 ApplyCopyright tool</li>
3107 <div align="center">
3108 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
3111 <td><em>Application</em>
3113 <li>New warning dialog when the Jalview Desktop cannot
3114 contact web services</li>
3115 <li>JABA service parameters for a preset are shown in
3116 service job window</li>
3117 <li>JABA Service menu entries reworded</li>
3121 <li>Modeller PIR IO broken - cannot correctly import a
3122 pir file emitted by Jalview</li>
3123 <li>Existing feature settings transferred to new
3124 alignment view created from cut'n'paste</li>
3125 <li>Improved test for mixed amino/nucleotide chains when
3126 parsing PDB files</li>
3127 <li>Consensus and conservation annotation rows
3128 occasionally become blank for all new windows</li>
3129 <li>Exception raised when right clicking above sequences
3130 in wrapped view mode</li>
3131 </ul> <em>Application</em>
3133 <li>multiple multiply aligned structure views cause cpu
3134 usage to hit 100% and computer to hang</li>
3135 <li>Web Service parameter layout breaks for long user
3136 parameter names</li>
3137 <li>Jaba service discovery hangs desktop if Jaba server
3144 <div align="center">
3145 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3148 <td><em>Application</em>
3150 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3151 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3154 <li>Web Services preference tab</li>
3155 <li>Analysis parameters dialog box and user defined
3157 <li>Improved speed and layout of Envision2 service menu</li>
3158 <li>Superpose structures using associated sequence
3160 <li>Export coordinates and projection as CSV from PCA
3162 </ul> <em>Applet</em>
3164 <li>enable javascript: execution by the applet via the
3165 link out mechanism</li>
3166 </ul> <em>Other</em>
3168 <li>Updated the Jmol Jalview interface to work with Jmol
3170 <li>The Jalview Desktop and JalviewLite applet now
3171 require Java 1.5</li>
3172 <li>Allow Jalview feature colour specification for GFF
3173 sequence annotation files</li>
3174 <li>New 'colour by label' keword in Jalview feature file
3175 type colour specification</li>
3176 <li>New Jalview Desktop Groovy API method that allows a
3177 script to check if it being run in an interactive session or
3178 in a batch operation from the Jalview command line</li>
3182 <li>clustalx colourscheme colours Ds preferentially when
3183 both D+E are present in over 50% of the column</li>
3184 </ul> <em>Application</em>
3186 <li>typo in AlignmentFrame->View->Hide->all but
3187 selected Regions menu item</li>
3188 <li>sequence fetcher replaces ',' for ';' when the ',' is
3189 part of a valid accession ID</li>
3190 <li>fatal OOM if object retrieved by sequence fetcher
3191 runs out of memory</li>
3192 <li>unhandled Out of Memory Error when viewing pca
3193 analysis results</li>
3194 <li>InstallAnywhere builds fail to launch on OS X java
3195 10.5 update 4 (due to apple Java 1.6 update)</li>
3196 <li>Installanywhere Jalview silently fails to launch</li>
3197 </ul> <em>Applet</em>
3199 <li>Jalview.getFeatureGroups() raises an
3200 ArrayIndexOutOfBoundsException if no feature groups are
3207 <div align="center">
3208 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3214 <li>Alignment prettyprinter doesn't cope with long
3216 <li>clustalx colourscheme colours Ds preferentially when
3217 both D+E are present in over 50% of the column</li>
3218 <li>nucleic acid structures retrieved from PDB do not
3219 import correctly</li>
3220 <li>More columns get selected than were clicked on when a
3221 number of columns are hidden</li>
3222 <li>annotation label popup menu not providing correct
3223 add/hide/show options when rows are hidden or none are
3225 <li>Stockholm format shown in list of readable formats,
3226 and parser copes better with alignments from RFAM.</li>
3227 <li>CSV output of consensus only includes the percentage
3228 of all symbols if sequence logo display is enabled</li>
3230 </ul> <em>Applet</em>
3232 <li>annotation panel disappears when annotation is
3234 </ul> <em>Application</em>
3236 <li>Alignment view not redrawn properly when new
3237 alignment opened where annotation panel is visible but no
3238 annotations are present on alignment</li>
3239 <li>pasted region containing hidden columns is
3240 incorrectly displayed in new alignment window</li>
3241 <li>Jalview slow to complete operations when stdout is
3242 flooded (fix is to close the Jalview console)</li>
3243 <li>typo in AlignmentFrame->View->Hide->all but
3244 selected Rregions menu item.</li>
3245 <li>inconsistent group submenu and Format submenu entry
3246 'Un' or 'Non'conserved</li>
3247 <li>Sequence feature settings are being shared by
3248 multiple distinct alignments</li>
3249 <li>group annotation not recreated when tree partition is
3251 <li>double click on group annotation to select sequences
3252 does not propagate to associated trees</li>
3253 <li>Mac OSX specific issues:
3255 <li>exception raised when mouse clicked on desktop
3256 window background</li>
3257 <li>Desktop menu placed on menu bar and application
3258 name set correctly</li>
3259 <li>sequence feature settings not wide enough for the
3260 save feature colourscheme button</li>
3269 <div align="center">
3270 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3273 <td><em>New Capabilities</em>
3275 <li>URL links generated from description line for
3276 regular-expression based URL links (applet and application)
3278 <li>Non-positional feature URL links are shown in link
3280 <li>Linked viewing of nucleic acid sequences and
3282 <li>Automatic Scrolling option in View menu to display
3283 the currently highlighted region of an alignment.</li>
3284 <li>Order an alignment by sequence length, or using the
3285 average score or total feature count for each sequence.</li>
3286 <li>Shading features by score or associated description</li>
3287 <li>Subdivide alignment and groups based on identity of
3288 selected subsequence (Make Groups from Selection).</li>
3289 <li>New hide/show options including Shift+Control+H to
3290 hide everything but the currently selected region.</li>
3291 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3292 </ul> <em>Application</em>
3294 <li>Fetch DB References capabilities and UI expanded to
3295 support retrieval from DAS sequence sources</li>
3296 <li>Local DAS Sequence sources can be added via the
3297 command line or via the Add local source dialog box.</li>
3298 <li>DAS Dbref and DbxRef feature types are parsed as
3299 database references and protein_name is parsed as
3300 description line (BioSapiens terms).</li>
3301 <li>Enable or disable non-positional feature and database
3302 references in sequence ID tooltip from View menu in
3304 <!-- <li>New hidden columns and rows and representatives capabilities
3305 in annotations file (in progress - not yet fully implemented)</li> -->
3306 <li>Group-associated consensus, sequence logos and
3307 conservation plots</li>
3308 <li>Symbol distributions for each column can be exported
3309 and visualized as sequence logos</li>
3310 <li>Optionally scale multi-character column labels to fit
3311 within each column of annotation row<!-- todo for applet -->
3313 <li>Optional automatic sort of associated alignment view
3314 when a new tree is opened.</li>
3315 <li>Jalview Java Console</li>
3316 <li>Better placement of desktop window when moving
3317 between different screens.</li>
3318 <li>New preference items for sequence ID tooltip and
3319 consensus annotation</li>
3320 <li>Client to submit sequences and IDs to Envision2
3322 <li><em>Vamsas Capabilities</em>
3324 <li>Improved VAMSAS synchronization (Jalview archive
3325 used to preserve views, structures, and tree display
3327 <li>Import of vamsas documents from disk or URL via
3329 <li>Sharing of selected regions between views and
3330 with other VAMSAS applications (Experimental feature!)</li>
3331 <li>Updated API to VAMSAS version 0.2</li>
3333 </ul> <em>Applet</em>
3335 <li>Middle button resizes annotation row height</li>
3338 <li>sortByTree (true/false) - automatically sort the
3339 associated alignment view by the tree when a new tree is
3341 <li>showTreeBootstraps (true/false) - show or hide
3342 branch bootstraps (default is to show them if available)</li>
3343 <li>showTreeDistances (true/false) - show or hide
3344 branch lengths (default is to show them if available)</li>
3345 <li>showUnlinkedTreeNodes (true/false) - indicate if
3346 unassociated nodes should be highlighted in the tree
3348 <li>heightScale and widthScale (1.0 or more) -
3349 increase the height or width of a cell in the alignment
3350 grid relative to the current font size.</li>
3353 <li>Non-positional features displayed in sequence ID
3355 </ul> <em>Other</em>
3357 <li>Features format: graduated colour definitions and
3358 specification of feature scores</li>
3359 <li>Alignment Annotations format: new keywords for group
3360 associated annotation (GROUP_REF) and annotation row display
3361 properties (ROW_PROPERTIES)</li>
3362 <li>XML formats extended to support graduated feature
3363 colourschemes, group associated annotation, and profile
3364 visualization settings.</li></td>
3367 <li>Source field in GFF files parsed as feature source
3368 rather than description</li>
3369 <li>Non-positional features are now included in sequence
3370 feature and gff files (controlled via non-positional feature
3371 visibility in tooltip).</li>
3372 <li>URL links generated for all feature links (bugfix)</li>
3373 <li>Added URL embedding instructions to features file
3375 <li>Codons containing ambiguous nucleotides translated as
3376 'X' in peptide product</li>
3377 <li>Match case switch in find dialog box works for both
3378 sequence ID and sequence string and query strings do not
3379 have to be in upper case to match case-insensitively.</li>
3380 <li>AMSA files only contain first column of
3381 multi-character column annotation labels</li>
3382 <li>Jalview Annotation File generation/parsing consistent
3383 with documentation (e.g. Stockholm annotation can be
3384 exported and re-imported)</li>
3385 <li>PDB files without embedded PDB IDs given a friendly
3387 <li>Find incrementally searches ID string matches as well
3388 as subsequence matches, and correctly reports total number
3392 <li>Better handling of exceptions during sequence
3394 <li>Dasobert generated non-positional feature URL
3395 link text excludes the start_end suffix</li>
3396 <li>DAS feature and source retrieval buttons disabled
3397 when fetch or registry operations in progress.</li>
3398 <li>PDB files retrieved from URLs are cached properly</li>
3399 <li>Sequence description lines properly shared via
3401 <li>Sequence fetcher fetches multiple records for all
3403 <li>Ensured that command line das feature retrieval
3404 completes before alignment figures are generated.</li>
3405 <li>Reduced time taken when opening file browser for
3407 <li>isAligned check prior to calculating tree, PCA or
3408 submitting an MSA to JNet now excludes hidden sequences.</li>
3409 <li>User defined group colours properly recovered
3410 from Jalview projects.</li>
3419 <div align="center">
3420 <strong>2.4.0.b2</strong><br> 28/10/2009
3425 <li>Experimental support for google analytics usage
3427 <li>Jalview privacy settings (user preferences and docs).</li>
3432 <li>Race condition in applet preventing startup in
3434 <li>Exception when feature created from selection beyond
3435 length of sequence.</li>
3436 <li>Allow synthetic PDB files to be imported gracefully</li>
3437 <li>Sequence associated annotation rows associate with
3438 all sequences with a given id</li>
3439 <li>Find function matches case-insensitively for sequence
3440 ID string searches</li>
3441 <li>Non-standard characters do not cause pairwise
3442 alignment to fail with exception</li>
3443 </ul> <em>Application Issues</em>
3445 <li>Sequences are now validated against EMBL database</li>
3446 <li>Sequence fetcher fetches multiple records for all
3448 </ul> <em>InstallAnywhere Issues</em>
3450 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3451 issue with installAnywhere mechanism)</li>
3452 <li>Command line launching of JARs from InstallAnywhere
3453 version (java class versioning error fixed)</li>
3460 <div align="center">
3461 <strong>2.4</strong><br> 27/8/2008
3464 <td><em>User Interface</em>
3466 <li>Linked highlighting of codon and amino acid from
3467 translation and protein products</li>
3468 <li>Linked highlighting of structure associated with
3469 residue mapping to codon position</li>
3470 <li>Sequence Fetcher provides example accession numbers
3471 and 'clear' button</li>
3472 <li>MemoryMonitor added as an option under Desktop's
3474 <li>Extract score function to parse whitespace separated
3475 numeric data in description line</li>
3476 <li>Column labels in alignment annotation can be centred.</li>
3477 <li>Tooltip for sequence associated annotation give name
3479 </ul> <em>Web Services and URL fetching</em>
3481 <li>JPred3 web service</li>
3482 <li>Prototype sequence search client (no public services
3484 <li>Fetch either seed alignment or full alignment from
3486 <li>URL Links created for matching database cross
3487 references as well as sequence ID</li>
3488 <li>URL Links can be created using regular-expressions</li>
3489 </ul> <em>Sequence Database Connectivity</em>
3491 <li>Retrieval of cross-referenced sequences from other
3493 <li>Generalised database reference retrieval and
3494 validation to all fetchable databases</li>
3495 <li>Fetch sequences from DAS sources supporting the
3496 sequence command</li>
3497 </ul> <em>Import and Export</em>
3498 <li>export annotation rows as CSV for spreadsheet import</li>
3499 <li>Jalview projects record alignment dataset associations,
3500 EMBL products, and cDNA sequence mappings</li>
3501 <li>Sequence Group colour can be specified in Annotation
3503 <li>Ad-hoc colouring of group in Annotation File using RGB
3504 triplet as name of colourscheme</li>
3505 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3507 <li>treenode binding for VAMSAS tree exchange</li>
3508 <li>local editing and update of sequences in VAMSAS
3509 alignments (experimental)</li>
3510 <li>Create new or select existing session to join</li>
3511 <li>load and save of vamsas documents</li>
3512 </ul> <em>Application command line</em>
3514 <li>-tree parameter to open trees (introduced for passing
3516 <li>-fetchfrom command line argument to specify nicknames
3517 of DAS servers to query for alignment features</li>
3518 <li>-dasserver command line argument to add new servers
3519 that are also automatically queried for features</li>
3520 <li>-groovy command line argument executes a given groovy
3521 script after all input data has been loaded and parsed</li>
3522 </ul> <em>Applet-Application data exchange</em>
3524 <li>Trees passed as applet parameters can be passed to
3525 application (when using "View in full
3526 application")</li>
3527 </ul> <em>Applet Parameters</em>
3529 <li>feature group display control parameter</li>
3530 <li>debug parameter</li>
3531 <li>showbutton parameter</li>
3532 </ul> <em>Applet API methods</em>
3534 <li>newView public method</li>
3535 <li>Window (current view) specific get/set public methods</li>
3536 <li>Feature display control methods</li>
3537 <li>get list of currently selected sequences</li>
3538 </ul> <em>New Jalview distribution features</em>
3540 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3541 <li>RELEASE file gives build properties for the latest
3542 Jalview release.</li>
3543 <li>Java 1.1 Applet build made easier and donotobfuscate
3544 property controls execution of obfuscator</li>
3545 <li>Build target for generating source distribution</li>
3546 <li>Debug flag for javacc</li>
3547 <li>.jalview_properties file is documented (slightly) in
3548 jalview.bin.Cache</li>
3549 <li>Continuous Build Integration for stable and
3550 development version of Application, Applet and source
3555 <li>selected region output includes visible annotations
3556 (for certain formats)</li>
3557 <li>edit label/displaychar contains existing label/char
3559 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3560 <li>shorter peptide product names from EMBL records</li>
3561 <li>Newick string generator makes compact representations</li>
3562 <li>bootstrap values parsed correctly for tree files with
3564 <li>pathological filechooser bug avoided by not allowing
3565 filenames containing a ':'</li>
3566 <li>Fixed exception when parsing GFF files containing
3567 global sequence features</li>
3568 <li>Alignment datasets are finalized only when number of
3569 references from alignment sequences goes to zero</li>
3570 <li>Close of tree branch colour box without colour
3571 selection causes cascading exceptions</li>
3572 <li>occasional negative imgwidth exceptions</li>
3573 <li>better reporting of non-fatal warnings to user when
3574 file parsing fails.</li>
3575 <li>Save works when Jalview project is default format</li>
3576 <li>Save as dialog opened if current alignment format is
3577 not a valid output format</li>
3578 <li>UniProt canonical names introduced for both das and
3580 <li>Histidine should be midblue (not pink!) in Zappo</li>
3581 <li>error messages passed up and output when data read
3583 <li>edit undo recovers previous dataset sequence when
3584 sequence is edited</li>
3585 <li>allow PDB files without pdb ID HEADER lines (like
3586 those generated by MODELLER) to be read in properly</li>
3587 <li>allow reading of JPred concise files as a normal
3589 <li>Stockholm annotation parsing and alignment properties
3590 import fixed for PFAM records</li>
3591 <li>Structure view windows have correct name in Desktop
3593 <li>annotation consisting of sequence associated scores
3594 can be read and written correctly to annotation file</li>
3595 <li>Aligned cDNA translation to aligned peptide works
3597 <li>Fixed display of hidden sequence markers and
3598 non-italic font for representatives in Applet</li>
3599 <li>Applet Menus are always embedded in applet window on
3601 <li>Newly shown features appear at top of stack (in
3603 <li>Annotations added via parameter not drawn properly
3604 due to null pointer exceptions</li>
3605 <li>Secondary structure lines are drawn starting from
3606 first column of alignment</li>
3607 <li>UniProt XML import updated for new schema release in
3609 <li>Sequence feature to sequence ID match for Features
3610 file is case-insensitive</li>
3611 <li>Sequence features read from Features file appended to
3612 all sequences with matching IDs</li>
3613 <li>PDB structure coloured correctly for associated views
3614 containing a sub-sequence</li>
3615 <li>PDB files can be retrieved by applet from Jar files</li>
3616 <li>feature and annotation file applet parameters
3617 referring to different directories are retrieved correctly</li>
3618 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3619 <li>Fixed application hang whilst waiting for
3620 splash-screen version check to complete</li>
3621 <li>Applet properly URLencodes input parameter values
3622 when passing them to the launchApp service</li>
3623 <li>display name and local features preserved in results
3624 retrieved from web service</li>
3625 <li>Visual delay indication for sequence retrieval and
3626 sequence fetcher initialisation</li>
3627 <li>updated Application to use DAS 1.53e version of
3628 dasobert DAS client</li>
3629 <li>Re-instated Full AMSA support and .amsa file
3631 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3639 <div align="center">
3640 <strong>2.3</strong><br> 9/5/07
3645 <li>Jmol 11.0.2 integration</li>
3646 <li>PDB views stored in Jalview XML files</li>
3647 <li>Slide sequences</li>
3648 <li>Edit sequence in place</li>
3649 <li>EMBL CDS features</li>
3650 <li>DAS Feature mapping</li>
3651 <li>Feature ordering</li>
3652 <li>Alignment Properties</li>
3653 <li>Annotation Scores</li>
3654 <li>Sort by scores</li>
3655 <li>Feature/annotation editing in applet</li>
3660 <li>Headless state operation in 2.2.1</li>
3661 <li>Incorrect and unstable DNA pairwise alignment</li>
3662 <li>Cut and paste of sequences with annotation</li>
3663 <li>Feature group display state in XML</li>
3664 <li>Feature ordering in XML</li>
3665 <li>blc file iteration selection using filename # suffix</li>
3666 <li>Stockholm alignment properties</li>
3667 <li>Stockhom alignment secondary structure annotation</li>
3668 <li>2.2.1 applet had no feature transparency</li>
3669 <li>Number pad keys can be used in cursor mode</li>
3670 <li>Structure Viewer mirror image resolved</li>
3677 <div align="center">
3678 <strong>2.2.1</strong><br> 12/2/07
3683 <li>Non standard characters can be read and displayed
3684 <li>Annotations/Features can be imported/exported to the
3686 <li>Applet allows editing of sequence/annotation/group
3687 name & description
3688 <li>Preference setting to display sequence name in
3690 <li>Annotation file format extended to allow
3691 Sequence_groups to be defined
3692 <li>Default opening of alignment overview panel can be
3693 specified in preferences
3694 <li>PDB residue numbering annotation added to associated
3700 <li>Applet crash under certain Linux OS with Java 1.6
3702 <li>Annotation file export / import bugs fixed
3703 <li>PNG / EPS image output bugs fixed
3709 <div align="center">
3710 <strong>2.2</strong><br> 27/11/06
3715 <li>Multiple views on alignment
3716 <li>Sequence feature editing
3717 <li>"Reload" alignment
3718 <li>"Save" to current filename
3719 <li>Background dependent text colour
3720 <li>Right align sequence ids
3721 <li>User-defined lower case residue colours
3724 <li>Menu item accelerator keys
3725 <li>Control-V pastes to current alignment
3726 <li>Cancel button for DAS Feature Fetching
3727 <li>PCA and PDB Viewers zoom via mouse roller
3728 <li>User-defined sub-tree colours and sub-tree selection
3730 <li>'New Window' button on the 'Output to Text box'
3735 <li>New memory efficient Undo/Redo System
3736 <li>Optimised symbol lookups and conservation/consensus
3738 <li>Region Conservation/Consensus recalculated after
3740 <li>Fixed Remove Empty Columns Bug (empty columns at end
3742 <li>Slowed DAS Feature Fetching for increased robustness.
3744 <li>Made angle brackets in ASCII feature descriptions
3746 <li>Re-instated Zoom function for PCA
3747 <li>Sequence descriptions conserved in web service
3749 <li>UniProt ID discoverer uses any word separated by
3751 <li>WsDbFetch query/result association resolved
3752 <li>Tree leaf to sequence mapping improved
3753 <li>Smooth fonts switch moved to FontChooser dialog box.
3760 <div align="center">
3761 <strong>2.1.1</strong><br> 12/9/06
3766 <li>Copy consensus sequence to clipboard</li>
3771 <li>Image output - rightmost residues are rendered if
3772 sequence id panel has been resized</li>
3773 <li>Image output - all offscreen group boundaries are
3775 <li>Annotation files with sequence references - all
3776 elements in file are relative to sequence position</li>
3777 <li>Mac Applet users can use Alt key for group editing</li>
3783 <div align="center">
3784 <strong>2.1</strong><br> 22/8/06
3789 <li>MAFFT Multiple Alignment in default Web Service list</li>
3790 <li>DAS Feature fetching</li>
3791 <li>Hide sequences and columns</li>
3792 <li>Export Annotations and Features</li>
3793 <li>GFF file reading / writing</li>
3794 <li>Associate structures with sequences from local PDB
3796 <li>Add sequences to exisiting alignment</li>
3797 <li>Recently opened files / URL lists</li>
3798 <li>Applet can launch the full application</li>
3799 <li>Applet has transparency for features (Java 1.2
3801 <li>Applet has user defined colours parameter</li>
3802 <li>Applet can load sequences from parameter
3803 "sequence<em>x</em>"
3809 <li>Redundancy Panel reinstalled in the Applet</li>
3810 <li>Monospaced font - EPS / rescaling bug fixed</li>
3811 <li>Annotation files with sequence references bug fixed</li>
3817 <div align="center">
3818 <strong>2.08.1</strong><br> 2/5/06
3823 <li>Change case of selected region from Popup menu</li>
3824 <li>Choose to match case when searching</li>
3825 <li>Middle mouse button and mouse movement can compress /
3826 expand the visible width and height of the alignment</li>
3831 <li>Annotation Panel displays complete JNet results</li>
3837 <div align="center">
3838 <strong>2.08b</strong><br> 18/4/06
3844 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3845 <li>Righthand label on wrapped alignments shows correct
3852 <div align="center">
3853 <strong>2.08</strong><br> 10/4/06
3858 <li>Editing can be locked to the selection area</li>
3859 <li>Keyboard editing</li>
3860 <li>Create sequence features from searches</li>
3861 <li>Precalculated annotations can be loaded onto
3863 <li>Features file allows grouping of features</li>
3864 <li>Annotation Colouring scheme added</li>
3865 <li>Smooth fonts off by default - Faster rendering</li>
3866 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3871 <li>Drag & Drop fixed on Linux</li>
3872 <li>Jalview Archive file faster to load/save, sequence
3873 descriptions saved.</li>
3879 <div align="center">
3880 <strong>2.07</strong><br> 12/12/05
3885 <li>PDB Structure Viewer enhanced</li>
3886 <li>Sequence Feature retrieval and display enhanced</li>
3887 <li>Choose to output sequence start-end after sequence
3888 name for file output</li>
3889 <li>Sequence Fetcher WSDBFetch@EBI</li>
3890 <li>Applet can read feature files, PDB files and can be
3891 used for HTML form input</li>
3896 <li>HTML output writes groups and features</li>
3897 <li>Group editing is Control and mouse click</li>
3898 <li>File IO bugs</li>
3904 <div align="center">
3905 <strong>2.06</strong><br> 28/9/05
3910 <li>View annotations in wrapped mode</li>
3911 <li>More options for PCA viewer</li>
3916 <li>GUI bugs resolved</li>
3917 <li>Runs with -nodisplay from command line</li>
3923 <div align="center">
3924 <strong>2.05b</strong><br> 15/9/05
3929 <li>Choose EPS export as lineart or text</li>
3930 <li>Jar files are executable</li>
3931 <li>Can read in Uracil - maps to unknown residue</li>
3936 <li>Known OutOfMemory errors give warning message</li>
3937 <li>Overview window calculated more efficiently</li>
3938 <li>Several GUI bugs resolved</li>
3944 <div align="center">
3945 <strong>2.05</strong><br> 30/8/05
3950 <li>Edit and annotate in "Wrapped" view</li>
3955 <li>Several GUI bugs resolved</li>
3961 <div align="center">
3962 <strong>2.04</strong><br> 24/8/05
3967 <li>Hold down mouse wheel & scroll to change font
3973 <li>Improved JPred client reliability</li>
3974 <li>Improved loading of Jalview files</li>
3980 <div align="center">
3981 <strong>2.03</strong><br> 18/8/05
3986 <li>Set Proxy server name and port in preferences</li>
3987 <li>Multiple URL links from sequence ids</li>
3988 <li>User Defined Colours can have a scheme name and added
3990 <li>Choose to ignore gaps in consensus calculation</li>
3991 <li>Unix users can set default web browser</li>
3992 <li>Runs without GUI for batch processing</li>
3993 <li>Dynamically generated Web Service Menus</li>
3998 <li>InstallAnywhere download for Sparc Solaris</li>
4004 <div align="center">
4005 <strong>2.02</strong><br> 18/7/05
4011 <li>Copy & Paste order of sequences maintains
4012 alignment order.</li>
4018 <div align="center">
4019 <strong>2.01</strong><br> 12/7/05
4024 <li>Use delete key for deleting selection.</li>
4025 <li>Use Mouse wheel to scroll sequences.</li>
4026 <li>Help file updated to describe how to add alignment
4028 <li>Version and build date written to build properties
4030 <li>InstallAnywhere installation will check for updates
4031 at launch of Jalview.</li>
4036 <li>Delete gaps bug fixed.</li>
4037 <li>FileChooser sorts columns.</li>
4038 <li>Can remove groups one by one.</li>
4039 <li>Filechooser icons installed.</li>
4040 <li>Finder ignores return character when searching.
4041 Return key will initiate a search.<br>
4048 <div align="center">
4049 <strong>2.0</strong><br> 20/6/05
4054 <li>New codebase</li>