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.2.10.4">2.10.4</a><br /> <em>1/05/2018</em></strong>
76 <td><div align="left">
80 <!-- JAL-1847 JAL-2944 -->Structure Chooser controls to
81 control superposition of multiple structures and open
82 structures in existing views
85 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
86 ID and annotation area margins can be click-dragged to
90 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
94 <!-- JAL-2759 -->Improved performance for large alignments
95 and lots of hidden columns
98 <!-- JAL-2593 -->Improved performance when rendering lots
104 <td><div align="left">
107 <!-- JAL-2899 -->Structure and Overview aren't updated
108 when Colour By Annotation threshold slider is adjusted
111 <!-- JAL-2778 -->Slow redraw when Overview panel shown
112 overlapping alignment panel
115 <!-- JAL-2929 -->overview doesn't show end of unpadded
119 <!-- JAL-2666 -->Linked scrolling via protein horizontal
120 scroll bar doesn't work for some CDS/Protein views
123 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
124 Java 1.8u153 onwards and Java 1.9u4+.
127 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
128 columns in annotation row
131 <!-- JAL-2913 -->Preferences panel's ID Width control is
132 honored in interactive and batch mode
135 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
136 for structures added to existing Jmol view
139 <!-- JAL-2223 -->'View Mappings' includes duplicate
140 entries after importing project with multiple views
143 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
144 protein sequences via SIFTS from associated PDB entries
145 with negative residue numbers or missing residues fails
148 <!-- JAL-2952 -->Exception when shading sequence with negative
149 Temperature Factor values from annotated PDB files (e.g.
150 as generated by CONSURF)
153 <!-- JAL-2922 -->Invert displayed features very slow when
154 structure and/or overview windows are also shown
157 <!-- JAL-2954 -->Selecting columns from highlighted regions
158 very slow for alignments with large numbers of sequences
161 <!-- JAL-2925 -->Copy Consensus fails for group consensus
162 with 'StringIndexOutOfBounds'
165 <!-- JAL-2976 -->VAqua(4) (<a
166 href="http://violetlib.org/vaqua/overview.html">download
167 here</a>) provided as fallback Look and Feel for OSX
168 platforms running Java 10
171 <!-- JAL-2960 -->Adding a structure to existing structure
172 view appears to do nothing because the view is hidden behind the alignment view
178 <!-- JAL-2926 -->Copy consensus sequence option in applet
179 should copy the group consensus when popup is opened on it
183 <em>New Known Defects</em>
186 <!-- JAL-2973 --> Exceptions occasionally raised when
187 editing a large alignment and overview is displayed
190 <!-- JAL-2974 -->'Overview updating' progress bar is shown
191 repeatedly after a series of edits even when the overview
192 is no longer reflecting updates
195 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
196 structures for protein subsequence (if 'Trim Retrieved
197 Sequences' enabled) or Ensembl isoforms (Workaround in
198 2.10.4 is to fail back to N&W mapping)
205 <td width="60" nowrap>
207 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
210 <td><div align="left">
211 <ul><li>Updated Certum Codesigning Certificate
212 (Valid till 30th November 2018)</li></ul></div></td>
213 <td><div align="left">
216 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
217 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
218 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
219 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
220 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
221 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
222 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
228 <td width="60" nowrap>
230 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
233 <td><div align="left">
237 <!-- JAL-2446 -->Faster and more efficient management and
238 rendering of sequence features
241 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
242 429 rate limit request hander
245 <!-- JAL-2773 -->Structure views don't get updated unless
246 their colours have changed
249 <!-- JAL-2495 -->All linked sequences are highlighted for
250 a structure mousover (Jmol) or selection (Chimera)
253 <!-- JAL-2790 -->'Cancel' button in progress bar for
254 JABAWS AACon, RNAAliFold and Disorder prediction jobs
257 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
258 view from Ensembl locus cross-references
261 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
265 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
266 feature can be disabled
269 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
270 PDB easier retrieval of sequences for lists of IDs
273 <!-- JAL-2758 -->Short names for sequences retrieved from
279 <li>Groovy interpreter updated to 2.4.12</li>
280 <li>Example groovy script for generating a matrix of
281 percent identity scores for current alignment.</li>
283 <em>Testing and Deployment</em>
286 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
290 <td><div align="left">
294 <!-- JAL-2643 -->Pressing tab after updating the colour
295 threshold text field doesn't trigger an update to the
299 <!-- JAL-2682 -->Race condition when parsing sequence ID
303 <!-- JAL-2608 -->Overview windows are also closed when
304 alignment window is closed
307 <!-- JAL-2548 -->Export of features doesn't always respect
311 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
312 takes a long time in Cursor mode
318 <!-- JAL-2777 -->Structures with whitespace chainCode
319 cannot be viewed in Chimera
322 <!-- JAL-2728 -->Protein annotation panel too high in
326 <!-- JAL-2757 -->Can't edit the query after the server
327 error warning icon is shown in Uniprot and PDB Free Text
331 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
334 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
337 <!-- JAL-2739 -->Hidden column marker in last column not
338 rendered when switching back from Wrapped to normal view
341 <!-- JAL-2768 -->Annotation display corrupted when
342 scrolling right in unwapped alignment view
345 <!-- JAL-2542 -->Existing features on subsequence
346 incorrectly relocated when full sequence retrieved from
350 <!-- JAL-2733 -->Last reported memory still shown when
351 Desktop->Show Memory is unticked (OSX only)
354 <!-- JAL-2658 -->Amend Features dialog doesn't allow
355 features of same type and group to be selected for
359 <!-- JAL-2524 -->Jalview becomes sluggish in wide
360 alignments when hidden columns are present
363 <!-- JAL-2392 -->Jalview freezes when loading and
364 displaying several structures
367 <!-- JAL-2732 -->Black outlines left after resizing or
371 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
372 within the Jalview desktop on OSX
375 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
376 when in wrapped alignment mode
379 <!-- JAL-2636 -->Scale mark not shown when close to right
380 hand end of alignment
383 <!-- JAL-2684 -->Pairwise alignment of selected regions of
384 each selected sequence do not have correct start/end
388 <!-- JAL-2793 -->Alignment ruler height set incorrectly
389 after canceling the Alignment Window's Font dialog
392 <!-- JAL-2036 -->Show cross-references not enabled after
393 restoring project until a new view is created
396 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
397 URL links appears when only default EMBL-EBI link is
398 configured (since 2.10.2b2)
401 <!-- JAL-2775 -->Overview redraws whole window when box
405 <!-- JAL-2225 -->Structure viewer doesn't map all chains
406 in a multi-chain structure when viewing alignment
407 involving more than one chain (since 2.10)
410 <!-- JAL-2811 -->Double residue highlights in cursor mode
411 if new selection moves alignment window
414 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
415 arrow key in cursor mode to pass hidden column marker
418 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
419 that produces correctly annotated transcripts and products
422 <!-- JAL-2776 -->Toggling a feature group after first time
423 doesn't update associated structure view
426 <em>Applet</em><br />
429 <!-- JAL-2687 -->Concurrent modification exception when
430 closing alignment panel
433 <em>BioJSON</em><br />
436 <!-- JAL-2546 -->BioJSON export does not preserve
437 non-positional features
440 <em>New Known Issues</em>
443 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
444 sequence features correctly (for many previous versions of
448 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
449 using cursor in wrapped panel other than top
452 <!-- JAL-2791 -->Select columns containing feature ignores
453 graduated colour threshold
456 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
457 always preserve numbering and sequence features
460 <em>Known Java 9 Issues</em>
463 <!-- JAL-2902 -->Groovy Console very slow to open and is
464 not responsive when entering characters (Webstart, Java
471 <td width="60" nowrap>
473 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
474 <em>2/10/2017</em></strong>
477 <td><div align="left">
478 <em>New features in Jalview Desktop</em>
481 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
483 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
487 <td><div align="left">
491 <td width="60" nowrap>
493 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
494 <em>7/9/2017</em></strong>
497 <td><div align="left">
501 <!-- JAL-2588 -->Show gaps in overview window by colouring
502 in grey (sequences used to be coloured grey, and gaps were
506 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
510 <!-- JAL-2587 -->Overview updates immediately on increase
511 in size and progress bar shown as higher resolution
512 overview is recalculated
517 <td><div align="left">
521 <!-- JAL-2664 -->Overview window redraws every hidden
522 column region row by row
525 <!-- JAL-2681 -->duplicate protein sequences shown after
526 retrieving Ensembl crossrefs for sequences from Uniprot
529 <!-- JAL-2603 -->Overview window throws NPE if show boxes
530 format setting is unticked
533 <!-- JAL-2610 -->Groups are coloured wrongly in overview
534 if group has show boxes format setting unticked
537 <!-- JAL-2672,JAL-2665 -->Redraw problems when
538 autoscrolling whilst dragging current selection group to
539 include sequences and columns not currently displayed
542 <!-- JAL-2691 -->Not all chains are mapped when multimeric
543 assemblies are imported via CIF file
546 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
547 displayed when threshold or conservation colouring is also
551 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
555 <!-- JAL-2673 -->Jalview continues to scroll after
556 dragging a selected region off the visible region of the
560 <!-- JAL-2724 -->Cannot apply annotation based
561 colourscheme to all groups in a view
564 <!-- JAL-2511 -->IDs don't line up with sequences
565 initially after font size change using the Font chooser or
572 <td width="60" nowrap>
574 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
577 <td><div align="left">
578 <em>Calculations</em>
582 <!-- JAL-1933 -->Occupancy annotation row shows number of
583 ungapped positions in each column of the alignment.
586 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
587 a calculation dialog box
590 <!-- JAL-2379 -->Revised implementation of PCA for speed
591 and memory efficiency (~30x faster)
594 <!-- JAL-2403 -->Revised implementation of sequence
595 similarity scores as used by Tree, PCA, Shading Consensus
596 and other calculations
599 <!-- JAL-2416 -->Score matrices are stored as resource
600 files within the Jalview codebase
603 <!-- JAL-2500 -->Trees computed on Sequence Feature
604 Similarity may have different topology due to increased
611 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
612 model for alignments and groups
615 <!-- JAL-384 -->Custom shading schemes created via groovy
622 <!-- JAL-2526 -->Efficiency improvements for interacting
623 with alignment and overview windows
626 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
630 <!-- JAL-2388 -->Hidden columns and sequences can be
634 <!-- JAL-2611 -->Click-drag in visible area allows fine
635 adjustment of visible position
639 <em>Data import/export</em>
642 <!-- JAL-2535 -->Posterior probability annotation from
643 Stockholm files imported as sequence associated annotation
646 <!-- JAL-2507 -->More robust per-sequence positional
647 annotation input/output via stockholm flatfile
650 <!-- JAL-2533 -->Sequence names don't include file
651 extension when importing structure files without embedded
652 names or PDB accessions
655 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
656 format sequence substitution matrices
659 <em>User Interface</em>
662 <!-- JAL-2447 --> Experimental Features Checkbox in
663 Desktop's Tools menu to hide or show untested features in
667 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
668 via Overview or sequence motif search operations
671 <!-- JAL-2547 -->Amend sequence features dialog box can be
672 opened by double clicking gaps within sequence feature
676 <!-- JAL-1476 -->Status bar message shown when not enough
677 aligned positions were available to create a 3D structure
681 <em>3D Structure</em>
684 <!-- JAL-2430 -->Hidden regions in alignment views are not
685 coloured in linked structure views
688 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
689 file-based command exchange
692 <!-- JAL-2375 -->Structure chooser automatically shows
693 Cached Structures rather than querying the PDBe if
694 structures are already available for sequences
697 <!-- JAL-2520 -->Structures imported via URL are cached in
698 the Jalview project rather than downloaded again when the
702 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
703 to transfer Chimera's structure attributes as Jalview
704 features, and vice-versa (<strong>Experimental
708 <em>Web Services</em>
711 <!-- JAL-2549 -->Updated JABAWS client to v2.2
714 <!-- JAL-2335 -->Filter non-standard amino acids and
715 nucleotides when submitting to AACon and other MSA
719 <!-- JAL-2316, -->URLs for viewing database
720 cross-references provided by identifiers.org and the
728 <!-- JAL-2344 -->FileFormatI interface for describing and
729 identifying file formats (instead of String constants)
732 <!-- JAL-2228 -->FeatureCounter script refactored for
733 efficiency when counting all displayed features (not
734 backwards compatible with 2.10.1)
737 <em>Example files</em>
740 <!-- JAL-2631 -->Graduated feature colour style example
741 included in the example feature file
744 <em>Documentation</em>
747 <!-- JAL-2339 -->Release notes reformatted for readability
748 with the built-in Java help viewer
751 <!-- JAL-1644 -->Find documentation updated with 'search
752 sequence description' option
758 <!-- JAL-2485, -->External service integration tests for
759 Uniprot REST Free Text Search Client
762 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
765 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
770 <td><div align="left">
771 <em>Calculations</em>
774 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
775 matrix - C->R should be '-3'<br />Old matrix restored
776 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
778 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
779 Jalview's treatment of gaps in PCA and substitution matrix
780 based Tree calculations.<br /> <br />In earlier versions
781 of Jalview, gaps matching gaps were penalised, and gaps
782 matching non-gaps penalised even more. In the PCA
783 calculation, gaps were actually treated as non-gaps - so
784 different costs were applied, which meant Jalview's PCAs
785 were different to those produced by SeqSpace.<br />Jalview
786 now treats gaps in the same way as SeqSpace (ie it scores
787 them as 0). <br /> <br />Enter the following in the
788 Groovy console to restore pre-2.10.2 behaviour:<br />
789 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
790 // for 2.10.1 mode <br />
791 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
792 // to restore 2.10.2 mode <br /> <br /> <em>Note:
793 these settings will affect all subsequent tree and PCA
794 calculations (not recommended)</em></li>
796 <!-- JAL-2424 -->Fixed off-by-one bug that affected
797 scaling of branch lengths for trees computed using
798 Sequence Feature Similarity.
801 <!-- JAL-2377 -->PCA calculation could hang when
802 generating output report when working with highly
806 <!-- JAL-2544 --> Sort by features includes features to
807 right of selected region when gaps present on right-hand
811 <em>User Interface</em>
814 <!-- JAL-2346 -->Reopening Colour by annotation dialog
815 doesn't reselect a specific sequence's associated
816 annotation after it was used for colouring a view
819 <!-- JAL-2419 -->Current selection lost if popup menu
820 opened on a region of alignment without groups
823 <!-- JAL-2374 -->Popup menu not always shown for regions
824 of an alignment with overlapping groups
827 <!-- JAL-2310 -->Finder double counts if both a sequence's
828 name and description match
831 <!-- JAL-2370 -->Hiding column selection containing two
832 hidden regions results in incorrect hidden regions
835 <!-- JAL-2386 -->'Apply to all groups' setting when
836 changing colour does not apply Conservation slider value
840 <!-- JAL-2373 -->Percentage identity and conservation menu
841 items do not show a tick or allow shading to be disabled
844 <!-- JAL-2385 -->Conservation shading or PID threshold
845 lost when base colourscheme changed if slider not visible
848 <!-- JAL-2547 -->Sequence features shown in tooltip for
849 gaps before start of features
852 <!-- JAL-2623 -->Graduated feature colour threshold not
853 restored to UI when feature colour is edited
856 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
857 a time when scrolling vertically in wrapped mode.
860 <!-- JAL-2630 -->Structure and alignment overview update
861 as graduate feature colour settings are modified via the
865 <!-- JAL-2034 -->Overview window doesn't always update
866 when a group defined on the alignment is resized
869 <!-- JAL-2605 -->Mouseovers on left/right scale region in
870 wrapped view result in positional status updates
874 <!-- JAL-2563 -->Status bar doesn't show position for
875 ambiguous amino acid and nucleotide symbols
878 <!-- JAL-2602 -->Copy consensus sequence failed if
879 alignment included gapped columns
882 <!-- JAL-2473 -->Minimum size set for Jalview windows so
883 widgets don't permanently disappear
886 <!-- JAL-2503 -->Cannot select or filter quantitative
887 annotation that are shown only as column labels (e.g.
888 T-Coffee column reliability scores)
891 <!-- JAL-2594 -->Exception thrown if trying to create a
892 sequence feature on gaps only
895 <!-- JAL-2504 -->Features created with 'New feature'
896 button from a Find inherit previously defined feature type
897 rather than the Find query string
900 <!-- JAL-2423 -->incorrect title in output window when
901 exporting tree calculated in Jalview
904 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
905 and then revealing them reorders sequences on the
909 <!-- JAL-964 -->Group panel in sequence feature settings
910 doesn't update to reflect available set of groups after
911 interactively adding or modifying features
914 <!-- JAL-2225 -->Sequence Database chooser unusable on
918 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
919 only excluded gaps in current sequence and ignored
926 <!-- JAL-2421 -->Overview window visible region moves
927 erratically when hidden rows or columns are present
930 <!-- JAL-2362 -->Per-residue colourschemes applied via the
931 Structure Viewer's colour menu don't correspond to
935 <!-- JAL-2405 -->Protein specific colours only offered in
936 colour and group colour menu for protein alignments
939 <!-- JAL-2385 -->Colour threshold slider doesn't update to
940 reflect currently selected view or group's shading
944 <!-- JAL-2624 -->Feature colour thresholds not respected
945 when rendered on overview and structures when opacity at
949 <!-- JAL-2589 -->User defined gap colour not shown in
950 overview when features overlaid on alignment
953 <em>Data import/export</em>
956 <!-- JAL-2576 -->Very large alignments take a long time to
960 <!-- JAL-2507 -->Per-sequence RNA secondary structures
961 added after a sequence was imported are not written to
965 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
966 when importing RNA secondary structure via Stockholm
969 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
970 not shown in correct direction for simple pseudoknots
973 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
974 with lightGray or darkGray via features file (but can
978 <!-- JAL-2383 -->Above PID colour threshold not recovered
979 when alignment view imported from project
982 <!-- JAL-2520,JAL-2465 -->No mappings generated between
983 structure and sequences extracted from structure files
984 imported via URL and viewed in Jmol
987 <!-- JAL-2520 -->Structures loaded via URL are saved in
988 Jalview Projects rather than fetched via URL again when
989 the project is loaded and the structure viewed
992 <em>Web Services</em>
995 <!-- JAL-2519 -->EnsemblGenomes example failing after
996 release of Ensembl v.88
999 <!-- JAL-2366 -->Proxy server address and port always
1000 appear enabled in Preferences->Connections
1003 <!-- JAL-2461 -->DAS registry not found exceptions
1004 removed from console output
1007 <!-- JAL-2582 -->Cannot retrieve protein products from
1008 Ensembl by Peptide ID
1011 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1012 created from SIFTs, and spurious 'Couldn't open structure
1013 in Chimera' errors raised after April 2017 update (problem
1014 due to 'null' string rather than empty string used for
1015 residues with no corresponding PDB mapping).
1018 <em>Application UI</em>
1021 <!-- JAL-2361 -->User Defined Colours not added to Colour
1025 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1026 case' residues (button in colourscheme editor debugged and
1027 new documentation and tooltips added)
1030 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1031 doesn't restore group-specific text colour thresholds
1034 <!-- JAL-2243 -->Feature settings panel does not update as
1035 new features are added to alignment
1038 <!-- JAL-2532 -->Cancel in feature settings reverts
1039 changes to feature colours via the Amend features dialog
1042 <!-- JAL-2506 -->Null pointer exception when attempting to
1043 edit graduated feature colour via amend features dialog
1047 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1048 selection menu changes colours of alignment views
1051 <!-- JAL-2426 -->Spurious exceptions in console raised
1052 from alignment calculation workers after alignment has
1056 <!-- JAL-1608 -->Typo in selection popup menu - Create
1057 groups now 'Create Group'
1060 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1061 Create/Undefine group doesn't always work
1064 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1065 shown again after pressing 'Cancel'
1068 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1069 adjusts start position in wrap mode
1072 <!-- JAL-2563 -->Status bar doesn't show positions for
1073 ambiguous amino acids
1076 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1077 CDS/Protein view after CDS sequences added for aligned
1081 <!-- JAL-2592 -->User defined colourschemes called 'User
1082 Defined' don't appear in Colours menu
1088 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1089 score models doesn't always result in an updated PCA plot
1092 <!-- JAL-2442 -->Features not rendered as transparent on
1093 overview or linked structure view
1096 <!-- JAL-2372 -->Colour group by conservation doesn't
1100 <!-- JAL-2517 -->Hitting Cancel after applying
1101 user-defined colourscheme doesn't restore original
1108 <!-- JAL-2314 -->Unit test failure:
1109 jalview.ws.jabaws.RNAStructExportImport setup fails
1112 <!-- JAL-2307 -->Unit test failure:
1113 jalview.ws.sifts.SiftsClientTest due to compatibility
1114 problems with deep array comparison equality asserts in
1115 successive versions of TestNG
1118 <!-- JAL-2479 -->Relocated StructureChooserTest and
1119 ParameterUtilsTest Unit tests to Network suite
1122 <em>New Known Issues</em>
1125 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1126 phase after a sequence motif find operation
1129 <!-- JAL-2550 -->Importing annotation file with rows
1130 containing just upper and lower case letters are
1131 interpreted as WUSS RNA secondary structure symbols
1134 <!-- JAL-2590 -->Cannot load and display Newick trees
1135 reliably from eggnog Ortholog database
1138 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1139 containing features of type Highlight' when 'B' is pressed
1140 to mark columns containing highlighted regions.
1143 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1144 doesn't always add secondary structure annotation.
1149 <td width="60" nowrap>
1150 <div align="center">
1151 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1154 <td><div align="left">
1158 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1159 for all consensus calculations
1162 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1165 <li>Updated Jalview's Certum code signing certificate
1168 <em>Application</em>
1171 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1172 set of database cross-references, sorted alphabetically
1175 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1176 from database cross references. Users with custom links
1177 will receive a <a href="webServices/urllinks.html#warning">warning
1178 dialog</a> asking them to update their preferences.
1181 <!-- JAL-2287-->Cancel button and escape listener on
1182 dialog warning user about disconnecting Jalview from a
1186 <!-- JAL-2320-->Jalview's Chimera control window closes if
1187 the Chimera it is connected to is shut down
1190 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1191 columns menu item to mark columns containing highlighted
1192 regions (e.g. from structure selections or results of a
1196 <!-- JAL-2284-->Command line option for batch-generation
1197 of HTML pages rendering alignment data with the BioJS
1207 <!-- JAL-2286 -->Columns with more than one modal residue
1208 are not coloured or thresholded according to percent
1209 identity (first observed in Jalview 2.8.2)
1212 <!-- JAL-2301 -->Threonine incorrectly reported as not
1216 <!-- JAL-2318 -->Updates to documentation pages (above PID
1217 threshold, amino acid properties)
1220 <!-- JAL-2292 -->Lower case residues in sequences are not
1221 reported as mapped to residues in a structure file in the
1225 <!--JAL-2324 -->Identical features with non-numeric scores
1226 could be added multiple times to a sequence
1229 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1230 bond features shown as two highlighted residues rather
1231 than a range in linked structure views, and treated
1232 correctly when selecting and computing trees from features
1235 <!-- JAL-2281-->Custom URL links for database
1236 cross-references are matched to database name regardless
1241 <em>Application</em>
1244 <!-- JAL-2282-->Custom URL links for specific database
1245 names without regular expressions also offer links from
1249 <!-- JAL-2315-->Removing a single configured link in the
1250 URL links pane in Connections preferences doesn't actually
1251 update Jalview configuration
1254 <!-- JAL-2272-->CTRL-Click on a selected region to open
1255 the alignment area popup menu doesn't work on El-Capitan
1258 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1259 files with similarly named sequences if dropped onto the
1263 <!-- JAL-2312 -->Additional mappings are shown for PDB
1264 entries where more chains exist in the PDB accession than
1265 are reported in the SIFTS file
1268 <!-- JAL-2317-->Certain structures do not get mapped to
1269 the structure view when displayed with Chimera
1272 <!-- JAL-2317-->No chains shown in the Chimera view
1273 panel's View->Show Chains submenu
1276 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1277 work for wrapped alignment views
1280 <!--JAL-2197 -->Rename UI components for running JPred
1281 predictions from 'JNet' to 'JPred'
1284 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1285 corrupted when annotation panel vertical scroll is not at
1286 first annotation row
1289 <!--JAL-2332 -->Attempting to view structure for Hen
1290 lysozyme results in a PDB Client error dialog box
1293 <!-- JAL-2319 -->Structure View's mapping report switched
1294 ranges for PDB and sequence for SIFTS
1297 SIFTS 'Not_Observed' residues mapped to non-existant
1301 <!-- <em>New Known Issues</em>
1308 <td width="60" nowrap>
1309 <div align="center">
1310 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1311 <em>25/10/2016</em></strong>
1314 <td><em>Application</em>
1316 <li>3D Structure chooser opens with 'Cached structures'
1317 view if structures already loaded</li>
1318 <li>Progress bar reports models as they are loaded to
1319 structure views</li>
1325 <li>Colour by conservation always enabled and no tick
1326 shown in menu when BLOSUM or PID shading applied</li>
1327 <li>FER1_ARATH and FER2_ARATH labels were switched in
1328 example sequences/projects/trees</li>
1330 <em>Application</em>
1332 <li>Jalview projects with views of local PDB structure
1333 files saved on Windows cannot be opened on OSX</li>
1334 <li>Multiple structure views can be opened and superposed
1335 without timeout for structures with multiple models or
1336 multiple sequences in alignment</li>
1337 <li>Cannot import or associated local PDB files without a
1338 PDB ID HEADER line</li>
1339 <li>RMSD is not output in Jmol console when superposition
1341 <li>Drag and drop of URL from Browser fails for Linux and
1342 OSX versions earlier than El Capitan</li>
1343 <li>ENA client ignores invalid content from ENA server</li>
1344 <li>Exceptions are not raised in console when ENA client
1345 attempts to fetch non-existent IDs via Fetch DB Refs UI
1347 <li>Exceptions are not raised in console when a new view
1348 is created on the alignment</li>
1349 <li>OSX right-click fixed for group selections: CMD-click
1350 to insert/remove gaps in groups and CTRL-click to open group
1353 <em>Build and deployment</em>
1355 <li>URL link checker now copes with multi-line anchor
1358 <em>New Known Issues</em>
1360 <li>Drag and drop from URL links in browsers do not work
1367 <td width="60" nowrap>
1368 <div align="center">
1369 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1372 <td><em>General</em>
1375 <!-- JAL-2124 -->Updated Spanish translations.
1378 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1379 for importing structure data to Jalview. Enables mmCIF and
1383 <!-- JAL-192 --->Alignment ruler shows positions relative to
1387 <!-- JAL-2202 -->Position/residue shown in status bar when
1388 mousing over sequence associated annotation
1391 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1395 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1396 '()', canonical '[]' and invalid '{}' base pair populations
1400 <!-- JAL-2092 -->Feature settings popup menu options for
1401 showing or hiding columns containing a feature
1404 <!-- JAL-1557 -->Edit selected group by double clicking on
1405 group and sequence associated annotation labels
1408 <!-- JAL-2236 -->Sequence name added to annotation label in
1409 select/hide columns by annotation and colour by annotation
1413 </ul> <em>Application</em>
1416 <!-- JAL-2050-->Automatically hide introns when opening a
1417 gene/transcript view
1420 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1424 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1425 structure mappings with the EMBL-EBI PDBe SIFTS database
1428 <!-- JAL-2079 -->Updated download sites used for Rfam and
1429 Pfam sources to xfam.org
1432 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1435 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1436 over sequences in Jalview
1439 <!-- JAL-2027-->Support for reverse-complement coding
1440 regions in ENA and EMBL
1443 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1444 for record retrieval via ENA rest API
1447 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1451 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1452 groovy script execution
1455 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1456 alignment window's Calculate menu
1459 <!-- JAL-1812 -->Allow groovy scripts that call
1460 Jalview.getAlignFrames() to run in headless mode
1463 <!-- JAL-2068 -->Support for creating new alignment
1464 calculation workers from groovy scripts
1467 <!-- JAL-1369 --->Store/restore reference sequence in
1471 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1472 associations are now saved/restored from project
1475 <!-- JAL-1993 -->Database selection dialog always shown
1476 before sequence fetcher is opened
1479 <!-- JAL-2183 -->Double click on an entry in Jalview's
1480 database chooser opens a sequence fetcher
1483 <!-- JAL-1563 -->Free-text search client for UniProt using
1484 the UniProt REST API
1487 <!-- JAL-2168 -->-nonews command line parameter to prevent
1488 the news reader opening
1491 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1492 querying stored in preferences
1495 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1499 <!-- JAL-1977-->Tooltips shown on database chooser
1502 <!-- JAL-391 -->Reverse complement function in calculate
1503 menu for nucleotide sequences
1506 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1507 and feature counts preserves alignment ordering (and
1508 debugged for complex feature sets).
1511 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1512 viewing structures with Jalview 2.10
1515 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1516 genome, transcript CCDS and gene ids via the Ensembl and
1517 Ensembl Genomes REST API
1520 <!-- JAL-2049 -->Protein sequence variant annotation
1521 computed for 'sequence_variant' annotation on CDS regions
1525 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1529 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1530 Ref Fetcher fails to match, or otherwise updates sequence
1531 data from external database records.
1534 <!-- JAL-2154 -->Revised Jalview Project format for
1535 efficient recovery of sequence coding and alignment
1536 annotation relationships.
1538 </ul> <!-- <em>Applet</em>
1549 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1553 <!-- JAL-2018-->Export features in Jalview format (again)
1554 includes graduated colourschemes
1557 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1558 working with big alignments and lots of hidden columns
1561 <!-- JAL-2053-->Hidden column markers not always rendered
1562 at right of alignment window
1565 <!-- JAL-2067 -->Tidied up links in help file table of
1569 <!-- JAL-2072 -->Feature based tree calculation not shown
1573 <!-- JAL-2075 -->Hidden columns ignored during feature
1574 based tree calculation
1577 <!-- JAL-2065 -->Alignment view stops updating when show
1578 unconserved enabled for group on alignment
1581 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1585 <!-- JAL-2146 -->Alignment column in status incorrectly
1586 shown as "Sequence position" when mousing over
1590 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1591 hidden columns present
1594 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1595 user created annotation added to alignment
1598 <!-- JAL-1841 -->RNA Structure consensus only computed for
1599 '()' base pair annotation
1602 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1603 in zero scores for all base pairs in RNA Structure
1607 <!-- JAL-2174-->Extend selection with columns containing
1611 <!-- JAL-2275 -->Pfam format writer puts extra space at
1612 beginning of sequence
1615 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1619 <!-- JAL-2238 -->Cannot create groups on an alignment from
1620 from a tree when t-coffee scores are shown
1623 <!-- JAL-1836,1967 -->Cannot import and view PDB
1624 structures with chains containing negative resnums (4q4h)
1627 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1631 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1632 to Clustal, PIR and PileUp output
1635 <!-- JAL-2008 -->Reordering sequence features that are
1636 not visible causes alignment window to repaint
1639 <!-- JAL-2006 -->Threshold sliders don't work in
1640 graduated colour and colour by annotation row for e-value
1641 scores associated with features and annotation rows
1644 <!-- JAL-1797 -->amino acid physicochemical conservation
1645 calculation should be case independent
1648 <!-- JAL-2173 -->Remove annotation also updates hidden
1652 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1653 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1654 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1657 <!-- JAL-2065 -->Null pointer exceptions and redraw
1658 problems when reference sequence defined and 'show
1659 non-conserved' enabled
1662 <!-- JAL-1306 -->Quality and Conservation are now shown on
1663 load even when Consensus calculation is disabled
1666 <!-- JAL-1932 -->Remove right on penultimate column of
1667 alignment does nothing
1670 <em>Application</em>
1673 <!-- JAL-1552-->URLs and links can't be imported by
1674 drag'n'drop on OSX when launched via webstart (note - not
1675 yet fixed for El Capitan)
1678 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1679 output when running on non-gb/us i18n platforms
1682 <!-- JAL-1944 -->Error thrown when exporting a view with
1683 hidden sequences as flat-file alignment
1686 <!-- JAL-2030-->InstallAnywhere distribution fails when
1690 <!-- JAL-2080-->Jalview very slow to launch via webstart
1691 (also hotfix for 2.9.0b2)
1694 <!-- JAL-2085 -->Cannot save project when view has a
1695 reference sequence defined
1698 <!-- JAL-1011 -->Columns are suddenly selected in other
1699 alignments and views when revealing hidden columns
1702 <!-- JAL-1989 -->Hide columns not mirrored in complement
1703 view in a cDNA/Protein splitframe
1706 <!-- JAL-1369 -->Cannot save/restore representative
1707 sequence from project when only one sequence is
1711 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1712 in Structure Chooser
1715 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1716 structure consensus didn't refresh annotation panel
1719 <!-- JAL-1962 -->View mapping in structure view shows
1720 mappings between sequence and all chains in a PDB file
1723 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1724 dialogs format columns correctly, don't display array
1725 data, sort columns according to type
1728 <!-- JAL-1975 -->Export complete shown after destination
1729 file chooser is cancelled during an image export
1732 <!-- JAL-2025 -->Error when querying PDB Service with
1733 sequence name containing special characters
1736 <!-- JAL-2024 -->Manual PDB structure querying should be
1740 <!-- JAL-2104 -->Large tooltips with broken HTML
1741 formatting don't wrap
1744 <!-- JAL-1128 -->Figures exported from wrapped view are
1745 truncated so L looks like I in consensus annotation
1748 <!-- JAL-2003 -->Export features should only export the
1749 currently displayed features for the current selection or
1753 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1754 after fetching cross-references, and restoring from
1758 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1759 followed in the structure viewer
1762 <!-- JAL-2163 -->Titles for individual alignments in
1763 splitframe not restored from project
1766 <!-- JAL-2145 -->missing autocalculated annotation at
1767 trailing end of protein alignment in transcript/product
1768 splitview when pad-gaps not enabled by default
1771 <!-- JAL-1797 -->amino acid physicochemical conservation
1775 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1776 article has been read (reopened issue due to
1777 internationalisation problems)
1780 <!-- JAL-1960 -->Only offer PDB structures in structure
1781 viewer based on sequence name, PDB and UniProt
1786 <!-- JAL-1976 -->No progress bar shown during export of
1790 <!-- JAL-2213 -->Structures not always superimposed after
1791 multiple structures are shown for one or more sequences.
1794 <!-- JAL-1370 -->Reference sequence characters should not
1795 be replaced with '.' when 'Show unconserved' format option
1799 <!-- JAL-1823 -->Cannot specify chain code when entering
1800 specific PDB id for sequence
1803 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1804 'Export hidden sequences' is enabled, but 'export hidden
1805 columns' is disabled.
1808 <!--JAL-2026-->Best Quality option in structure chooser
1809 selects lowest rather than highest resolution structures
1813 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1814 to sequence mapping in 'View Mappings' report
1817 <!-- JAL-2284 -->Unable to read old Jalview projects that
1818 contain non-XML data added after Jalvew wrote project.
1821 <!-- JAL-2118 -->Newly created annotation row reorders
1822 after clicking on it to create new annotation for a
1826 <!-- JAL-1980 -->Null Pointer Exception raised when
1827 pressing Add on an orphaned cut'n'paste window.
1829 <!-- may exclude, this is an external service stability issue JAL-1941
1830 -- > RNA 3D structure not added via DSSR service</li> -->
1835 <!-- JAL-2151 -->Incorrect columns are selected when
1836 hidden columns present before start of sequence
1839 <!-- JAL-1986 -->Missing dependencies on applet pages
1843 <!-- JAL-1947 -->Overview pixel size changes when
1844 sequences are hidden in applet
1847 <!-- JAL-1996 -->Updated instructions for applet
1848 deployment on examples pages.
1855 <td width="60" nowrap>
1856 <div align="center">
1857 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1858 <em>16/10/2015</em></strong>
1861 <td><em>General</em>
1863 <li>Time stamps for signed Jalview application and applet
1868 <em>Application</em>
1870 <li>Duplicate group consensus and conservation rows
1871 shown when tree is partitioned</li>
1872 <li>Erratic behaviour when tree partitions made with
1873 multiple cDNA/Protein split views</li>
1879 <td width="60" nowrap>
1880 <div align="center">
1881 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1882 <em>8/10/2015</em></strong>
1885 <td><em>General</em>
1887 <li>Updated Spanish translations of localized text for
1889 </ul> <em>Application</em>
1891 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1892 <li>Signed OSX InstallAnywhere installer<br></li>
1893 <li>Support for per-sequence based annotations in BioJSON</li>
1894 </ul> <em>Applet</em>
1896 <li>Split frame example added to applet examples page</li>
1897 </ul> <em>Build and Deployment</em>
1900 <!-- JAL-1888 -->New ant target for running Jalview's test
1908 <li>Mapping of cDNA to protein in split frames
1909 incorrect when sequence start > 1</li>
1910 <li>Broken images in filter column by annotation dialog
1912 <li>Feature colours not parsed from features file</li>
1913 <li>Exceptions and incomplete link URLs recovered when
1914 loading a features file containing HTML tags in feature
1918 <em>Application</em>
1920 <li>Annotations corrupted after BioJS export and
1922 <li>Incorrect sequence limits after Fetch DB References
1923 with 'trim retrieved sequences'</li>
1924 <li>Incorrect warning about deleting all data when
1925 deleting selected columns</li>
1926 <li>Patch to build system for shipping properly signed
1927 JNLP templates for webstart launch</li>
1928 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1929 unreleased structures for download or viewing</li>
1930 <li>Tab/space/return keystroke operation of EMBL-PDBe
1931 fetcher/viewer dialogs works correctly</li>
1932 <li>Disabled 'minimise' button on Jalview windows
1933 running on OSX to workaround redraw hang bug</li>
1934 <li>Split cDNA/Protein view position and geometry not
1935 recovered from jalview project</li>
1936 <li>Initial enabled/disabled state of annotation menu
1937 sorter 'show autocalculated first/last' corresponds to
1939 <li>Restoring of Clustal, RNA Helices and T-Coffee
1940 color schemes from BioJSON</li>
1944 <li>Reorder sequences mirrored in cDNA/Protein split
1946 <li>Applet with Jmol examples not loading correctly</li>
1952 <td><div align="center">
1953 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1955 <td><em>General</em>
1957 <li>Linked visualisation and analysis of DNA and Protein
1960 <li>Translated cDNA alignments shown as split protein
1961 and DNA alignment views</li>
1962 <li>Codon consensus annotation for linked protein and
1963 cDNA alignment views</li>
1964 <li>Link cDNA or Protein product sequences by loading
1965 them onto Protein or cDNA alignments</li>
1966 <li>Reconstruct linked cDNA alignment from aligned
1967 protein sequences</li>
1970 <li>Jmol integration updated to Jmol v14.2.14</li>
1971 <li>Import and export of Jalview alignment views as <a
1972 href="features/bioJsonFormat.html">BioJSON</a></li>
1973 <li>New alignment annotation file statements for
1974 reference sequences and marking hidden columns</li>
1975 <li>Reference sequence based alignment shading to
1976 highlight variation</li>
1977 <li>Select or hide columns according to alignment
1979 <li>Find option for locating sequences by description</li>
1980 <li>Conserved physicochemical properties shown in amino
1981 acid conservation row</li>
1982 <li>Alignments can be sorted by number of RNA helices</li>
1983 </ul> <em>Application</em>
1985 <li>New cDNA/Protein analysis capabilities
1987 <li>Get Cross-References should open a Split Frame
1988 view with cDNA/Protein</li>
1989 <li>Detect when nucleotide sequences and protein
1990 sequences are placed in the same alignment</li>
1991 <li>Split cDNA/Protein views are saved in Jalview
1996 <li>Use REST API to talk to Chimera</li>
1997 <li>Selected regions in Chimera are highlighted in linked
1998 Jalview windows</li>
2000 <li>VARNA RNA viewer updated to v3.93</li>
2001 <li>VARNA views are saved in Jalview Projects</li>
2002 <li>Pseudoknots displayed as Jalview RNA annotation can
2003 be shown in VARNA</li>
2005 <li>Make groups for selection uses marked columns as well
2006 as the active selected region</li>
2008 <li>Calculate UPGMA and NJ trees using sequence feature
2010 <li>New Export options
2012 <li>New Export Settings dialog to control hidden
2013 region export in flat file generation</li>
2015 <li>Export alignment views for display with the <a
2016 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2018 <li>Export scrollable SVG in HTML page</li>
2019 <li>Optional embedding of BioJSON data when exporting
2020 alignment figures to HTML</li>
2022 <li>3D structure retrieval and display
2024 <li>Free text and structured queries with the PDBe
2026 <li>PDBe Search API based discovery and selection of
2027 PDB structures for a sequence set</li>
2031 <li>JPred4 employed for protein secondary structure
2033 <li>Hide Insertions menu option to hide unaligned columns
2034 for one or a group of sequences</li>
2035 <li>Automatically hide insertions in alignments imported
2036 from the JPred4 web server</li>
2037 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2038 system on OSX<br />LGPL libraries courtesy of <a
2039 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2041 <li>changed 'View nucleotide structure' submenu to 'View
2042 VARNA 2D Structure'</li>
2043 <li>change "View protein structure" menu option to "3D
2046 </ul> <em>Applet</em>
2048 <li>New layout for applet example pages</li>
2049 <li>New parameters to enable SplitFrame view
2050 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2051 <li>New example demonstrating linked viewing of cDNA and
2052 Protein alignments</li>
2053 </ul> <em>Development and deployment</em>
2055 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2056 <li>Include installation type and git revision in build
2057 properties and console log output</li>
2058 <li>Jalview Github organisation, and new github site for
2059 storing BioJsMSA Templates</li>
2060 <li>Jalview's unit tests now managed with TestNG</li>
2063 <!-- <em>General</em>
2065 </ul> --> <!-- issues resolved --> <em>Application</em>
2067 <li>Escape should close any open find dialogs</li>
2068 <li>Typo in select-by-features status report</li>
2069 <li>Consensus RNA secondary secondary structure
2070 predictions are not highlighted in amber</li>
2071 <li>Missing gap character in v2.7 example file means
2072 alignment appears unaligned when pad-gaps is not enabled</li>
2073 <li>First switch to RNA Helices colouring doesn't colour
2074 associated structure views</li>
2075 <li>ID width preference option is greyed out when auto
2076 width checkbox not enabled</li>
2077 <li>Stopped a warning dialog from being shown when
2078 creating user defined colours</li>
2079 <li>'View Mapping' in structure viewer shows sequence
2080 mappings for just that viewer's sequences</li>
2081 <li>Workaround for superposing PDB files containing
2082 multiple models in Chimera</li>
2083 <li>Report sequence position in status bar when hovering
2084 over Jmol structure</li>
2085 <li>Cannot output gaps as '.' symbols with Selection ->
2086 output to text box</li>
2087 <li>Flat file exports of alignments with hidden columns
2088 have incorrect sequence start/end</li>
2089 <li>'Aligning' a second chain to a Chimera structure from
2091 <li>Colour schemes applied to structure viewers don't
2092 work for nucleotide</li>
2093 <li>Loading/cut'n'pasting an empty or invalid file leads
2094 to a grey/invisible alignment window</li>
2095 <li>Exported Jpred annotation from a sequence region
2096 imports to different position</li>
2097 <li>Space at beginning of sequence feature tooltips shown
2098 on some platforms</li>
2099 <li>Chimera viewer 'View | Show Chain' menu is not
2101 <li>'New View' fails with a Null Pointer Exception in
2102 console if Chimera has been opened</li>
2103 <li>Mouseover to Chimera not working</li>
2104 <li>Miscellaneous ENA XML feature qualifiers not
2106 <li>NPE in annotation renderer after 'Extract Scores'</li>
2107 <li>If two structures in one Chimera window, mouseover of
2108 either sequence shows on first structure</li>
2109 <li>'Show annotations' options should not make
2110 non-positional annotations visible</li>
2111 <li>Subsequence secondary structure annotation not shown
2112 in right place after 'view flanking regions'</li>
2113 <li>File Save As type unset when current file format is
2115 <li>Save as '.jar' option removed for saving Jalview
2117 <li>Colour by Sequence colouring in Chimera more
2119 <li>Cannot 'add reference annotation' for a sequence in
2120 several views on same alignment</li>
2121 <li>Cannot show linked products for EMBL / ENA records</li>
2122 <li>Jalview's tooltip wraps long texts containing no
2124 </ul> <em>Applet</em>
2126 <li>Jmol to JalviewLite mouseover/link not working</li>
2127 <li>JalviewLite can't import sequences with ID
2128 descriptions containing angle brackets</li>
2129 </ul> <em>General</em>
2131 <li>Cannot export and reimport RNA secondary structure
2132 via jalview annotation file</li>
2133 <li>Random helix colour palette for colour by annotation
2134 with RNA secondary structure</li>
2135 <li>Mouseover to cDNA from STOP residue in protein
2136 translation doesn't work.</li>
2137 <li>hints when using the select by annotation dialog box</li>
2138 <li>Jmol alignment incorrect if PDB file has alternate CA
2140 <li>FontChooser message dialog appears to hang after
2141 choosing 1pt font</li>
2142 <li>Peptide secondary structure incorrectly imported from
2143 annotation file when annotation display text includes 'e' or
2145 <li>Cannot set colour of new feature type whilst creating
2147 <li>cDNA translation alignment should not be sequence
2148 order dependent</li>
2149 <li>'Show unconserved' doesn't work for lower case
2151 <li>Nucleotide ambiguity codes involving R not recognised</li>
2152 </ul> <em>Deployment and Documentation</em>
2154 <li>Applet example pages appear different to the rest of
2155 www.jalview.org</li>
2156 </ul> <em>Application Known issues</em>
2158 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2159 <li>Misleading message appears after trying to delete
2161 <li>Jalview icon not shown in dock after InstallAnywhere
2162 version launches</li>
2163 <li>Fetching EMBL reference for an RNA sequence results
2164 fails with a sequence mismatch</li>
2165 <li>Corrupted or unreadable alignment display when
2166 scrolling alignment to right</li>
2167 <li>ArrayIndexOutOfBoundsException thrown when remove
2168 empty columns called on alignment with ragged gapped ends</li>
2169 <li>auto calculated alignment annotation rows do not get
2170 placed above or below non-autocalculated rows</li>
2171 <li>Jalview dekstop becomes sluggish at full screen in
2172 ultra-high resolution</li>
2173 <li>Cannot disable consensus calculation independently of
2174 quality and conservation</li>
2175 <li>Mouseover highlighting between cDNA and protein can
2176 become sluggish with more than one splitframe shown</li>
2177 </ul> <em>Applet Known Issues</em>
2179 <li>Core PDB parsing code requires Jmol</li>
2180 <li>Sequence canvas panel goes white when alignment
2181 window is being resized</li>
2187 <td><div align="center">
2188 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2190 <td><em>General</em>
2192 <li>Updated Java code signing certificate donated by
2194 <li>Features and annotation preserved when performing
2195 pairwise alignment</li>
2196 <li>RNA pseudoknot annotation can be
2197 imported/exported/displayed</li>
2198 <li>'colour by annotation' can colour by RNA and
2199 protein secondary structure</li>
2200 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2201 post-hoc with 2.9 release</em>)
2204 </ul> <em>Application</em>
2206 <li>Extract and display secondary structure for sequences
2207 with 3D structures</li>
2208 <li>Support for parsing RNAML</li>
2209 <li>Annotations menu for layout
2211 <li>sort sequence annotation rows by alignment</li>
2212 <li>place sequence annotation above/below alignment
2215 <li>Output in Stockholm format</li>
2216 <li>Internationalisation: improved Spanish (es)
2218 <li>Structure viewer preferences tab</li>
2219 <li>Disorder and Secondary Structure annotation tracks
2220 shared between alignments</li>
2221 <li>UCSF Chimera launch and linked highlighting from
2223 <li>Show/hide all sequence associated annotation rows for
2224 all or current selection</li>
2225 <li>disorder and secondary structure predictions
2226 available as dataset annotation</li>
2227 <li>Per-sequence rna helices colouring</li>
2230 <li>Sequence database accessions imported when fetching
2231 alignments from Rfam</li>
2232 <li>update VARNA version to 3.91</li>
2234 <li>New groovy scripts for exporting aligned positions,
2235 conservation values, and calculating sum of pairs scores.</li>
2236 <li>Command line argument to set default JABAWS server</li>
2237 <li>include installation type in build properties and
2238 console log output</li>
2239 <li>Updated Jalview project format to preserve dataset
2243 <!-- issues resolved --> <em>Application</em>
2245 <li>Distinguish alignment and sequence associated RNA
2246 structure in structure->view->VARNA</li>
2247 <li>Raise dialog box if user deletes all sequences in an
2249 <li>Pressing F1 results in documentation opening twice</li>
2250 <li>Sequence feature tooltip is wrapped</li>
2251 <li>Double click on sequence associated annotation
2252 selects only first column</li>
2253 <li>Redundancy removal doesn't result in unlinked
2254 leaves shown in tree</li>
2255 <li>Undos after several redundancy removals don't undo
2257 <li>Hide sequence doesn't hide associated annotation</li>
2258 <li>User defined colours dialog box too big to fit on
2259 screen and buttons not visible</li>
2260 <li>author list isn't updated if already written to
2261 Jalview properties</li>
2262 <li>Popup menu won't open after retrieving sequence
2264 <li>File open window for associate PDB doesn't open</li>
2265 <li>Left-then-right click on a sequence id opens a
2266 browser search window</li>
2267 <li>Cannot open sequence feature shading/sort popup menu
2268 in feature settings dialog</li>
2269 <li>better tooltip placement for some areas of Jalview
2271 <li>Allow addition of JABAWS Server which doesn't
2272 pass validation</li>
2273 <li>Web services parameters dialog box is too large to
2275 <li>Muscle nucleotide alignment preset obscured by
2277 <li>JABAWS preset submenus don't contain newly
2278 defined user preset</li>
2279 <li>MSA web services warns user if they were launched
2280 with invalid input</li>
2281 <li>Jalview cannot contact DAS Registy when running on
2284 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2285 'Superpose with' submenu not shown when new view
2289 </ul> <!-- <em>Applet</em>
2291 </ul> <em>General</em>
2293 </ul>--> <em>Deployment and Documentation</em>
2295 <li>2G and 1G options in launchApp have no effect on
2296 memory allocation</li>
2297 <li>launchApp service doesn't automatically open
2298 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2300 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2301 InstallAnywhere reports cannot find valid JVM when Java
2302 1.7_055 is available
2304 </ul> <em>Application Known issues</em>
2307 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2308 corrupted or unreadable alignment display when scrolling
2312 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2313 retrieval fails but progress bar continues for DAS retrieval
2314 with large number of ID
2317 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2318 flatfile output of visible region has incorrect sequence
2322 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2323 rna structure consensus doesn't update when secondary
2324 structure tracks are rearranged
2327 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2328 invalid rna structure positional highlighting does not
2329 highlight position of invalid base pairs
2332 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2333 out of memory errors are not raised when saving Jalview
2334 project from alignment window file menu
2337 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2338 Switching to RNA Helices colouring doesn't propagate to
2342 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2343 colour by RNA Helices not enabled when user created
2344 annotation added to alignment
2347 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2348 Jalview icon not shown on dock in Mountain Lion/Webstart
2350 </ul> <em>Applet Known Issues</em>
2353 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2354 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2357 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2358 Jalview and Jmol example not compatible with IE9
2361 <li>Sort by annotation score doesn't reverse order
2367 <td><div align="center">
2368 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2371 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2374 <li>Internationalisation of user interface (usually
2375 called i18n support) and translation for Spanish locale</li>
2376 <li>Define/Undefine group on current selection with
2377 Ctrl-G/Shift Ctrl-G</li>
2378 <li>Improved group creation/removal options in
2379 alignment/sequence Popup menu</li>
2380 <li>Sensible precision for symbol distribution
2381 percentages shown in logo tooltip.</li>
2382 <li>Annotation panel height set according to amount of
2383 annotation when alignment first opened</li>
2384 </ul> <em>Application</em>
2386 <li>Interactive consensus RNA secondary structure
2387 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2388 <li>Select columns containing particular features from
2389 Feature Settings dialog</li>
2390 <li>View all 'representative' PDB structures for selected
2392 <li>Update Jalview project format:
2394 <li>New file extension for Jalview projects '.jvp'</li>
2395 <li>Preserve sequence and annotation dataset (to
2396 store secondary structure annotation,etc)</li>
2397 <li>Per group and alignment annotation and RNA helix
2401 <li>New similarity measures for PCA and Tree calculation
2403 <li>Experimental support for retrieval and viewing of
2404 flanking regions for an alignment</li>
2408 <!-- issues resolved --> <em>Application</em>
2410 <li>logo keeps spinning and status remains at queued or
2411 running after job is cancelled</li>
2412 <li>cannot export features from alignments imported from
2413 Jalview/VAMSAS projects</li>
2414 <li>Buggy slider for web service parameters that take
2416 <li>Newly created RNA secondary structure line doesn't
2417 have 'display all symbols' flag set</li>
2418 <li>T-COFFEE alignment score shading scheme and other
2419 annotation shading not saved in Jalview project</li>
2420 <li>Local file cannot be loaded in freshly downloaded
2422 <li>Jalview icon not shown on dock in Mountain
2424 <li>Load file from desktop file browser fails</li>
2425 <li>Occasional NPE thrown when calculating large trees</li>
2426 <li>Cannot reorder or slide sequences after dragging an
2427 alignment onto desktop</li>
2428 <li>Colour by annotation dialog throws NPE after using
2429 'extract scores' function</li>
2430 <li>Loading/cut'n'pasting an empty file leads to a grey
2431 alignment window</li>
2432 <li>Disorder thresholds rendered incorrectly after
2433 performing IUPred disorder prediction</li>
2434 <li>Multiple group annotated consensus rows shown when
2435 changing 'normalise logo' display setting</li>
2436 <li>Find shows blank dialog after 'finished searching' if
2437 nothing matches query</li>
2438 <li>Null Pointer Exceptions raised when sorting by
2439 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2441 <li>Errors in Jmol console when structures in alignment
2442 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2444 <li>Not all working JABAWS services are shown in
2446 <li>JAVAWS version of Jalview fails to launch with
2447 'invalid literal/length code'</li>
2448 <li>Annotation/RNA Helix colourschemes cannot be applied
2449 to alignment with groups (actually fixed in 2.8.0b1)</li>
2450 <li>RNA Helices and T-Coffee Scores available as default
2453 </ul> <em>Applet</em>
2455 <li>Remove group option is shown even when selection is
2457 <li>Apply to all groups ticked but colourscheme changes
2458 don't affect groups</li>
2459 <li>Documented RNA Helices and T-Coffee Scores as valid
2460 colourscheme name</li>
2461 <li>Annotation labels drawn on sequence IDs when
2462 Annotation panel is not displayed</li>
2463 <li>Increased font size for dropdown menus on OSX and
2464 embedded windows</li>
2465 </ul> <em>Other</em>
2467 <li>Consensus sequence for alignments/groups with a
2468 single sequence were not calculated</li>
2469 <li>annotation files that contain only groups imported as
2470 annotation and junk sequences</li>
2471 <li>Fasta files with sequences containing '*' incorrectly
2472 recognised as PFAM or BLC</li>
2473 <li>conservation/PID slider apply all groups option
2474 doesn't affect background (2.8.0b1)
2476 <li>redundancy highlighting is erratic at 0% and 100%</li>
2477 <li>Remove gapped columns fails for sequences with ragged
2479 <li>AMSA annotation row with leading spaces is not
2480 registered correctly on import</li>
2481 <li>Jalview crashes when selecting PCA analysis for
2482 certain alignments</li>
2483 <li>Opening the colour by annotation dialog for an
2484 existing annotation based 'use original colours'
2485 colourscheme loses original colours setting</li>
2490 <td><div align="center">
2491 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2492 <em>30/1/2014</em></strong>
2496 <li>Trusted certificates for JalviewLite applet and
2497 Jalview Desktop application<br />Certificate was donated by
2498 <a href="https://www.certum.eu">Certum</a> to the Jalview
2499 open source project).
2501 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2502 <li>Output in Stockholm format</li>
2503 <li>Allow import of data from gzipped files</li>
2504 <li>Export/import group and sequence associated line
2505 graph thresholds</li>
2506 <li>Nucleotide substitution matrix that supports RNA and
2507 ambiguity codes</li>
2508 <li>Allow disorder predictions to be made on the current
2509 selection (or visible selection) in the same way that JPred
2511 <li>Groovy scripting for headless Jalview operation</li>
2512 </ul> <em>Other improvements</em>
2514 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2515 <li>COMBINE statement uses current SEQUENCE_REF and
2516 GROUP_REF scope to group annotation rows</li>
2517 <li>Support '' style escaping of quotes in Newick
2519 <li>Group options for JABAWS service by command line name</li>
2520 <li>Empty tooltip shown for JABA service options with a
2521 link but no description</li>
2522 <li>Select primary source when selecting authority in
2523 database fetcher GUI</li>
2524 <li>Add .mfa to FASTA file extensions recognised by
2526 <li>Annotation label tooltip text wrap</li>
2531 <li>Slow scrolling when lots of annotation rows are
2533 <li>Lots of NPE (and slowness) after creating RNA
2534 secondary structure annotation line</li>
2535 <li>Sequence database accessions not imported when
2536 fetching alignments from Rfam</li>
2537 <li>Incorrect SHMR submission for sequences with
2539 <li>View all structures does not always superpose
2541 <li>Option widgets in service parameters not updated to
2542 reflect user or preset settings</li>
2543 <li>Null pointer exceptions for some services without
2544 presets or adjustable parameters</li>
2545 <li>Discover PDB IDs entry in structure menu doesn't
2546 discover PDB xRefs</li>
2547 <li>Exception encountered while trying to retrieve
2548 features with DAS</li>
2549 <li>Lowest value in annotation row isn't coloured
2550 when colour by annotation (per sequence) is coloured</li>
2551 <li>Keyboard mode P jumps to start of gapped region when
2552 residue follows a gap</li>
2553 <li>Jalview appears to hang importing an alignment with
2554 Wrap as default or after enabling Wrap</li>
2555 <li>'Right click to add annotations' message
2556 shown in wrap mode when no annotations present</li>
2557 <li>Disorder predictions fail with NPE if no automatic
2558 annotation already exists on alignment</li>
2559 <li>oninit javascript function should be called after
2560 initialisation completes</li>
2561 <li>Remove redundancy after disorder prediction corrupts
2562 alignment window display</li>
2563 <li>Example annotation file in documentation is invalid</li>
2564 <li>Grouped line graph annotation rows are not exported
2565 to annotation file</li>
2566 <li>Multi-harmony analysis cannot be run when only two
2568 <li>Cannot create multiple groups of line graphs with
2569 several 'combine' statements in annotation file</li>
2570 <li>Pressing return several times causes Number Format
2571 exceptions in keyboard mode</li>
2572 <li>Multi-harmony (SHMMR) method doesn't submit
2573 correct partitions for input data</li>
2574 <li>Translation from DNA to Amino Acids fails</li>
2575 <li>Jalview fail to load newick tree with quoted label</li>
2576 <li>--headless flag isn't understood</li>
2577 <li>ClassCastException when generating EPS in headless
2579 <li>Adjusting sequence-associated shading threshold only
2580 changes one row's threshold</li>
2581 <li>Preferences and Feature settings panel panel
2582 doesn't open</li>
2583 <li>hide consensus histogram also hides conservation and
2584 quality histograms</li>
2589 <td><div align="center">
2590 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2592 <td><em>Application</em>
2594 <li>Support for JABAWS 2.0 Services (AACon alignment
2595 conservation, protein disorder and Clustal Omega)</li>
2596 <li>JABAWS server status indicator in Web Services
2598 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2599 in Jalview alignment window</li>
2600 <li>Updated Jalview build and deploy framework for OSX
2601 mountain lion, windows 7, and 8</li>
2602 <li>Nucleotide substitution matrix for PCA that supports
2603 RNA and ambiguity codes</li>
2605 <li>Improved sequence database retrieval GUI</li>
2606 <li>Support fetching and database reference look up
2607 against multiple DAS sources (Fetch all from in 'fetch db
2609 <li>Jalview project improvements
2611 <li>Store and retrieve the 'belowAlignment'
2612 flag for annotation</li>
2613 <li>calcId attribute to group annotation rows on the
2615 <li>Store AACon calculation settings for a view in
2616 Jalview project</li>
2620 <li>horizontal scrolling gesture support</li>
2621 <li>Visual progress indicator when PCA calculation is
2623 <li>Simpler JABA web services menus</li>
2624 <li>visual indication that web service results are still
2625 being retrieved from server</li>
2626 <li>Serialise the dialogs that are shown when Jalview
2627 starts up for first time</li>
2628 <li>Jalview user agent string for interacting with HTTP
2630 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2632 <li>Examples directory and Groovy library included in
2633 InstallAnywhere distribution</li>
2634 </ul> <em>Applet</em>
2636 <li>RNA alignment and secondary structure annotation
2637 visualization applet example</li>
2638 </ul> <em>General</em>
2640 <li>Normalise option for consensus sequence logo</li>
2641 <li>Reset button in PCA window to return dimensions to
2643 <li>Allow seqspace or Jalview variant of alignment PCA
2645 <li>PCA with either nucleic acid and protein substitution
2647 <li>Allow windows containing HTML reports to be exported
2649 <li>Interactive display and editing of RNA secondary
2650 structure contacts</li>
2651 <li>RNA Helix Alignment Colouring</li>
2652 <li>RNA base pair logo consensus</li>
2653 <li>Parse sequence associated secondary structure
2654 information in Stockholm files</li>
2655 <li>HTML Export database accessions and annotation
2656 information presented in tooltip for sequences</li>
2657 <li>Import secondary structure from LOCARNA clustalw
2658 style RNA alignment files</li>
2659 <li>import and visualise T-COFFEE quality scores for an
2661 <li>'colour by annotation' per sequence option to
2662 shade each sequence according to its associated alignment
2664 <li>New Jalview Logo</li>
2665 </ul> <em>Documentation and Development</em>
2667 <li>documentation for score matrices used in Jalview</li>
2668 <li>New Website!</li>
2670 <td><em>Application</em>
2672 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2673 wsdbfetch REST service</li>
2674 <li>Stop windows being moved outside desktop on OSX</li>
2675 <li>Filetype associations not installed for webstart
2677 <li>Jalview does not always retrieve progress of a JABAWS
2678 job execution in full once it is complete</li>
2679 <li>revise SHMR RSBS definition to ensure alignment is
2680 uploaded via ali_file parameter</li>
2681 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2682 <li>View all structures superposed fails with exception</li>
2683 <li>Jnet job queues forever if a very short sequence is
2684 submitted for prediction</li>
2685 <li>Cut and paste menu not opened when mouse clicked on
2687 <li>Putting fractional value into integer text box in
2688 alignment parameter dialog causes Jalview to hang</li>
2689 <li>Structure view highlighting doesn't work on
2691 <li>View all structures fails with exception shown in
2693 <li>Characters in filename associated with PDBEntry not
2694 escaped in a platform independent way</li>
2695 <li>Jalview desktop fails to launch with exception when
2697 <li>Tree calculation reports 'you must have 2 or more
2698 sequences selected' when selection is empty</li>
2699 <li>Jalview desktop fails to launch with jar signature
2700 failure when java web start temporary file caching is
2702 <li>DAS Sequence retrieval with range qualification
2703 results in sequence xref which includes range qualification</li>
2704 <li>Errors during processing of command line arguments
2705 cause progress bar (JAL-898) to be removed</li>
2706 <li>Replace comma for semi-colon option not disabled for
2707 DAS sources in sequence fetcher</li>
2708 <li>Cannot close news reader when JABAWS server warning
2709 dialog is shown</li>
2710 <li>Option widgets not updated to reflect user settings</li>
2711 <li>Edited sequence not submitted to web service</li>
2712 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2713 <li>InstallAnywhere installer doesn't unpack and run
2714 on OSX Mountain Lion</li>
2715 <li>Annotation panel not given a scroll bar when
2716 sequences with alignment annotation are pasted into the
2718 <li>Sequence associated annotation rows not associated
2719 when loaded from Jalview project</li>
2720 <li>Browser launch fails with NPE on java 1.7</li>
2721 <li>JABAWS alignment marked as finished when job was
2722 cancelled or job failed due to invalid input</li>
2723 <li>NPE with v2.7 example when clicking on Tree
2724 associated with all views</li>
2725 <li>Exceptions when copy/paste sequences with grouped
2726 annotation rows to new window</li>
2727 </ul> <em>Applet</em>
2729 <li>Sequence features are momentarily displayed before
2730 they are hidden using hidefeaturegroups applet parameter</li>
2731 <li>loading features via javascript API automatically
2732 enables feature display</li>
2733 <li>scrollToColumnIn javascript API method doesn't
2735 </ul> <em>General</em>
2737 <li>Redundancy removal fails for rna alignment</li>
2738 <li>PCA calculation fails when sequence has been selected
2739 and then deselected</li>
2740 <li>PCA window shows grey box when first opened on OSX</li>
2741 <li>Letters coloured pink in sequence logo when alignment
2742 coloured with clustalx</li>
2743 <li>Choosing fonts without letter symbols defined causes
2744 exceptions and redraw errors</li>
2745 <li>Initial PCA plot view is not same as manually
2746 reconfigured view</li>
2747 <li>Grouped annotation graph label has incorrect line
2749 <li>Grouped annotation graph label display is corrupted
2750 for lots of labels</li>
2755 <div align="center">
2756 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2759 <td><em>Application</em>
2761 <li>Jalview Desktop News Reader</li>
2762 <li>Tweaked default layout of web services menu</li>
2763 <li>View/alignment association menu to enable user to
2764 easily specify which alignment a multi-structure view takes
2765 its colours/correspondences from</li>
2766 <li>Allow properties file location to be specified as URL</li>
2767 <li>Extend Jalview project to preserve associations
2768 between many alignment views and a single Jmol display</li>
2769 <li>Store annotation row height in Jalview project file</li>
2770 <li>Annotation row column label formatting attributes
2771 stored in project file</li>
2772 <li>Annotation row order for auto-calculated annotation
2773 rows preserved in Jalview project file</li>
2774 <li>Visual progress indication when Jalview state is
2775 saved using Desktop window menu</li>
2776 <li>Visual indication that command line arguments are
2777 still being processed</li>
2778 <li>Groovy script execution from URL</li>
2779 <li>Colour by annotation default min and max colours in
2781 <li>Automatically associate PDB files dragged onto an
2782 alignment with sequences that have high similarity and
2784 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2785 <li>'view structures' option to open many
2786 structures in same window</li>
2787 <li>Sort associated views menu option for tree panel</li>
2788 <li>Group all JABA and non-JABA services for a particular
2789 analysis function in its own submenu</li>
2790 </ul> <em>Applet</em>
2792 <li>Userdefined and autogenerated annotation rows for
2794 <li>Adjustment of alignment annotation pane height</li>
2795 <li>Annotation scrollbar for annotation panel</li>
2796 <li>Drag to reorder annotation rows in annotation panel</li>
2797 <li>'automaticScrolling' parameter</li>
2798 <li>Allow sequences with partial ID string matches to be
2799 annotated from GFF/Jalview features files</li>
2800 <li>Sequence logo annotation row in applet</li>
2801 <li>Absolute paths relative to host server in applet
2802 parameters are treated as such</li>
2803 <li>New in the JalviewLite javascript API:
2805 <li>JalviewLite.js javascript library</li>
2806 <li>Javascript callbacks for
2808 <li>Applet initialisation</li>
2809 <li>Sequence/alignment mouse-overs and selections</li>
2812 <li>scrollTo row and column alignment scrolling
2814 <li>Select sequence/alignment regions from javascript</li>
2815 <li>javascript structure viewer harness to pass
2816 messages between Jmol and Jalview when running as
2817 distinct applets</li>
2818 <li>sortBy method</li>
2819 <li>Set of applet and application examples shipped
2820 with documentation</li>
2821 <li>New example to demonstrate JalviewLite and Jmol
2822 javascript message exchange</li>
2824 </ul> <em>General</em>
2826 <li>Enable Jmol displays to be associated with multiple
2827 multiple alignments</li>
2828 <li>Option to automatically sort alignment with new tree</li>
2829 <li>User configurable link to enable redirects to a
2830 www.Jalview.org mirror</li>
2831 <li>Jmol colours option for Jmol displays</li>
2832 <li>Configurable newline string when writing alignment
2833 and other flat files</li>
2834 <li>Allow alignment annotation description lines to
2835 contain html tags</li>
2836 </ul> <em>Documentation and Development</em>
2838 <li>Add groovy test harness for bulk load testing to
2840 <li>Groovy script to load and align a set of sequences
2841 using a web service before displaying the result in the
2842 Jalview desktop</li>
2843 <li>Restructured javascript and applet api documentation</li>
2844 <li>Ant target to publish example html files with applet
2846 <li>Netbeans project for building Jalview from source</li>
2847 <li>ant task to create online javadoc for Jalview source</li>
2849 <td><em>Application</em>
2851 <li>User defined colourscheme throws exception when
2852 current built in colourscheme is saved as new scheme</li>
2853 <li>AlignFrame->Save in application pops up save
2854 dialog for valid filename/format</li>
2855 <li>Cannot view associated structure for UniProt sequence</li>
2856 <li>PDB file association breaks for UniProt sequence
2858 <li>Associate PDB from file dialog does not tell you
2859 which sequence is to be associated with the file</li>
2860 <li>Find All raises null pointer exception when query
2861 only matches sequence IDs</li>
2862 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2863 <li>Jalview project with Jmol views created with Jalview
2864 2.4 cannot be loaded</li>
2865 <li>Filetype associations not installed for webstart
2867 <li>Two or more chains in a single PDB file associated
2868 with sequences in different alignments do not get coloured
2869 by their associated sequence</li>
2870 <li>Visibility status of autocalculated annotation row
2871 not preserved when project is loaded</li>
2872 <li>Annotation row height and visibility attributes not
2873 stored in Jalview project</li>
2874 <li>Tree bootstraps are not preserved when saved as a
2875 Jalview project</li>
2876 <li>Envision2 workflow tooltips are corrupted</li>
2877 <li>Enabling show group conservation also enables colour
2878 by conservation</li>
2879 <li>Duplicate group associated conservation or consensus
2880 created on new view</li>
2881 <li>Annotation scrollbar not displayed after 'show
2882 all hidden annotation rows' option selected</li>
2883 <li>Alignment quality not updated after alignment
2884 annotation row is hidden then shown</li>
2885 <li>Preserve colouring of structures coloured by
2886 sequences in pre Jalview 2.7 projects</li>
2887 <li>Web service job parameter dialog is not laid out
2889 <li>Web services menu not refreshed after 'reset
2890 services' button is pressed in preferences</li>
2891 <li>Annotation off by one in Jalview v2_3 example project</li>
2892 <li>Structures imported from file and saved in project
2893 get name like jalview_pdb1234.txt when reloaded</li>
2894 <li>Jalview does not always retrieve progress of a JABAWS
2895 job execution in full once it is complete</li>
2896 </ul> <em>Applet</em>
2898 <li>Alignment height set incorrectly when lots of
2899 annotation rows are displayed</li>
2900 <li>Relative URLs in feature HTML text not resolved to
2902 <li>View follows highlighting does not work for positions
2904 <li><= shown as = in tooltip</li>
2905 <li>Export features raises exception when no features
2907 <li>Separator string used for serialising lists of IDs
2908 for javascript api is modified when separator string
2909 provided as parameter</li>
2910 <li>Null pointer exception when selecting tree leaves for
2911 alignment with no existing selection</li>
2912 <li>Relative URLs for datasources assumed to be relative
2913 to applet's codebase</li>
2914 <li>Status bar not updated after finished searching and
2915 search wraps around to first result</li>
2916 <li>StructureSelectionManager instance shared between
2917 several Jalview applets causes race conditions and memory
2919 <li>Hover tooltip and mouseover of position on structure
2920 not sent from Jmol in applet</li>
2921 <li>Certain sequences of javascript method calls to
2922 applet API fatally hang browser</li>
2923 </ul> <em>General</em>
2925 <li>View follows structure mouseover scrolls beyond
2926 position with wrapped view and hidden regions</li>
2927 <li>Find sequence position moves to wrong residue
2928 with/without hidden columns</li>
2929 <li>Sequence length given in alignment properties window
2931 <li>InvalidNumberFormat exceptions thrown when trying to
2932 import PDB like structure files</li>
2933 <li>Positional search results are only highlighted
2934 between user-supplied sequence start/end bounds</li>
2935 <li>End attribute of sequence is not validated</li>
2936 <li>Find dialog only finds first sequence containing a
2937 given sequence position</li>
2938 <li>Sequence numbering not preserved in MSF alignment
2940 <li>Jalview PDB file reader does not extract sequence
2941 from nucleotide chains correctly</li>
2942 <li>Structure colours not updated when tree partition
2943 changed in alignment</li>
2944 <li>Sequence associated secondary structure not correctly
2945 parsed in interleaved stockholm</li>
2946 <li>Colour by annotation dialog does not restore current
2948 <li>Hiding (nearly) all sequences doesn't work
2950 <li>Sequences containing lowercase letters are not
2951 properly associated with their pdb files</li>
2952 </ul> <em>Documentation and Development</em>
2954 <li>schemas/JalviewWsParamSet.xsd corrupted by
2955 ApplyCopyright tool</li>
2960 <div align="center">
2961 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2964 <td><em>Application</em>
2966 <li>New warning dialog when the Jalview Desktop cannot
2967 contact web services</li>
2968 <li>JABA service parameters for a preset are shown in
2969 service job window</li>
2970 <li>JABA Service menu entries reworded</li>
2974 <li>Modeller PIR IO broken - cannot correctly import a
2975 pir file emitted by Jalview</li>
2976 <li>Existing feature settings transferred to new
2977 alignment view created from cut'n'paste</li>
2978 <li>Improved test for mixed amino/nucleotide chains when
2979 parsing PDB files</li>
2980 <li>Consensus and conservation annotation rows
2981 occasionally become blank for all new windows</li>
2982 <li>Exception raised when right clicking above sequences
2983 in wrapped view mode</li>
2984 </ul> <em>Application</em>
2986 <li>multiple multiply aligned structure views cause cpu
2987 usage to hit 100% and computer to hang</li>
2988 <li>Web Service parameter layout breaks for long user
2989 parameter names</li>
2990 <li>Jaba service discovery hangs desktop if Jaba server
2997 <div align="center">
2998 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
3001 <td><em>Application</em>
3003 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
3004 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
3007 <li>Web Services preference tab</li>
3008 <li>Analysis parameters dialog box and user defined
3010 <li>Improved speed and layout of Envision2 service menu</li>
3011 <li>Superpose structures using associated sequence
3013 <li>Export coordinates and projection as CSV from PCA
3015 </ul> <em>Applet</em>
3017 <li>enable javascript: execution by the applet via the
3018 link out mechanism</li>
3019 </ul> <em>Other</em>
3021 <li>Updated the Jmol Jalview interface to work with Jmol
3023 <li>The Jalview Desktop and JalviewLite applet now
3024 require Java 1.5</li>
3025 <li>Allow Jalview feature colour specification for GFF
3026 sequence annotation files</li>
3027 <li>New 'colour by label' keword in Jalview feature file
3028 type colour specification</li>
3029 <li>New Jalview Desktop Groovy API method that allows a
3030 script to check if it being run in an interactive session or
3031 in a batch operation from the Jalview command line</li>
3035 <li>clustalx colourscheme colours Ds preferentially when
3036 both D+E are present in over 50% of the column</li>
3037 </ul> <em>Application</em>
3039 <li>typo in AlignmentFrame->View->Hide->all but
3040 selected Regions menu item</li>
3041 <li>sequence fetcher replaces ',' for ';' when the ',' is
3042 part of a valid accession ID</li>
3043 <li>fatal OOM if object retrieved by sequence fetcher
3044 runs out of memory</li>
3045 <li>unhandled Out of Memory Error when viewing pca
3046 analysis results</li>
3047 <li>InstallAnywhere builds fail to launch on OS X java
3048 10.5 update 4 (due to apple Java 1.6 update)</li>
3049 <li>Installanywhere Jalview silently fails to launch</li>
3050 </ul> <em>Applet</em>
3052 <li>Jalview.getFeatureGroups() raises an
3053 ArrayIndexOutOfBoundsException if no feature groups are
3060 <div align="center">
3061 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3067 <li>Alignment prettyprinter doesn't cope with long
3069 <li>clustalx colourscheme colours Ds preferentially when
3070 both D+E are present in over 50% of the column</li>
3071 <li>nucleic acid structures retrieved from PDB do not
3072 import correctly</li>
3073 <li>More columns get selected than were clicked on when a
3074 number of columns are hidden</li>
3075 <li>annotation label popup menu not providing correct
3076 add/hide/show options when rows are hidden or none are
3078 <li>Stockholm format shown in list of readable formats,
3079 and parser copes better with alignments from RFAM.</li>
3080 <li>CSV output of consensus only includes the percentage
3081 of all symbols if sequence logo display is enabled</li>
3083 </ul> <em>Applet</em>
3085 <li>annotation panel disappears when annotation is
3087 </ul> <em>Application</em>
3089 <li>Alignment view not redrawn properly when new
3090 alignment opened where annotation panel is visible but no
3091 annotations are present on alignment</li>
3092 <li>pasted region containing hidden columns is
3093 incorrectly displayed in new alignment window</li>
3094 <li>Jalview slow to complete operations when stdout is
3095 flooded (fix is to close the Jalview console)</li>
3096 <li>typo in AlignmentFrame->View->Hide->all but
3097 selected Rregions menu item.</li>
3098 <li>inconsistent group submenu and Format submenu entry
3099 'Un' or 'Non'conserved</li>
3100 <li>Sequence feature settings are being shared by
3101 multiple distinct alignments</li>
3102 <li>group annotation not recreated when tree partition is
3104 <li>double click on group annotation to select sequences
3105 does not propagate to associated trees</li>
3106 <li>Mac OSX specific issues:
3108 <li>exception raised when mouse clicked on desktop
3109 window background</li>
3110 <li>Desktop menu placed on menu bar and application
3111 name set correctly</li>
3112 <li>sequence feature settings not wide enough for the
3113 save feature colourscheme button</li>
3122 <div align="center">
3123 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3126 <td><em>New Capabilities</em>
3128 <li>URL links generated from description line for
3129 regular-expression based URL links (applet and application)
3131 <li>Non-positional feature URL links are shown in link
3133 <li>Linked viewing of nucleic acid sequences and
3135 <li>Automatic Scrolling option in View menu to display
3136 the currently highlighted region of an alignment.</li>
3137 <li>Order an alignment by sequence length, or using the
3138 average score or total feature count for each sequence.</li>
3139 <li>Shading features by score or associated description</li>
3140 <li>Subdivide alignment and groups based on identity of
3141 selected subsequence (Make Groups from Selection).</li>
3142 <li>New hide/show options including Shift+Control+H to
3143 hide everything but the currently selected region.</li>
3144 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3145 </ul> <em>Application</em>
3147 <li>Fetch DB References capabilities and UI expanded to
3148 support retrieval from DAS sequence sources</li>
3149 <li>Local DAS Sequence sources can be added via the
3150 command line or via the Add local source dialog box.</li>
3151 <li>DAS Dbref and DbxRef feature types are parsed as
3152 database references and protein_name is parsed as
3153 description line (BioSapiens terms).</li>
3154 <li>Enable or disable non-positional feature and database
3155 references in sequence ID tooltip from View menu in
3157 <!-- <li>New hidden columns and rows and representatives capabilities
3158 in annotations file (in progress - not yet fully implemented)</li> -->
3159 <li>Group-associated consensus, sequence logos and
3160 conservation plots</li>
3161 <li>Symbol distributions for each column can be exported
3162 and visualized as sequence logos</li>
3163 <li>Optionally scale multi-character column labels to fit
3164 within each column of annotation row<!-- todo for applet -->
3166 <li>Optional automatic sort of associated alignment view
3167 when a new tree is opened.</li>
3168 <li>Jalview Java Console</li>
3169 <li>Better placement of desktop window when moving
3170 between different screens.</li>
3171 <li>New preference items for sequence ID tooltip and
3172 consensus annotation</li>
3173 <li>Client to submit sequences and IDs to Envision2
3175 <li><em>Vamsas Capabilities</em>
3177 <li>Improved VAMSAS synchronization (Jalview archive
3178 used to preserve views, structures, and tree display
3180 <li>Import of vamsas documents from disk or URL via
3182 <li>Sharing of selected regions between views and
3183 with other VAMSAS applications (Experimental feature!)</li>
3184 <li>Updated API to VAMSAS version 0.2</li>
3186 </ul> <em>Applet</em>
3188 <li>Middle button resizes annotation row height</li>
3191 <li>sortByTree (true/false) - automatically sort the
3192 associated alignment view by the tree when a new tree is
3194 <li>showTreeBootstraps (true/false) - show or hide
3195 branch bootstraps (default is to show them if available)</li>
3196 <li>showTreeDistances (true/false) - show or hide
3197 branch lengths (default is to show them if available)</li>
3198 <li>showUnlinkedTreeNodes (true/false) - indicate if
3199 unassociated nodes should be highlighted in the tree
3201 <li>heightScale and widthScale (1.0 or more) -
3202 increase the height or width of a cell in the alignment
3203 grid relative to the current font size.</li>
3206 <li>Non-positional features displayed in sequence ID
3208 </ul> <em>Other</em>
3210 <li>Features format: graduated colour definitions and
3211 specification of feature scores</li>
3212 <li>Alignment Annotations format: new keywords for group
3213 associated annotation (GROUP_REF) and annotation row display
3214 properties (ROW_PROPERTIES)</li>
3215 <li>XML formats extended to support graduated feature
3216 colourschemes, group associated annotation, and profile
3217 visualization settings.</li></td>
3220 <li>Source field in GFF files parsed as feature source
3221 rather than description</li>
3222 <li>Non-positional features are now included in sequence
3223 feature and gff files (controlled via non-positional feature
3224 visibility in tooltip).</li>
3225 <li>URL links generated for all feature links (bugfix)</li>
3226 <li>Added URL embedding instructions to features file
3228 <li>Codons containing ambiguous nucleotides translated as
3229 'X' in peptide product</li>
3230 <li>Match case switch in find dialog box works for both
3231 sequence ID and sequence string and query strings do not
3232 have to be in upper case to match case-insensitively.</li>
3233 <li>AMSA files only contain first column of
3234 multi-character column annotation labels</li>
3235 <li>Jalview Annotation File generation/parsing consistent
3236 with documentation (e.g. Stockholm annotation can be
3237 exported and re-imported)</li>
3238 <li>PDB files without embedded PDB IDs given a friendly
3240 <li>Find incrementally searches ID string matches as well
3241 as subsequence matches, and correctly reports total number
3245 <li>Better handling of exceptions during sequence
3247 <li>Dasobert generated non-positional feature URL
3248 link text excludes the start_end suffix</li>
3249 <li>DAS feature and source retrieval buttons disabled
3250 when fetch or registry operations in progress.</li>
3251 <li>PDB files retrieved from URLs are cached properly</li>
3252 <li>Sequence description lines properly shared via
3254 <li>Sequence fetcher fetches multiple records for all
3256 <li>Ensured that command line das feature retrieval
3257 completes before alignment figures are generated.</li>
3258 <li>Reduced time taken when opening file browser for
3260 <li>isAligned check prior to calculating tree, PCA or
3261 submitting an MSA to JNet now excludes hidden sequences.</li>
3262 <li>User defined group colours properly recovered
3263 from Jalview projects.</li>
3272 <div align="center">
3273 <strong>2.4.0.b2</strong><br> 28/10/2009
3278 <li>Experimental support for google analytics usage
3280 <li>Jalview privacy settings (user preferences and docs).</li>
3285 <li>Race condition in applet preventing startup in
3287 <li>Exception when feature created from selection beyond
3288 length of sequence.</li>
3289 <li>Allow synthetic PDB files to be imported gracefully</li>
3290 <li>Sequence associated annotation rows associate with
3291 all sequences with a given id</li>
3292 <li>Find function matches case-insensitively for sequence
3293 ID string searches</li>
3294 <li>Non-standard characters do not cause pairwise
3295 alignment to fail with exception</li>
3296 </ul> <em>Application Issues</em>
3298 <li>Sequences are now validated against EMBL database</li>
3299 <li>Sequence fetcher fetches multiple records for all
3301 </ul> <em>InstallAnywhere Issues</em>
3303 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3304 issue with installAnywhere mechanism)</li>
3305 <li>Command line launching of JARs from InstallAnywhere
3306 version (java class versioning error fixed)</li>
3313 <div align="center">
3314 <strong>2.4</strong><br> 27/8/2008
3317 <td><em>User Interface</em>
3319 <li>Linked highlighting of codon and amino acid from
3320 translation and protein products</li>
3321 <li>Linked highlighting of structure associated with
3322 residue mapping to codon position</li>
3323 <li>Sequence Fetcher provides example accession numbers
3324 and 'clear' button</li>
3325 <li>MemoryMonitor added as an option under Desktop's
3327 <li>Extract score function to parse whitespace separated
3328 numeric data in description line</li>
3329 <li>Column labels in alignment annotation can be centred.</li>
3330 <li>Tooltip for sequence associated annotation give name
3332 </ul> <em>Web Services and URL fetching</em>
3334 <li>JPred3 web service</li>
3335 <li>Prototype sequence search client (no public services
3337 <li>Fetch either seed alignment or full alignment from
3339 <li>URL Links created for matching database cross
3340 references as well as sequence ID</li>
3341 <li>URL Links can be created using regular-expressions</li>
3342 </ul> <em>Sequence Database Connectivity</em>
3344 <li>Retrieval of cross-referenced sequences from other
3346 <li>Generalised database reference retrieval and
3347 validation to all fetchable databases</li>
3348 <li>Fetch sequences from DAS sources supporting the
3349 sequence command</li>
3350 </ul> <em>Import and Export</em>
3351 <li>export annotation rows as CSV for spreadsheet import</li>
3352 <li>Jalview projects record alignment dataset associations,
3353 EMBL products, and cDNA sequence mappings</li>
3354 <li>Sequence Group colour can be specified in Annotation
3356 <li>Ad-hoc colouring of group in Annotation File using RGB
3357 triplet as name of colourscheme</li>
3358 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3360 <li>treenode binding for VAMSAS tree exchange</li>
3361 <li>local editing and update of sequences in VAMSAS
3362 alignments (experimental)</li>
3363 <li>Create new or select existing session to join</li>
3364 <li>load and save of vamsas documents</li>
3365 </ul> <em>Application command line</em>
3367 <li>-tree parameter to open trees (introduced for passing
3369 <li>-fetchfrom command line argument to specify nicknames
3370 of DAS servers to query for alignment features</li>
3371 <li>-dasserver command line argument to add new servers
3372 that are also automatically queried for features</li>
3373 <li>-groovy command line argument executes a given groovy
3374 script after all input data has been loaded and parsed</li>
3375 </ul> <em>Applet-Application data exchange</em>
3377 <li>Trees passed as applet parameters can be passed to
3378 application (when using "View in full
3379 application")</li>
3380 </ul> <em>Applet Parameters</em>
3382 <li>feature group display control parameter</li>
3383 <li>debug parameter</li>
3384 <li>showbutton parameter</li>
3385 </ul> <em>Applet API methods</em>
3387 <li>newView public method</li>
3388 <li>Window (current view) specific get/set public methods</li>
3389 <li>Feature display control methods</li>
3390 <li>get list of currently selected sequences</li>
3391 </ul> <em>New Jalview distribution features</em>
3393 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3394 <li>RELEASE file gives build properties for the latest
3395 Jalview release.</li>
3396 <li>Java 1.1 Applet build made easier and donotobfuscate
3397 property controls execution of obfuscator</li>
3398 <li>Build target for generating source distribution</li>
3399 <li>Debug flag for javacc</li>
3400 <li>.jalview_properties file is documented (slightly) in
3401 jalview.bin.Cache</li>
3402 <li>Continuous Build Integration for stable and
3403 development version of Application, Applet and source
3408 <li>selected region output includes visible annotations
3409 (for certain formats)</li>
3410 <li>edit label/displaychar contains existing label/char
3412 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3413 <li>shorter peptide product names from EMBL records</li>
3414 <li>Newick string generator makes compact representations</li>
3415 <li>bootstrap values parsed correctly for tree files with
3417 <li>pathological filechooser bug avoided by not allowing
3418 filenames containing a ':'</li>
3419 <li>Fixed exception when parsing GFF files containing
3420 global sequence features</li>
3421 <li>Alignment datasets are finalized only when number of
3422 references from alignment sequences goes to zero</li>
3423 <li>Close of tree branch colour box without colour
3424 selection causes cascading exceptions</li>
3425 <li>occasional negative imgwidth exceptions</li>
3426 <li>better reporting of non-fatal warnings to user when
3427 file parsing fails.</li>
3428 <li>Save works when Jalview project is default format</li>
3429 <li>Save as dialog opened if current alignment format is
3430 not a valid output format</li>
3431 <li>UniProt canonical names introduced for both das and
3433 <li>Histidine should be midblue (not pink!) in Zappo</li>
3434 <li>error messages passed up and output when data read
3436 <li>edit undo recovers previous dataset sequence when
3437 sequence is edited</li>
3438 <li>allow PDB files without pdb ID HEADER lines (like
3439 those generated by MODELLER) to be read in properly</li>
3440 <li>allow reading of JPred concise files as a normal
3442 <li>Stockholm annotation parsing and alignment properties
3443 import fixed for PFAM records</li>
3444 <li>Structure view windows have correct name in Desktop
3446 <li>annotation consisting of sequence associated scores
3447 can be read and written correctly to annotation file</li>
3448 <li>Aligned cDNA translation to aligned peptide works
3450 <li>Fixed display of hidden sequence markers and
3451 non-italic font for representatives in Applet</li>
3452 <li>Applet Menus are always embedded in applet window on
3454 <li>Newly shown features appear at top of stack (in
3456 <li>Annotations added via parameter not drawn properly
3457 due to null pointer exceptions</li>
3458 <li>Secondary structure lines are drawn starting from
3459 first column of alignment</li>
3460 <li>UniProt XML import updated for new schema release in
3462 <li>Sequence feature to sequence ID match for Features
3463 file is case-insensitive</li>
3464 <li>Sequence features read from Features file appended to
3465 all sequences with matching IDs</li>
3466 <li>PDB structure coloured correctly for associated views
3467 containing a sub-sequence</li>
3468 <li>PDB files can be retrieved by applet from Jar files</li>
3469 <li>feature and annotation file applet parameters
3470 referring to different directories are retrieved correctly</li>
3471 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3472 <li>Fixed application hang whilst waiting for
3473 splash-screen version check to complete</li>
3474 <li>Applet properly URLencodes input parameter values
3475 when passing them to the launchApp service</li>
3476 <li>display name and local features preserved in results
3477 retrieved from web service</li>
3478 <li>Visual delay indication for sequence retrieval and
3479 sequence fetcher initialisation</li>
3480 <li>updated Application to use DAS 1.53e version of
3481 dasobert DAS client</li>
3482 <li>Re-instated Full AMSA support and .amsa file
3484 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3492 <div align="center">
3493 <strong>2.3</strong><br> 9/5/07
3498 <li>Jmol 11.0.2 integration</li>
3499 <li>PDB views stored in Jalview XML files</li>
3500 <li>Slide sequences</li>
3501 <li>Edit sequence in place</li>
3502 <li>EMBL CDS features</li>
3503 <li>DAS Feature mapping</li>
3504 <li>Feature ordering</li>
3505 <li>Alignment Properties</li>
3506 <li>Annotation Scores</li>
3507 <li>Sort by scores</li>
3508 <li>Feature/annotation editing in applet</li>
3513 <li>Headless state operation in 2.2.1</li>
3514 <li>Incorrect and unstable DNA pairwise alignment</li>
3515 <li>Cut and paste of sequences with annotation</li>
3516 <li>Feature group display state in XML</li>
3517 <li>Feature ordering in XML</li>
3518 <li>blc file iteration selection using filename # suffix</li>
3519 <li>Stockholm alignment properties</li>
3520 <li>Stockhom alignment secondary structure annotation</li>
3521 <li>2.2.1 applet had no feature transparency</li>
3522 <li>Number pad keys can be used in cursor mode</li>
3523 <li>Structure Viewer mirror image resolved</li>
3530 <div align="center">
3531 <strong>2.2.1</strong><br> 12/2/07
3536 <li>Non standard characters can be read and displayed
3537 <li>Annotations/Features can be imported/exported to the
3539 <li>Applet allows editing of sequence/annotation/group
3540 name & description
3541 <li>Preference setting to display sequence name in
3543 <li>Annotation file format extended to allow
3544 Sequence_groups to be defined
3545 <li>Default opening of alignment overview panel can be
3546 specified in preferences
3547 <li>PDB residue numbering annotation added to associated
3553 <li>Applet crash under certain Linux OS with Java 1.6
3555 <li>Annotation file export / import bugs fixed
3556 <li>PNG / EPS image output bugs fixed
3562 <div align="center">
3563 <strong>2.2</strong><br> 27/11/06
3568 <li>Multiple views on alignment
3569 <li>Sequence feature editing
3570 <li>"Reload" alignment
3571 <li>"Save" to current filename
3572 <li>Background dependent text colour
3573 <li>Right align sequence ids
3574 <li>User-defined lower case residue colours
3577 <li>Menu item accelerator keys
3578 <li>Control-V pastes to current alignment
3579 <li>Cancel button for DAS Feature Fetching
3580 <li>PCA and PDB Viewers zoom via mouse roller
3581 <li>User-defined sub-tree colours and sub-tree selection
3583 <li>'New Window' button on the 'Output to Text box'
3588 <li>New memory efficient Undo/Redo System
3589 <li>Optimised symbol lookups and conservation/consensus
3591 <li>Region Conservation/Consensus recalculated after
3593 <li>Fixed Remove Empty Columns Bug (empty columns at end
3595 <li>Slowed DAS Feature Fetching for increased robustness.
3597 <li>Made angle brackets in ASCII feature descriptions
3599 <li>Re-instated Zoom function for PCA
3600 <li>Sequence descriptions conserved in web service
3602 <li>UniProt ID discoverer uses any word separated by
3604 <li>WsDbFetch query/result association resolved
3605 <li>Tree leaf to sequence mapping improved
3606 <li>Smooth fonts switch moved to FontChooser dialog box.
3613 <div align="center">
3614 <strong>2.1.1</strong><br> 12/9/06
3619 <li>Copy consensus sequence to clipboard</li>
3624 <li>Image output - rightmost residues are rendered if
3625 sequence id panel has been resized</li>
3626 <li>Image output - all offscreen group boundaries are
3628 <li>Annotation files with sequence references - all
3629 elements in file are relative to sequence position</li>
3630 <li>Mac Applet users can use Alt key for group editing</li>
3636 <div align="center">
3637 <strong>2.1</strong><br> 22/8/06
3642 <li>MAFFT Multiple Alignment in default Web Service list</li>
3643 <li>DAS Feature fetching</li>
3644 <li>Hide sequences and columns</li>
3645 <li>Export Annotations and Features</li>
3646 <li>GFF file reading / writing</li>
3647 <li>Associate structures with sequences from local PDB
3649 <li>Add sequences to exisiting alignment</li>
3650 <li>Recently opened files / URL lists</li>
3651 <li>Applet can launch the full application</li>
3652 <li>Applet has transparency for features (Java 1.2
3654 <li>Applet has user defined colours parameter</li>
3655 <li>Applet can load sequences from parameter
3656 "sequence<em>x</em>"
3662 <li>Redundancy Panel reinstalled in the Applet</li>
3663 <li>Monospaced font - EPS / rescaling bug fixed</li>
3664 <li>Annotation files with sequence references bug fixed</li>
3670 <div align="center">
3671 <strong>2.08.1</strong><br> 2/5/06
3676 <li>Change case of selected region from Popup menu</li>
3677 <li>Choose to match case when searching</li>
3678 <li>Middle mouse button and mouse movement can compress /
3679 expand the visible width and height of the alignment</li>
3684 <li>Annotation Panel displays complete JNet results</li>
3690 <div align="center">
3691 <strong>2.08b</strong><br> 18/4/06
3697 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3698 <li>Righthand label on wrapped alignments shows correct
3705 <div align="center">
3706 <strong>2.08</strong><br> 10/4/06
3711 <li>Editing can be locked to the selection area</li>
3712 <li>Keyboard editing</li>
3713 <li>Create sequence features from searches</li>
3714 <li>Precalculated annotations can be loaded onto
3716 <li>Features file allows grouping of features</li>
3717 <li>Annotation Colouring scheme added</li>
3718 <li>Smooth fonts off by default - Faster rendering</li>
3719 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3724 <li>Drag & Drop fixed on Linux</li>
3725 <li>Jalview Archive file faster to load/save, sequence
3726 descriptions saved.</li>
3732 <div align="center">
3733 <strong>2.07</strong><br> 12/12/05
3738 <li>PDB Structure Viewer enhanced</li>
3739 <li>Sequence Feature retrieval and display enhanced</li>
3740 <li>Choose to output sequence start-end after sequence
3741 name for file output</li>
3742 <li>Sequence Fetcher WSDBFetch@EBI</li>
3743 <li>Applet can read feature files, PDB files and can be
3744 used for HTML form input</li>
3749 <li>HTML output writes groups and features</li>
3750 <li>Group editing is Control and mouse click</li>
3751 <li>File IO bugs</li>
3757 <div align="center">
3758 <strong>2.06</strong><br> 28/9/05
3763 <li>View annotations in wrapped mode</li>
3764 <li>More options for PCA viewer</li>
3769 <li>GUI bugs resolved</li>
3770 <li>Runs with -nodisplay from command line</li>
3776 <div align="center">
3777 <strong>2.05b</strong><br> 15/9/05
3782 <li>Choose EPS export as lineart or text</li>
3783 <li>Jar files are executable</li>
3784 <li>Can read in Uracil - maps to unknown residue</li>
3789 <li>Known OutOfMemory errors give warning message</li>
3790 <li>Overview window calculated more efficiently</li>
3791 <li>Several GUI bugs resolved</li>
3797 <div align="center">
3798 <strong>2.05</strong><br> 30/8/05
3803 <li>Edit and annotate in "Wrapped" view</li>
3808 <li>Several GUI bugs resolved</li>
3814 <div align="center">
3815 <strong>2.04</strong><br> 24/8/05
3820 <li>Hold down mouse wheel & scroll to change font
3826 <li>Improved JPred client reliability</li>
3827 <li>Improved loading of Jalview files</li>
3833 <div align="center">
3834 <strong>2.03</strong><br> 18/8/05
3839 <li>Set Proxy server name and port in preferences</li>
3840 <li>Multiple URL links from sequence ids</li>
3841 <li>User Defined Colours can have a scheme name and added
3843 <li>Choose to ignore gaps in consensus calculation</li>
3844 <li>Unix users can set default web browser</li>
3845 <li>Runs without GUI for batch processing</li>
3846 <li>Dynamically generated Web Service Menus</li>
3851 <li>InstallAnywhere download for Sparc Solaris</li>
3857 <div align="center">
3858 <strong>2.02</strong><br> 18/7/05
3864 <li>Copy & Paste order of sequences maintains
3865 alignment order.</li>
3871 <div align="center">
3872 <strong>2.01</strong><br> 12/7/05
3877 <li>Use delete key for deleting selection.</li>
3878 <li>Use Mouse wheel to scroll sequences.</li>
3879 <li>Help file updated to describe how to add alignment
3881 <li>Version and build date written to build properties
3883 <li>InstallAnywhere installation will check for updates
3884 at launch of Jalview.</li>
3889 <li>Delete gaps bug fixed.</li>
3890 <li>FileChooser sorts columns.</li>
3891 <li>Can remove groups one by one.</li>
3892 <li>Filechooser icons installed.</li>
3893 <li>Finder ignores return character when searching.
3894 Return key will initiate a search.<br>
3901 <div align="center">
3902 <strong>2.0</strong><br> 20/6/05
3907 <li>New codebase</li>