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-2666 -->Linked scrolling via protein horizontal
116 scroll bar doesn't work for some CDS/Protein views
119 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
120 Java 1.8u153 onwards and Java 1.9u4+.
123 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
124 columns in annotation row
127 <!-- JAL-2913 -->Preferences panel's ID Width control is
128 honored in interactive and batch mode
131 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
132 for structures added to existing Jmol view
135 <!-- JAL-2223 -->'View Mappings' includes duplicate
136 entries after importing project with multiple views
139 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
140 protein sequences via SIFTS from associated PDB entries
141 with negative residue numbers or missing residues fails
144 <!-- JAL-2952 -->Exception when shading sequence with negative
145 Temperature Factor values from annotated PDB files (e.g.
146 as generated by CONSURF)
149 <!-- JAL-2954 -->Selecting columns from highlighted regions
150 very slow for alignments with large numbers of sequences
153 <!-- JAL-2925 -->Copy Consensus fails for group consensus
154 with 'StringIndexOutOfBounds'
157 <!-- JAL-2976 -->VAqua(4) (<a
158 href="http://violetlib.org/vaqua/overview.html">download
159 here</a>) provided as fallback Look and Feel for OSX
160 platforms running Java 10
163 <!-- JAL-2960 -->Adding a structure to existing structure
164 view appears to do nothing because the view is hidden behind the alignment view
170 <!-- JAL-2926 -->Copy consensus sequence option in applet
171 should copy the group consensus when popup is opened on it
175 <em>New Known Defects</em>
178 <!-- JAL-2973 --> Exceptions occasionally raised when
179 editing a large alignment and overview is displayed
182 <!-- JAL-2974 -->'Overview updating' progress bar is shown
183 repeatedly after a series of edits even when the overview
184 is no longer reflecting updates
187 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
188 structures for protein subsequence (if 'Trim Retrieved
189 Sequences' enabled) or Ensembl isoforms (Workaround in
190 2.10.4 is to fail back to N&W mapping)
197 <td width="60" nowrap>
199 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
202 <td><div align="left">
203 <ul><li>Updated Certum Codesigning Certificate
204 (Valid till 30th November 2018)</li></ul></div></td>
205 <td><div align="left">
208 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
209 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
210 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
211 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
212 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
213 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
214 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
220 <td width="60" nowrap>
222 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
225 <td><div align="left">
229 <!-- JAL-2446 -->Faster and more efficient management and
230 rendering of sequence features
233 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
234 429 rate limit request hander
237 <!-- JAL-2773 -->Structure views don't get updated unless
238 their colours have changed
241 <!-- JAL-2495 -->All linked sequences are highlighted for
242 a structure mousover (Jmol) or selection (Chimera)
245 <!-- JAL-2790 -->'Cancel' button in progress bar for
246 JABAWS AACon, RNAAliFold and Disorder prediction jobs
249 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
250 view from Ensembl locus cross-references
253 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
257 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
258 feature can be disabled
261 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
262 PDB easier retrieval of sequences for lists of IDs
265 <!-- JAL-2758 -->Short names for sequences retrieved from
271 <li>Groovy interpreter updated to 2.4.12</li>
272 <li>Example groovy script for generating a matrix of
273 percent identity scores for current alignment.</li>
275 <em>Testing and Deployment</em>
278 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
282 <td><div align="left">
286 <!-- JAL-2643 -->Pressing tab after updating the colour
287 threshold text field doesn't trigger an update to the
291 <!-- JAL-2682 -->Race condition when parsing sequence ID
295 <!-- JAL-2608 -->Overview windows are also closed when
296 alignment window is closed
299 <!-- JAL-2548 -->Export of features doesn't always respect
303 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
304 takes a long time in Cursor mode
310 <!-- JAL-2777 -->Structures with whitespace chainCode
311 cannot be viewed in Chimera
314 <!-- JAL-2728 -->Protein annotation panel too high in
318 <!-- JAL-2757 -->Can't edit the query after the server
319 error warning icon is shown in Uniprot and PDB Free Text
323 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
326 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
329 <!-- JAL-2739 -->Hidden column marker in last column not
330 rendered when switching back from Wrapped to normal view
333 <!-- JAL-2768 -->Annotation display corrupted when
334 scrolling right in unwapped alignment view
337 <!-- JAL-2542 -->Existing features on subsequence
338 incorrectly relocated when full sequence retrieved from
342 <!-- JAL-2733 -->Last reported memory still shown when
343 Desktop->Show Memory is unticked (OSX only)
346 <!-- JAL-2658 -->Amend Features dialog doesn't allow
347 features of same type and group to be selected for
351 <!-- JAL-2524 -->Jalview becomes sluggish in wide
352 alignments when hidden columns are present
355 <!-- JAL-2392 -->Jalview freezes when loading and
356 displaying several structures
359 <!-- JAL-2732 -->Black outlines left after resizing or
363 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
364 within the Jalview desktop on OSX
367 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
368 when in wrapped alignment mode
371 <!-- JAL-2636 -->Scale mark not shown when close to right
372 hand end of alignment
375 <!-- JAL-2684 -->Pairwise alignment of selected regions of
376 each selected sequence do not have correct start/end
380 <!-- JAL-2793 -->Alignment ruler height set incorrectly
381 after canceling the Alignment Window's Font dialog
384 <!-- JAL-2036 -->Show cross-references not enabled after
385 restoring project until a new view is created
388 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
389 URL links appears when only default EMBL-EBI link is
390 configured (since 2.10.2b2)
393 <!-- JAL-2775 -->Overview redraws whole window when box
397 <!-- JAL-2225 -->Structure viewer doesn't map all chains
398 in a multi-chain structure when viewing alignment
399 involving more than one chain (since 2.10)
402 <!-- JAL-2811 -->Double residue highlights in cursor mode
403 if new selection moves alignment window
406 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
407 arrow key in cursor mode to pass hidden column marker
410 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
411 that produces correctly annotated transcripts and products
414 <!-- JAL-2776 -->Toggling a feature group after first time
415 doesn't update associated structure view
418 <em>Applet</em><br />
421 <!-- JAL-2687 -->Concurrent modification exception when
422 closing alignment panel
425 <em>BioJSON</em><br />
428 <!-- JAL-2546 -->BioJSON export does not preserve
429 non-positional features
432 <em>New Known Issues</em>
435 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
436 sequence features correctly (for many previous versions of
440 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
441 using cursor in wrapped panel other than top
444 <!-- JAL-2791 -->Select columns containing feature ignores
445 graduated colour threshold
448 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
449 always preserve numbering and sequence features
452 <em>Known Java 9 Issues</em>
455 <!-- JAL-2902 -->Groovy Console very slow to open and is
456 not responsive when entering characters (Webstart, Java
463 <td width="60" nowrap>
465 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
466 <em>2/10/2017</em></strong>
469 <td><div align="left">
470 <em>New features in Jalview Desktop</em>
473 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
475 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
479 <td><div align="left">
483 <td width="60" nowrap>
485 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
486 <em>7/9/2017</em></strong>
489 <td><div align="left">
493 <!-- JAL-2588 -->Show gaps in overview window by colouring
494 in grey (sequences used to be coloured grey, and gaps were
498 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
502 <!-- JAL-2587 -->Overview updates immediately on increase
503 in size and progress bar shown as higher resolution
504 overview is recalculated
509 <td><div align="left">
513 <!-- JAL-2664 -->Overview window redraws every hidden
514 column region row by row
517 <!-- JAL-2681 -->duplicate protein sequences shown after
518 retrieving Ensembl crossrefs for sequences from Uniprot
521 <!-- JAL-2603 -->Overview window throws NPE if show boxes
522 format setting is unticked
525 <!-- JAL-2610 -->Groups are coloured wrongly in overview
526 if group has show boxes format setting unticked
529 <!-- JAL-2672,JAL-2665 -->Redraw problems when
530 autoscrolling whilst dragging current selection group to
531 include sequences and columns not currently displayed
534 <!-- JAL-2691 -->Not all chains are mapped when multimeric
535 assemblies are imported via CIF file
538 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
539 displayed when threshold or conservation colouring is also
543 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
547 <!-- JAL-2673 -->Jalview continues to scroll after
548 dragging a selected region off the visible region of the
552 <!-- JAL-2724 -->Cannot apply annotation based
553 colourscheme to all groups in a view
556 <!-- JAL-2511 -->IDs don't line up with sequences
557 initially after font size change using the Font chooser or
564 <td width="60" nowrap>
566 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
569 <td><div align="left">
570 <em>Calculations</em>
574 <!-- JAL-1933 -->Occupancy annotation row shows number of
575 ungapped positions in each column of the alignment.
578 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
579 a calculation dialog box
582 <!-- JAL-2379 -->Revised implementation of PCA for speed
583 and memory efficiency (~30x faster)
586 <!-- JAL-2403 -->Revised implementation of sequence
587 similarity scores as used by Tree, PCA, Shading Consensus
588 and other calculations
591 <!-- JAL-2416 -->Score matrices are stored as resource
592 files within the Jalview codebase
595 <!-- JAL-2500 -->Trees computed on Sequence Feature
596 Similarity may have different topology due to increased
603 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
604 model for alignments and groups
607 <!-- JAL-384 -->Custom shading schemes created via groovy
614 <!-- JAL-2526 -->Efficiency improvements for interacting
615 with alignment and overview windows
618 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
622 <!-- JAL-2388 -->Hidden columns and sequences can be
626 <!-- JAL-2611 -->Click-drag in visible area allows fine
627 adjustment of visible position
631 <em>Data import/export</em>
634 <!-- JAL-2535 -->Posterior probability annotation from
635 Stockholm files imported as sequence associated annotation
638 <!-- JAL-2507 -->More robust per-sequence positional
639 annotation input/output via stockholm flatfile
642 <!-- JAL-2533 -->Sequence names don't include file
643 extension when importing structure files without embedded
644 names or PDB accessions
647 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
648 format sequence substitution matrices
651 <em>User Interface</em>
654 <!-- JAL-2447 --> Experimental Features Checkbox in
655 Desktop's Tools menu to hide or show untested features in
659 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
660 via Overview or sequence motif search operations
663 <!-- JAL-2547 -->Amend sequence features dialog box can be
664 opened by double clicking gaps within sequence feature
668 <!-- JAL-1476 -->Status bar message shown when not enough
669 aligned positions were available to create a 3D structure
673 <em>3D Structure</em>
676 <!-- JAL-2430 -->Hidden regions in alignment views are not
677 coloured in linked structure views
680 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
681 file-based command exchange
684 <!-- JAL-2375 -->Structure chooser automatically shows
685 Cached Structures rather than querying the PDBe if
686 structures are already available for sequences
689 <!-- JAL-2520 -->Structures imported via URL are cached in
690 the Jalview project rather than downloaded again when the
694 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
695 to transfer Chimera's structure attributes as Jalview
696 features, and vice-versa (<strong>Experimental
700 <em>Web Services</em>
703 <!-- JAL-2549 -->Updated JABAWS client to v2.2
706 <!-- JAL-2335 -->Filter non-standard amino acids and
707 nucleotides when submitting to AACon and other MSA
711 <!-- JAL-2316, -->URLs for viewing database
712 cross-references provided by identifiers.org and the
720 <!-- JAL-2344 -->FileFormatI interface for describing and
721 identifying file formats (instead of String constants)
724 <!-- JAL-2228 -->FeatureCounter script refactored for
725 efficiency when counting all displayed features (not
726 backwards compatible with 2.10.1)
729 <em>Example files</em>
732 <!-- JAL-2631 -->Graduated feature colour style example
733 included in the example feature file
736 <em>Documentation</em>
739 <!-- JAL-2339 -->Release notes reformatted for readability
740 with the built-in Java help viewer
743 <!-- JAL-1644 -->Find documentation updated with 'search
744 sequence description' option
750 <!-- JAL-2485, -->External service integration tests for
751 Uniprot REST Free Text Search Client
754 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
757 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
762 <td><div align="left">
763 <em>Calculations</em>
766 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
767 matrix - C->R should be '-3'<br />Old matrix restored
768 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
770 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
771 Jalview's treatment of gaps in PCA and substitution matrix
772 based Tree calculations.<br /> <br />In earlier versions
773 of Jalview, gaps matching gaps were penalised, and gaps
774 matching non-gaps penalised even more. In the PCA
775 calculation, gaps were actually treated as non-gaps - so
776 different costs were applied, which meant Jalview's PCAs
777 were different to those produced by SeqSpace.<br />Jalview
778 now treats gaps in the same way as SeqSpace (ie it scores
779 them as 0). <br /> <br />Enter the following in the
780 Groovy console to restore pre-2.10.2 behaviour:<br />
781 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
782 // for 2.10.1 mode <br />
783 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
784 // to restore 2.10.2 mode <br /> <br /> <em>Note:
785 these settings will affect all subsequent tree and PCA
786 calculations (not recommended)</em></li>
788 <!-- JAL-2424 -->Fixed off-by-one bug that affected
789 scaling of branch lengths for trees computed using
790 Sequence Feature Similarity.
793 <!-- JAL-2377 -->PCA calculation could hang when
794 generating output report when working with highly
798 <!-- JAL-2544 --> Sort by features includes features to
799 right of selected region when gaps present on right-hand
803 <em>User Interface</em>
806 <!-- JAL-2346 -->Reopening Colour by annotation dialog
807 doesn't reselect a specific sequence's associated
808 annotation after it was used for colouring a view
811 <!-- JAL-2419 -->Current selection lost if popup menu
812 opened on a region of alignment without groups
815 <!-- JAL-2374 -->Popup menu not always shown for regions
816 of an alignment with overlapping groups
819 <!-- JAL-2310 -->Finder double counts if both a sequence's
820 name and description match
823 <!-- JAL-2370 -->Hiding column selection containing two
824 hidden regions results in incorrect hidden regions
827 <!-- JAL-2386 -->'Apply to all groups' setting when
828 changing colour does not apply Conservation slider value
832 <!-- JAL-2373 -->Percentage identity and conservation menu
833 items do not show a tick or allow shading to be disabled
836 <!-- JAL-2385 -->Conservation shading or PID threshold
837 lost when base colourscheme changed if slider not visible
840 <!-- JAL-2547 -->Sequence features shown in tooltip for
841 gaps before start of features
844 <!-- JAL-2623 -->Graduated feature colour threshold not
845 restored to UI when feature colour is edited
848 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
849 a time when scrolling vertically in wrapped mode.
852 <!-- JAL-2630 -->Structure and alignment overview update
853 as graduate feature colour settings are modified via the
857 <!-- JAL-2034 -->Overview window doesn't always update
858 when a group defined on the alignment is resized
861 <!-- JAL-2605 -->Mouseovers on left/right scale region in
862 wrapped view result in positional status updates
866 <!-- JAL-2563 -->Status bar doesn't show position for
867 ambiguous amino acid and nucleotide symbols
870 <!-- JAL-2602 -->Copy consensus sequence failed if
871 alignment included gapped columns
874 <!-- JAL-2473 -->Minimum size set for Jalview windows so
875 widgets don't permanently disappear
878 <!-- JAL-2503 -->Cannot select or filter quantitative
879 annotation that are shown only as column labels (e.g.
880 T-Coffee column reliability scores)
883 <!-- JAL-2594 -->Exception thrown if trying to create a
884 sequence feature on gaps only
887 <!-- JAL-2504 -->Features created with 'New feature'
888 button from a Find inherit previously defined feature type
889 rather than the Find query string
892 <!-- JAL-2423 -->incorrect title in output window when
893 exporting tree calculated in Jalview
896 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
897 and then revealing them reorders sequences on the
901 <!-- JAL-964 -->Group panel in sequence feature settings
902 doesn't update to reflect available set of groups after
903 interactively adding or modifying features
906 <!-- JAL-2225 -->Sequence Database chooser unusable on
910 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
911 only excluded gaps in current sequence and ignored
918 <!-- JAL-2421 -->Overview window visible region moves
919 erratically when hidden rows or columns are present
922 <!-- JAL-2362 -->Per-residue colourschemes applied via the
923 Structure Viewer's colour menu don't correspond to
927 <!-- JAL-2405 -->Protein specific colours only offered in
928 colour and group colour menu for protein alignments
931 <!-- JAL-2385 -->Colour threshold slider doesn't update to
932 reflect currently selected view or group's shading
936 <!-- JAL-2624 -->Feature colour thresholds not respected
937 when rendered on overview and structures when opacity at
941 <!-- JAL-2589 -->User defined gap colour not shown in
942 overview when features overlaid on alignment
945 <em>Data import/export</em>
948 <!-- JAL-2576 -->Very large alignments take a long time to
952 <!-- JAL-2507 -->Per-sequence RNA secondary structures
953 added after a sequence was imported are not written to
957 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
958 when importing RNA secondary structure via Stockholm
961 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
962 not shown in correct direction for simple pseudoknots
965 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
966 with lightGray or darkGray via features file (but can
970 <!-- JAL-2383 -->Above PID colour threshold not recovered
971 when alignment view imported from project
974 <!-- JAL-2520,JAL-2465 -->No mappings generated between
975 structure and sequences extracted from structure files
976 imported via URL and viewed in Jmol
979 <!-- JAL-2520 -->Structures loaded via URL are saved in
980 Jalview Projects rather than fetched via URL again when
981 the project is loaded and the structure viewed
984 <em>Web Services</em>
987 <!-- JAL-2519 -->EnsemblGenomes example failing after
988 release of Ensembl v.88
991 <!-- JAL-2366 -->Proxy server address and port always
992 appear enabled in Preferences->Connections
995 <!-- JAL-2461 -->DAS registry not found exceptions
996 removed from console output
999 <!-- JAL-2582 -->Cannot retrieve protein products from
1000 Ensembl by Peptide ID
1003 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
1004 created from SIFTs, and spurious 'Couldn't open structure
1005 in Chimera' errors raised after April 2017 update (problem
1006 due to 'null' string rather than empty string used for
1007 residues with no corresponding PDB mapping).
1010 <em>Application UI</em>
1013 <!-- JAL-2361 -->User Defined Colours not added to Colour
1017 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1018 case' residues (button in colourscheme editor debugged and
1019 new documentation and tooltips added)
1022 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1023 doesn't restore group-specific text colour thresholds
1026 <!-- JAL-2243 -->Feature settings panel does not update as
1027 new features are added to alignment
1030 <!-- JAL-2532 -->Cancel in feature settings reverts
1031 changes to feature colours via the Amend features dialog
1034 <!-- JAL-2506 -->Null pointer exception when attempting to
1035 edit graduated feature colour via amend features dialog
1039 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1040 selection menu changes colours of alignment views
1043 <!-- JAL-2426 -->Spurious exceptions in console raised
1044 from alignment calculation workers after alignment has
1048 <!-- JAL-1608 -->Typo in selection popup menu - Create
1049 groups now 'Create Group'
1052 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1053 Create/Undefine group doesn't always work
1056 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1057 shown again after pressing 'Cancel'
1060 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1061 adjusts start position in wrap mode
1064 <!-- JAL-2563 -->Status bar doesn't show positions for
1065 ambiguous amino acids
1068 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1069 CDS/Protein view after CDS sequences added for aligned
1073 <!-- JAL-2592 -->User defined colourschemes called 'User
1074 Defined' don't appear in Colours menu
1080 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1081 score models doesn't always result in an updated PCA plot
1084 <!-- JAL-2442 -->Features not rendered as transparent on
1085 overview or linked structure view
1088 <!-- JAL-2372 -->Colour group by conservation doesn't
1092 <!-- JAL-2517 -->Hitting Cancel after applying
1093 user-defined colourscheme doesn't restore original
1100 <!-- JAL-2314 -->Unit test failure:
1101 jalview.ws.jabaws.RNAStructExportImport setup fails
1104 <!-- JAL-2307 -->Unit test failure:
1105 jalview.ws.sifts.SiftsClientTest due to compatibility
1106 problems with deep array comparison equality asserts in
1107 successive versions of TestNG
1110 <!-- JAL-2479 -->Relocated StructureChooserTest and
1111 ParameterUtilsTest Unit tests to Network suite
1114 <em>New Known Issues</em>
1117 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1118 phase after a sequence motif find operation
1121 <!-- JAL-2550 -->Importing annotation file with rows
1122 containing just upper and lower case letters are
1123 interpreted as WUSS RNA secondary structure symbols
1126 <!-- JAL-2590 -->Cannot load and display Newick trees
1127 reliably from eggnog Ortholog database
1130 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1131 containing features of type Highlight' when 'B' is pressed
1132 to mark columns containing highlighted regions.
1135 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1136 doesn't always add secondary structure annotation.
1141 <td width="60" nowrap>
1142 <div align="center">
1143 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1146 <td><div align="left">
1150 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1151 for all consensus calculations
1154 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1157 <li>Updated Jalview's Certum code signing certificate
1160 <em>Application</em>
1163 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1164 set of database cross-references, sorted alphabetically
1167 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1168 from database cross references. Users with custom links
1169 will receive a <a href="webServices/urllinks.html#warning">warning
1170 dialog</a> asking them to update their preferences.
1173 <!-- JAL-2287-->Cancel button and escape listener on
1174 dialog warning user about disconnecting Jalview from a
1178 <!-- JAL-2320-->Jalview's Chimera control window closes if
1179 the Chimera it is connected to is shut down
1182 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1183 columns menu item to mark columns containing highlighted
1184 regions (e.g. from structure selections or results of a
1188 <!-- JAL-2284-->Command line option for batch-generation
1189 of HTML pages rendering alignment data with the BioJS
1199 <!-- JAL-2286 -->Columns with more than one modal residue
1200 are not coloured or thresholded according to percent
1201 identity (first observed in Jalview 2.8.2)
1204 <!-- JAL-2301 -->Threonine incorrectly reported as not
1208 <!-- JAL-2318 -->Updates to documentation pages (above PID
1209 threshold, amino acid properties)
1212 <!-- JAL-2292 -->Lower case residues in sequences are not
1213 reported as mapped to residues in a structure file in the
1217 <!--JAL-2324 -->Identical features with non-numeric scores
1218 could be added multiple times to a sequence
1221 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1222 bond features shown as two highlighted residues rather
1223 than a range in linked structure views, and treated
1224 correctly when selecting and computing trees from features
1227 <!-- JAL-2281-->Custom URL links for database
1228 cross-references are matched to database name regardless
1233 <em>Application</em>
1236 <!-- JAL-2282-->Custom URL links for specific database
1237 names without regular expressions also offer links from
1241 <!-- JAL-2315-->Removing a single configured link in the
1242 URL links pane in Connections preferences doesn't actually
1243 update Jalview configuration
1246 <!-- JAL-2272-->CTRL-Click on a selected region to open
1247 the alignment area popup menu doesn't work on El-Capitan
1250 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1251 files with similarly named sequences if dropped onto the
1255 <!-- JAL-2312 -->Additional mappings are shown for PDB
1256 entries where more chains exist in the PDB accession than
1257 are reported in the SIFTS file
1260 <!-- JAL-2317-->Certain structures do not get mapped to
1261 the structure view when displayed with Chimera
1264 <!-- JAL-2317-->No chains shown in the Chimera view
1265 panel's View->Show Chains submenu
1268 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1269 work for wrapped alignment views
1272 <!--JAL-2197 -->Rename UI components for running JPred
1273 predictions from 'JNet' to 'JPred'
1276 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1277 corrupted when annotation panel vertical scroll is not at
1278 first annotation row
1281 <!--JAL-2332 -->Attempting to view structure for Hen
1282 lysozyme results in a PDB Client error dialog box
1285 <!-- JAL-2319 -->Structure View's mapping report switched
1286 ranges for PDB and sequence for SIFTS
1289 SIFTS 'Not_Observed' residues mapped to non-existant
1293 <!-- <em>New Known Issues</em>
1300 <td width="60" nowrap>
1301 <div align="center">
1302 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1303 <em>25/10/2016</em></strong>
1306 <td><em>Application</em>
1308 <li>3D Structure chooser opens with 'Cached structures'
1309 view if structures already loaded</li>
1310 <li>Progress bar reports models as they are loaded to
1311 structure views</li>
1317 <li>Colour by conservation always enabled and no tick
1318 shown in menu when BLOSUM or PID shading applied</li>
1319 <li>FER1_ARATH and FER2_ARATH labels were switched in
1320 example sequences/projects/trees</li>
1322 <em>Application</em>
1324 <li>Jalview projects with views of local PDB structure
1325 files saved on Windows cannot be opened on OSX</li>
1326 <li>Multiple structure views can be opened and superposed
1327 without timeout for structures with multiple models or
1328 multiple sequences in alignment</li>
1329 <li>Cannot import or associated local PDB files without a
1330 PDB ID HEADER line</li>
1331 <li>RMSD is not output in Jmol console when superposition
1333 <li>Drag and drop of URL from Browser fails for Linux and
1334 OSX versions earlier than El Capitan</li>
1335 <li>ENA client ignores invalid content from ENA server</li>
1336 <li>Exceptions are not raised in console when ENA client
1337 attempts to fetch non-existent IDs via Fetch DB Refs UI
1339 <li>Exceptions are not raised in console when a new view
1340 is created on the alignment</li>
1341 <li>OSX right-click fixed for group selections: CMD-click
1342 to insert/remove gaps in groups and CTRL-click to open group
1345 <em>Build and deployment</em>
1347 <li>URL link checker now copes with multi-line anchor
1350 <em>New Known Issues</em>
1352 <li>Drag and drop from URL links in browsers do not work
1359 <td width="60" nowrap>
1360 <div align="center">
1361 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1364 <td><em>General</em>
1367 <!-- JAL-2124 -->Updated Spanish translations.
1370 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1371 for importing structure data to Jalview. Enables mmCIF and
1375 <!-- JAL-192 --->Alignment ruler shows positions relative to
1379 <!-- JAL-2202 -->Position/residue shown in status bar when
1380 mousing over sequence associated annotation
1383 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1387 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1388 '()', canonical '[]' and invalid '{}' base pair populations
1392 <!-- JAL-2092 -->Feature settings popup menu options for
1393 showing or hiding columns containing a feature
1396 <!-- JAL-1557 -->Edit selected group by double clicking on
1397 group and sequence associated annotation labels
1400 <!-- JAL-2236 -->Sequence name added to annotation label in
1401 select/hide columns by annotation and colour by annotation
1405 </ul> <em>Application</em>
1408 <!-- JAL-2050-->Automatically hide introns when opening a
1409 gene/transcript view
1412 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1416 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1417 structure mappings with the EMBL-EBI PDBe SIFTS database
1420 <!-- JAL-2079 -->Updated download sites used for Rfam and
1421 Pfam sources to xfam.org
1424 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1427 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1428 over sequences in Jalview
1431 <!-- JAL-2027-->Support for reverse-complement coding
1432 regions in ENA and EMBL
1435 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1436 for record retrieval via ENA rest API
1439 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1443 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1444 groovy script execution
1447 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1448 alignment window's Calculate menu
1451 <!-- JAL-1812 -->Allow groovy scripts that call
1452 Jalview.getAlignFrames() to run in headless mode
1455 <!-- JAL-2068 -->Support for creating new alignment
1456 calculation workers from groovy scripts
1459 <!-- JAL-1369 --->Store/restore reference sequence in
1463 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1464 associations are now saved/restored from project
1467 <!-- JAL-1993 -->Database selection dialog always shown
1468 before sequence fetcher is opened
1471 <!-- JAL-2183 -->Double click on an entry in Jalview's
1472 database chooser opens a sequence fetcher
1475 <!-- JAL-1563 -->Free-text search client for UniProt using
1476 the UniProt REST API
1479 <!-- JAL-2168 -->-nonews command line parameter to prevent
1480 the news reader opening
1483 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1484 querying stored in preferences
1487 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1491 <!-- JAL-1977-->Tooltips shown on database chooser
1494 <!-- JAL-391 -->Reverse complement function in calculate
1495 menu for nucleotide sequences
1498 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1499 and feature counts preserves alignment ordering (and
1500 debugged for complex feature sets).
1503 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1504 viewing structures with Jalview 2.10
1507 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1508 genome, transcript CCDS and gene ids via the Ensembl and
1509 Ensembl Genomes REST API
1512 <!-- JAL-2049 -->Protein sequence variant annotation
1513 computed for 'sequence_variant' annotation on CDS regions
1517 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1521 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1522 Ref Fetcher fails to match, or otherwise updates sequence
1523 data from external database records.
1526 <!-- JAL-2154 -->Revised Jalview Project format for
1527 efficient recovery of sequence coding and alignment
1528 annotation relationships.
1530 </ul> <!-- <em>Applet</em>
1541 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1545 <!-- JAL-2018-->Export features in Jalview format (again)
1546 includes graduated colourschemes
1549 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1550 working with big alignments and lots of hidden columns
1553 <!-- JAL-2053-->Hidden column markers not always rendered
1554 at right of alignment window
1557 <!-- JAL-2067 -->Tidied up links in help file table of
1561 <!-- JAL-2072 -->Feature based tree calculation not shown
1565 <!-- JAL-2075 -->Hidden columns ignored during feature
1566 based tree calculation
1569 <!-- JAL-2065 -->Alignment view stops updating when show
1570 unconserved enabled for group on alignment
1573 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1577 <!-- JAL-2146 -->Alignment column in status incorrectly
1578 shown as "Sequence position" when mousing over
1582 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1583 hidden columns present
1586 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1587 user created annotation added to alignment
1590 <!-- JAL-1841 -->RNA Structure consensus only computed for
1591 '()' base pair annotation
1594 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1595 in zero scores for all base pairs in RNA Structure
1599 <!-- JAL-2174-->Extend selection with columns containing
1603 <!-- JAL-2275 -->Pfam format writer puts extra space at
1604 beginning of sequence
1607 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1611 <!-- JAL-2238 -->Cannot create groups on an alignment from
1612 from a tree when t-coffee scores are shown
1615 <!-- JAL-1836,1967 -->Cannot import and view PDB
1616 structures with chains containing negative resnums (4q4h)
1619 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1623 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1624 to Clustal, PIR and PileUp output
1627 <!-- JAL-2008 -->Reordering sequence features that are
1628 not visible causes alignment window to repaint
1631 <!-- JAL-2006 -->Threshold sliders don't work in
1632 graduated colour and colour by annotation row for e-value
1633 scores associated with features and annotation rows
1636 <!-- JAL-1797 -->amino acid physicochemical conservation
1637 calculation should be case independent
1640 <!-- JAL-2173 -->Remove annotation also updates hidden
1644 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1645 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1646 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1649 <!-- JAL-2065 -->Null pointer exceptions and redraw
1650 problems when reference sequence defined and 'show
1651 non-conserved' enabled
1654 <!-- JAL-1306 -->Quality and Conservation are now shown on
1655 load even when Consensus calculation is disabled
1658 <!-- JAL-1932 -->Remove right on penultimate column of
1659 alignment does nothing
1662 <em>Application</em>
1665 <!-- JAL-1552-->URLs and links can't be imported by
1666 drag'n'drop on OSX when launched via webstart (note - not
1667 yet fixed for El Capitan)
1670 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1671 output when running on non-gb/us i18n platforms
1674 <!-- JAL-1944 -->Error thrown when exporting a view with
1675 hidden sequences as flat-file alignment
1678 <!-- JAL-2030-->InstallAnywhere distribution fails when
1682 <!-- JAL-2080-->Jalview very slow to launch via webstart
1683 (also hotfix for 2.9.0b2)
1686 <!-- JAL-2085 -->Cannot save project when view has a
1687 reference sequence defined
1690 <!-- JAL-1011 -->Columns are suddenly selected in other
1691 alignments and views when revealing hidden columns
1694 <!-- JAL-1989 -->Hide columns not mirrored in complement
1695 view in a cDNA/Protein splitframe
1698 <!-- JAL-1369 -->Cannot save/restore representative
1699 sequence from project when only one sequence is
1703 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1704 in Structure Chooser
1707 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1708 structure consensus didn't refresh annotation panel
1711 <!-- JAL-1962 -->View mapping in structure view shows
1712 mappings between sequence and all chains in a PDB file
1715 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1716 dialogs format columns correctly, don't display array
1717 data, sort columns according to type
1720 <!-- JAL-1975 -->Export complete shown after destination
1721 file chooser is cancelled during an image export
1724 <!-- JAL-2025 -->Error when querying PDB Service with
1725 sequence name containing special characters
1728 <!-- JAL-2024 -->Manual PDB structure querying should be
1732 <!-- JAL-2104 -->Large tooltips with broken HTML
1733 formatting don't wrap
1736 <!-- JAL-1128 -->Figures exported from wrapped view are
1737 truncated so L looks like I in consensus annotation
1740 <!-- JAL-2003 -->Export features should only export the
1741 currently displayed features for the current selection or
1745 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1746 after fetching cross-references, and restoring from
1750 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1751 followed in the structure viewer
1754 <!-- JAL-2163 -->Titles for individual alignments in
1755 splitframe not restored from project
1758 <!-- JAL-2145 -->missing autocalculated annotation at
1759 trailing end of protein alignment in transcript/product
1760 splitview when pad-gaps not enabled by default
1763 <!-- JAL-1797 -->amino acid physicochemical conservation
1767 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1768 article has been read (reopened issue due to
1769 internationalisation problems)
1772 <!-- JAL-1960 -->Only offer PDB structures in structure
1773 viewer based on sequence name, PDB and UniProt
1778 <!-- JAL-1976 -->No progress bar shown during export of
1782 <!-- JAL-2213 -->Structures not always superimposed after
1783 multiple structures are shown for one or more sequences.
1786 <!-- JAL-1370 -->Reference sequence characters should not
1787 be replaced with '.' when 'Show unconserved' format option
1791 <!-- JAL-1823 -->Cannot specify chain code when entering
1792 specific PDB id for sequence
1795 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1796 'Export hidden sequences' is enabled, but 'export hidden
1797 columns' is disabled.
1800 <!--JAL-2026-->Best Quality option in structure chooser
1801 selects lowest rather than highest resolution structures
1805 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1806 to sequence mapping in 'View Mappings' report
1809 <!-- JAL-2284 -->Unable to read old Jalview projects that
1810 contain non-XML data added after Jalvew wrote project.
1813 <!-- JAL-2118 -->Newly created annotation row reorders
1814 after clicking on it to create new annotation for a
1818 <!-- JAL-1980 -->Null Pointer Exception raised when
1819 pressing Add on an orphaned cut'n'paste window.
1821 <!-- may exclude, this is an external service stability issue JAL-1941
1822 -- > RNA 3D structure not added via DSSR service</li> -->
1827 <!-- JAL-2151 -->Incorrect columns are selected when
1828 hidden columns present before start of sequence
1831 <!-- JAL-1986 -->Missing dependencies on applet pages
1835 <!-- JAL-1947 -->Overview pixel size changes when
1836 sequences are hidden in applet
1839 <!-- JAL-1996 -->Updated instructions for applet
1840 deployment on examples pages.
1847 <td width="60" nowrap>
1848 <div align="center">
1849 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1850 <em>16/10/2015</em></strong>
1853 <td><em>General</em>
1855 <li>Time stamps for signed Jalview application and applet
1860 <em>Application</em>
1862 <li>Duplicate group consensus and conservation rows
1863 shown when tree is partitioned</li>
1864 <li>Erratic behaviour when tree partitions made with
1865 multiple cDNA/Protein split views</li>
1871 <td width="60" nowrap>
1872 <div align="center">
1873 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1874 <em>8/10/2015</em></strong>
1877 <td><em>General</em>
1879 <li>Updated Spanish translations of localized text for
1881 </ul> <em>Application</em>
1883 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1884 <li>Signed OSX InstallAnywhere installer<br></li>
1885 <li>Support for per-sequence based annotations in BioJSON</li>
1886 </ul> <em>Applet</em>
1888 <li>Split frame example added to applet examples page</li>
1889 </ul> <em>Build and Deployment</em>
1892 <!-- JAL-1888 -->New ant target for running Jalview's test
1900 <li>Mapping of cDNA to protein in split frames
1901 incorrect when sequence start > 1</li>
1902 <li>Broken images in filter column by annotation dialog
1904 <li>Feature colours not parsed from features file</li>
1905 <li>Exceptions and incomplete link URLs recovered when
1906 loading a features file containing HTML tags in feature
1910 <em>Application</em>
1912 <li>Annotations corrupted after BioJS export and
1914 <li>Incorrect sequence limits after Fetch DB References
1915 with 'trim retrieved sequences'</li>
1916 <li>Incorrect warning about deleting all data when
1917 deleting selected columns</li>
1918 <li>Patch to build system for shipping properly signed
1919 JNLP templates for webstart launch</li>
1920 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1921 unreleased structures for download or viewing</li>
1922 <li>Tab/space/return keystroke operation of EMBL-PDBe
1923 fetcher/viewer dialogs works correctly</li>
1924 <li>Disabled 'minimise' button on Jalview windows
1925 running on OSX to workaround redraw hang bug</li>
1926 <li>Split cDNA/Protein view position and geometry not
1927 recovered from jalview project</li>
1928 <li>Initial enabled/disabled state of annotation menu
1929 sorter 'show autocalculated first/last' corresponds to
1931 <li>Restoring of Clustal, RNA Helices and T-Coffee
1932 color schemes from BioJSON</li>
1936 <li>Reorder sequences mirrored in cDNA/Protein split
1938 <li>Applet with Jmol examples not loading correctly</li>
1944 <td><div align="center">
1945 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1947 <td><em>General</em>
1949 <li>Linked visualisation and analysis of DNA and Protein
1952 <li>Translated cDNA alignments shown as split protein
1953 and DNA alignment views</li>
1954 <li>Codon consensus annotation for linked protein and
1955 cDNA alignment views</li>
1956 <li>Link cDNA or Protein product sequences by loading
1957 them onto Protein or cDNA alignments</li>
1958 <li>Reconstruct linked cDNA alignment from aligned
1959 protein sequences</li>
1962 <li>Jmol integration updated to Jmol v14.2.14</li>
1963 <li>Import and export of Jalview alignment views as <a
1964 href="features/bioJsonFormat.html">BioJSON</a></li>
1965 <li>New alignment annotation file statements for
1966 reference sequences and marking hidden columns</li>
1967 <li>Reference sequence based alignment shading to
1968 highlight variation</li>
1969 <li>Select or hide columns according to alignment
1971 <li>Find option for locating sequences by description</li>
1972 <li>Conserved physicochemical properties shown in amino
1973 acid conservation row</li>
1974 <li>Alignments can be sorted by number of RNA helices</li>
1975 </ul> <em>Application</em>
1977 <li>New cDNA/Protein analysis capabilities
1979 <li>Get Cross-References should open a Split Frame
1980 view with cDNA/Protein</li>
1981 <li>Detect when nucleotide sequences and protein
1982 sequences are placed in the same alignment</li>
1983 <li>Split cDNA/Protein views are saved in Jalview
1988 <li>Use REST API to talk to Chimera</li>
1989 <li>Selected regions in Chimera are highlighted in linked
1990 Jalview windows</li>
1992 <li>VARNA RNA viewer updated to v3.93</li>
1993 <li>VARNA views are saved in Jalview Projects</li>
1994 <li>Pseudoknots displayed as Jalview RNA annotation can
1995 be shown in VARNA</li>
1997 <li>Make groups for selection uses marked columns as well
1998 as the active selected region</li>
2000 <li>Calculate UPGMA and NJ trees using sequence feature
2002 <li>New Export options
2004 <li>New Export Settings dialog to control hidden
2005 region export in flat file generation</li>
2007 <li>Export alignment views for display with the <a
2008 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
2010 <li>Export scrollable SVG in HTML page</li>
2011 <li>Optional embedding of BioJSON data when exporting
2012 alignment figures to HTML</li>
2014 <li>3D structure retrieval and display
2016 <li>Free text and structured queries with the PDBe
2018 <li>PDBe Search API based discovery and selection of
2019 PDB structures for a sequence set</li>
2023 <li>JPred4 employed for protein secondary structure
2025 <li>Hide Insertions menu option to hide unaligned columns
2026 for one or a group of sequences</li>
2027 <li>Automatically hide insertions in alignments imported
2028 from the JPred4 web server</li>
2029 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2030 system on OSX<br />LGPL libraries courtesy of <a
2031 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2033 <li>changed 'View nucleotide structure' submenu to 'View
2034 VARNA 2D Structure'</li>
2035 <li>change "View protein structure" menu option to "3D
2038 </ul> <em>Applet</em>
2040 <li>New layout for applet example pages</li>
2041 <li>New parameters to enable SplitFrame view
2042 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2043 <li>New example demonstrating linked viewing of cDNA and
2044 Protein alignments</li>
2045 </ul> <em>Development and deployment</em>
2047 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2048 <li>Include installation type and git revision in build
2049 properties and console log output</li>
2050 <li>Jalview Github organisation, and new github site for
2051 storing BioJsMSA Templates</li>
2052 <li>Jalview's unit tests now managed with TestNG</li>
2055 <!-- <em>General</em>
2057 </ul> --> <!-- issues resolved --> <em>Application</em>
2059 <li>Escape should close any open find dialogs</li>
2060 <li>Typo in select-by-features status report</li>
2061 <li>Consensus RNA secondary secondary structure
2062 predictions are not highlighted in amber</li>
2063 <li>Missing gap character in v2.7 example file means
2064 alignment appears unaligned when pad-gaps is not enabled</li>
2065 <li>First switch to RNA Helices colouring doesn't colour
2066 associated structure views</li>
2067 <li>ID width preference option is greyed out when auto
2068 width checkbox not enabled</li>
2069 <li>Stopped a warning dialog from being shown when
2070 creating user defined colours</li>
2071 <li>'View Mapping' in structure viewer shows sequence
2072 mappings for just that viewer's sequences</li>
2073 <li>Workaround for superposing PDB files containing
2074 multiple models in Chimera</li>
2075 <li>Report sequence position in status bar when hovering
2076 over Jmol structure</li>
2077 <li>Cannot output gaps as '.' symbols with Selection ->
2078 output to text box</li>
2079 <li>Flat file exports of alignments with hidden columns
2080 have incorrect sequence start/end</li>
2081 <li>'Aligning' a second chain to a Chimera structure from
2083 <li>Colour schemes applied to structure viewers don't
2084 work for nucleotide</li>
2085 <li>Loading/cut'n'pasting an empty or invalid file leads
2086 to a grey/invisible alignment window</li>
2087 <li>Exported Jpred annotation from a sequence region
2088 imports to different position</li>
2089 <li>Space at beginning of sequence feature tooltips shown
2090 on some platforms</li>
2091 <li>Chimera viewer 'View | Show Chain' menu is not
2093 <li>'New View' fails with a Null Pointer Exception in
2094 console if Chimera has been opened</li>
2095 <li>Mouseover to Chimera not working</li>
2096 <li>Miscellaneous ENA XML feature qualifiers not
2098 <li>NPE in annotation renderer after 'Extract Scores'</li>
2099 <li>If two structures in one Chimera window, mouseover of
2100 either sequence shows on first structure</li>
2101 <li>'Show annotations' options should not make
2102 non-positional annotations visible</li>
2103 <li>Subsequence secondary structure annotation not shown
2104 in right place after 'view flanking regions'</li>
2105 <li>File Save As type unset when current file format is
2107 <li>Save as '.jar' option removed for saving Jalview
2109 <li>Colour by Sequence colouring in Chimera more
2111 <li>Cannot 'add reference annotation' for a sequence in
2112 several views on same alignment</li>
2113 <li>Cannot show linked products for EMBL / ENA records</li>
2114 <li>Jalview's tooltip wraps long texts containing no
2116 </ul> <em>Applet</em>
2118 <li>Jmol to JalviewLite mouseover/link not working</li>
2119 <li>JalviewLite can't import sequences with ID
2120 descriptions containing angle brackets</li>
2121 </ul> <em>General</em>
2123 <li>Cannot export and reimport RNA secondary structure
2124 via jalview annotation file</li>
2125 <li>Random helix colour palette for colour by annotation
2126 with RNA secondary structure</li>
2127 <li>Mouseover to cDNA from STOP residue in protein
2128 translation doesn't work.</li>
2129 <li>hints when using the select by annotation dialog box</li>
2130 <li>Jmol alignment incorrect if PDB file has alternate CA
2132 <li>FontChooser message dialog appears to hang after
2133 choosing 1pt font</li>
2134 <li>Peptide secondary structure incorrectly imported from
2135 annotation file when annotation display text includes 'e' or
2137 <li>Cannot set colour of new feature type whilst creating
2139 <li>cDNA translation alignment should not be sequence
2140 order dependent</li>
2141 <li>'Show unconserved' doesn't work for lower case
2143 <li>Nucleotide ambiguity codes involving R not recognised</li>
2144 </ul> <em>Deployment and Documentation</em>
2146 <li>Applet example pages appear different to the rest of
2147 www.jalview.org</li>
2148 </ul> <em>Application Known issues</em>
2150 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2151 <li>Misleading message appears after trying to delete
2153 <li>Jalview icon not shown in dock after InstallAnywhere
2154 version launches</li>
2155 <li>Fetching EMBL reference for an RNA sequence results
2156 fails with a sequence mismatch</li>
2157 <li>Corrupted or unreadable alignment display when
2158 scrolling alignment to right</li>
2159 <li>ArrayIndexOutOfBoundsException thrown when remove
2160 empty columns called on alignment with ragged gapped ends</li>
2161 <li>auto calculated alignment annotation rows do not get
2162 placed above or below non-autocalculated rows</li>
2163 <li>Jalview dekstop becomes sluggish at full screen in
2164 ultra-high resolution</li>
2165 <li>Cannot disable consensus calculation independently of
2166 quality and conservation</li>
2167 <li>Mouseover highlighting between cDNA and protein can
2168 become sluggish with more than one splitframe shown</li>
2169 </ul> <em>Applet Known Issues</em>
2171 <li>Core PDB parsing code requires Jmol</li>
2172 <li>Sequence canvas panel goes white when alignment
2173 window is being resized</li>
2179 <td><div align="center">
2180 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2182 <td><em>General</em>
2184 <li>Updated Java code signing certificate donated by
2186 <li>Features and annotation preserved when performing
2187 pairwise alignment</li>
2188 <li>RNA pseudoknot annotation can be
2189 imported/exported/displayed</li>
2190 <li>'colour by annotation' can colour by RNA and
2191 protein secondary structure</li>
2192 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2193 post-hoc with 2.9 release</em>)
2196 </ul> <em>Application</em>
2198 <li>Extract and display secondary structure for sequences
2199 with 3D structures</li>
2200 <li>Support for parsing RNAML</li>
2201 <li>Annotations menu for layout
2203 <li>sort sequence annotation rows by alignment</li>
2204 <li>place sequence annotation above/below alignment
2207 <li>Output in Stockholm format</li>
2208 <li>Internationalisation: improved Spanish (es)
2210 <li>Structure viewer preferences tab</li>
2211 <li>Disorder and Secondary Structure annotation tracks
2212 shared between alignments</li>
2213 <li>UCSF Chimera launch and linked highlighting from
2215 <li>Show/hide all sequence associated annotation rows for
2216 all or current selection</li>
2217 <li>disorder and secondary structure predictions
2218 available as dataset annotation</li>
2219 <li>Per-sequence rna helices colouring</li>
2222 <li>Sequence database accessions imported when fetching
2223 alignments from Rfam</li>
2224 <li>update VARNA version to 3.91</li>
2226 <li>New groovy scripts for exporting aligned positions,
2227 conservation values, and calculating sum of pairs scores.</li>
2228 <li>Command line argument to set default JABAWS server</li>
2229 <li>include installation type in build properties and
2230 console log output</li>
2231 <li>Updated Jalview project format to preserve dataset
2235 <!-- issues resolved --> <em>Application</em>
2237 <li>Distinguish alignment and sequence associated RNA
2238 structure in structure->view->VARNA</li>
2239 <li>Raise dialog box if user deletes all sequences in an
2241 <li>Pressing F1 results in documentation opening twice</li>
2242 <li>Sequence feature tooltip is wrapped</li>
2243 <li>Double click on sequence associated annotation
2244 selects only first column</li>
2245 <li>Redundancy removal doesn't result in unlinked
2246 leaves shown in tree</li>
2247 <li>Undos after several redundancy removals don't undo
2249 <li>Hide sequence doesn't hide associated annotation</li>
2250 <li>User defined colours dialog box too big to fit on
2251 screen and buttons not visible</li>
2252 <li>author list isn't updated if already written to
2253 Jalview properties</li>
2254 <li>Popup menu won't open after retrieving sequence
2256 <li>File open window for associate PDB doesn't open</li>
2257 <li>Left-then-right click on a sequence id opens a
2258 browser search window</li>
2259 <li>Cannot open sequence feature shading/sort popup menu
2260 in feature settings dialog</li>
2261 <li>better tooltip placement for some areas of Jalview
2263 <li>Allow addition of JABAWS Server which doesn't
2264 pass validation</li>
2265 <li>Web services parameters dialog box is too large to
2267 <li>Muscle nucleotide alignment preset obscured by
2269 <li>JABAWS preset submenus don't contain newly
2270 defined user preset</li>
2271 <li>MSA web services warns user if they were launched
2272 with invalid input</li>
2273 <li>Jalview cannot contact DAS Registy when running on
2276 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2277 'Superpose with' submenu not shown when new view
2281 </ul> <!-- <em>Applet</em>
2283 </ul> <em>General</em>
2285 </ul>--> <em>Deployment and Documentation</em>
2287 <li>2G and 1G options in launchApp have no effect on
2288 memory allocation</li>
2289 <li>launchApp service doesn't automatically open
2290 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2292 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2293 InstallAnywhere reports cannot find valid JVM when Java
2294 1.7_055 is available
2296 </ul> <em>Application Known issues</em>
2299 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2300 corrupted or unreadable alignment display when scrolling
2304 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2305 retrieval fails but progress bar continues for DAS retrieval
2306 with large number of ID
2309 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2310 flatfile output of visible region has incorrect sequence
2314 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2315 rna structure consensus doesn't update when secondary
2316 structure tracks are rearranged
2319 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2320 invalid rna structure positional highlighting does not
2321 highlight position of invalid base pairs
2324 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2325 out of memory errors are not raised when saving Jalview
2326 project from alignment window file menu
2329 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2330 Switching to RNA Helices colouring doesn't propagate to
2334 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2335 colour by RNA Helices not enabled when user created
2336 annotation added to alignment
2339 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2340 Jalview icon not shown on dock in Mountain Lion/Webstart
2342 </ul> <em>Applet Known Issues</em>
2345 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2346 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2349 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2350 Jalview and Jmol example not compatible with IE9
2353 <li>Sort by annotation score doesn't reverse order
2359 <td><div align="center">
2360 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2363 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2366 <li>Internationalisation of user interface (usually
2367 called i18n support) and translation for Spanish locale</li>
2368 <li>Define/Undefine group on current selection with
2369 Ctrl-G/Shift Ctrl-G</li>
2370 <li>Improved group creation/removal options in
2371 alignment/sequence Popup menu</li>
2372 <li>Sensible precision for symbol distribution
2373 percentages shown in logo tooltip.</li>
2374 <li>Annotation panel height set according to amount of
2375 annotation when alignment first opened</li>
2376 </ul> <em>Application</em>
2378 <li>Interactive consensus RNA secondary structure
2379 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2380 <li>Select columns containing particular features from
2381 Feature Settings dialog</li>
2382 <li>View all 'representative' PDB structures for selected
2384 <li>Update Jalview project format:
2386 <li>New file extension for Jalview projects '.jvp'</li>
2387 <li>Preserve sequence and annotation dataset (to
2388 store secondary structure annotation,etc)</li>
2389 <li>Per group and alignment annotation and RNA helix
2393 <li>New similarity measures for PCA and Tree calculation
2395 <li>Experimental support for retrieval and viewing of
2396 flanking regions for an alignment</li>
2400 <!-- issues resolved --> <em>Application</em>
2402 <li>logo keeps spinning and status remains at queued or
2403 running after job is cancelled</li>
2404 <li>cannot export features from alignments imported from
2405 Jalview/VAMSAS projects</li>
2406 <li>Buggy slider for web service parameters that take
2408 <li>Newly created RNA secondary structure line doesn't
2409 have 'display all symbols' flag set</li>
2410 <li>T-COFFEE alignment score shading scheme and other
2411 annotation shading not saved in Jalview project</li>
2412 <li>Local file cannot be loaded in freshly downloaded
2414 <li>Jalview icon not shown on dock in Mountain
2416 <li>Load file from desktop file browser fails</li>
2417 <li>Occasional NPE thrown when calculating large trees</li>
2418 <li>Cannot reorder or slide sequences after dragging an
2419 alignment onto desktop</li>
2420 <li>Colour by annotation dialog throws NPE after using
2421 'extract scores' function</li>
2422 <li>Loading/cut'n'pasting an empty file leads to a grey
2423 alignment window</li>
2424 <li>Disorder thresholds rendered incorrectly after
2425 performing IUPred disorder prediction</li>
2426 <li>Multiple group annotated consensus rows shown when
2427 changing 'normalise logo' display setting</li>
2428 <li>Find shows blank dialog after 'finished searching' if
2429 nothing matches query</li>
2430 <li>Null Pointer Exceptions raised when sorting by
2431 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2433 <li>Errors in Jmol console when structures in alignment
2434 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2436 <li>Not all working JABAWS services are shown in
2438 <li>JAVAWS version of Jalview fails to launch with
2439 'invalid literal/length code'</li>
2440 <li>Annotation/RNA Helix colourschemes cannot be applied
2441 to alignment with groups (actually fixed in 2.8.0b1)</li>
2442 <li>RNA Helices and T-Coffee Scores available as default
2445 </ul> <em>Applet</em>
2447 <li>Remove group option is shown even when selection is
2449 <li>Apply to all groups ticked but colourscheme changes
2450 don't affect groups</li>
2451 <li>Documented RNA Helices and T-Coffee Scores as valid
2452 colourscheme name</li>
2453 <li>Annotation labels drawn on sequence IDs when
2454 Annotation panel is not displayed</li>
2455 <li>Increased font size for dropdown menus on OSX and
2456 embedded windows</li>
2457 </ul> <em>Other</em>
2459 <li>Consensus sequence for alignments/groups with a
2460 single sequence were not calculated</li>
2461 <li>annotation files that contain only groups imported as
2462 annotation and junk sequences</li>
2463 <li>Fasta files with sequences containing '*' incorrectly
2464 recognised as PFAM or BLC</li>
2465 <li>conservation/PID slider apply all groups option
2466 doesn't affect background (2.8.0b1)
2468 <li>redundancy highlighting is erratic at 0% and 100%</li>
2469 <li>Remove gapped columns fails for sequences with ragged
2471 <li>AMSA annotation row with leading spaces is not
2472 registered correctly on import</li>
2473 <li>Jalview crashes when selecting PCA analysis for
2474 certain alignments</li>
2475 <li>Opening the colour by annotation dialog for an
2476 existing annotation based 'use original colours'
2477 colourscheme loses original colours setting</li>
2482 <td><div align="center">
2483 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2484 <em>30/1/2014</em></strong>
2488 <li>Trusted certificates for JalviewLite applet and
2489 Jalview Desktop application<br />Certificate was donated by
2490 <a href="https://www.certum.eu">Certum</a> to the Jalview
2491 open source project).
2493 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2494 <li>Output in Stockholm format</li>
2495 <li>Allow import of data from gzipped files</li>
2496 <li>Export/import group and sequence associated line
2497 graph thresholds</li>
2498 <li>Nucleotide substitution matrix that supports RNA and
2499 ambiguity codes</li>
2500 <li>Allow disorder predictions to be made on the current
2501 selection (or visible selection) in the same way that JPred
2503 <li>Groovy scripting for headless Jalview operation</li>
2504 </ul> <em>Other improvements</em>
2506 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2507 <li>COMBINE statement uses current SEQUENCE_REF and
2508 GROUP_REF scope to group annotation rows</li>
2509 <li>Support '' style escaping of quotes in Newick
2511 <li>Group options for JABAWS service by command line name</li>
2512 <li>Empty tooltip shown for JABA service options with a
2513 link but no description</li>
2514 <li>Select primary source when selecting authority in
2515 database fetcher GUI</li>
2516 <li>Add .mfa to FASTA file extensions recognised by
2518 <li>Annotation label tooltip text wrap</li>
2523 <li>Slow scrolling when lots of annotation rows are
2525 <li>Lots of NPE (and slowness) after creating RNA
2526 secondary structure annotation line</li>
2527 <li>Sequence database accessions not imported when
2528 fetching alignments from Rfam</li>
2529 <li>Incorrect SHMR submission for sequences with
2531 <li>View all structures does not always superpose
2533 <li>Option widgets in service parameters not updated to
2534 reflect user or preset settings</li>
2535 <li>Null pointer exceptions for some services without
2536 presets or adjustable parameters</li>
2537 <li>Discover PDB IDs entry in structure menu doesn't
2538 discover PDB xRefs</li>
2539 <li>Exception encountered while trying to retrieve
2540 features with DAS</li>
2541 <li>Lowest value in annotation row isn't coloured
2542 when colour by annotation (per sequence) is coloured</li>
2543 <li>Keyboard mode P jumps to start of gapped region when
2544 residue follows a gap</li>
2545 <li>Jalview appears to hang importing an alignment with
2546 Wrap as default or after enabling Wrap</li>
2547 <li>'Right click to add annotations' message
2548 shown in wrap mode when no annotations present</li>
2549 <li>Disorder predictions fail with NPE if no automatic
2550 annotation already exists on alignment</li>
2551 <li>oninit javascript function should be called after
2552 initialisation completes</li>
2553 <li>Remove redundancy after disorder prediction corrupts
2554 alignment window display</li>
2555 <li>Example annotation file in documentation is invalid</li>
2556 <li>Grouped line graph annotation rows are not exported
2557 to annotation file</li>
2558 <li>Multi-harmony analysis cannot be run when only two
2560 <li>Cannot create multiple groups of line graphs with
2561 several 'combine' statements in annotation file</li>
2562 <li>Pressing return several times causes Number Format
2563 exceptions in keyboard mode</li>
2564 <li>Multi-harmony (SHMMR) method doesn't submit
2565 correct partitions for input data</li>
2566 <li>Translation from DNA to Amino Acids fails</li>
2567 <li>Jalview fail to load newick tree with quoted label</li>
2568 <li>--headless flag isn't understood</li>
2569 <li>ClassCastException when generating EPS in headless
2571 <li>Adjusting sequence-associated shading threshold only
2572 changes one row's threshold</li>
2573 <li>Preferences and Feature settings panel panel
2574 doesn't open</li>
2575 <li>hide consensus histogram also hides conservation and
2576 quality histograms</li>
2581 <td><div align="center">
2582 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2584 <td><em>Application</em>
2586 <li>Support for JABAWS 2.0 Services (AACon alignment
2587 conservation, protein disorder and Clustal Omega)</li>
2588 <li>JABAWS server status indicator in Web Services
2590 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2591 in Jalview alignment window</li>
2592 <li>Updated Jalview build and deploy framework for OSX
2593 mountain lion, windows 7, and 8</li>
2594 <li>Nucleotide substitution matrix for PCA that supports
2595 RNA and ambiguity codes</li>
2597 <li>Improved sequence database retrieval GUI</li>
2598 <li>Support fetching and database reference look up
2599 against multiple DAS sources (Fetch all from in 'fetch db
2601 <li>Jalview project improvements
2603 <li>Store and retrieve the 'belowAlignment'
2604 flag for annotation</li>
2605 <li>calcId attribute to group annotation rows on the
2607 <li>Store AACon calculation settings for a view in
2608 Jalview project</li>
2612 <li>horizontal scrolling gesture support</li>
2613 <li>Visual progress indicator when PCA calculation is
2615 <li>Simpler JABA web services menus</li>
2616 <li>visual indication that web service results are still
2617 being retrieved from server</li>
2618 <li>Serialise the dialogs that are shown when Jalview
2619 starts up for first time</li>
2620 <li>Jalview user agent string for interacting with HTTP
2622 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2624 <li>Examples directory and Groovy library included in
2625 InstallAnywhere distribution</li>
2626 </ul> <em>Applet</em>
2628 <li>RNA alignment and secondary structure annotation
2629 visualization applet example</li>
2630 </ul> <em>General</em>
2632 <li>Normalise option for consensus sequence logo</li>
2633 <li>Reset button in PCA window to return dimensions to
2635 <li>Allow seqspace or Jalview variant of alignment PCA
2637 <li>PCA with either nucleic acid and protein substitution
2639 <li>Allow windows containing HTML reports to be exported
2641 <li>Interactive display and editing of RNA secondary
2642 structure contacts</li>
2643 <li>RNA Helix Alignment Colouring</li>
2644 <li>RNA base pair logo consensus</li>
2645 <li>Parse sequence associated secondary structure
2646 information in Stockholm files</li>
2647 <li>HTML Export database accessions and annotation
2648 information presented in tooltip for sequences</li>
2649 <li>Import secondary structure from LOCARNA clustalw
2650 style RNA alignment files</li>
2651 <li>import and visualise T-COFFEE quality scores for an
2653 <li>'colour by annotation' per sequence option to
2654 shade each sequence according to its associated alignment
2656 <li>New Jalview Logo</li>
2657 </ul> <em>Documentation and Development</em>
2659 <li>documentation for score matrices used in Jalview</li>
2660 <li>New Website!</li>
2662 <td><em>Application</em>
2664 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2665 wsdbfetch REST service</li>
2666 <li>Stop windows being moved outside desktop on OSX</li>
2667 <li>Filetype associations not installed for webstart
2669 <li>Jalview does not always retrieve progress of a JABAWS
2670 job execution in full once it is complete</li>
2671 <li>revise SHMR RSBS definition to ensure alignment is
2672 uploaded via ali_file parameter</li>
2673 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2674 <li>View all structures superposed fails with exception</li>
2675 <li>Jnet job queues forever if a very short sequence is
2676 submitted for prediction</li>
2677 <li>Cut and paste menu not opened when mouse clicked on
2679 <li>Putting fractional value into integer text box in
2680 alignment parameter dialog causes Jalview to hang</li>
2681 <li>Structure view highlighting doesn't work on
2683 <li>View all structures fails with exception shown in
2685 <li>Characters in filename associated with PDBEntry not
2686 escaped in a platform independent way</li>
2687 <li>Jalview desktop fails to launch with exception when
2689 <li>Tree calculation reports 'you must have 2 or more
2690 sequences selected' when selection is empty</li>
2691 <li>Jalview desktop fails to launch with jar signature
2692 failure when java web start temporary file caching is
2694 <li>DAS Sequence retrieval with range qualification
2695 results in sequence xref which includes range qualification</li>
2696 <li>Errors during processing of command line arguments
2697 cause progress bar (JAL-898) to be removed</li>
2698 <li>Replace comma for semi-colon option not disabled for
2699 DAS sources in sequence fetcher</li>
2700 <li>Cannot close news reader when JABAWS server warning
2701 dialog is shown</li>
2702 <li>Option widgets not updated to reflect user settings</li>
2703 <li>Edited sequence not submitted to web service</li>
2704 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2705 <li>InstallAnywhere installer doesn't unpack and run
2706 on OSX Mountain Lion</li>
2707 <li>Annotation panel not given a scroll bar when
2708 sequences with alignment annotation are pasted into the
2710 <li>Sequence associated annotation rows not associated
2711 when loaded from Jalview project</li>
2712 <li>Browser launch fails with NPE on java 1.7</li>
2713 <li>JABAWS alignment marked as finished when job was
2714 cancelled or job failed due to invalid input</li>
2715 <li>NPE with v2.7 example when clicking on Tree
2716 associated with all views</li>
2717 <li>Exceptions when copy/paste sequences with grouped
2718 annotation rows to new window</li>
2719 </ul> <em>Applet</em>
2721 <li>Sequence features are momentarily displayed before
2722 they are hidden using hidefeaturegroups applet parameter</li>
2723 <li>loading features via javascript API automatically
2724 enables feature display</li>
2725 <li>scrollToColumnIn javascript API method doesn't
2727 </ul> <em>General</em>
2729 <li>Redundancy removal fails for rna alignment</li>
2730 <li>PCA calculation fails when sequence has been selected
2731 and then deselected</li>
2732 <li>PCA window shows grey box when first opened on OSX</li>
2733 <li>Letters coloured pink in sequence logo when alignment
2734 coloured with clustalx</li>
2735 <li>Choosing fonts without letter symbols defined causes
2736 exceptions and redraw errors</li>
2737 <li>Initial PCA plot view is not same as manually
2738 reconfigured view</li>
2739 <li>Grouped annotation graph label has incorrect line
2741 <li>Grouped annotation graph label display is corrupted
2742 for lots of labels</li>
2747 <div align="center">
2748 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2751 <td><em>Application</em>
2753 <li>Jalview Desktop News Reader</li>
2754 <li>Tweaked default layout of web services menu</li>
2755 <li>View/alignment association menu to enable user to
2756 easily specify which alignment a multi-structure view takes
2757 its colours/correspondences from</li>
2758 <li>Allow properties file location to be specified as URL</li>
2759 <li>Extend Jalview project to preserve associations
2760 between many alignment views and a single Jmol display</li>
2761 <li>Store annotation row height in Jalview project file</li>
2762 <li>Annotation row column label formatting attributes
2763 stored in project file</li>
2764 <li>Annotation row order for auto-calculated annotation
2765 rows preserved in Jalview project file</li>
2766 <li>Visual progress indication when Jalview state is
2767 saved using Desktop window menu</li>
2768 <li>Visual indication that command line arguments are
2769 still being processed</li>
2770 <li>Groovy script execution from URL</li>
2771 <li>Colour by annotation default min and max colours in
2773 <li>Automatically associate PDB files dragged onto an
2774 alignment with sequences that have high similarity and
2776 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2777 <li>'view structures' option to open many
2778 structures in same window</li>
2779 <li>Sort associated views menu option for tree panel</li>
2780 <li>Group all JABA and non-JABA services for a particular
2781 analysis function in its own submenu</li>
2782 </ul> <em>Applet</em>
2784 <li>Userdefined and autogenerated annotation rows for
2786 <li>Adjustment of alignment annotation pane height</li>
2787 <li>Annotation scrollbar for annotation panel</li>
2788 <li>Drag to reorder annotation rows in annotation panel</li>
2789 <li>'automaticScrolling' parameter</li>
2790 <li>Allow sequences with partial ID string matches to be
2791 annotated from GFF/Jalview features files</li>
2792 <li>Sequence logo annotation row in applet</li>
2793 <li>Absolute paths relative to host server in applet
2794 parameters are treated as such</li>
2795 <li>New in the JalviewLite javascript API:
2797 <li>JalviewLite.js javascript library</li>
2798 <li>Javascript callbacks for
2800 <li>Applet initialisation</li>
2801 <li>Sequence/alignment mouse-overs and selections</li>
2804 <li>scrollTo row and column alignment scrolling
2806 <li>Select sequence/alignment regions from javascript</li>
2807 <li>javascript structure viewer harness to pass
2808 messages between Jmol and Jalview when running as
2809 distinct applets</li>
2810 <li>sortBy method</li>
2811 <li>Set of applet and application examples shipped
2812 with documentation</li>
2813 <li>New example to demonstrate JalviewLite and Jmol
2814 javascript message exchange</li>
2816 </ul> <em>General</em>
2818 <li>Enable Jmol displays to be associated with multiple
2819 multiple alignments</li>
2820 <li>Option to automatically sort alignment with new tree</li>
2821 <li>User configurable link to enable redirects to a
2822 www.Jalview.org mirror</li>
2823 <li>Jmol colours option for Jmol displays</li>
2824 <li>Configurable newline string when writing alignment
2825 and other flat files</li>
2826 <li>Allow alignment annotation description lines to
2827 contain html tags</li>
2828 </ul> <em>Documentation and Development</em>
2830 <li>Add groovy test harness for bulk load testing to
2832 <li>Groovy script to load and align a set of sequences
2833 using a web service before displaying the result in the
2834 Jalview desktop</li>
2835 <li>Restructured javascript and applet api documentation</li>
2836 <li>Ant target to publish example html files with applet
2838 <li>Netbeans project for building Jalview from source</li>
2839 <li>ant task to create online javadoc for Jalview source</li>
2841 <td><em>Application</em>
2843 <li>User defined colourscheme throws exception when
2844 current built in colourscheme is saved as new scheme</li>
2845 <li>AlignFrame->Save in application pops up save
2846 dialog for valid filename/format</li>
2847 <li>Cannot view associated structure for UniProt sequence</li>
2848 <li>PDB file association breaks for UniProt sequence
2850 <li>Associate PDB from file dialog does not tell you
2851 which sequence is to be associated with the file</li>
2852 <li>Find All raises null pointer exception when query
2853 only matches sequence IDs</li>
2854 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2855 <li>Jalview project with Jmol views created with Jalview
2856 2.4 cannot be loaded</li>
2857 <li>Filetype associations not installed for webstart
2859 <li>Two or more chains in a single PDB file associated
2860 with sequences in different alignments do not get coloured
2861 by their associated sequence</li>
2862 <li>Visibility status of autocalculated annotation row
2863 not preserved when project is loaded</li>
2864 <li>Annotation row height and visibility attributes not
2865 stored in Jalview project</li>
2866 <li>Tree bootstraps are not preserved when saved as a
2867 Jalview project</li>
2868 <li>Envision2 workflow tooltips are corrupted</li>
2869 <li>Enabling show group conservation also enables colour
2870 by conservation</li>
2871 <li>Duplicate group associated conservation or consensus
2872 created on new view</li>
2873 <li>Annotation scrollbar not displayed after 'show
2874 all hidden annotation rows' option selected</li>
2875 <li>Alignment quality not updated after alignment
2876 annotation row is hidden then shown</li>
2877 <li>Preserve colouring of structures coloured by
2878 sequences in pre Jalview 2.7 projects</li>
2879 <li>Web service job parameter dialog is not laid out
2881 <li>Web services menu not refreshed after 'reset
2882 services' button is pressed in preferences</li>
2883 <li>Annotation off by one in Jalview v2_3 example project</li>
2884 <li>Structures imported from file and saved in project
2885 get name like jalview_pdb1234.txt when reloaded</li>
2886 <li>Jalview does not always retrieve progress of a JABAWS
2887 job execution in full once it is complete</li>
2888 </ul> <em>Applet</em>
2890 <li>Alignment height set incorrectly when lots of
2891 annotation rows are displayed</li>
2892 <li>Relative URLs in feature HTML text not resolved to
2894 <li>View follows highlighting does not work for positions
2896 <li><= shown as = in tooltip</li>
2897 <li>Export features raises exception when no features
2899 <li>Separator string used for serialising lists of IDs
2900 for javascript api is modified when separator string
2901 provided as parameter</li>
2902 <li>Null pointer exception when selecting tree leaves for
2903 alignment with no existing selection</li>
2904 <li>Relative URLs for datasources assumed to be relative
2905 to applet's codebase</li>
2906 <li>Status bar not updated after finished searching and
2907 search wraps around to first result</li>
2908 <li>StructureSelectionManager instance shared between
2909 several Jalview applets causes race conditions and memory
2911 <li>Hover tooltip and mouseover of position on structure
2912 not sent from Jmol in applet</li>
2913 <li>Certain sequences of javascript method calls to
2914 applet API fatally hang browser</li>
2915 </ul> <em>General</em>
2917 <li>View follows structure mouseover scrolls beyond
2918 position with wrapped view and hidden regions</li>
2919 <li>Find sequence position moves to wrong residue
2920 with/without hidden columns</li>
2921 <li>Sequence length given in alignment properties window
2923 <li>InvalidNumberFormat exceptions thrown when trying to
2924 import PDB like structure files</li>
2925 <li>Positional search results are only highlighted
2926 between user-supplied sequence start/end bounds</li>
2927 <li>End attribute of sequence is not validated</li>
2928 <li>Find dialog only finds first sequence containing a
2929 given sequence position</li>
2930 <li>Sequence numbering not preserved in MSF alignment
2932 <li>Jalview PDB file reader does not extract sequence
2933 from nucleotide chains correctly</li>
2934 <li>Structure colours not updated when tree partition
2935 changed in alignment</li>
2936 <li>Sequence associated secondary structure not correctly
2937 parsed in interleaved stockholm</li>
2938 <li>Colour by annotation dialog does not restore current
2940 <li>Hiding (nearly) all sequences doesn't work
2942 <li>Sequences containing lowercase letters are not
2943 properly associated with their pdb files</li>
2944 </ul> <em>Documentation and Development</em>
2946 <li>schemas/JalviewWsParamSet.xsd corrupted by
2947 ApplyCopyright tool</li>
2952 <div align="center">
2953 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2956 <td><em>Application</em>
2958 <li>New warning dialog when the Jalview Desktop cannot
2959 contact web services</li>
2960 <li>JABA service parameters for a preset are shown in
2961 service job window</li>
2962 <li>JABA Service menu entries reworded</li>
2966 <li>Modeller PIR IO broken - cannot correctly import a
2967 pir file emitted by Jalview</li>
2968 <li>Existing feature settings transferred to new
2969 alignment view created from cut'n'paste</li>
2970 <li>Improved test for mixed amino/nucleotide chains when
2971 parsing PDB files</li>
2972 <li>Consensus and conservation annotation rows
2973 occasionally become blank for all new windows</li>
2974 <li>Exception raised when right clicking above sequences
2975 in wrapped view mode</li>
2976 </ul> <em>Application</em>
2978 <li>multiple multiply aligned structure views cause cpu
2979 usage to hit 100% and computer to hang</li>
2980 <li>Web Service parameter layout breaks for long user
2981 parameter names</li>
2982 <li>Jaba service discovery hangs desktop if Jaba server
2989 <div align="center">
2990 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2993 <td><em>Application</em>
2995 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2996 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2999 <li>Web Services preference tab</li>
3000 <li>Analysis parameters dialog box and user defined
3002 <li>Improved speed and layout of Envision2 service menu</li>
3003 <li>Superpose structures using associated sequence
3005 <li>Export coordinates and projection as CSV from PCA
3007 </ul> <em>Applet</em>
3009 <li>enable javascript: execution by the applet via the
3010 link out mechanism</li>
3011 </ul> <em>Other</em>
3013 <li>Updated the Jmol Jalview interface to work with Jmol
3015 <li>The Jalview Desktop and JalviewLite applet now
3016 require Java 1.5</li>
3017 <li>Allow Jalview feature colour specification for GFF
3018 sequence annotation files</li>
3019 <li>New 'colour by label' keword in Jalview feature file
3020 type colour specification</li>
3021 <li>New Jalview Desktop Groovy API method that allows a
3022 script to check if it being run in an interactive session or
3023 in a batch operation from the Jalview command line</li>
3027 <li>clustalx colourscheme colours Ds preferentially when
3028 both D+E are present in over 50% of the column</li>
3029 </ul> <em>Application</em>
3031 <li>typo in AlignmentFrame->View->Hide->all but
3032 selected Regions menu item</li>
3033 <li>sequence fetcher replaces ',' for ';' when the ',' is
3034 part of a valid accession ID</li>
3035 <li>fatal OOM if object retrieved by sequence fetcher
3036 runs out of memory</li>
3037 <li>unhandled Out of Memory Error when viewing pca
3038 analysis results</li>
3039 <li>InstallAnywhere builds fail to launch on OS X java
3040 10.5 update 4 (due to apple Java 1.6 update)</li>
3041 <li>Installanywhere Jalview silently fails to launch</li>
3042 </ul> <em>Applet</em>
3044 <li>Jalview.getFeatureGroups() raises an
3045 ArrayIndexOutOfBoundsException if no feature groups are
3052 <div align="center">
3053 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3059 <li>Alignment prettyprinter doesn't cope with long
3061 <li>clustalx colourscheme colours Ds preferentially when
3062 both D+E are present in over 50% of the column</li>
3063 <li>nucleic acid structures retrieved from PDB do not
3064 import correctly</li>
3065 <li>More columns get selected than were clicked on when a
3066 number of columns are hidden</li>
3067 <li>annotation label popup menu not providing correct
3068 add/hide/show options when rows are hidden or none are
3070 <li>Stockholm format shown in list of readable formats,
3071 and parser copes better with alignments from RFAM.</li>
3072 <li>CSV output of consensus only includes the percentage
3073 of all symbols if sequence logo display is enabled</li>
3075 </ul> <em>Applet</em>
3077 <li>annotation panel disappears when annotation is
3079 </ul> <em>Application</em>
3081 <li>Alignment view not redrawn properly when new
3082 alignment opened where annotation panel is visible but no
3083 annotations are present on alignment</li>
3084 <li>pasted region containing hidden columns is
3085 incorrectly displayed in new alignment window</li>
3086 <li>Jalview slow to complete operations when stdout is
3087 flooded (fix is to close the Jalview console)</li>
3088 <li>typo in AlignmentFrame->View->Hide->all but
3089 selected Rregions menu item.</li>
3090 <li>inconsistent group submenu and Format submenu entry
3091 'Un' or 'Non'conserved</li>
3092 <li>Sequence feature settings are being shared by
3093 multiple distinct alignments</li>
3094 <li>group annotation not recreated when tree partition is
3096 <li>double click on group annotation to select sequences
3097 does not propagate to associated trees</li>
3098 <li>Mac OSX specific issues:
3100 <li>exception raised when mouse clicked on desktop
3101 window background</li>
3102 <li>Desktop menu placed on menu bar and application
3103 name set correctly</li>
3104 <li>sequence feature settings not wide enough for the
3105 save feature colourscheme button</li>
3114 <div align="center">
3115 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3118 <td><em>New Capabilities</em>
3120 <li>URL links generated from description line for
3121 regular-expression based URL links (applet and application)
3123 <li>Non-positional feature URL links are shown in link
3125 <li>Linked viewing of nucleic acid sequences and
3127 <li>Automatic Scrolling option in View menu to display
3128 the currently highlighted region of an alignment.</li>
3129 <li>Order an alignment by sequence length, or using the
3130 average score or total feature count for each sequence.</li>
3131 <li>Shading features by score or associated description</li>
3132 <li>Subdivide alignment and groups based on identity of
3133 selected subsequence (Make Groups from Selection).</li>
3134 <li>New hide/show options including Shift+Control+H to
3135 hide everything but the currently selected region.</li>
3136 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3137 </ul> <em>Application</em>
3139 <li>Fetch DB References capabilities and UI expanded to
3140 support retrieval from DAS sequence sources</li>
3141 <li>Local DAS Sequence sources can be added via the
3142 command line or via the Add local source dialog box.</li>
3143 <li>DAS Dbref and DbxRef feature types are parsed as
3144 database references and protein_name is parsed as
3145 description line (BioSapiens terms).</li>
3146 <li>Enable or disable non-positional feature and database
3147 references in sequence ID tooltip from View menu in
3149 <!-- <li>New hidden columns and rows and representatives capabilities
3150 in annotations file (in progress - not yet fully implemented)</li> -->
3151 <li>Group-associated consensus, sequence logos and
3152 conservation plots</li>
3153 <li>Symbol distributions for each column can be exported
3154 and visualized as sequence logos</li>
3155 <li>Optionally scale multi-character column labels to fit
3156 within each column of annotation row<!-- todo for applet -->
3158 <li>Optional automatic sort of associated alignment view
3159 when a new tree is opened.</li>
3160 <li>Jalview Java Console</li>
3161 <li>Better placement of desktop window when moving
3162 between different screens.</li>
3163 <li>New preference items for sequence ID tooltip and
3164 consensus annotation</li>
3165 <li>Client to submit sequences and IDs to Envision2
3167 <li><em>Vamsas Capabilities</em>
3169 <li>Improved VAMSAS synchronization (Jalview archive
3170 used to preserve views, structures, and tree display
3172 <li>Import of vamsas documents from disk or URL via
3174 <li>Sharing of selected regions between views and
3175 with other VAMSAS applications (Experimental feature!)</li>
3176 <li>Updated API to VAMSAS version 0.2</li>
3178 </ul> <em>Applet</em>
3180 <li>Middle button resizes annotation row height</li>
3183 <li>sortByTree (true/false) - automatically sort the
3184 associated alignment view by the tree when a new tree is
3186 <li>showTreeBootstraps (true/false) - show or hide
3187 branch bootstraps (default is to show them if available)</li>
3188 <li>showTreeDistances (true/false) - show or hide
3189 branch lengths (default is to show them if available)</li>
3190 <li>showUnlinkedTreeNodes (true/false) - indicate if
3191 unassociated nodes should be highlighted in the tree
3193 <li>heightScale and widthScale (1.0 or more) -
3194 increase the height or width of a cell in the alignment
3195 grid relative to the current font size.</li>
3198 <li>Non-positional features displayed in sequence ID
3200 </ul> <em>Other</em>
3202 <li>Features format: graduated colour definitions and
3203 specification of feature scores</li>
3204 <li>Alignment Annotations format: new keywords for group
3205 associated annotation (GROUP_REF) and annotation row display
3206 properties (ROW_PROPERTIES)</li>
3207 <li>XML formats extended to support graduated feature
3208 colourschemes, group associated annotation, and profile
3209 visualization settings.</li></td>
3212 <li>Source field in GFF files parsed as feature source
3213 rather than description</li>
3214 <li>Non-positional features are now included in sequence
3215 feature and gff files (controlled via non-positional feature
3216 visibility in tooltip).</li>
3217 <li>URL links generated for all feature links (bugfix)</li>
3218 <li>Added URL embedding instructions to features file
3220 <li>Codons containing ambiguous nucleotides translated as
3221 'X' in peptide product</li>
3222 <li>Match case switch in find dialog box works for both
3223 sequence ID and sequence string and query strings do not
3224 have to be in upper case to match case-insensitively.</li>
3225 <li>AMSA files only contain first column of
3226 multi-character column annotation labels</li>
3227 <li>Jalview Annotation File generation/parsing consistent
3228 with documentation (e.g. Stockholm annotation can be
3229 exported and re-imported)</li>
3230 <li>PDB files without embedded PDB IDs given a friendly
3232 <li>Find incrementally searches ID string matches as well
3233 as subsequence matches, and correctly reports total number
3237 <li>Better handling of exceptions during sequence
3239 <li>Dasobert generated non-positional feature URL
3240 link text excludes the start_end suffix</li>
3241 <li>DAS feature and source retrieval buttons disabled
3242 when fetch or registry operations in progress.</li>
3243 <li>PDB files retrieved from URLs are cached properly</li>
3244 <li>Sequence description lines properly shared via
3246 <li>Sequence fetcher fetches multiple records for all
3248 <li>Ensured that command line das feature retrieval
3249 completes before alignment figures are generated.</li>
3250 <li>Reduced time taken when opening file browser for
3252 <li>isAligned check prior to calculating tree, PCA or
3253 submitting an MSA to JNet now excludes hidden sequences.</li>
3254 <li>User defined group colours properly recovered
3255 from Jalview projects.</li>
3264 <div align="center">
3265 <strong>2.4.0.b2</strong><br> 28/10/2009
3270 <li>Experimental support for google analytics usage
3272 <li>Jalview privacy settings (user preferences and docs).</li>
3277 <li>Race condition in applet preventing startup in
3279 <li>Exception when feature created from selection beyond
3280 length of sequence.</li>
3281 <li>Allow synthetic PDB files to be imported gracefully</li>
3282 <li>Sequence associated annotation rows associate with
3283 all sequences with a given id</li>
3284 <li>Find function matches case-insensitively for sequence
3285 ID string searches</li>
3286 <li>Non-standard characters do not cause pairwise
3287 alignment to fail with exception</li>
3288 </ul> <em>Application Issues</em>
3290 <li>Sequences are now validated against EMBL database</li>
3291 <li>Sequence fetcher fetches multiple records for all
3293 </ul> <em>InstallAnywhere Issues</em>
3295 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3296 issue with installAnywhere mechanism)</li>
3297 <li>Command line launching of JARs from InstallAnywhere
3298 version (java class versioning error fixed)</li>
3305 <div align="center">
3306 <strong>2.4</strong><br> 27/8/2008
3309 <td><em>User Interface</em>
3311 <li>Linked highlighting of codon and amino acid from
3312 translation and protein products</li>
3313 <li>Linked highlighting of structure associated with
3314 residue mapping to codon position</li>
3315 <li>Sequence Fetcher provides example accession numbers
3316 and 'clear' button</li>
3317 <li>MemoryMonitor added as an option under Desktop's
3319 <li>Extract score function to parse whitespace separated
3320 numeric data in description line</li>
3321 <li>Column labels in alignment annotation can be centred.</li>
3322 <li>Tooltip for sequence associated annotation give name
3324 </ul> <em>Web Services and URL fetching</em>
3326 <li>JPred3 web service</li>
3327 <li>Prototype sequence search client (no public services
3329 <li>Fetch either seed alignment or full alignment from
3331 <li>URL Links created for matching database cross
3332 references as well as sequence ID</li>
3333 <li>URL Links can be created using regular-expressions</li>
3334 </ul> <em>Sequence Database Connectivity</em>
3336 <li>Retrieval of cross-referenced sequences from other
3338 <li>Generalised database reference retrieval and
3339 validation to all fetchable databases</li>
3340 <li>Fetch sequences from DAS sources supporting the
3341 sequence command</li>
3342 </ul> <em>Import and Export</em>
3343 <li>export annotation rows as CSV for spreadsheet import</li>
3344 <li>Jalview projects record alignment dataset associations,
3345 EMBL products, and cDNA sequence mappings</li>
3346 <li>Sequence Group colour can be specified in Annotation
3348 <li>Ad-hoc colouring of group in Annotation File using RGB
3349 triplet as name of colourscheme</li>
3350 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3352 <li>treenode binding for VAMSAS tree exchange</li>
3353 <li>local editing and update of sequences in VAMSAS
3354 alignments (experimental)</li>
3355 <li>Create new or select existing session to join</li>
3356 <li>load and save of vamsas documents</li>
3357 </ul> <em>Application command line</em>
3359 <li>-tree parameter to open trees (introduced for passing
3361 <li>-fetchfrom command line argument to specify nicknames
3362 of DAS servers to query for alignment features</li>
3363 <li>-dasserver command line argument to add new servers
3364 that are also automatically queried for features</li>
3365 <li>-groovy command line argument executes a given groovy
3366 script after all input data has been loaded and parsed</li>
3367 </ul> <em>Applet-Application data exchange</em>
3369 <li>Trees passed as applet parameters can be passed to
3370 application (when using "View in full
3371 application")</li>
3372 </ul> <em>Applet Parameters</em>
3374 <li>feature group display control parameter</li>
3375 <li>debug parameter</li>
3376 <li>showbutton parameter</li>
3377 </ul> <em>Applet API methods</em>
3379 <li>newView public method</li>
3380 <li>Window (current view) specific get/set public methods</li>
3381 <li>Feature display control methods</li>
3382 <li>get list of currently selected sequences</li>
3383 </ul> <em>New Jalview distribution features</em>
3385 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3386 <li>RELEASE file gives build properties for the latest
3387 Jalview release.</li>
3388 <li>Java 1.1 Applet build made easier and donotobfuscate
3389 property controls execution of obfuscator</li>
3390 <li>Build target for generating source distribution</li>
3391 <li>Debug flag for javacc</li>
3392 <li>.jalview_properties file is documented (slightly) in
3393 jalview.bin.Cache</li>
3394 <li>Continuous Build Integration for stable and
3395 development version of Application, Applet and source
3400 <li>selected region output includes visible annotations
3401 (for certain formats)</li>
3402 <li>edit label/displaychar contains existing label/char
3404 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3405 <li>shorter peptide product names from EMBL records</li>
3406 <li>Newick string generator makes compact representations</li>
3407 <li>bootstrap values parsed correctly for tree files with
3409 <li>pathological filechooser bug avoided by not allowing
3410 filenames containing a ':'</li>
3411 <li>Fixed exception when parsing GFF files containing
3412 global sequence features</li>
3413 <li>Alignment datasets are finalized only when number of
3414 references from alignment sequences goes to zero</li>
3415 <li>Close of tree branch colour box without colour
3416 selection causes cascading exceptions</li>
3417 <li>occasional negative imgwidth exceptions</li>
3418 <li>better reporting of non-fatal warnings to user when
3419 file parsing fails.</li>
3420 <li>Save works when Jalview project is default format</li>
3421 <li>Save as dialog opened if current alignment format is
3422 not a valid output format</li>
3423 <li>UniProt canonical names introduced for both das and
3425 <li>Histidine should be midblue (not pink!) in Zappo</li>
3426 <li>error messages passed up and output when data read
3428 <li>edit undo recovers previous dataset sequence when
3429 sequence is edited</li>
3430 <li>allow PDB files without pdb ID HEADER lines (like
3431 those generated by MODELLER) to be read in properly</li>
3432 <li>allow reading of JPred concise files as a normal
3434 <li>Stockholm annotation parsing and alignment properties
3435 import fixed for PFAM records</li>
3436 <li>Structure view windows have correct name in Desktop
3438 <li>annotation consisting of sequence associated scores
3439 can be read and written correctly to annotation file</li>
3440 <li>Aligned cDNA translation to aligned peptide works
3442 <li>Fixed display of hidden sequence markers and
3443 non-italic font for representatives in Applet</li>
3444 <li>Applet Menus are always embedded in applet window on
3446 <li>Newly shown features appear at top of stack (in
3448 <li>Annotations added via parameter not drawn properly
3449 due to null pointer exceptions</li>
3450 <li>Secondary structure lines are drawn starting from
3451 first column of alignment</li>
3452 <li>UniProt XML import updated for new schema release in
3454 <li>Sequence feature to sequence ID match for Features
3455 file is case-insensitive</li>
3456 <li>Sequence features read from Features file appended to
3457 all sequences with matching IDs</li>
3458 <li>PDB structure coloured correctly for associated views
3459 containing a sub-sequence</li>
3460 <li>PDB files can be retrieved by applet from Jar files</li>
3461 <li>feature and annotation file applet parameters
3462 referring to different directories are retrieved correctly</li>
3463 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3464 <li>Fixed application hang whilst waiting for
3465 splash-screen version check to complete</li>
3466 <li>Applet properly URLencodes input parameter values
3467 when passing them to the launchApp service</li>
3468 <li>display name and local features preserved in results
3469 retrieved from web service</li>
3470 <li>Visual delay indication for sequence retrieval and
3471 sequence fetcher initialisation</li>
3472 <li>updated Application to use DAS 1.53e version of
3473 dasobert DAS client</li>
3474 <li>Re-instated Full AMSA support and .amsa file
3476 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3484 <div align="center">
3485 <strong>2.3</strong><br> 9/5/07
3490 <li>Jmol 11.0.2 integration</li>
3491 <li>PDB views stored in Jalview XML files</li>
3492 <li>Slide sequences</li>
3493 <li>Edit sequence in place</li>
3494 <li>EMBL CDS features</li>
3495 <li>DAS Feature mapping</li>
3496 <li>Feature ordering</li>
3497 <li>Alignment Properties</li>
3498 <li>Annotation Scores</li>
3499 <li>Sort by scores</li>
3500 <li>Feature/annotation editing in applet</li>
3505 <li>Headless state operation in 2.2.1</li>
3506 <li>Incorrect and unstable DNA pairwise alignment</li>
3507 <li>Cut and paste of sequences with annotation</li>
3508 <li>Feature group display state in XML</li>
3509 <li>Feature ordering in XML</li>
3510 <li>blc file iteration selection using filename # suffix</li>
3511 <li>Stockholm alignment properties</li>
3512 <li>Stockhom alignment secondary structure annotation</li>
3513 <li>2.2.1 applet had no feature transparency</li>
3514 <li>Number pad keys can be used in cursor mode</li>
3515 <li>Structure Viewer mirror image resolved</li>
3522 <div align="center">
3523 <strong>2.2.1</strong><br> 12/2/07
3528 <li>Non standard characters can be read and displayed
3529 <li>Annotations/Features can be imported/exported to the
3531 <li>Applet allows editing of sequence/annotation/group
3532 name & description
3533 <li>Preference setting to display sequence name in
3535 <li>Annotation file format extended to allow
3536 Sequence_groups to be defined
3537 <li>Default opening of alignment overview panel can be
3538 specified in preferences
3539 <li>PDB residue numbering annotation added to associated
3545 <li>Applet crash under certain Linux OS with Java 1.6
3547 <li>Annotation file export / import bugs fixed
3548 <li>PNG / EPS image output bugs fixed
3554 <div align="center">
3555 <strong>2.2</strong><br> 27/11/06
3560 <li>Multiple views on alignment
3561 <li>Sequence feature editing
3562 <li>"Reload" alignment
3563 <li>"Save" to current filename
3564 <li>Background dependent text colour
3565 <li>Right align sequence ids
3566 <li>User-defined lower case residue colours
3569 <li>Menu item accelerator keys
3570 <li>Control-V pastes to current alignment
3571 <li>Cancel button for DAS Feature Fetching
3572 <li>PCA and PDB Viewers zoom via mouse roller
3573 <li>User-defined sub-tree colours and sub-tree selection
3575 <li>'New Window' button on the 'Output to Text box'
3580 <li>New memory efficient Undo/Redo System
3581 <li>Optimised symbol lookups and conservation/consensus
3583 <li>Region Conservation/Consensus recalculated after
3585 <li>Fixed Remove Empty Columns Bug (empty columns at end
3587 <li>Slowed DAS Feature Fetching for increased robustness.
3589 <li>Made angle brackets in ASCII feature descriptions
3591 <li>Re-instated Zoom function for PCA
3592 <li>Sequence descriptions conserved in web service
3594 <li>UniProt ID discoverer uses any word separated by
3596 <li>WsDbFetch query/result association resolved
3597 <li>Tree leaf to sequence mapping improved
3598 <li>Smooth fonts switch moved to FontChooser dialog box.
3605 <div align="center">
3606 <strong>2.1.1</strong><br> 12/9/06
3611 <li>Copy consensus sequence to clipboard</li>
3616 <li>Image output - rightmost residues are rendered if
3617 sequence id panel has been resized</li>
3618 <li>Image output - all offscreen group boundaries are
3620 <li>Annotation files with sequence references - all
3621 elements in file are relative to sequence position</li>
3622 <li>Mac Applet users can use Alt key for group editing</li>
3628 <div align="center">
3629 <strong>2.1</strong><br> 22/8/06
3634 <li>MAFFT Multiple Alignment in default Web Service list</li>
3635 <li>DAS Feature fetching</li>
3636 <li>Hide sequences and columns</li>
3637 <li>Export Annotations and Features</li>
3638 <li>GFF file reading / writing</li>
3639 <li>Associate structures with sequences from local PDB
3641 <li>Add sequences to exisiting alignment</li>
3642 <li>Recently opened files / URL lists</li>
3643 <li>Applet can launch the full application</li>
3644 <li>Applet has transparency for features (Java 1.2
3646 <li>Applet has user defined colours parameter</li>
3647 <li>Applet can load sequences from parameter
3648 "sequence<em>x</em>"
3654 <li>Redundancy Panel reinstalled in the Applet</li>
3655 <li>Monospaced font - EPS / rescaling bug fixed</li>
3656 <li>Annotation files with sequence references bug fixed</li>
3662 <div align="center">
3663 <strong>2.08.1</strong><br> 2/5/06
3668 <li>Change case of selected region from Popup menu</li>
3669 <li>Choose to match case when searching</li>
3670 <li>Middle mouse button and mouse movement can compress /
3671 expand the visible width and height of the alignment</li>
3676 <li>Annotation Panel displays complete JNet results</li>
3682 <div align="center">
3683 <strong>2.08b</strong><br> 18/4/06
3689 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3690 <li>Righthand label on wrapped alignments shows correct
3697 <div align="center">
3698 <strong>2.08</strong><br> 10/4/06
3703 <li>Editing can be locked to the selection area</li>
3704 <li>Keyboard editing</li>
3705 <li>Create sequence features from searches</li>
3706 <li>Precalculated annotations can be loaded onto
3708 <li>Features file allows grouping of features</li>
3709 <li>Annotation Colouring scheme added</li>
3710 <li>Smooth fonts off by default - Faster rendering</li>
3711 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3716 <li>Drag & Drop fixed on Linux</li>
3717 <li>Jalview Archive file faster to load/save, sequence
3718 descriptions saved.</li>
3724 <div align="center">
3725 <strong>2.07</strong><br> 12/12/05
3730 <li>PDB Structure Viewer enhanced</li>
3731 <li>Sequence Feature retrieval and display enhanced</li>
3732 <li>Choose to output sequence start-end after sequence
3733 name for file output</li>
3734 <li>Sequence Fetcher WSDBFetch@EBI</li>
3735 <li>Applet can read feature files, PDB files and can be
3736 used for HTML form input</li>
3741 <li>HTML output writes groups and features</li>
3742 <li>Group editing is Control and mouse click</li>
3743 <li>File IO bugs</li>
3749 <div align="center">
3750 <strong>2.06</strong><br> 28/9/05
3755 <li>View annotations in wrapped mode</li>
3756 <li>More options for PCA viewer</li>
3761 <li>GUI bugs resolved</li>
3762 <li>Runs with -nodisplay from command line</li>
3768 <div align="center">
3769 <strong>2.05b</strong><br> 15/9/05
3774 <li>Choose EPS export as lineart or text</li>
3775 <li>Jar files are executable</li>
3776 <li>Can read in Uracil - maps to unknown residue</li>
3781 <li>Known OutOfMemory errors give warning message</li>
3782 <li>Overview window calculated more efficiently</li>
3783 <li>Several GUI bugs resolved</li>
3789 <div align="center">
3790 <strong>2.05</strong><br> 30/8/05
3795 <li>Edit and annotate in "Wrapped" view</li>
3800 <li>Several GUI bugs resolved</li>
3806 <div align="center">
3807 <strong>2.04</strong><br> 24/8/05
3812 <li>Hold down mouse wheel & scroll to change font
3818 <li>Improved JPred client reliability</li>
3819 <li>Improved loading of Jalview files</li>
3825 <div align="center">
3826 <strong>2.03</strong><br> 18/8/05
3831 <li>Set Proxy server name and port in preferences</li>
3832 <li>Multiple URL links from sequence ids</li>
3833 <li>User Defined Colours can have a scheme name and added
3835 <li>Choose to ignore gaps in consensus calculation</li>
3836 <li>Unix users can set default web browser</li>
3837 <li>Runs without GUI for batch processing</li>
3838 <li>Dynamically generated Web Service Menus</li>
3843 <li>InstallAnywhere download for Sparc Solaris</li>
3849 <div align="center">
3850 <strong>2.02</strong><br> 18/7/05
3856 <li>Copy & Paste order of sequences maintains
3857 alignment order.</li>
3863 <div align="center">
3864 <strong>2.01</strong><br> 12/7/05
3869 <li>Use delete key for deleting selection.</li>
3870 <li>Use Mouse wheel to scroll sequences.</li>
3871 <li>Help file updated to describe how to add alignment
3873 <li>Version and build date written to build properties
3875 <li>InstallAnywhere installation will check for updates
3876 at launch of Jalview.</li>
3881 <li>Delete gaps bug fixed.</li>
3882 <li>FileChooser sorts columns.</li>
3883 <li>Can remove groups one by one.</li>
3884 <li>Filechooser icons installed.</li>
3885 <li>Finder ignores return character when searching.
3886 Return key will initiate a search.<br>
3893 <div align="center">
3894 <strong>2.0</strong><br> 20/6/05
3899 <li>New codebase</li>