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-2778 -->Slow redraw when Overview panel shown
108 overlapping alignment panel
111 <!-- JAL-2666 -->Linked scrolling via protein horizontal
112 scroll bar doesn't work for some CDS/Protein views
115 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
116 Java 1.8u153 onwards and Java 1.9u4+.
119 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
120 columns in annotation row
123 <!-- JAL-2913 -->Preferences panel's ID Width control is
124 honored in interactive and batch mode
127 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
128 for structures added to existing Jmol view
131 <!-- JAL-2223 -->'View Mappings' includes duplicate
132 entries after importing project with multiple views
135 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
136 protein sequences via SIFTS from associated PDB entries
137 with negative residue numbers or missing residues fails
140 <!-- JAL-2952 -->Exception when shading sequence with negative
141 Temperature Factor values from annotated PDB files (e.g.
142 as generated by CONSURF)
145 <!-- JAL-2954 -->Selecting columns from highlighted regions
146 very slow for alignments with large numbers of sequences
148 <li><!-- JAL-2925 -->Copy Consensus fails for group consensus with 'StringIndexOutOfBounds'</li>
149 <li><em>New Defects</em>
152 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
153 structures for protein subsequence (if 'Trim Retrieved
154 Sequences' enabled) or Ensembl isoforms (Workaround in
155 2.10.4 is to fail back to N&W mapping)
162 <!-- JAL-2926 -->Copy consensus sequence option in applet
163 should copy the group consensus when popup is opened on it
167 <em>New Known Defects</em>
170 <!-- JAL-2973 --> Exceptions occasionally raised when
171 editing a large alignment and overview is displayed
174 <!-- JAL-2974 -->'Overview updating' progress bar is shown
175 repeatedly after a series of edits even when the overview
176 is no longer reflecting updates
183 <td width="60" nowrap>
185 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
188 <td><div align="left">
189 <ul><li>Updated Certum Codesigning Certificate
190 (Valid till 30th November 2018)</li></ul></div></td>
191 <td><div align="left">
194 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
195 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
196 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
197 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
198 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
199 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
200 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
206 <td width="60" nowrap>
208 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
211 <td><div align="left">
215 <!-- JAL-2446 -->Faster and more efficient management and
216 rendering of sequence features
219 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
220 429 rate limit request hander
223 <!-- JAL-2773 -->Structure views don't get updated unless
224 their colours have changed
227 <!-- JAL-2495 -->All linked sequences are highlighted for
228 a structure mousover (Jmol) or selection (Chimera)
231 <!-- JAL-2790 -->'Cancel' button in progress bar for
232 JABAWS AACon, RNAAliFold and Disorder prediction jobs
235 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
236 view from Ensembl locus cross-references
239 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
243 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
244 feature can be disabled
247 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
248 PDB easier retrieval of sequences for lists of IDs
251 <!-- JAL-2758 -->Short names for sequences retrieved from
257 <li>Groovy interpreter updated to 2.4.12</li>
258 <li>Example groovy script for generating a matrix of
259 percent identity scores for current alignment.</li>
261 <em>Testing and Deployment</em>
264 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
268 <td><div align="left">
272 <!-- JAL-2643 -->Pressing tab after updating the colour
273 threshold text field doesn't trigger an update to the
277 <!-- JAL-2682 -->Race condition when parsing sequence ID
281 <!-- JAL-2608 -->Overview windows are also closed when
282 alignment window is closed
285 <!-- JAL-2548 -->Export of features doesn't always respect
289 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
290 takes a long time in Cursor mode
296 <!-- JAL-2777 -->Structures with whitespace chainCode
297 cannot be viewed in Chimera
300 <!-- JAL-2728 -->Protein annotation panel too high in
304 <!-- JAL-2757 -->Can't edit the query after the server
305 error warning icon is shown in Uniprot and PDB Free Text
309 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
312 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
315 <!-- JAL-2739 -->Hidden column marker in last column not
316 rendered when switching back from Wrapped to normal view
319 <!-- JAL-2768 -->Annotation display corrupted when
320 scrolling right in unwapped alignment view
323 <!-- JAL-2542 -->Existing features on subsequence
324 incorrectly relocated when full sequence retrieved from
328 <!-- JAL-2733 -->Last reported memory still shown when
329 Desktop->Show Memory is unticked (OSX only)
332 <!-- JAL-2658 -->Amend Features dialog doesn't allow
333 features of same type and group to be selected for
337 <!-- JAL-2524 -->Jalview becomes sluggish in wide
338 alignments when hidden columns are present
341 <!-- JAL-2392 -->Jalview freezes when loading and
342 displaying several structures
345 <!-- JAL-2732 -->Black outlines left after resizing or
349 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
350 within the Jalview desktop on OSX
353 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
354 when in wrapped alignment mode
357 <!-- JAL-2636 -->Scale mark not shown when close to right
358 hand end of alignment
361 <!-- JAL-2684 -->Pairwise alignment of selected regions of
362 each selected sequence do not have correct start/end
366 <!-- JAL-2793 -->Alignment ruler height set incorrectly
367 after canceling the Alignment Window's Font dialog
370 <!-- JAL-2036 -->Show cross-references not enabled after
371 restoring project until a new view is created
374 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
375 URL links appears when only default EMBL-EBI link is
376 configured (since 2.10.2b2)
379 <!-- JAL-2775 -->Overview redraws whole window when box
383 <!-- JAL-2225 -->Structure viewer doesn't map all chains
384 in a multi-chain structure when viewing alignment
385 involving more than one chain (since 2.10)
388 <!-- JAL-2811 -->Double residue highlights in cursor mode
389 if new selection moves alignment window
392 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
393 arrow key in cursor mode to pass hidden column marker
396 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
397 that produces correctly annotated transcripts and products
400 <!-- JAL-2776 -->Toggling a feature group after first time
401 doesn't update associated structure view
404 <em>Applet</em><br />
407 <!-- JAL-2687 -->Concurrent modification exception when
408 closing alignment panel
411 <em>BioJSON</em><br />
414 <!-- JAL-2546 -->BioJSON export does not preserve
415 non-positional features
418 <em>New Known Issues</em>
421 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
422 sequence features correctly (for many previous versions of
426 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
427 using cursor in wrapped panel other than top
430 <!-- JAL-2791 -->Select columns containing feature ignores
431 graduated colour threshold
434 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
435 always preserve numbering and sequence features
438 <em>Known Java 9 Issues</em>
441 <!-- JAL-2902 -->Groovy Console very slow to open and is
442 not responsive when entering characters (Webstart, Java
449 <td width="60" nowrap>
451 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
452 <em>2/10/2017</em></strong>
455 <td><div align="left">
456 <em>New features in Jalview Desktop</em>
459 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
461 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
465 <td><div align="left">
469 <td width="60" nowrap>
471 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
472 <em>7/9/2017</em></strong>
475 <td><div align="left">
479 <!-- JAL-2588 -->Show gaps in overview window by colouring
480 in grey (sequences used to be coloured grey, and gaps were
484 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
488 <!-- JAL-2587 -->Overview updates immediately on increase
489 in size and progress bar shown as higher resolution
490 overview is recalculated
495 <td><div align="left">
499 <!-- JAL-2664 -->Overview window redraws every hidden
500 column region row by row
503 <!-- JAL-2681 -->duplicate protein sequences shown after
504 retrieving Ensembl crossrefs for sequences from Uniprot
507 <!-- JAL-2603 -->Overview window throws NPE if show boxes
508 format setting is unticked
511 <!-- JAL-2610 -->Groups are coloured wrongly in overview
512 if group has show boxes format setting unticked
515 <!-- JAL-2672,JAL-2665 -->Redraw problems when
516 autoscrolling whilst dragging current selection group to
517 include sequences and columns not currently displayed
520 <!-- JAL-2691 -->Not all chains are mapped when multimeric
521 assemblies are imported via CIF file
524 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
525 displayed when threshold or conservation colouring is also
529 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
533 <!-- JAL-2673 -->Jalview continues to scroll after
534 dragging a selected region off the visible region of the
538 <!-- JAL-2724 -->Cannot apply annotation based
539 colourscheme to all groups in a view
542 <!-- JAL-2511 -->IDs don't line up with sequences
543 initially after font size change using the Font chooser or
550 <td width="60" nowrap>
552 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
555 <td><div align="left">
556 <em>Calculations</em>
560 <!-- JAL-1933 -->Occupancy annotation row shows number of
561 ungapped positions in each column of the alignment.
564 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
565 a calculation dialog box
568 <!-- JAL-2379 -->Revised implementation of PCA for speed
569 and memory efficiency (~30x faster)
572 <!-- JAL-2403 -->Revised implementation of sequence
573 similarity scores as used by Tree, PCA, Shading Consensus
574 and other calculations
577 <!-- JAL-2416 -->Score matrices are stored as resource
578 files within the Jalview codebase
581 <!-- JAL-2500 -->Trees computed on Sequence Feature
582 Similarity may have different topology due to increased
589 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
590 model for alignments and groups
593 <!-- JAL-384 -->Custom shading schemes created via groovy
600 <!-- JAL-2526 -->Efficiency improvements for interacting
601 with alignment and overview windows
604 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
608 <!-- JAL-2388 -->Hidden columns and sequences can be
612 <!-- JAL-2611 -->Click-drag in visible area allows fine
613 adjustment of visible position
617 <em>Data import/export</em>
620 <!-- JAL-2535 -->Posterior probability annotation from
621 Stockholm files imported as sequence associated annotation
624 <!-- JAL-2507 -->More robust per-sequence positional
625 annotation input/output via stockholm flatfile
628 <!-- JAL-2533 -->Sequence names don't include file
629 extension when importing structure files without embedded
630 names or PDB accessions
633 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
634 format sequence substitution matrices
637 <em>User Interface</em>
640 <!-- JAL-2447 --> Experimental Features Checkbox in
641 Desktop's Tools menu to hide or show untested features in
645 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
646 via Overview or sequence motif search operations
649 <!-- JAL-2547 -->Amend sequence features dialog box can be
650 opened by double clicking gaps within sequence feature
654 <!-- JAL-1476 -->Status bar message shown when not enough
655 aligned positions were available to create a 3D structure
659 <em>3D Structure</em>
662 <!-- JAL-2430 -->Hidden regions in alignment views are not
663 coloured in linked structure views
666 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
667 file-based command exchange
670 <!-- JAL-2375 -->Structure chooser automatically shows
671 Cached Structures rather than querying the PDBe if
672 structures are already available for sequences
675 <!-- JAL-2520 -->Structures imported via URL are cached in
676 the Jalview project rather than downloaded again when the
680 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
681 to transfer Chimera's structure attributes as Jalview
682 features, and vice-versa (<strong>Experimental
686 <em>Web Services</em>
689 <!-- JAL-2549 -->Updated JABAWS client to v2.2
692 <!-- JAL-2335 -->Filter non-standard amino acids and
693 nucleotides when submitting to AACon and other MSA
697 <!-- JAL-2316, -->URLs for viewing database
698 cross-references provided by identifiers.org and the
706 <!-- JAL-2344 -->FileFormatI interface for describing and
707 identifying file formats (instead of String constants)
710 <!-- JAL-2228 -->FeatureCounter script refactored for
711 efficiency when counting all displayed features (not
712 backwards compatible with 2.10.1)
715 <em>Example files</em>
718 <!-- JAL-2631 -->Graduated feature colour style example
719 included in the example feature file
722 <em>Documentation</em>
725 <!-- JAL-2339 -->Release notes reformatted for readability
726 with the built-in Java help viewer
729 <!-- JAL-1644 -->Find documentation updated with 'search
730 sequence description' option
736 <!-- JAL-2485, -->External service integration tests for
737 Uniprot REST Free Text Search Client
740 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
743 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
748 <td><div align="left">
749 <em>Calculations</em>
752 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
753 matrix - C->R should be '-3'<br />Old matrix restored
754 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
756 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
757 Jalview's treatment of gaps in PCA and substitution matrix
758 based Tree calculations.<br /> <br />In earlier versions
759 of Jalview, gaps matching gaps were penalised, and gaps
760 matching non-gaps penalised even more. In the PCA
761 calculation, gaps were actually treated as non-gaps - so
762 different costs were applied, which meant Jalview's PCAs
763 were different to those produced by SeqSpace.<br />Jalview
764 now treats gaps in the same way as SeqSpace (ie it scores
765 them as 0). <br /> <br />Enter the following in the
766 Groovy console to restore pre-2.10.2 behaviour:<br />
767 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
768 // for 2.10.1 mode <br />
769 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
770 // to restore 2.10.2 mode <br /> <br /> <em>Note:
771 these settings will affect all subsequent tree and PCA
772 calculations (not recommended)</em></li>
774 <!-- JAL-2424 -->Fixed off-by-one bug that affected
775 scaling of branch lengths for trees computed using
776 Sequence Feature Similarity.
779 <!-- JAL-2377 -->PCA calculation could hang when
780 generating output report when working with highly
784 <!-- JAL-2544 --> Sort by features includes features to
785 right of selected region when gaps present on right-hand
789 <em>User Interface</em>
792 <!-- JAL-2346 -->Reopening Colour by annotation dialog
793 doesn't reselect a specific sequence's associated
794 annotation after it was used for colouring a view
797 <!-- JAL-2419 -->Current selection lost if popup menu
798 opened on a region of alignment without groups
801 <!-- JAL-2374 -->Popup menu not always shown for regions
802 of an alignment with overlapping groups
805 <!-- JAL-2310 -->Finder double counts if both a sequence's
806 name and description match
809 <!-- JAL-2370 -->Hiding column selection containing two
810 hidden regions results in incorrect hidden regions
813 <!-- JAL-2386 -->'Apply to all groups' setting when
814 changing colour does not apply Conservation slider value
818 <!-- JAL-2373 -->Percentage identity and conservation menu
819 items do not show a tick or allow shading to be disabled
822 <!-- JAL-2385 -->Conservation shading or PID threshold
823 lost when base colourscheme changed if slider not visible
826 <!-- JAL-2547 -->Sequence features shown in tooltip for
827 gaps before start of features
830 <!-- JAL-2623 -->Graduated feature colour threshold not
831 restored to UI when feature colour is edited
834 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
835 a time when scrolling vertically in wrapped mode.
838 <!-- JAL-2630 -->Structure and alignment overview update
839 as graduate feature colour settings are modified via the
843 <!-- JAL-2034 -->Overview window doesn't always update
844 when a group defined on the alignment is resized
847 <!-- JAL-2605 -->Mouseovers on left/right scale region in
848 wrapped view result in positional status updates
852 <!-- JAL-2563 -->Status bar doesn't show position for
853 ambiguous amino acid and nucleotide symbols
856 <!-- JAL-2602 -->Copy consensus sequence failed if
857 alignment included gapped columns
860 <!-- JAL-2473 -->Minimum size set for Jalview windows so
861 widgets don't permanently disappear
864 <!-- JAL-2503 -->Cannot select or filter quantitative
865 annotation that are shown only as column labels (e.g.
866 T-Coffee column reliability scores)
869 <!-- JAL-2594 -->Exception thrown if trying to create a
870 sequence feature on gaps only
873 <!-- JAL-2504 -->Features created with 'New feature'
874 button from a Find inherit previously defined feature type
875 rather than the Find query string
878 <!-- JAL-2423 -->incorrect title in output window when
879 exporting tree calculated in Jalview
882 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
883 and then revealing them reorders sequences on the
887 <!-- JAL-964 -->Group panel in sequence feature settings
888 doesn't update to reflect available set of groups after
889 interactively adding or modifying features
892 <!-- JAL-2225 -->Sequence Database chooser unusable on
896 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
897 only excluded gaps in current sequence and ignored
904 <!-- JAL-2421 -->Overview window visible region moves
905 erratically when hidden rows or columns are present
908 <!-- JAL-2362 -->Per-residue colourschemes applied via the
909 Structure Viewer's colour menu don't correspond to
913 <!-- JAL-2405 -->Protein specific colours only offered in
914 colour and group colour menu for protein alignments
917 <!-- JAL-2385 -->Colour threshold slider doesn't update to
918 reflect currently selected view or group's shading
922 <!-- JAL-2624 -->Feature colour thresholds not respected
923 when rendered on overview and structures when opacity at
927 <!-- JAL-2589 -->User defined gap colour not shown in
928 overview when features overlaid on alignment
931 <em>Data import/export</em>
934 <!-- JAL-2576 -->Very large alignments take a long time to
938 <!-- JAL-2507 -->Per-sequence RNA secondary structures
939 added after a sequence was imported are not written to
943 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
944 when importing RNA secondary structure via Stockholm
947 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
948 not shown in correct direction for simple pseudoknots
951 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
952 with lightGray or darkGray via features file (but can
956 <!-- JAL-2383 -->Above PID colour threshold not recovered
957 when alignment view imported from project
960 <!-- JAL-2520,JAL-2465 -->No mappings generated between
961 structure and sequences extracted from structure files
962 imported via URL and viewed in Jmol
965 <!-- JAL-2520 -->Structures loaded via URL are saved in
966 Jalview Projects rather than fetched via URL again when
967 the project is loaded and the structure viewed
970 <em>Web Services</em>
973 <!-- JAL-2519 -->EnsemblGenomes example failing after
974 release of Ensembl v.88
977 <!-- JAL-2366 -->Proxy server address and port always
978 appear enabled in Preferences->Connections
981 <!-- JAL-2461 -->DAS registry not found exceptions
982 removed from console output
985 <!-- JAL-2582 -->Cannot retrieve protein products from
986 Ensembl by Peptide ID
989 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
990 created from SIFTs, and spurious 'Couldn't open structure
991 in Chimera' errors raised after April 2017 update (problem
992 due to 'null' string rather than empty string used for
993 residues with no corresponding PDB mapping).
996 <em>Application UI</em>
999 <!-- JAL-2361 -->User Defined Colours not added to Colour
1003 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
1004 case' residues (button in colourscheme editor debugged and
1005 new documentation and tooltips added)
1008 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
1009 doesn't restore group-specific text colour thresholds
1012 <!-- JAL-2243 -->Feature settings panel does not update as
1013 new features are added to alignment
1016 <!-- JAL-2532 -->Cancel in feature settings reverts
1017 changes to feature colours via the Amend features dialog
1020 <!-- JAL-2506 -->Null pointer exception when attempting to
1021 edit graduated feature colour via amend features dialog
1025 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
1026 selection menu changes colours of alignment views
1029 <!-- JAL-2426 -->Spurious exceptions in console raised
1030 from alignment calculation workers after alignment has
1034 <!-- JAL-1608 -->Typo in selection popup menu - Create
1035 groups now 'Create Group'
1038 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
1039 Create/Undefine group doesn't always work
1042 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
1043 shown again after pressing 'Cancel'
1046 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
1047 adjusts start position in wrap mode
1050 <!-- JAL-2563 -->Status bar doesn't show positions for
1051 ambiguous amino acids
1054 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
1055 CDS/Protein view after CDS sequences added for aligned
1059 <!-- JAL-2592 -->User defined colourschemes called 'User
1060 Defined' don't appear in Colours menu
1066 <!-- JAL-2468 -->Switching between Nucleotide and Protein
1067 score models doesn't always result in an updated PCA plot
1070 <!-- JAL-2442 -->Features not rendered as transparent on
1071 overview or linked structure view
1074 <!-- JAL-2372 -->Colour group by conservation doesn't
1078 <!-- JAL-2517 -->Hitting Cancel after applying
1079 user-defined colourscheme doesn't restore original
1086 <!-- JAL-2314 -->Unit test failure:
1087 jalview.ws.jabaws.RNAStructExportImport setup fails
1090 <!-- JAL-2307 -->Unit test failure:
1091 jalview.ws.sifts.SiftsClientTest due to compatibility
1092 problems with deep array comparison equality asserts in
1093 successive versions of TestNG
1096 <!-- JAL-2479 -->Relocated StructureChooserTest and
1097 ParameterUtilsTest Unit tests to Network suite
1100 <em>New Known Issues</em>
1103 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1104 phase after a sequence motif find operation
1107 <!-- JAL-2550 -->Importing annotation file with rows
1108 containing just upper and lower case letters are
1109 interpreted as WUSS RNA secondary structure symbols
1112 <!-- JAL-2590 -->Cannot load and display Newick trees
1113 reliably from eggnog Ortholog database
1116 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1117 containing features of type Highlight' when 'B' is pressed
1118 to mark columns containing highlighted regions.
1121 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1122 doesn't always add secondary structure annotation.
1127 <td width="60" nowrap>
1128 <div align="center">
1129 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1132 <td><div align="left">
1136 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1137 for all consensus calculations
1140 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1143 <li>Updated Jalview's Certum code signing certificate
1146 <em>Application</em>
1149 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1150 set of database cross-references, sorted alphabetically
1153 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1154 from database cross references. Users with custom links
1155 will receive a <a href="webServices/urllinks.html#warning">warning
1156 dialog</a> asking them to update their preferences.
1159 <!-- JAL-2287-->Cancel button and escape listener on
1160 dialog warning user about disconnecting Jalview from a
1164 <!-- JAL-2320-->Jalview's Chimera control window closes if
1165 the Chimera it is connected to is shut down
1168 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1169 columns menu item to mark columns containing highlighted
1170 regions (e.g. from structure selections or results of a
1174 <!-- JAL-2284-->Command line option for batch-generation
1175 of HTML pages rendering alignment data with the BioJS
1185 <!-- JAL-2286 -->Columns with more than one modal residue
1186 are not coloured or thresholded according to percent
1187 identity (first observed in Jalview 2.8.2)
1190 <!-- JAL-2301 -->Threonine incorrectly reported as not
1194 <!-- JAL-2318 -->Updates to documentation pages (above PID
1195 threshold, amino acid properties)
1198 <!-- JAL-2292 -->Lower case residues in sequences are not
1199 reported as mapped to residues in a structure file in the
1203 <!--JAL-2324 -->Identical features with non-numeric scores
1204 could be added multiple times to a sequence
1207 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1208 bond features shown as two highlighted residues rather
1209 than a range in linked structure views, and treated
1210 correctly when selecting and computing trees from features
1213 <!-- JAL-2281-->Custom URL links for database
1214 cross-references are matched to database name regardless
1219 <em>Application</em>
1222 <!-- JAL-2282-->Custom URL links for specific database
1223 names without regular expressions also offer links from
1227 <!-- JAL-2315-->Removing a single configured link in the
1228 URL links pane in Connections preferences doesn't actually
1229 update Jalview configuration
1232 <!-- JAL-2272-->CTRL-Click on a selected region to open
1233 the alignment area popup menu doesn't work on El-Capitan
1236 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1237 files with similarly named sequences if dropped onto the
1241 <!-- JAL-2312 -->Additional mappings are shown for PDB
1242 entries where more chains exist in the PDB accession than
1243 are reported in the SIFTS file
1246 <!-- JAL-2317-->Certain structures do not get mapped to
1247 the structure view when displayed with Chimera
1250 <!-- JAL-2317-->No chains shown in the Chimera view
1251 panel's View->Show Chains submenu
1254 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1255 work for wrapped alignment views
1258 <!--JAL-2197 -->Rename UI components for running JPred
1259 predictions from 'JNet' to 'JPred'
1262 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1263 corrupted when annotation panel vertical scroll is not at
1264 first annotation row
1267 <!--JAL-2332 -->Attempting to view structure for Hen
1268 lysozyme results in a PDB Client error dialog box
1271 <!-- JAL-2319 -->Structure View's mapping report switched
1272 ranges for PDB and sequence for SIFTS
1275 SIFTS 'Not_Observed' residues mapped to non-existant
1279 <!-- <em>New Known Issues</em>
1286 <td width="60" nowrap>
1287 <div align="center">
1288 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1289 <em>25/10/2016</em></strong>
1292 <td><em>Application</em>
1294 <li>3D Structure chooser opens with 'Cached structures'
1295 view if structures already loaded</li>
1296 <li>Progress bar reports models as they are loaded to
1297 structure views</li>
1303 <li>Colour by conservation always enabled and no tick
1304 shown in menu when BLOSUM or PID shading applied</li>
1305 <li>FER1_ARATH and FER2_ARATH labels were switched in
1306 example sequences/projects/trees</li>
1308 <em>Application</em>
1310 <li>Jalview projects with views of local PDB structure
1311 files saved on Windows cannot be opened on OSX</li>
1312 <li>Multiple structure views can be opened and superposed
1313 without timeout for structures with multiple models or
1314 multiple sequences in alignment</li>
1315 <li>Cannot import or associated local PDB files without a
1316 PDB ID HEADER line</li>
1317 <li>RMSD is not output in Jmol console when superposition
1319 <li>Drag and drop of URL from Browser fails for Linux and
1320 OSX versions earlier than El Capitan</li>
1321 <li>ENA client ignores invalid content from ENA server</li>
1322 <li>Exceptions are not raised in console when ENA client
1323 attempts to fetch non-existent IDs via Fetch DB Refs UI
1325 <li>Exceptions are not raised in console when a new view
1326 is created on the alignment</li>
1327 <li>OSX right-click fixed for group selections: CMD-click
1328 to insert/remove gaps in groups and CTRL-click to open group
1331 <em>Build and deployment</em>
1333 <li>URL link checker now copes with multi-line anchor
1336 <em>New Known Issues</em>
1338 <li>Drag and drop from URL links in browsers do not work
1345 <td width="60" nowrap>
1346 <div align="center">
1347 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1350 <td><em>General</em>
1353 <!-- JAL-2124 -->Updated Spanish translations.
1356 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1357 for importing structure data to Jalview. Enables mmCIF and
1361 <!-- JAL-192 --->Alignment ruler shows positions relative to
1365 <!-- JAL-2202 -->Position/residue shown in status bar when
1366 mousing over sequence associated annotation
1369 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1373 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1374 '()', canonical '[]' and invalid '{}' base pair populations
1378 <!-- JAL-2092 -->Feature settings popup menu options for
1379 showing or hiding columns containing a feature
1382 <!-- JAL-1557 -->Edit selected group by double clicking on
1383 group and sequence associated annotation labels
1386 <!-- JAL-2236 -->Sequence name added to annotation label in
1387 select/hide columns by annotation and colour by annotation
1391 </ul> <em>Application</em>
1394 <!-- JAL-2050-->Automatically hide introns when opening a
1395 gene/transcript view
1398 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1402 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1403 structure mappings with the EMBL-EBI PDBe SIFTS database
1406 <!-- JAL-2079 -->Updated download sites used for Rfam and
1407 Pfam sources to xfam.org
1410 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1413 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1414 over sequences in Jalview
1417 <!-- JAL-2027-->Support for reverse-complement coding
1418 regions in ENA and EMBL
1421 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1422 for record retrieval via ENA rest API
1425 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1429 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1430 groovy script execution
1433 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1434 alignment window's Calculate menu
1437 <!-- JAL-1812 -->Allow groovy scripts that call
1438 Jalview.getAlignFrames() to run in headless mode
1441 <!-- JAL-2068 -->Support for creating new alignment
1442 calculation workers from groovy scripts
1445 <!-- JAL-1369 --->Store/restore reference sequence in
1449 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1450 associations are now saved/restored from project
1453 <!-- JAL-1993 -->Database selection dialog always shown
1454 before sequence fetcher is opened
1457 <!-- JAL-2183 -->Double click on an entry in Jalview's
1458 database chooser opens a sequence fetcher
1461 <!-- JAL-1563 -->Free-text search client for UniProt using
1462 the UniProt REST API
1465 <!-- JAL-2168 -->-nonews command line parameter to prevent
1466 the news reader opening
1469 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1470 querying stored in preferences
1473 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1477 <!-- JAL-1977-->Tooltips shown on database chooser
1480 <!-- JAL-391 -->Reverse complement function in calculate
1481 menu for nucleotide sequences
1484 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1485 and feature counts preserves alignment ordering (and
1486 debugged for complex feature sets).
1489 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1490 viewing structures with Jalview 2.10
1493 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1494 genome, transcript CCDS and gene ids via the Ensembl and
1495 Ensembl Genomes REST API
1498 <!-- JAL-2049 -->Protein sequence variant annotation
1499 computed for 'sequence_variant' annotation on CDS regions
1503 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1507 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1508 Ref Fetcher fails to match, or otherwise updates sequence
1509 data from external database records.
1512 <!-- JAL-2154 -->Revised Jalview Project format for
1513 efficient recovery of sequence coding and alignment
1514 annotation relationships.
1516 </ul> <!-- <em>Applet</em>
1527 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1531 <!-- JAL-2018-->Export features in Jalview format (again)
1532 includes graduated colourschemes
1535 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1536 working with big alignments and lots of hidden columns
1539 <!-- JAL-2053-->Hidden column markers not always rendered
1540 at right of alignment window
1543 <!-- JAL-2067 -->Tidied up links in help file table of
1547 <!-- JAL-2072 -->Feature based tree calculation not shown
1551 <!-- JAL-2075 -->Hidden columns ignored during feature
1552 based tree calculation
1555 <!-- JAL-2065 -->Alignment view stops updating when show
1556 unconserved enabled for group on alignment
1559 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1563 <!-- JAL-2146 -->Alignment column in status incorrectly
1564 shown as "Sequence position" when mousing over
1568 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1569 hidden columns present
1572 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1573 user created annotation added to alignment
1576 <!-- JAL-1841 -->RNA Structure consensus only computed for
1577 '()' base pair annotation
1580 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1581 in zero scores for all base pairs in RNA Structure
1585 <!-- JAL-2174-->Extend selection with columns containing
1589 <!-- JAL-2275 -->Pfam format writer puts extra space at
1590 beginning of sequence
1593 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1597 <!-- JAL-2238 -->Cannot create groups on an alignment from
1598 from a tree when t-coffee scores are shown
1601 <!-- JAL-1836,1967 -->Cannot import and view PDB
1602 structures with chains containing negative resnums (4q4h)
1605 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1609 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1610 to Clustal, PIR and PileUp output
1613 <!-- JAL-2008 -->Reordering sequence features that are
1614 not visible causes alignment window to repaint
1617 <!-- JAL-2006 -->Threshold sliders don't work in
1618 graduated colour and colour by annotation row for e-value
1619 scores associated with features and annotation rows
1622 <!-- JAL-1797 -->amino acid physicochemical conservation
1623 calculation should be case independent
1626 <!-- JAL-2173 -->Remove annotation also updates hidden
1630 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1631 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1632 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1635 <!-- JAL-2065 -->Null pointer exceptions and redraw
1636 problems when reference sequence defined and 'show
1637 non-conserved' enabled
1640 <!-- JAL-1306 -->Quality and Conservation are now shown on
1641 load even when Consensus calculation is disabled
1644 <!-- JAL-1932 -->Remove right on penultimate column of
1645 alignment does nothing
1648 <em>Application</em>
1651 <!-- JAL-1552-->URLs and links can't be imported by
1652 drag'n'drop on OSX when launched via webstart (note - not
1653 yet fixed for El Capitan)
1656 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1657 output when running on non-gb/us i18n platforms
1660 <!-- JAL-1944 -->Error thrown when exporting a view with
1661 hidden sequences as flat-file alignment
1664 <!-- JAL-2030-->InstallAnywhere distribution fails when
1668 <!-- JAL-2080-->Jalview very slow to launch via webstart
1669 (also hotfix for 2.9.0b2)
1672 <!-- JAL-2085 -->Cannot save project when view has a
1673 reference sequence defined
1676 <!-- JAL-1011 -->Columns are suddenly selected in other
1677 alignments and views when revealing hidden columns
1680 <!-- JAL-1989 -->Hide columns not mirrored in complement
1681 view in a cDNA/Protein splitframe
1684 <!-- JAL-1369 -->Cannot save/restore representative
1685 sequence from project when only one sequence is
1689 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1690 in Structure Chooser
1693 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1694 structure consensus didn't refresh annotation panel
1697 <!-- JAL-1962 -->View mapping in structure view shows
1698 mappings between sequence and all chains in a PDB file
1701 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1702 dialogs format columns correctly, don't display array
1703 data, sort columns according to type
1706 <!-- JAL-1975 -->Export complete shown after destination
1707 file chooser is cancelled during an image export
1710 <!-- JAL-2025 -->Error when querying PDB Service with
1711 sequence name containing special characters
1714 <!-- JAL-2024 -->Manual PDB structure querying should be
1718 <!-- JAL-2104 -->Large tooltips with broken HTML
1719 formatting don't wrap
1722 <!-- JAL-1128 -->Figures exported from wrapped view are
1723 truncated so L looks like I in consensus annotation
1726 <!-- JAL-2003 -->Export features should only export the
1727 currently displayed features for the current selection or
1731 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1732 after fetching cross-references, and restoring from
1736 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1737 followed in the structure viewer
1740 <!-- JAL-2163 -->Titles for individual alignments in
1741 splitframe not restored from project
1744 <!-- JAL-2145 -->missing autocalculated annotation at
1745 trailing end of protein alignment in transcript/product
1746 splitview when pad-gaps not enabled by default
1749 <!-- JAL-1797 -->amino acid physicochemical conservation
1753 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1754 article has been read (reopened issue due to
1755 internationalisation problems)
1758 <!-- JAL-1960 -->Only offer PDB structures in structure
1759 viewer based on sequence name, PDB and UniProt
1764 <!-- JAL-1976 -->No progress bar shown during export of
1768 <!-- JAL-2213 -->Structures not always superimposed after
1769 multiple structures are shown for one or more sequences.
1772 <!-- JAL-1370 -->Reference sequence characters should not
1773 be replaced with '.' when 'Show unconserved' format option
1777 <!-- JAL-1823 -->Cannot specify chain code when entering
1778 specific PDB id for sequence
1781 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1782 'Export hidden sequences' is enabled, but 'export hidden
1783 columns' is disabled.
1786 <!--JAL-2026-->Best Quality option in structure chooser
1787 selects lowest rather than highest resolution structures
1791 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1792 to sequence mapping in 'View Mappings' report
1795 <!-- JAL-2284 -->Unable to read old Jalview projects that
1796 contain non-XML data added after Jalvew wrote project.
1799 <!-- JAL-2118 -->Newly created annotation row reorders
1800 after clicking on it to create new annotation for a
1804 <!-- JAL-1980 -->Null Pointer Exception raised when
1805 pressing Add on an orphaned cut'n'paste window.
1807 <!-- may exclude, this is an external service stability issue JAL-1941
1808 -- > RNA 3D structure not added via DSSR service</li> -->
1813 <!-- JAL-2151 -->Incorrect columns are selected when
1814 hidden columns present before start of sequence
1817 <!-- JAL-1986 -->Missing dependencies on applet pages
1821 <!-- JAL-1947 -->Overview pixel size changes when
1822 sequences are hidden in applet
1825 <!-- JAL-1996 -->Updated instructions for applet
1826 deployment on examples pages.
1833 <td width="60" nowrap>
1834 <div align="center">
1835 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1836 <em>16/10/2015</em></strong>
1839 <td><em>General</em>
1841 <li>Time stamps for signed Jalview application and applet
1846 <em>Application</em>
1848 <li>Duplicate group consensus and conservation rows
1849 shown when tree is partitioned</li>
1850 <li>Erratic behaviour when tree partitions made with
1851 multiple cDNA/Protein split views</li>
1857 <td width="60" nowrap>
1858 <div align="center">
1859 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1860 <em>8/10/2015</em></strong>
1863 <td><em>General</em>
1865 <li>Updated Spanish translations of localized text for
1867 </ul> <em>Application</em>
1869 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1870 <li>Signed OSX InstallAnywhere installer<br></li>
1871 <li>Support for per-sequence based annotations in BioJSON</li>
1872 </ul> <em>Applet</em>
1874 <li>Split frame example added to applet examples page</li>
1875 </ul> <em>Build and Deployment</em>
1878 <!-- JAL-1888 -->New ant target for running Jalview's test
1886 <li>Mapping of cDNA to protein in split frames
1887 incorrect when sequence start > 1</li>
1888 <li>Broken images in filter column by annotation dialog
1890 <li>Feature colours not parsed from features file</li>
1891 <li>Exceptions and incomplete link URLs recovered when
1892 loading a features file containing HTML tags in feature
1896 <em>Application</em>
1898 <li>Annotations corrupted after BioJS export and
1900 <li>Incorrect sequence limits after Fetch DB References
1901 with 'trim retrieved sequences'</li>
1902 <li>Incorrect warning about deleting all data when
1903 deleting selected columns</li>
1904 <li>Patch to build system for shipping properly signed
1905 JNLP templates for webstart launch</li>
1906 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1907 unreleased structures for download or viewing</li>
1908 <li>Tab/space/return keystroke operation of EMBL-PDBe
1909 fetcher/viewer dialogs works correctly</li>
1910 <li>Disabled 'minimise' button on Jalview windows
1911 running on OSX to workaround redraw hang bug</li>
1912 <li>Split cDNA/Protein view position and geometry not
1913 recovered from jalview project</li>
1914 <li>Initial enabled/disabled state of annotation menu
1915 sorter 'show autocalculated first/last' corresponds to
1917 <li>Restoring of Clustal, RNA Helices and T-Coffee
1918 color schemes from BioJSON</li>
1922 <li>Reorder sequences mirrored in cDNA/Protein split
1924 <li>Applet with Jmol examples not loading correctly</li>
1930 <td><div align="center">
1931 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1933 <td><em>General</em>
1935 <li>Linked visualisation and analysis of DNA and Protein
1938 <li>Translated cDNA alignments shown as split protein
1939 and DNA alignment views</li>
1940 <li>Codon consensus annotation for linked protein and
1941 cDNA alignment views</li>
1942 <li>Link cDNA or Protein product sequences by loading
1943 them onto Protein or cDNA alignments</li>
1944 <li>Reconstruct linked cDNA alignment from aligned
1945 protein sequences</li>
1948 <li>Jmol integration updated to Jmol v14.2.14</li>
1949 <li>Import and export of Jalview alignment views as <a
1950 href="features/bioJsonFormat.html">BioJSON</a></li>
1951 <li>New alignment annotation file statements for
1952 reference sequences and marking hidden columns</li>
1953 <li>Reference sequence based alignment shading to
1954 highlight variation</li>
1955 <li>Select or hide columns according to alignment
1957 <li>Find option for locating sequences by description</li>
1958 <li>Conserved physicochemical properties shown in amino
1959 acid conservation row</li>
1960 <li>Alignments can be sorted by number of RNA helices</li>
1961 </ul> <em>Application</em>
1963 <li>New cDNA/Protein analysis capabilities
1965 <li>Get Cross-References should open a Split Frame
1966 view with cDNA/Protein</li>
1967 <li>Detect when nucleotide sequences and protein
1968 sequences are placed in the same alignment</li>
1969 <li>Split cDNA/Protein views are saved in Jalview
1974 <li>Use REST API to talk to Chimera</li>
1975 <li>Selected regions in Chimera are highlighted in linked
1976 Jalview windows</li>
1978 <li>VARNA RNA viewer updated to v3.93</li>
1979 <li>VARNA views are saved in Jalview Projects</li>
1980 <li>Pseudoknots displayed as Jalview RNA annotation can
1981 be shown in VARNA</li>
1983 <li>Make groups for selection uses marked columns as well
1984 as the active selected region</li>
1986 <li>Calculate UPGMA and NJ trees using sequence feature
1988 <li>New Export options
1990 <li>New Export Settings dialog to control hidden
1991 region export in flat file generation</li>
1993 <li>Export alignment views for display with the <a
1994 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1996 <li>Export scrollable SVG in HTML page</li>
1997 <li>Optional embedding of BioJSON data when exporting
1998 alignment figures to HTML</li>
2000 <li>3D structure retrieval and display
2002 <li>Free text and structured queries with the PDBe
2004 <li>PDBe Search API based discovery and selection of
2005 PDB structures for a sequence set</li>
2009 <li>JPred4 employed for protein secondary structure
2011 <li>Hide Insertions menu option to hide unaligned columns
2012 for one or a group of sequences</li>
2013 <li>Automatically hide insertions in alignments imported
2014 from the JPred4 web server</li>
2015 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
2016 system on OSX<br />LGPL libraries courtesy of <a
2017 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
2019 <li>changed 'View nucleotide structure' submenu to 'View
2020 VARNA 2D Structure'</li>
2021 <li>change "View protein structure" menu option to "3D
2024 </ul> <em>Applet</em>
2026 <li>New layout for applet example pages</li>
2027 <li>New parameters to enable SplitFrame view
2028 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
2029 <li>New example demonstrating linked viewing of cDNA and
2030 Protein alignments</li>
2031 </ul> <em>Development and deployment</em>
2033 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
2034 <li>Include installation type and git revision in build
2035 properties and console log output</li>
2036 <li>Jalview Github organisation, and new github site for
2037 storing BioJsMSA Templates</li>
2038 <li>Jalview's unit tests now managed with TestNG</li>
2041 <!-- <em>General</em>
2043 </ul> --> <!-- issues resolved --> <em>Application</em>
2045 <li>Escape should close any open find dialogs</li>
2046 <li>Typo in select-by-features status report</li>
2047 <li>Consensus RNA secondary secondary structure
2048 predictions are not highlighted in amber</li>
2049 <li>Missing gap character in v2.7 example file means
2050 alignment appears unaligned when pad-gaps is not enabled</li>
2051 <li>First switch to RNA Helices colouring doesn't colour
2052 associated structure views</li>
2053 <li>ID width preference option is greyed out when auto
2054 width checkbox not enabled</li>
2055 <li>Stopped a warning dialog from being shown when
2056 creating user defined colours</li>
2057 <li>'View Mapping' in structure viewer shows sequence
2058 mappings for just that viewer's sequences</li>
2059 <li>Workaround for superposing PDB files containing
2060 multiple models in Chimera</li>
2061 <li>Report sequence position in status bar when hovering
2062 over Jmol structure</li>
2063 <li>Cannot output gaps as '.' symbols with Selection ->
2064 output to text box</li>
2065 <li>Flat file exports of alignments with hidden columns
2066 have incorrect sequence start/end</li>
2067 <li>'Aligning' a second chain to a Chimera structure from
2069 <li>Colour schemes applied to structure viewers don't
2070 work for nucleotide</li>
2071 <li>Loading/cut'n'pasting an empty or invalid file leads
2072 to a grey/invisible alignment window</li>
2073 <li>Exported Jpred annotation from a sequence region
2074 imports to different position</li>
2075 <li>Space at beginning of sequence feature tooltips shown
2076 on some platforms</li>
2077 <li>Chimera viewer 'View | Show Chain' menu is not
2079 <li>'New View' fails with a Null Pointer Exception in
2080 console if Chimera has been opened</li>
2081 <li>Mouseover to Chimera not working</li>
2082 <li>Miscellaneous ENA XML feature qualifiers not
2084 <li>NPE in annotation renderer after 'Extract Scores'</li>
2085 <li>If two structures in one Chimera window, mouseover of
2086 either sequence shows on first structure</li>
2087 <li>'Show annotations' options should not make
2088 non-positional annotations visible</li>
2089 <li>Subsequence secondary structure annotation not shown
2090 in right place after 'view flanking regions'</li>
2091 <li>File Save As type unset when current file format is
2093 <li>Save as '.jar' option removed for saving Jalview
2095 <li>Colour by Sequence colouring in Chimera more
2097 <li>Cannot 'add reference annotation' for a sequence in
2098 several views on same alignment</li>
2099 <li>Cannot show linked products for EMBL / ENA records</li>
2100 <li>Jalview's tooltip wraps long texts containing no
2102 </ul> <em>Applet</em>
2104 <li>Jmol to JalviewLite mouseover/link not working</li>
2105 <li>JalviewLite can't import sequences with ID
2106 descriptions containing angle brackets</li>
2107 </ul> <em>General</em>
2109 <li>Cannot export and reimport RNA secondary structure
2110 via jalview annotation file</li>
2111 <li>Random helix colour palette for colour by annotation
2112 with RNA secondary structure</li>
2113 <li>Mouseover to cDNA from STOP residue in protein
2114 translation doesn't work.</li>
2115 <li>hints when using the select by annotation dialog box</li>
2116 <li>Jmol alignment incorrect if PDB file has alternate CA
2118 <li>FontChooser message dialog appears to hang after
2119 choosing 1pt font</li>
2120 <li>Peptide secondary structure incorrectly imported from
2121 annotation file when annotation display text includes 'e' or
2123 <li>Cannot set colour of new feature type whilst creating
2125 <li>cDNA translation alignment should not be sequence
2126 order dependent</li>
2127 <li>'Show unconserved' doesn't work for lower case
2129 <li>Nucleotide ambiguity codes involving R not recognised</li>
2130 </ul> <em>Deployment and Documentation</em>
2132 <li>Applet example pages appear different to the rest of
2133 www.jalview.org</li>
2134 </ul> <em>Application Known issues</em>
2136 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2137 <li>Misleading message appears after trying to delete
2139 <li>Jalview icon not shown in dock after InstallAnywhere
2140 version launches</li>
2141 <li>Fetching EMBL reference for an RNA sequence results
2142 fails with a sequence mismatch</li>
2143 <li>Corrupted or unreadable alignment display when
2144 scrolling alignment to right</li>
2145 <li>ArrayIndexOutOfBoundsException thrown when remove
2146 empty columns called on alignment with ragged gapped ends</li>
2147 <li>auto calculated alignment annotation rows do not get
2148 placed above or below non-autocalculated rows</li>
2149 <li>Jalview dekstop becomes sluggish at full screen in
2150 ultra-high resolution</li>
2151 <li>Cannot disable consensus calculation independently of
2152 quality and conservation</li>
2153 <li>Mouseover highlighting between cDNA and protein can
2154 become sluggish with more than one splitframe shown</li>
2155 </ul> <em>Applet Known Issues</em>
2157 <li>Core PDB parsing code requires Jmol</li>
2158 <li>Sequence canvas panel goes white when alignment
2159 window is being resized</li>
2165 <td><div align="center">
2166 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2168 <td><em>General</em>
2170 <li>Updated Java code signing certificate donated by
2172 <li>Features and annotation preserved when performing
2173 pairwise alignment</li>
2174 <li>RNA pseudoknot annotation can be
2175 imported/exported/displayed</li>
2176 <li>'colour by annotation' can colour by RNA and
2177 protein secondary structure</li>
2178 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2179 post-hoc with 2.9 release</em>)
2182 </ul> <em>Application</em>
2184 <li>Extract and display secondary structure for sequences
2185 with 3D structures</li>
2186 <li>Support for parsing RNAML</li>
2187 <li>Annotations menu for layout
2189 <li>sort sequence annotation rows by alignment</li>
2190 <li>place sequence annotation above/below alignment
2193 <li>Output in Stockholm format</li>
2194 <li>Internationalisation: improved Spanish (es)
2196 <li>Structure viewer preferences tab</li>
2197 <li>Disorder and Secondary Structure annotation tracks
2198 shared between alignments</li>
2199 <li>UCSF Chimera launch and linked highlighting from
2201 <li>Show/hide all sequence associated annotation rows for
2202 all or current selection</li>
2203 <li>disorder and secondary structure predictions
2204 available as dataset annotation</li>
2205 <li>Per-sequence rna helices colouring</li>
2208 <li>Sequence database accessions imported when fetching
2209 alignments from Rfam</li>
2210 <li>update VARNA version to 3.91</li>
2212 <li>New groovy scripts for exporting aligned positions,
2213 conservation values, and calculating sum of pairs scores.</li>
2214 <li>Command line argument to set default JABAWS server</li>
2215 <li>include installation type in build properties and
2216 console log output</li>
2217 <li>Updated Jalview project format to preserve dataset
2221 <!-- issues resolved --> <em>Application</em>
2223 <li>Distinguish alignment and sequence associated RNA
2224 structure in structure->view->VARNA</li>
2225 <li>Raise dialog box if user deletes all sequences in an
2227 <li>Pressing F1 results in documentation opening twice</li>
2228 <li>Sequence feature tooltip is wrapped</li>
2229 <li>Double click on sequence associated annotation
2230 selects only first column</li>
2231 <li>Redundancy removal doesn't result in unlinked
2232 leaves shown in tree</li>
2233 <li>Undos after several redundancy removals don't undo
2235 <li>Hide sequence doesn't hide associated annotation</li>
2236 <li>User defined colours dialog box too big to fit on
2237 screen and buttons not visible</li>
2238 <li>author list isn't updated if already written to
2239 Jalview properties</li>
2240 <li>Popup menu won't open after retrieving sequence
2242 <li>File open window for associate PDB doesn't open</li>
2243 <li>Left-then-right click on a sequence id opens a
2244 browser search window</li>
2245 <li>Cannot open sequence feature shading/sort popup menu
2246 in feature settings dialog</li>
2247 <li>better tooltip placement for some areas of Jalview
2249 <li>Allow addition of JABAWS Server which doesn't
2250 pass validation</li>
2251 <li>Web services parameters dialog box is too large to
2253 <li>Muscle nucleotide alignment preset obscured by
2255 <li>JABAWS preset submenus don't contain newly
2256 defined user preset</li>
2257 <li>MSA web services warns user if they were launched
2258 with invalid input</li>
2259 <li>Jalview cannot contact DAS Registy when running on
2262 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2263 'Superpose with' submenu not shown when new view
2267 </ul> <!-- <em>Applet</em>
2269 </ul> <em>General</em>
2271 </ul>--> <em>Deployment and Documentation</em>
2273 <li>2G and 1G options in launchApp have no effect on
2274 memory allocation</li>
2275 <li>launchApp service doesn't automatically open
2276 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2278 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2279 InstallAnywhere reports cannot find valid JVM when Java
2280 1.7_055 is available
2282 </ul> <em>Application Known issues</em>
2285 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2286 corrupted or unreadable alignment display when scrolling
2290 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2291 retrieval fails but progress bar continues for DAS retrieval
2292 with large number of ID
2295 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2296 flatfile output of visible region has incorrect sequence
2300 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2301 rna structure consensus doesn't update when secondary
2302 structure tracks are rearranged
2305 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2306 invalid rna structure positional highlighting does not
2307 highlight position of invalid base pairs
2310 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2311 out of memory errors are not raised when saving Jalview
2312 project from alignment window file menu
2315 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2316 Switching to RNA Helices colouring doesn't propagate to
2320 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2321 colour by RNA Helices not enabled when user created
2322 annotation added to alignment
2325 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2326 Jalview icon not shown on dock in Mountain Lion/Webstart
2328 </ul> <em>Applet Known Issues</em>
2331 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2332 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2335 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2336 Jalview and Jmol example not compatible with IE9
2339 <li>Sort by annotation score doesn't reverse order
2345 <td><div align="center">
2346 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2349 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2352 <li>Internationalisation of user interface (usually
2353 called i18n support) and translation for Spanish locale</li>
2354 <li>Define/Undefine group on current selection with
2355 Ctrl-G/Shift Ctrl-G</li>
2356 <li>Improved group creation/removal options in
2357 alignment/sequence Popup menu</li>
2358 <li>Sensible precision for symbol distribution
2359 percentages shown in logo tooltip.</li>
2360 <li>Annotation panel height set according to amount of
2361 annotation when alignment first opened</li>
2362 </ul> <em>Application</em>
2364 <li>Interactive consensus RNA secondary structure
2365 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2366 <li>Select columns containing particular features from
2367 Feature Settings dialog</li>
2368 <li>View all 'representative' PDB structures for selected
2370 <li>Update Jalview project format:
2372 <li>New file extension for Jalview projects '.jvp'</li>
2373 <li>Preserve sequence and annotation dataset (to
2374 store secondary structure annotation,etc)</li>
2375 <li>Per group and alignment annotation and RNA helix
2379 <li>New similarity measures for PCA and Tree calculation
2381 <li>Experimental support for retrieval and viewing of
2382 flanking regions for an alignment</li>
2386 <!-- issues resolved --> <em>Application</em>
2388 <li>logo keeps spinning and status remains at queued or
2389 running after job is cancelled</li>
2390 <li>cannot export features from alignments imported from
2391 Jalview/VAMSAS projects</li>
2392 <li>Buggy slider for web service parameters that take
2394 <li>Newly created RNA secondary structure line doesn't
2395 have 'display all symbols' flag set</li>
2396 <li>T-COFFEE alignment score shading scheme and other
2397 annotation shading not saved in Jalview project</li>
2398 <li>Local file cannot be loaded in freshly downloaded
2400 <li>Jalview icon not shown on dock in Mountain
2402 <li>Load file from desktop file browser fails</li>
2403 <li>Occasional NPE thrown when calculating large trees</li>
2404 <li>Cannot reorder or slide sequences after dragging an
2405 alignment onto desktop</li>
2406 <li>Colour by annotation dialog throws NPE after using
2407 'extract scores' function</li>
2408 <li>Loading/cut'n'pasting an empty file leads to a grey
2409 alignment window</li>
2410 <li>Disorder thresholds rendered incorrectly after
2411 performing IUPred disorder prediction</li>
2412 <li>Multiple group annotated consensus rows shown when
2413 changing 'normalise logo' display setting</li>
2414 <li>Find shows blank dialog after 'finished searching' if
2415 nothing matches query</li>
2416 <li>Null Pointer Exceptions raised when sorting by
2417 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2419 <li>Errors in Jmol console when structures in alignment
2420 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2422 <li>Not all working JABAWS services are shown in
2424 <li>JAVAWS version of Jalview fails to launch with
2425 'invalid literal/length code'</li>
2426 <li>Annotation/RNA Helix colourschemes cannot be applied
2427 to alignment with groups (actually fixed in 2.8.0b1)</li>
2428 <li>RNA Helices and T-Coffee Scores available as default
2431 </ul> <em>Applet</em>
2433 <li>Remove group option is shown even when selection is
2435 <li>Apply to all groups ticked but colourscheme changes
2436 don't affect groups</li>
2437 <li>Documented RNA Helices and T-Coffee Scores as valid
2438 colourscheme name</li>
2439 <li>Annotation labels drawn on sequence IDs when
2440 Annotation panel is not displayed</li>
2441 <li>Increased font size for dropdown menus on OSX and
2442 embedded windows</li>
2443 </ul> <em>Other</em>
2445 <li>Consensus sequence for alignments/groups with a
2446 single sequence were not calculated</li>
2447 <li>annotation files that contain only groups imported as
2448 annotation and junk sequences</li>
2449 <li>Fasta files with sequences containing '*' incorrectly
2450 recognised as PFAM or BLC</li>
2451 <li>conservation/PID slider apply all groups option
2452 doesn't affect background (2.8.0b1)
2454 <li>redundancy highlighting is erratic at 0% and 100%</li>
2455 <li>Remove gapped columns fails for sequences with ragged
2457 <li>AMSA annotation row with leading spaces is not
2458 registered correctly on import</li>
2459 <li>Jalview crashes when selecting PCA analysis for
2460 certain alignments</li>
2461 <li>Opening the colour by annotation dialog for an
2462 existing annotation based 'use original colours'
2463 colourscheme loses original colours setting</li>
2468 <td><div align="center">
2469 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2470 <em>30/1/2014</em></strong>
2474 <li>Trusted certificates for JalviewLite applet and
2475 Jalview Desktop application<br />Certificate was donated by
2476 <a href="https://www.certum.eu">Certum</a> to the Jalview
2477 open source project).
2479 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2480 <li>Output in Stockholm format</li>
2481 <li>Allow import of data from gzipped files</li>
2482 <li>Export/import group and sequence associated line
2483 graph thresholds</li>
2484 <li>Nucleotide substitution matrix that supports RNA and
2485 ambiguity codes</li>
2486 <li>Allow disorder predictions to be made on the current
2487 selection (or visible selection) in the same way that JPred
2489 <li>Groovy scripting for headless Jalview operation</li>
2490 </ul> <em>Other improvements</em>
2492 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2493 <li>COMBINE statement uses current SEQUENCE_REF and
2494 GROUP_REF scope to group annotation rows</li>
2495 <li>Support '' style escaping of quotes in Newick
2497 <li>Group options for JABAWS service by command line name</li>
2498 <li>Empty tooltip shown for JABA service options with a
2499 link but no description</li>
2500 <li>Select primary source when selecting authority in
2501 database fetcher GUI</li>
2502 <li>Add .mfa to FASTA file extensions recognised by
2504 <li>Annotation label tooltip text wrap</li>
2509 <li>Slow scrolling when lots of annotation rows are
2511 <li>Lots of NPE (and slowness) after creating RNA
2512 secondary structure annotation line</li>
2513 <li>Sequence database accessions not imported when
2514 fetching alignments from Rfam</li>
2515 <li>Incorrect SHMR submission for sequences with
2517 <li>View all structures does not always superpose
2519 <li>Option widgets in service parameters not updated to
2520 reflect user or preset settings</li>
2521 <li>Null pointer exceptions for some services without
2522 presets or adjustable parameters</li>
2523 <li>Discover PDB IDs entry in structure menu doesn't
2524 discover PDB xRefs</li>
2525 <li>Exception encountered while trying to retrieve
2526 features with DAS</li>
2527 <li>Lowest value in annotation row isn't coloured
2528 when colour by annotation (per sequence) is coloured</li>
2529 <li>Keyboard mode P jumps to start of gapped region when
2530 residue follows a gap</li>
2531 <li>Jalview appears to hang importing an alignment with
2532 Wrap as default or after enabling Wrap</li>
2533 <li>'Right click to add annotations' message
2534 shown in wrap mode when no annotations present</li>
2535 <li>Disorder predictions fail with NPE if no automatic
2536 annotation already exists on alignment</li>
2537 <li>oninit javascript function should be called after
2538 initialisation completes</li>
2539 <li>Remove redundancy after disorder prediction corrupts
2540 alignment window display</li>
2541 <li>Example annotation file in documentation is invalid</li>
2542 <li>Grouped line graph annotation rows are not exported
2543 to annotation file</li>
2544 <li>Multi-harmony analysis cannot be run when only two
2546 <li>Cannot create multiple groups of line graphs with
2547 several 'combine' statements in annotation file</li>
2548 <li>Pressing return several times causes Number Format
2549 exceptions in keyboard mode</li>
2550 <li>Multi-harmony (SHMMR) method doesn't submit
2551 correct partitions for input data</li>
2552 <li>Translation from DNA to Amino Acids fails</li>
2553 <li>Jalview fail to load newick tree with quoted label</li>
2554 <li>--headless flag isn't understood</li>
2555 <li>ClassCastException when generating EPS in headless
2557 <li>Adjusting sequence-associated shading threshold only
2558 changes one row's threshold</li>
2559 <li>Preferences and Feature settings panel panel
2560 doesn't open</li>
2561 <li>hide consensus histogram also hides conservation and
2562 quality histograms</li>
2567 <td><div align="center">
2568 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2570 <td><em>Application</em>
2572 <li>Support for JABAWS 2.0 Services (AACon alignment
2573 conservation, protein disorder and Clustal Omega)</li>
2574 <li>JABAWS server status indicator in Web Services
2576 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2577 in Jalview alignment window</li>
2578 <li>Updated Jalview build and deploy framework for OSX
2579 mountain lion, windows 7, and 8</li>
2580 <li>Nucleotide substitution matrix for PCA that supports
2581 RNA and ambiguity codes</li>
2583 <li>Improved sequence database retrieval GUI</li>
2584 <li>Support fetching and database reference look up
2585 against multiple DAS sources (Fetch all from in 'fetch db
2587 <li>Jalview project improvements
2589 <li>Store and retrieve the 'belowAlignment'
2590 flag for annotation</li>
2591 <li>calcId attribute to group annotation rows on the
2593 <li>Store AACon calculation settings for a view in
2594 Jalview project</li>
2598 <li>horizontal scrolling gesture support</li>
2599 <li>Visual progress indicator when PCA calculation is
2601 <li>Simpler JABA web services menus</li>
2602 <li>visual indication that web service results are still
2603 being retrieved from server</li>
2604 <li>Serialise the dialogs that are shown when Jalview
2605 starts up for first time</li>
2606 <li>Jalview user agent string for interacting with HTTP
2608 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2610 <li>Examples directory and Groovy library included in
2611 InstallAnywhere distribution</li>
2612 </ul> <em>Applet</em>
2614 <li>RNA alignment and secondary structure annotation
2615 visualization applet example</li>
2616 </ul> <em>General</em>
2618 <li>Normalise option for consensus sequence logo</li>
2619 <li>Reset button in PCA window to return dimensions to
2621 <li>Allow seqspace or Jalview variant of alignment PCA
2623 <li>PCA with either nucleic acid and protein substitution
2625 <li>Allow windows containing HTML reports to be exported
2627 <li>Interactive display and editing of RNA secondary
2628 structure contacts</li>
2629 <li>RNA Helix Alignment Colouring</li>
2630 <li>RNA base pair logo consensus</li>
2631 <li>Parse sequence associated secondary structure
2632 information in Stockholm files</li>
2633 <li>HTML Export database accessions and annotation
2634 information presented in tooltip for sequences</li>
2635 <li>Import secondary structure from LOCARNA clustalw
2636 style RNA alignment files</li>
2637 <li>import and visualise T-COFFEE quality scores for an
2639 <li>'colour by annotation' per sequence option to
2640 shade each sequence according to its associated alignment
2642 <li>New Jalview Logo</li>
2643 </ul> <em>Documentation and Development</em>
2645 <li>documentation for score matrices used in Jalview</li>
2646 <li>New Website!</li>
2648 <td><em>Application</em>
2650 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2651 wsdbfetch REST service</li>
2652 <li>Stop windows being moved outside desktop on OSX</li>
2653 <li>Filetype associations not installed for webstart
2655 <li>Jalview does not always retrieve progress of a JABAWS
2656 job execution in full once it is complete</li>
2657 <li>revise SHMR RSBS definition to ensure alignment is
2658 uploaded via ali_file parameter</li>
2659 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2660 <li>View all structures superposed fails with exception</li>
2661 <li>Jnet job queues forever if a very short sequence is
2662 submitted for prediction</li>
2663 <li>Cut and paste menu not opened when mouse clicked on
2665 <li>Putting fractional value into integer text box in
2666 alignment parameter dialog causes Jalview to hang</li>
2667 <li>Structure view highlighting doesn't work on
2669 <li>View all structures fails with exception shown in
2671 <li>Characters in filename associated with PDBEntry not
2672 escaped in a platform independent way</li>
2673 <li>Jalview desktop fails to launch with exception when
2675 <li>Tree calculation reports 'you must have 2 or more
2676 sequences selected' when selection is empty</li>
2677 <li>Jalview desktop fails to launch with jar signature
2678 failure when java web start temporary file caching is
2680 <li>DAS Sequence retrieval with range qualification
2681 results in sequence xref which includes range qualification</li>
2682 <li>Errors during processing of command line arguments
2683 cause progress bar (JAL-898) to be removed</li>
2684 <li>Replace comma for semi-colon option not disabled for
2685 DAS sources in sequence fetcher</li>
2686 <li>Cannot close news reader when JABAWS server warning
2687 dialog is shown</li>
2688 <li>Option widgets not updated to reflect user settings</li>
2689 <li>Edited sequence not submitted to web service</li>
2690 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2691 <li>InstallAnywhere installer doesn't unpack and run
2692 on OSX Mountain Lion</li>
2693 <li>Annotation panel not given a scroll bar when
2694 sequences with alignment annotation are pasted into the
2696 <li>Sequence associated annotation rows not associated
2697 when loaded from Jalview project</li>
2698 <li>Browser launch fails with NPE on java 1.7</li>
2699 <li>JABAWS alignment marked as finished when job was
2700 cancelled or job failed due to invalid input</li>
2701 <li>NPE with v2.7 example when clicking on Tree
2702 associated with all views</li>
2703 <li>Exceptions when copy/paste sequences with grouped
2704 annotation rows to new window</li>
2705 </ul> <em>Applet</em>
2707 <li>Sequence features are momentarily displayed before
2708 they are hidden using hidefeaturegroups applet parameter</li>
2709 <li>loading features via javascript API automatically
2710 enables feature display</li>
2711 <li>scrollToColumnIn javascript API method doesn't
2713 </ul> <em>General</em>
2715 <li>Redundancy removal fails for rna alignment</li>
2716 <li>PCA calculation fails when sequence has been selected
2717 and then deselected</li>
2718 <li>PCA window shows grey box when first opened on OSX</li>
2719 <li>Letters coloured pink in sequence logo when alignment
2720 coloured with clustalx</li>
2721 <li>Choosing fonts without letter symbols defined causes
2722 exceptions and redraw errors</li>
2723 <li>Initial PCA plot view is not same as manually
2724 reconfigured view</li>
2725 <li>Grouped annotation graph label has incorrect line
2727 <li>Grouped annotation graph label display is corrupted
2728 for lots of labels</li>
2733 <div align="center">
2734 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2737 <td><em>Application</em>
2739 <li>Jalview Desktop News Reader</li>
2740 <li>Tweaked default layout of web services menu</li>
2741 <li>View/alignment association menu to enable user to
2742 easily specify which alignment a multi-structure view takes
2743 its colours/correspondences from</li>
2744 <li>Allow properties file location to be specified as URL</li>
2745 <li>Extend Jalview project to preserve associations
2746 between many alignment views and a single Jmol display</li>
2747 <li>Store annotation row height in Jalview project file</li>
2748 <li>Annotation row column label formatting attributes
2749 stored in project file</li>
2750 <li>Annotation row order for auto-calculated annotation
2751 rows preserved in Jalview project file</li>
2752 <li>Visual progress indication when Jalview state is
2753 saved using Desktop window menu</li>
2754 <li>Visual indication that command line arguments are
2755 still being processed</li>
2756 <li>Groovy script execution from URL</li>
2757 <li>Colour by annotation default min and max colours in
2759 <li>Automatically associate PDB files dragged onto an
2760 alignment with sequences that have high similarity and
2762 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2763 <li>'view structures' option to open many
2764 structures in same window</li>
2765 <li>Sort associated views menu option for tree panel</li>
2766 <li>Group all JABA and non-JABA services for a particular
2767 analysis function in its own submenu</li>
2768 </ul> <em>Applet</em>
2770 <li>Userdefined and autogenerated annotation rows for
2772 <li>Adjustment of alignment annotation pane height</li>
2773 <li>Annotation scrollbar for annotation panel</li>
2774 <li>Drag to reorder annotation rows in annotation panel</li>
2775 <li>'automaticScrolling' parameter</li>
2776 <li>Allow sequences with partial ID string matches to be
2777 annotated from GFF/Jalview features files</li>
2778 <li>Sequence logo annotation row in applet</li>
2779 <li>Absolute paths relative to host server in applet
2780 parameters are treated as such</li>
2781 <li>New in the JalviewLite javascript API:
2783 <li>JalviewLite.js javascript library</li>
2784 <li>Javascript callbacks for
2786 <li>Applet initialisation</li>
2787 <li>Sequence/alignment mouse-overs and selections</li>
2790 <li>scrollTo row and column alignment scrolling
2792 <li>Select sequence/alignment regions from javascript</li>
2793 <li>javascript structure viewer harness to pass
2794 messages between Jmol and Jalview when running as
2795 distinct applets</li>
2796 <li>sortBy method</li>
2797 <li>Set of applet and application examples shipped
2798 with documentation</li>
2799 <li>New example to demonstrate JalviewLite and Jmol
2800 javascript message exchange</li>
2802 </ul> <em>General</em>
2804 <li>Enable Jmol displays to be associated with multiple
2805 multiple alignments</li>
2806 <li>Option to automatically sort alignment with new tree</li>
2807 <li>User configurable link to enable redirects to a
2808 www.Jalview.org mirror</li>
2809 <li>Jmol colours option for Jmol displays</li>
2810 <li>Configurable newline string when writing alignment
2811 and other flat files</li>
2812 <li>Allow alignment annotation description lines to
2813 contain html tags</li>
2814 </ul> <em>Documentation and Development</em>
2816 <li>Add groovy test harness for bulk load testing to
2818 <li>Groovy script to load and align a set of sequences
2819 using a web service before displaying the result in the
2820 Jalview desktop</li>
2821 <li>Restructured javascript and applet api documentation</li>
2822 <li>Ant target to publish example html files with applet
2824 <li>Netbeans project for building Jalview from source</li>
2825 <li>ant task to create online javadoc for Jalview source</li>
2827 <td><em>Application</em>
2829 <li>User defined colourscheme throws exception when
2830 current built in colourscheme is saved as new scheme</li>
2831 <li>AlignFrame->Save in application pops up save
2832 dialog for valid filename/format</li>
2833 <li>Cannot view associated structure for UniProt sequence</li>
2834 <li>PDB file association breaks for UniProt sequence
2836 <li>Associate PDB from file dialog does not tell you
2837 which sequence is to be associated with the file</li>
2838 <li>Find All raises null pointer exception when query
2839 only matches sequence IDs</li>
2840 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2841 <li>Jalview project with Jmol views created with Jalview
2842 2.4 cannot be loaded</li>
2843 <li>Filetype associations not installed for webstart
2845 <li>Two or more chains in a single PDB file associated
2846 with sequences in different alignments do not get coloured
2847 by their associated sequence</li>
2848 <li>Visibility status of autocalculated annotation row
2849 not preserved when project is loaded</li>
2850 <li>Annotation row height and visibility attributes not
2851 stored in Jalview project</li>
2852 <li>Tree bootstraps are not preserved when saved as a
2853 Jalview project</li>
2854 <li>Envision2 workflow tooltips are corrupted</li>
2855 <li>Enabling show group conservation also enables colour
2856 by conservation</li>
2857 <li>Duplicate group associated conservation or consensus
2858 created on new view</li>
2859 <li>Annotation scrollbar not displayed after 'show
2860 all hidden annotation rows' option selected</li>
2861 <li>Alignment quality not updated after alignment
2862 annotation row is hidden then shown</li>
2863 <li>Preserve colouring of structures coloured by
2864 sequences in pre Jalview 2.7 projects</li>
2865 <li>Web service job parameter dialog is not laid out
2867 <li>Web services menu not refreshed after 'reset
2868 services' button is pressed in preferences</li>
2869 <li>Annotation off by one in Jalview v2_3 example project</li>
2870 <li>Structures imported from file and saved in project
2871 get name like jalview_pdb1234.txt when reloaded</li>
2872 <li>Jalview does not always retrieve progress of a JABAWS
2873 job execution in full once it is complete</li>
2874 </ul> <em>Applet</em>
2876 <li>Alignment height set incorrectly when lots of
2877 annotation rows are displayed</li>
2878 <li>Relative URLs in feature HTML text not resolved to
2880 <li>View follows highlighting does not work for positions
2882 <li><= shown as = in tooltip</li>
2883 <li>Export features raises exception when no features
2885 <li>Separator string used for serialising lists of IDs
2886 for javascript api is modified when separator string
2887 provided as parameter</li>
2888 <li>Null pointer exception when selecting tree leaves for
2889 alignment with no existing selection</li>
2890 <li>Relative URLs for datasources assumed to be relative
2891 to applet's codebase</li>
2892 <li>Status bar not updated after finished searching and
2893 search wraps around to first result</li>
2894 <li>StructureSelectionManager instance shared between
2895 several Jalview applets causes race conditions and memory
2897 <li>Hover tooltip and mouseover of position on structure
2898 not sent from Jmol in applet</li>
2899 <li>Certain sequences of javascript method calls to
2900 applet API fatally hang browser</li>
2901 </ul> <em>General</em>
2903 <li>View follows structure mouseover scrolls beyond
2904 position with wrapped view and hidden regions</li>
2905 <li>Find sequence position moves to wrong residue
2906 with/without hidden columns</li>
2907 <li>Sequence length given in alignment properties window
2909 <li>InvalidNumberFormat exceptions thrown when trying to
2910 import PDB like structure files</li>
2911 <li>Positional search results are only highlighted
2912 between user-supplied sequence start/end bounds</li>
2913 <li>End attribute of sequence is not validated</li>
2914 <li>Find dialog only finds first sequence containing a
2915 given sequence position</li>
2916 <li>Sequence numbering not preserved in MSF alignment
2918 <li>Jalview PDB file reader does not extract sequence
2919 from nucleotide chains correctly</li>
2920 <li>Structure colours not updated when tree partition
2921 changed in alignment</li>
2922 <li>Sequence associated secondary structure not correctly
2923 parsed in interleaved stockholm</li>
2924 <li>Colour by annotation dialog does not restore current
2926 <li>Hiding (nearly) all sequences doesn't work
2928 <li>Sequences containing lowercase letters are not
2929 properly associated with their pdb files</li>
2930 </ul> <em>Documentation and Development</em>
2932 <li>schemas/JalviewWsParamSet.xsd corrupted by
2933 ApplyCopyright tool</li>
2938 <div align="center">
2939 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2942 <td><em>Application</em>
2944 <li>New warning dialog when the Jalview Desktop cannot
2945 contact web services</li>
2946 <li>JABA service parameters for a preset are shown in
2947 service job window</li>
2948 <li>JABA Service menu entries reworded</li>
2952 <li>Modeller PIR IO broken - cannot correctly import a
2953 pir file emitted by Jalview</li>
2954 <li>Existing feature settings transferred to new
2955 alignment view created from cut'n'paste</li>
2956 <li>Improved test for mixed amino/nucleotide chains when
2957 parsing PDB files</li>
2958 <li>Consensus and conservation annotation rows
2959 occasionally become blank for all new windows</li>
2960 <li>Exception raised when right clicking above sequences
2961 in wrapped view mode</li>
2962 </ul> <em>Application</em>
2964 <li>multiple multiply aligned structure views cause cpu
2965 usage to hit 100% and computer to hang</li>
2966 <li>Web Service parameter layout breaks for long user
2967 parameter names</li>
2968 <li>Jaba service discovery hangs desktop if Jaba server
2975 <div align="center">
2976 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2979 <td><em>Application</em>
2981 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2982 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2985 <li>Web Services preference tab</li>
2986 <li>Analysis parameters dialog box and user defined
2988 <li>Improved speed and layout of Envision2 service menu</li>
2989 <li>Superpose structures using associated sequence
2991 <li>Export coordinates and projection as CSV from PCA
2993 </ul> <em>Applet</em>
2995 <li>enable javascript: execution by the applet via the
2996 link out mechanism</li>
2997 </ul> <em>Other</em>
2999 <li>Updated the Jmol Jalview interface to work with Jmol
3001 <li>The Jalview Desktop and JalviewLite applet now
3002 require Java 1.5</li>
3003 <li>Allow Jalview feature colour specification for GFF
3004 sequence annotation files</li>
3005 <li>New 'colour by label' keword in Jalview feature file
3006 type colour specification</li>
3007 <li>New Jalview Desktop Groovy API method that allows a
3008 script to check if it being run in an interactive session or
3009 in a batch operation from the Jalview command line</li>
3013 <li>clustalx colourscheme colours Ds preferentially when
3014 both D+E are present in over 50% of the column</li>
3015 </ul> <em>Application</em>
3017 <li>typo in AlignmentFrame->View->Hide->all but
3018 selected Regions menu item</li>
3019 <li>sequence fetcher replaces ',' for ';' when the ',' is
3020 part of a valid accession ID</li>
3021 <li>fatal OOM if object retrieved by sequence fetcher
3022 runs out of memory</li>
3023 <li>unhandled Out of Memory Error when viewing pca
3024 analysis results</li>
3025 <li>InstallAnywhere builds fail to launch on OS X java
3026 10.5 update 4 (due to apple Java 1.6 update)</li>
3027 <li>Installanywhere Jalview silently fails to launch</li>
3028 </ul> <em>Applet</em>
3030 <li>Jalview.getFeatureGroups() raises an
3031 ArrayIndexOutOfBoundsException if no feature groups are
3038 <div align="center">
3039 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
3045 <li>Alignment prettyprinter doesn't cope with long
3047 <li>clustalx colourscheme colours Ds preferentially when
3048 both D+E are present in over 50% of the column</li>
3049 <li>nucleic acid structures retrieved from PDB do not
3050 import correctly</li>
3051 <li>More columns get selected than were clicked on when a
3052 number of columns are hidden</li>
3053 <li>annotation label popup menu not providing correct
3054 add/hide/show options when rows are hidden or none are
3056 <li>Stockholm format shown in list of readable formats,
3057 and parser copes better with alignments from RFAM.</li>
3058 <li>CSV output of consensus only includes the percentage
3059 of all symbols if sequence logo display is enabled</li>
3061 </ul> <em>Applet</em>
3063 <li>annotation panel disappears when annotation is
3065 </ul> <em>Application</em>
3067 <li>Alignment view not redrawn properly when new
3068 alignment opened where annotation panel is visible but no
3069 annotations are present on alignment</li>
3070 <li>pasted region containing hidden columns is
3071 incorrectly displayed in new alignment window</li>
3072 <li>Jalview slow to complete operations when stdout is
3073 flooded (fix is to close the Jalview console)</li>
3074 <li>typo in AlignmentFrame->View->Hide->all but
3075 selected Rregions menu item.</li>
3076 <li>inconsistent group submenu and Format submenu entry
3077 'Un' or 'Non'conserved</li>
3078 <li>Sequence feature settings are being shared by
3079 multiple distinct alignments</li>
3080 <li>group annotation not recreated when tree partition is
3082 <li>double click on group annotation to select sequences
3083 does not propagate to associated trees</li>
3084 <li>Mac OSX specific issues:
3086 <li>exception raised when mouse clicked on desktop
3087 window background</li>
3088 <li>Desktop menu placed on menu bar and application
3089 name set correctly</li>
3090 <li>sequence feature settings not wide enough for the
3091 save feature colourscheme button</li>
3100 <div align="center">
3101 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3104 <td><em>New Capabilities</em>
3106 <li>URL links generated from description line for
3107 regular-expression based URL links (applet and application)
3109 <li>Non-positional feature URL links are shown in link
3111 <li>Linked viewing of nucleic acid sequences and
3113 <li>Automatic Scrolling option in View menu to display
3114 the currently highlighted region of an alignment.</li>
3115 <li>Order an alignment by sequence length, or using the
3116 average score or total feature count for each sequence.</li>
3117 <li>Shading features by score or associated description</li>
3118 <li>Subdivide alignment and groups based on identity of
3119 selected subsequence (Make Groups from Selection).</li>
3120 <li>New hide/show options including Shift+Control+H to
3121 hide everything but the currently selected region.</li>
3122 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3123 </ul> <em>Application</em>
3125 <li>Fetch DB References capabilities and UI expanded to
3126 support retrieval from DAS sequence sources</li>
3127 <li>Local DAS Sequence sources can be added via the
3128 command line or via the Add local source dialog box.</li>
3129 <li>DAS Dbref and DbxRef feature types are parsed as
3130 database references and protein_name is parsed as
3131 description line (BioSapiens terms).</li>
3132 <li>Enable or disable non-positional feature and database
3133 references in sequence ID tooltip from View menu in
3135 <!-- <li>New hidden columns and rows and representatives capabilities
3136 in annotations file (in progress - not yet fully implemented)</li> -->
3137 <li>Group-associated consensus, sequence logos and
3138 conservation plots</li>
3139 <li>Symbol distributions for each column can be exported
3140 and visualized as sequence logos</li>
3141 <li>Optionally scale multi-character column labels to fit
3142 within each column of annotation row<!-- todo for applet -->
3144 <li>Optional automatic sort of associated alignment view
3145 when a new tree is opened.</li>
3146 <li>Jalview Java Console</li>
3147 <li>Better placement of desktop window when moving
3148 between different screens.</li>
3149 <li>New preference items for sequence ID tooltip and
3150 consensus annotation</li>
3151 <li>Client to submit sequences and IDs to Envision2
3153 <li><em>Vamsas Capabilities</em>
3155 <li>Improved VAMSAS synchronization (Jalview archive
3156 used to preserve views, structures, and tree display
3158 <li>Import of vamsas documents from disk or URL via
3160 <li>Sharing of selected regions between views and
3161 with other VAMSAS applications (Experimental feature!)</li>
3162 <li>Updated API to VAMSAS version 0.2</li>
3164 </ul> <em>Applet</em>
3166 <li>Middle button resizes annotation row height</li>
3169 <li>sortByTree (true/false) - automatically sort the
3170 associated alignment view by the tree when a new tree is
3172 <li>showTreeBootstraps (true/false) - show or hide
3173 branch bootstraps (default is to show them if available)</li>
3174 <li>showTreeDistances (true/false) - show or hide
3175 branch lengths (default is to show them if available)</li>
3176 <li>showUnlinkedTreeNodes (true/false) - indicate if
3177 unassociated nodes should be highlighted in the tree
3179 <li>heightScale and widthScale (1.0 or more) -
3180 increase the height or width of a cell in the alignment
3181 grid relative to the current font size.</li>
3184 <li>Non-positional features displayed in sequence ID
3186 </ul> <em>Other</em>
3188 <li>Features format: graduated colour definitions and
3189 specification of feature scores</li>
3190 <li>Alignment Annotations format: new keywords for group
3191 associated annotation (GROUP_REF) and annotation row display
3192 properties (ROW_PROPERTIES)</li>
3193 <li>XML formats extended to support graduated feature
3194 colourschemes, group associated annotation, and profile
3195 visualization settings.</li></td>
3198 <li>Source field in GFF files parsed as feature source
3199 rather than description</li>
3200 <li>Non-positional features are now included in sequence
3201 feature and gff files (controlled via non-positional feature
3202 visibility in tooltip).</li>
3203 <li>URL links generated for all feature links (bugfix)</li>
3204 <li>Added URL embedding instructions to features file
3206 <li>Codons containing ambiguous nucleotides translated as
3207 'X' in peptide product</li>
3208 <li>Match case switch in find dialog box works for both
3209 sequence ID and sequence string and query strings do not
3210 have to be in upper case to match case-insensitively.</li>
3211 <li>AMSA files only contain first column of
3212 multi-character column annotation labels</li>
3213 <li>Jalview Annotation File generation/parsing consistent
3214 with documentation (e.g. Stockholm annotation can be
3215 exported and re-imported)</li>
3216 <li>PDB files without embedded PDB IDs given a friendly
3218 <li>Find incrementally searches ID string matches as well
3219 as subsequence matches, and correctly reports total number
3223 <li>Better handling of exceptions during sequence
3225 <li>Dasobert generated non-positional feature URL
3226 link text excludes the start_end suffix</li>
3227 <li>DAS feature and source retrieval buttons disabled
3228 when fetch or registry operations in progress.</li>
3229 <li>PDB files retrieved from URLs are cached properly</li>
3230 <li>Sequence description lines properly shared via
3232 <li>Sequence fetcher fetches multiple records for all
3234 <li>Ensured that command line das feature retrieval
3235 completes before alignment figures are generated.</li>
3236 <li>Reduced time taken when opening file browser for
3238 <li>isAligned check prior to calculating tree, PCA or
3239 submitting an MSA to JNet now excludes hidden sequences.</li>
3240 <li>User defined group colours properly recovered
3241 from Jalview projects.</li>
3250 <div align="center">
3251 <strong>2.4.0.b2</strong><br> 28/10/2009
3256 <li>Experimental support for google analytics usage
3258 <li>Jalview privacy settings (user preferences and docs).</li>
3263 <li>Race condition in applet preventing startup in
3265 <li>Exception when feature created from selection beyond
3266 length of sequence.</li>
3267 <li>Allow synthetic PDB files to be imported gracefully</li>
3268 <li>Sequence associated annotation rows associate with
3269 all sequences with a given id</li>
3270 <li>Find function matches case-insensitively for sequence
3271 ID string searches</li>
3272 <li>Non-standard characters do not cause pairwise
3273 alignment to fail with exception</li>
3274 </ul> <em>Application Issues</em>
3276 <li>Sequences are now validated against EMBL database</li>
3277 <li>Sequence fetcher fetches multiple records for all
3279 </ul> <em>InstallAnywhere Issues</em>
3281 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3282 issue with installAnywhere mechanism)</li>
3283 <li>Command line launching of JARs from InstallAnywhere
3284 version (java class versioning error fixed)</li>
3291 <div align="center">
3292 <strong>2.4</strong><br> 27/8/2008
3295 <td><em>User Interface</em>
3297 <li>Linked highlighting of codon and amino acid from
3298 translation and protein products</li>
3299 <li>Linked highlighting of structure associated with
3300 residue mapping to codon position</li>
3301 <li>Sequence Fetcher provides example accession numbers
3302 and 'clear' button</li>
3303 <li>MemoryMonitor added as an option under Desktop's
3305 <li>Extract score function to parse whitespace separated
3306 numeric data in description line</li>
3307 <li>Column labels in alignment annotation can be centred.</li>
3308 <li>Tooltip for sequence associated annotation give name
3310 </ul> <em>Web Services and URL fetching</em>
3312 <li>JPred3 web service</li>
3313 <li>Prototype sequence search client (no public services
3315 <li>Fetch either seed alignment or full alignment from
3317 <li>URL Links created for matching database cross
3318 references as well as sequence ID</li>
3319 <li>URL Links can be created using regular-expressions</li>
3320 </ul> <em>Sequence Database Connectivity</em>
3322 <li>Retrieval of cross-referenced sequences from other
3324 <li>Generalised database reference retrieval and
3325 validation to all fetchable databases</li>
3326 <li>Fetch sequences from DAS sources supporting the
3327 sequence command</li>
3328 </ul> <em>Import and Export</em>
3329 <li>export annotation rows as CSV for spreadsheet import</li>
3330 <li>Jalview projects record alignment dataset associations,
3331 EMBL products, and cDNA sequence mappings</li>
3332 <li>Sequence Group colour can be specified in Annotation
3334 <li>Ad-hoc colouring of group in Annotation File using RGB
3335 triplet as name of colourscheme</li>
3336 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3338 <li>treenode binding for VAMSAS tree exchange</li>
3339 <li>local editing and update of sequences in VAMSAS
3340 alignments (experimental)</li>
3341 <li>Create new or select existing session to join</li>
3342 <li>load and save of vamsas documents</li>
3343 </ul> <em>Application command line</em>
3345 <li>-tree parameter to open trees (introduced for passing
3347 <li>-fetchfrom command line argument to specify nicknames
3348 of DAS servers to query for alignment features</li>
3349 <li>-dasserver command line argument to add new servers
3350 that are also automatically queried for features</li>
3351 <li>-groovy command line argument executes a given groovy
3352 script after all input data has been loaded and parsed</li>
3353 </ul> <em>Applet-Application data exchange</em>
3355 <li>Trees passed as applet parameters can be passed to
3356 application (when using "View in full
3357 application")</li>
3358 </ul> <em>Applet Parameters</em>
3360 <li>feature group display control parameter</li>
3361 <li>debug parameter</li>
3362 <li>showbutton parameter</li>
3363 </ul> <em>Applet API methods</em>
3365 <li>newView public method</li>
3366 <li>Window (current view) specific get/set public methods</li>
3367 <li>Feature display control methods</li>
3368 <li>get list of currently selected sequences</li>
3369 </ul> <em>New Jalview distribution features</em>
3371 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3372 <li>RELEASE file gives build properties for the latest
3373 Jalview release.</li>
3374 <li>Java 1.1 Applet build made easier and donotobfuscate
3375 property controls execution of obfuscator</li>
3376 <li>Build target for generating source distribution</li>
3377 <li>Debug flag for javacc</li>
3378 <li>.jalview_properties file is documented (slightly) in
3379 jalview.bin.Cache</li>
3380 <li>Continuous Build Integration for stable and
3381 development version of Application, Applet and source
3386 <li>selected region output includes visible annotations
3387 (for certain formats)</li>
3388 <li>edit label/displaychar contains existing label/char
3390 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3391 <li>shorter peptide product names from EMBL records</li>
3392 <li>Newick string generator makes compact representations</li>
3393 <li>bootstrap values parsed correctly for tree files with
3395 <li>pathological filechooser bug avoided by not allowing
3396 filenames containing a ':'</li>
3397 <li>Fixed exception when parsing GFF files containing
3398 global sequence features</li>
3399 <li>Alignment datasets are finalized only when number of
3400 references from alignment sequences goes to zero</li>
3401 <li>Close of tree branch colour box without colour
3402 selection causes cascading exceptions</li>
3403 <li>occasional negative imgwidth exceptions</li>
3404 <li>better reporting of non-fatal warnings to user when
3405 file parsing fails.</li>
3406 <li>Save works when Jalview project is default format</li>
3407 <li>Save as dialog opened if current alignment format is
3408 not a valid output format</li>
3409 <li>UniProt canonical names introduced for both das and
3411 <li>Histidine should be midblue (not pink!) in Zappo</li>
3412 <li>error messages passed up and output when data read
3414 <li>edit undo recovers previous dataset sequence when
3415 sequence is edited</li>
3416 <li>allow PDB files without pdb ID HEADER lines (like
3417 those generated by MODELLER) to be read in properly</li>
3418 <li>allow reading of JPred concise files as a normal
3420 <li>Stockholm annotation parsing and alignment properties
3421 import fixed for PFAM records</li>
3422 <li>Structure view windows have correct name in Desktop
3424 <li>annotation consisting of sequence associated scores
3425 can be read and written correctly to annotation file</li>
3426 <li>Aligned cDNA translation to aligned peptide works
3428 <li>Fixed display of hidden sequence markers and
3429 non-italic font for representatives in Applet</li>
3430 <li>Applet Menus are always embedded in applet window on
3432 <li>Newly shown features appear at top of stack (in
3434 <li>Annotations added via parameter not drawn properly
3435 due to null pointer exceptions</li>
3436 <li>Secondary structure lines are drawn starting from
3437 first column of alignment</li>
3438 <li>UniProt XML import updated for new schema release in
3440 <li>Sequence feature to sequence ID match for Features
3441 file is case-insensitive</li>
3442 <li>Sequence features read from Features file appended to
3443 all sequences with matching IDs</li>
3444 <li>PDB structure coloured correctly for associated views
3445 containing a sub-sequence</li>
3446 <li>PDB files can be retrieved by applet from Jar files</li>
3447 <li>feature and annotation file applet parameters
3448 referring to different directories are retrieved correctly</li>
3449 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3450 <li>Fixed application hang whilst waiting for
3451 splash-screen version check to complete</li>
3452 <li>Applet properly URLencodes input parameter values
3453 when passing them to the launchApp service</li>
3454 <li>display name and local features preserved in results
3455 retrieved from web service</li>
3456 <li>Visual delay indication for sequence retrieval and
3457 sequence fetcher initialisation</li>
3458 <li>updated Application to use DAS 1.53e version of
3459 dasobert DAS client</li>
3460 <li>Re-instated Full AMSA support and .amsa file
3462 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3470 <div align="center">
3471 <strong>2.3</strong><br> 9/5/07
3476 <li>Jmol 11.0.2 integration</li>
3477 <li>PDB views stored in Jalview XML files</li>
3478 <li>Slide sequences</li>
3479 <li>Edit sequence in place</li>
3480 <li>EMBL CDS features</li>
3481 <li>DAS Feature mapping</li>
3482 <li>Feature ordering</li>
3483 <li>Alignment Properties</li>
3484 <li>Annotation Scores</li>
3485 <li>Sort by scores</li>
3486 <li>Feature/annotation editing in applet</li>
3491 <li>Headless state operation in 2.2.1</li>
3492 <li>Incorrect and unstable DNA pairwise alignment</li>
3493 <li>Cut and paste of sequences with annotation</li>
3494 <li>Feature group display state in XML</li>
3495 <li>Feature ordering in XML</li>
3496 <li>blc file iteration selection using filename # suffix</li>
3497 <li>Stockholm alignment properties</li>
3498 <li>Stockhom alignment secondary structure annotation</li>
3499 <li>2.2.1 applet had no feature transparency</li>
3500 <li>Number pad keys can be used in cursor mode</li>
3501 <li>Structure Viewer mirror image resolved</li>
3508 <div align="center">
3509 <strong>2.2.1</strong><br> 12/2/07
3514 <li>Non standard characters can be read and displayed
3515 <li>Annotations/Features can be imported/exported to the
3517 <li>Applet allows editing of sequence/annotation/group
3518 name & description
3519 <li>Preference setting to display sequence name in
3521 <li>Annotation file format extended to allow
3522 Sequence_groups to be defined
3523 <li>Default opening of alignment overview panel can be
3524 specified in preferences
3525 <li>PDB residue numbering annotation added to associated
3531 <li>Applet crash under certain Linux OS with Java 1.6
3533 <li>Annotation file export / import bugs fixed
3534 <li>PNG / EPS image output bugs fixed
3540 <div align="center">
3541 <strong>2.2</strong><br> 27/11/06
3546 <li>Multiple views on alignment
3547 <li>Sequence feature editing
3548 <li>"Reload" alignment
3549 <li>"Save" to current filename
3550 <li>Background dependent text colour
3551 <li>Right align sequence ids
3552 <li>User-defined lower case residue colours
3555 <li>Menu item accelerator keys
3556 <li>Control-V pastes to current alignment
3557 <li>Cancel button for DAS Feature Fetching
3558 <li>PCA and PDB Viewers zoom via mouse roller
3559 <li>User-defined sub-tree colours and sub-tree selection
3561 <li>'New Window' button on the 'Output to Text box'
3566 <li>New memory efficient Undo/Redo System
3567 <li>Optimised symbol lookups and conservation/consensus
3569 <li>Region Conservation/Consensus recalculated after
3571 <li>Fixed Remove Empty Columns Bug (empty columns at end
3573 <li>Slowed DAS Feature Fetching for increased robustness.
3575 <li>Made angle brackets in ASCII feature descriptions
3577 <li>Re-instated Zoom function for PCA
3578 <li>Sequence descriptions conserved in web service
3580 <li>UniProt ID discoverer uses any word separated by
3582 <li>WsDbFetch query/result association resolved
3583 <li>Tree leaf to sequence mapping improved
3584 <li>Smooth fonts switch moved to FontChooser dialog box.
3591 <div align="center">
3592 <strong>2.1.1</strong><br> 12/9/06
3597 <li>Copy consensus sequence to clipboard</li>
3602 <li>Image output - rightmost residues are rendered if
3603 sequence id panel has been resized</li>
3604 <li>Image output - all offscreen group boundaries are
3606 <li>Annotation files with sequence references - all
3607 elements in file are relative to sequence position</li>
3608 <li>Mac Applet users can use Alt key for group editing</li>
3614 <div align="center">
3615 <strong>2.1</strong><br> 22/8/06
3620 <li>MAFFT Multiple Alignment in default Web Service list</li>
3621 <li>DAS Feature fetching</li>
3622 <li>Hide sequences and columns</li>
3623 <li>Export Annotations and Features</li>
3624 <li>GFF file reading / writing</li>
3625 <li>Associate structures with sequences from local PDB
3627 <li>Add sequences to exisiting alignment</li>
3628 <li>Recently opened files / URL lists</li>
3629 <li>Applet can launch the full application</li>
3630 <li>Applet has transparency for features (Java 1.2
3632 <li>Applet has user defined colours parameter</li>
3633 <li>Applet can load sequences from parameter
3634 "sequence<em>x</em>"
3640 <li>Redundancy Panel reinstalled in the Applet</li>
3641 <li>Monospaced font - EPS / rescaling bug fixed</li>
3642 <li>Annotation files with sequence references bug fixed</li>
3648 <div align="center">
3649 <strong>2.08.1</strong><br> 2/5/06
3654 <li>Change case of selected region from Popup menu</li>
3655 <li>Choose to match case when searching</li>
3656 <li>Middle mouse button and mouse movement can compress /
3657 expand the visible width and height of the alignment</li>
3662 <li>Annotation Panel displays complete JNet results</li>
3668 <div align="center">
3669 <strong>2.08b</strong><br> 18/4/06
3675 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3676 <li>Righthand label on wrapped alignments shows correct
3683 <div align="center">
3684 <strong>2.08</strong><br> 10/4/06
3689 <li>Editing can be locked to the selection area</li>
3690 <li>Keyboard editing</li>
3691 <li>Create sequence features from searches</li>
3692 <li>Precalculated annotations can be loaded onto
3694 <li>Features file allows grouping of features</li>
3695 <li>Annotation Colouring scheme added</li>
3696 <li>Smooth fonts off by default - Faster rendering</li>
3697 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3702 <li>Drag & Drop fixed on Linux</li>
3703 <li>Jalview Archive file faster to load/save, sequence
3704 descriptions saved.</li>
3710 <div align="center">
3711 <strong>2.07</strong><br> 12/12/05
3716 <li>PDB Structure Viewer enhanced</li>
3717 <li>Sequence Feature retrieval and display enhanced</li>
3718 <li>Choose to output sequence start-end after sequence
3719 name for file output</li>
3720 <li>Sequence Fetcher WSDBFetch@EBI</li>
3721 <li>Applet can read feature files, PDB files and can be
3722 used for HTML form input</li>
3727 <li>HTML output writes groups and features</li>
3728 <li>Group editing is Control and mouse click</li>
3729 <li>File IO bugs</li>
3735 <div align="center">
3736 <strong>2.06</strong><br> 28/9/05
3741 <li>View annotations in wrapped mode</li>
3742 <li>More options for PCA viewer</li>
3747 <li>GUI bugs resolved</li>
3748 <li>Runs with -nodisplay from command line</li>
3754 <div align="center">
3755 <strong>2.05b</strong><br> 15/9/05
3760 <li>Choose EPS export as lineart or text</li>
3761 <li>Jar files are executable</li>
3762 <li>Can read in Uracil - maps to unknown residue</li>
3767 <li>Known OutOfMemory errors give warning message</li>
3768 <li>Overview window calculated more efficiently</li>
3769 <li>Several GUI bugs resolved</li>
3775 <div align="center">
3776 <strong>2.05</strong><br> 30/8/05
3781 <li>Edit and annotate in "Wrapped" view</li>
3786 <li>Several GUI bugs resolved</li>
3792 <div align="center">
3793 <strong>2.04</strong><br> 24/8/05
3798 <li>Hold down mouse wheel & scroll to change font
3804 <li>Improved JPred client reliability</li>
3805 <li>Improved loading of Jalview files</li>
3811 <div align="center">
3812 <strong>2.03</strong><br> 18/8/05
3817 <li>Set Proxy server name and port in preferences</li>
3818 <li>Multiple URL links from sequence ids</li>
3819 <li>User Defined Colours can have a scheme name and added
3821 <li>Choose to ignore gaps in consensus calculation</li>
3822 <li>Unix users can set default web browser</li>
3823 <li>Runs without GUI for batch processing</li>
3824 <li>Dynamically generated Web Service Menus</li>
3829 <li>InstallAnywhere download for Sparc Solaris</li>
3835 <div align="center">
3836 <strong>2.02</strong><br> 18/7/05
3842 <li>Copy & Paste order of sequences maintains
3843 alignment order.</li>
3849 <div align="center">
3850 <strong>2.01</strong><br> 12/7/05
3855 <li>Use delete key for deleting selection.</li>
3856 <li>Use Mouse wheel to scroll sequences.</li>
3857 <li>Help file updated to describe how to add alignment
3859 <li>Version and build date written to build properties
3861 <li>InstallAnywhere installation will check for updates
3862 at launch of Jalview.</li>
3867 <li>Delete gaps bug fixed.</li>
3868 <li>FileChooser sorts columns.</li>
3869 <li>Can remove groups one by one.</li>
3870 <li>Filechooser icons installed.</li>
3871 <li>Finder ignores return character when searching.
3872 Return key will initiate a search.<br>
3879 <div align="center">
3880 <strong>2.0</strong><br> 20/6/05
3885 <li>New codebase</li>