3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
76 <td><div align="left">
84 <td><div align="left">
87 <!-- JAL-2778 -->Slow redraw when Overview panel shown operlapping alignment panel
94 <td width="60" nowrap>
96 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
99 <td><div align="left">
100 <ul><li>Updated Certum Codesigning Certificate
101 (Valid till 30th November 2018)</li></ul></div></td>
102 <td><div align="left">
105 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
106 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
107 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
108 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
109 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
110 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
111 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
117 <td width="60" nowrap>
119 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
122 <td><div align="left">
126 <!-- JAL-2446 -->Faster and more efficient management and
127 rendering of sequence features
130 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
131 429 rate limit request hander
134 <!-- JAL-2773 -->Structure views don't get updated unless
135 their colours have changed
138 <!-- JAL-2495 -->All linked sequences are highlighted for
139 a structure mousover (Jmol) or selection (Chimera)
142 <!-- JAL-2790 -->'Cancel' button in progress bar for
143 JABAWS AACon, RNAAliFold and Disorder prediction jobs
146 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
147 view from Ensembl locus cross-references
150 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
154 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
155 feature can be disabled
158 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
159 PDB easier retrieval of sequences for lists of IDs
162 <!-- JAL-2758 -->Short names for sequences retrieved from
168 <li>Groovy interpreter updated to 2.4.12</li>
169 <li>Example groovy script for generating a matrix of
170 percent identity scores for current alignment.</li>
172 <em>Testing and Deployment</em>
175 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
179 <td><div align="left">
183 <!-- JAL-2643 -->Pressing tab after updating the colour
184 threshold text field doesn't trigger an update to the
188 <!-- JAL-2682 -->Race condition when parsing sequence ID
192 <!-- JAL-2608 -->Overview windows are also closed when
193 alignment window is closed
196 <!-- JAL-2548 -->Export of features doesn't always respect
200 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
201 takes a long time in Cursor mode
207 <!-- JAL-2777 -->Structures with whitespace chainCode
208 cannot be viewed in Chimera
211 <!-- JAL-2728 -->Protein annotation panel too high in
215 <!-- JAL-2757 -->Can't edit the query after the server
216 error warning icon is shown in Uniprot and PDB Free Text
220 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
223 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
226 <!-- JAL-2739 -->Hidden column marker in last column not
227 rendered when switching back from Wrapped to normal view
230 <!-- JAL-2768 -->Annotation display corrupted when
231 scrolling right in unwapped alignment view
234 <!-- JAL-2542 -->Existing features on subsequence
235 incorrectly relocated when full sequence retrieved from
239 <!-- JAL-2733 -->Last reported memory still shown when
240 Desktop->Show Memory is unticked (OSX only)
243 <!-- JAL-2658 -->Amend Features dialog doesn't allow
244 features of same type and group to be selected for
248 <!-- JAL-2524 -->Jalview becomes sluggish in wide
249 alignments when hidden columns are present
252 <!-- JAL-2392 -->Jalview freezes when loading and
253 displaying several structures
256 <!-- JAL-2732 -->Black outlines left after resizing or
260 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
261 within the Jalview desktop on OSX
264 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
265 when in wrapped alignment mode
268 <!-- JAL-2636 -->Scale mark not shown when close to right
269 hand end of alignment
272 <!-- JAL-2684 -->Pairwise alignment of selected regions of
273 each selected sequence do not have correct start/end
277 <!-- JAL-2793 -->Alignment ruler height set incorrectly
278 after canceling the Alignment Window's Font dialog
281 <!-- JAL-2036 -->Show cross-references not enabled after
282 restoring project until a new view is created
285 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
286 URL links appears when only default EMBL-EBI link is
287 configured (since 2.10.2b2)
290 <!-- JAL-2775 -->Overview redraws whole window when box
294 <!-- JAL-2225 -->Structure viewer doesn't map all chains
295 in a multi-chain structure when viewing alignment
296 involving more than one chain (since 2.10)
299 <!-- JAL-2811 -->Double residue highlights in cursor mode
300 if new selection moves alignment window
303 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
304 arrow key in cursor mode to pass hidden column marker
307 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
308 that produces correctly annotated transcripts and products
311 <!-- JAL-2776 -->Toggling a feature group after first time
312 doesn't update associated structure view
315 <em>Applet</em><br />
318 <!-- JAL-2687 -->Concurrent modification exception when
319 closing alignment panel
322 <em>BioJSON</em><br />
325 <!-- JAL-2546 -->BioJSON export does not preserve
326 non-positional features
329 <em>New Known Issues</em>
332 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
333 sequence features correctly (for many previous versions of
337 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
338 using cursor in wrapped panel other than top
341 <!-- JAL-2791 -->Select columns containing feature ignores
342 graduated colour threshold
345 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
346 always preserve numbering and sequence features
349 <em>Known Java 9 Issues</em>
352 <!-- JAL-2902 -->Groovy Console very slow to open and is
353 not responsive when entering characters (Webstart, Java
360 <td width="60" nowrap>
362 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
363 <em>2/10/2017</em></strong>
366 <td><div align="left">
367 <em>New features in Jalview Desktop</em>
370 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
372 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
376 <td><div align="left">
380 <td width="60" nowrap>
382 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
383 <em>7/9/2017</em></strong>
386 <td><div align="left">
390 <!-- JAL-2588 -->Show gaps in overview window by colouring
391 in grey (sequences used to be coloured grey, and gaps were
395 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
399 <!-- JAL-2587 -->Overview updates immediately on increase
400 in size and progress bar shown as higher resolution
401 overview is recalculated
406 <td><div align="left">
410 <!-- JAL-2664 -->Overview window redraws every hidden
411 column region row by row
414 <!-- JAL-2681 -->duplicate protein sequences shown after
415 retrieving Ensembl crossrefs for sequences from Uniprot
418 <!-- JAL-2603 -->Overview window throws NPE if show boxes
419 format setting is unticked
422 <!-- JAL-2610 -->Groups are coloured wrongly in overview
423 if group has show boxes format setting unticked
426 <!-- JAL-2672,JAL-2665 -->Redraw problems when
427 autoscrolling whilst dragging current selection group to
428 include sequences and columns not currently displayed
431 <!-- JAL-2691 -->Not all chains are mapped when multimeric
432 assemblies are imported via CIF file
435 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
436 displayed when threshold or conservation colouring is also
440 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
444 <!-- JAL-2673 -->Jalview continues to scroll after
445 dragging a selected region off the visible region of the
449 <!-- JAL-2724 -->Cannot apply annotation based
450 colourscheme to all groups in a view
453 <!-- JAL-2511 -->IDs don't line up with sequences
454 initially after font size change using the Font chooser or
461 <td width="60" nowrap>
463 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
466 <td><div align="left">
467 <em>Calculations</em>
471 <!-- JAL-1933 -->Occupancy annotation row shows number of
472 ungapped positions in each column of the alignment.
475 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
476 a calculation dialog box
479 <!-- JAL-2379 -->Revised implementation of PCA for speed
480 and memory efficiency (~30x faster)
483 <!-- JAL-2403 -->Revised implementation of sequence
484 similarity scores as used by Tree, PCA, Shading Consensus
485 and other calculations
488 <!-- JAL-2416 -->Score matrices are stored as resource
489 files within the Jalview codebase
492 <!-- JAL-2500 -->Trees computed on Sequence Feature
493 Similarity may have different topology due to increased
500 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
501 model for alignments and groups
504 <!-- JAL-384 -->Custom shading schemes created via groovy
511 <!-- JAL-2526 -->Efficiency improvements for interacting
512 with alignment and overview windows
515 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
519 <!-- JAL-2388 -->Hidden columns and sequences can be
523 <!-- JAL-2611 -->Click-drag in visible area allows fine
524 adjustment of visible position
528 <em>Data import/export</em>
531 <!-- JAL-2535 -->Posterior probability annotation from
532 Stockholm files imported as sequence associated annotation
535 <!-- JAL-2507 -->More robust per-sequence positional
536 annotation input/output via stockholm flatfile
539 <!-- JAL-2533 -->Sequence names don't include file
540 extension when importing structure files without embedded
541 names or PDB accessions
544 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
545 format sequence substitution matrices
548 <em>User Interface</em>
551 <!-- JAL-2447 --> Experimental Features Checkbox in
552 Desktop's Tools menu to hide or show untested features in
556 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
557 via Overview or sequence motif search operations
560 <!-- JAL-2547 -->Amend sequence features dialog box can be
561 opened by double clicking gaps within sequence feature
565 <!-- JAL-1476 -->Status bar message shown when not enough
566 aligned positions were available to create a 3D structure
570 <em>3D Structure</em>
573 <!-- JAL-2430 -->Hidden regions in alignment views are not
574 coloured in linked structure views
577 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
578 file-based command exchange
581 <!-- JAL-2375 -->Structure chooser automatically shows
582 Cached Structures rather than querying the PDBe if
583 structures are already available for sequences
586 <!-- JAL-2520 -->Structures imported via URL are cached in
587 the Jalview project rather than downloaded again when the
591 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
592 to transfer Chimera's structure attributes as Jalview
593 features, and vice-versa (<strong>Experimental
597 <em>Web Services</em>
600 <!-- JAL-2549 -->Updated JABAWS client to v2.2
603 <!-- JAL-2335 -->Filter non-standard amino acids and
604 nucleotides when submitting to AACon and other MSA
608 <!-- JAL-2316, -->URLs for viewing database
609 cross-references provided by identifiers.org and the
617 <!-- JAL-2344 -->FileFormatI interface for describing and
618 identifying file formats (instead of String constants)
621 <!-- JAL-2228 -->FeatureCounter script refactored for
622 efficiency when counting all displayed features (not
623 backwards compatible with 2.10.1)
626 <em>Example files</em>
629 <!-- JAL-2631 -->Graduated feature colour style example
630 included in the example feature file
633 <em>Documentation</em>
636 <!-- JAL-2339 -->Release notes reformatted for readability
637 with the built-in Java help viewer
640 <!-- JAL-1644 -->Find documentation updated with 'search
641 sequence description' option
647 <!-- JAL-2485, -->External service integration tests for
648 Uniprot REST Free Text Search Client
651 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
654 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
659 <td><div align="left">
660 <em>Calculations</em>
663 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
664 matrix - C->R should be '-3'<br />Old matrix restored
665 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
667 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
668 Jalview's treatment of gaps in PCA and substitution matrix
669 based Tree calculations.<br /> <br />In earlier versions
670 of Jalview, gaps matching gaps were penalised, and gaps
671 matching non-gaps penalised even more. In the PCA
672 calculation, gaps were actually treated as non-gaps - so
673 different costs were applied, which meant Jalview's PCAs
674 were different to those produced by SeqSpace.<br />Jalview
675 now treats gaps in the same way as SeqSpace (ie it scores
676 them as 0). <br /> <br />Enter the following in the
677 Groovy console to restore pre-2.10.2 behaviour:<br />
678 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
679 // for 2.10.1 mode <br />
680 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
681 // to restore 2.10.2 mode <br /> <br /> <em>Note:
682 these settings will affect all subsequent tree and PCA
683 calculations (not recommended)</em></li>
685 <!-- JAL-2424 -->Fixed off-by-one bug that affected
686 scaling of branch lengths for trees computed using
687 Sequence Feature Similarity.
690 <!-- JAL-2377 -->PCA calculation could hang when
691 generating output report when working with highly
695 <!-- JAL-2544 --> Sort by features includes features to
696 right of selected region when gaps present on right-hand
700 <em>User Interface</em>
703 <!-- JAL-2346 -->Reopening Colour by annotation dialog
704 doesn't reselect a specific sequence's associated
705 annotation after it was used for colouring a view
708 <!-- JAL-2419 -->Current selection lost if popup menu
709 opened on a region of alignment without groups
712 <!-- JAL-2374 -->Popup menu not always shown for regions
713 of an alignment with overlapping groups
716 <!-- JAL-2310 -->Finder double counts if both a sequence's
717 name and description match
720 <!-- JAL-2370 -->Hiding column selection containing two
721 hidden regions results in incorrect hidden regions
724 <!-- JAL-2386 -->'Apply to all groups' setting when
725 changing colour does not apply Conservation slider value
729 <!-- JAL-2373 -->Percentage identity and conservation menu
730 items do not show a tick or allow shading to be disabled
733 <!-- JAL-2385 -->Conservation shading or PID threshold
734 lost when base colourscheme changed if slider not visible
737 <!-- JAL-2547 -->Sequence features shown in tooltip for
738 gaps before start of features
741 <!-- JAL-2623 -->Graduated feature colour threshold not
742 restored to UI when feature colour is edited
745 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
746 a time when scrolling vertically in wrapped mode.
749 <!-- JAL-2630 -->Structure and alignment overview update
750 as graduate feature colour settings are modified via the
754 <!-- JAL-2034 -->Overview window doesn't always update
755 when a group defined on the alignment is resized
758 <!-- JAL-2605 -->Mouseovers on left/right scale region in
759 wrapped view result in positional status updates
763 <!-- JAL-2563 -->Status bar doesn't show position for
764 ambiguous amino acid and nucleotide symbols
767 <!-- JAL-2602 -->Copy consensus sequence failed if
768 alignment included gapped columns
771 <!-- JAL-2473 -->Minimum size set for Jalview windows so
772 widgets don't permanently disappear
775 <!-- JAL-2503 -->Cannot select or filter quantitative
776 annotation that are shown only as column labels (e.g.
777 T-Coffee column reliability scores)
780 <!-- JAL-2594 -->Exception thrown if trying to create a
781 sequence feature on gaps only
784 <!-- JAL-2504 -->Features created with 'New feature'
785 button from a Find inherit previously defined feature type
786 rather than the Find query string
789 <!-- JAL-2423 -->incorrect title in output window when
790 exporting tree calculated in Jalview
793 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
794 and then revealing them reorders sequences on the
798 <!-- JAL-964 -->Group panel in sequence feature settings
799 doesn't update to reflect available set of groups after
800 interactively adding or modifying features
803 <!-- JAL-2225 -->Sequence Database chooser unusable on
807 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
808 only excluded gaps in current sequence and ignored
815 <!-- JAL-2421 -->Overview window visible region moves
816 erratically when hidden rows or columns are present
819 <!-- JAL-2362 -->Per-residue colourschemes applied via the
820 Structure Viewer's colour menu don't correspond to
824 <!-- JAL-2405 -->Protein specific colours only offered in
825 colour and group colour menu for protein alignments
828 <!-- JAL-2385 -->Colour threshold slider doesn't update to
829 reflect currently selected view or group's shading
833 <!-- JAL-2624 -->Feature colour thresholds not respected
834 when rendered on overview and structures when opacity at
838 <!-- JAL-2589 -->User defined gap colour not shown in
839 overview when features overlaid on alignment
842 <em>Data import/export</em>
845 <!-- JAL-2576 -->Very large alignments take a long time to
849 <!-- JAL-2507 -->Per-sequence RNA secondary structures
850 added after a sequence was imported are not written to
854 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
855 when importing RNA secondary structure via Stockholm
858 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
859 not shown in correct direction for simple pseudoknots
862 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
863 with lightGray or darkGray via features file (but can
867 <!-- JAL-2383 -->Above PID colour threshold not recovered
868 when alignment view imported from project
871 <!-- JAL-2520,JAL-2465 -->No mappings generated between
872 structure and sequences extracted from structure files
873 imported via URL and viewed in Jmol
876 <!-- JAL-2520 -->Structures loaded via URL are saved in
877 Jalview Projects rather than fetched via URL again when
878 the project is loaded and the structure viewed
881 <em>Web Services</em>
884 <!-- JAL-2519 -->EnsemblGenomes example failing after
885 release of Ensembl v.88
888 <!-- JAL-2366 -->Proxy server address and port always
889 appear enabled in Preferences->Connections
892 <!-- JAL-2461 -->DAS registry not found exceptions
893 removed from console output
896 <!-- JAL-2582 -->Cannot retrieve protein products from
897 Ensembl by Peptide ID
900 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
901 created from SIFTs, and spurious 'Couldn't open structure
902 in Chimera' errors raised after April 2017 update (problem
903 due to 'null' string rather than empty string used for
904 residues with no corresponding PDB mapping).
907 <em>Application UI</em>
910 <!-- JAL-2361 -->User Defined Colours not added to Colour
914 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
915 case' residues (button in colourscheme editor debugged and
916 new documentation and tooltips added)
919 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
920 doesn't restore group-specific text colour thresholds
923 <!-- JAL-2243 -->Feature settings panel does not update as
924 new features are added to alignment
927 <!-- JAL-2532 -->Cancel in feature settings reverts
928 changes to feature colours via the Amend features dialog
931 <!-- JAL-2506 -->Null pointer exception when attempting to
932 edit graduated feature colour via amend features dialog
936 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
937 selection menu changes colours of alignment views
940 <!-- JAL-2426 -->Spurious exceptions in console raised
941 from alignment calculation workers after alignment has
945 <!-- JAL-1608 -->Typo in selection popup menu - Create
946 groups now 'Create Group'
949 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
950 Create/Undefine group doesn't always work
953 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
954 shown again after pressing 'Cancel'
957 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
958 adjusts start position in wrap mode
961 <!-- JAL-2563 -->Status bar doesn't show positions for
962 ambiguous amino acids
965 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
966 CDS/Protein view after CDS sequences added for aligned
970 <!-- JAL-2592 -->User defined colourschemes called 'User
971 Defined' don't appear in Colours menu
977 <!-- JAL-2468 -->Switching between Nucleotide and Protein
978 score models doesn't always result in an updated PCA plot
981 <!-- JAL-2442 -->Features not rendered as transparent on
982 overview or linked structure view
985 <!-- JAL-2372 -->Colour group by conservation doesn't
989 <!-- JAL-2517 -->Hitting Cancel after applying
990 user-defined colourscheme doesn't restore original
997 <!-- JAL-2314 -->Unit test failure:
998 jalview.ws.jabaws.RNAStructExportImport setup fails
1001 <!-- JAL-2307 -->Unit test failure:
1002 jalview.ws.sifts.SiftsClientTest due to compatibility
1003 problems with deep array comparison equality asserts in
1004 successive versions of TestNG
1007 <!-- JAL-2479 -->Relocated StructureChooserTest and
1008 ParameterUtilsTest Unit tests to Network suite
1011 <em>New Known Issues</em>
1014 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1015 phase after a sequence motif find operation
1018 <!-- JAL-2550 -->Importing annotation file with rows
1019 containing just upper and lower case letters are
1020 interpreted as WUSS RNA secondary structure symbols
1023 <!-- JAL-2590 -->Cannot load and display Newick trees
1024 reliably from eggnog Ortholog database
1027 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1028 containing features of type Highlight' when 'B' is pressed
1029 to mark columns containing highlighted regions.
1032 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1033 doesn't always add secondary structure annotation.
1038 <td width="60" nowrap>
1039 <div align="center">
1040 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1043 <td><div align="left">
1047 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1048 for all consensus calculations
1051 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1054 <li>Updated Jalview's Certum code signing certificate
1057 <em>Application</em>
1060 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1061 set of database cross-references, sorted alphabetically
1064 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1065 from database cross references. Users with custom links
1066 will receive a <a href="webServices/urllinks.html#warning">warning
1067 dialog</a> asking them to update their preferences.
1070 <!-- JAL-2287-->Cancel button and escape listener on
1071 dialog warning user about disconnecting Jalview from a
1075 <!-- JAL-2320-->Jalview's Chimera control window closes if
1076 the Chimera it is connected to is shut down
1079 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1080 columns menu item to mark columns containing highlighted
1081 regions (e.g. from structure selections or results of a
1085 <!-- JAL-2284-->Command line option for batch-generation
1086 of HTML pages rendering alignment data with the BioJS
1096 <!-- JAL-2286 -->Columns with more than one modal residue
1097 are not coloured or thresholded according to percent
1098 identity (first observed in Jalview 2.8.2)
1101 <!-- JAL-2301 -->Threonine incorrectly reported as not
1105 <!-- JAL-2318 -->Updates to documentation pages (above PID
1106 threshold, amino acid properties)
1109 <!-- JAL-2292 -->Lower case residues in sequences are not
1110 reported as mapped to residues in a structure file in the
1114 <!--JAL-2324 -->Identical features with non-numeric scores
1115 could be added multiple times to a sequence
1118 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1119 bond features shown as two highlighted residues rather
1120 than a range in linked structure views, and treated
1121 correctly when selecting and computing trees from features
1124 <!-- JAL-2281-->Custom URL links for database
1125 cross-references are matched to database name regardless
1130 <em>Application</em>
1133 <!-- JAL-2282-->Custom URL links for specific database
1134 names without regular expressions also offer links from
1138 <!-- JAL-2315-->Removing a single configured link in the
1139 URL links pane in Connections preferences doesn't actually
1140 update Jalview configuration
1143 <!-- JAL-2272-->CTRL-Click on a selected region to open
1144 the alignment area popup menu doesn't work on El-Capitan
1147 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1148 files with similarly named sequences if dropped onto the
1152 <!-- JAL-2312 -->Additional mappings are shown for PDB
1153 entries where more chains exist in the PDB accession than
1154 are reported in the SIFTS file
1157 <!-- JAL-2317-->Certain structures do not get mapped to
1158 the structure view when displayed with Chimera
1161 <!-- JAL-2317-->No chains shown in the Chimera view
1162 panel's View->Show Chains submenu
1165 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1166 work for wrapped alignment views
1169 <!--JAL-2197 -->Rename UI components for running JPred
1170 predictions from 'JNet' to 'JPred'
1173 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1174 corrupted when annotation panel vertical scroll is not at
1175 first annotation row
1178 <!--JAL-2332 -->Attempting to view structure for Hen
1179 lysozyme results in a PDB Client error dialog box
1182 <!-- JAL-2319 -->Structure View's mapping report switched
1183 ranges for PDB and sequence for SIFTS
1186 SIFTS 'Not_Observed' residues mapped to non-existant
1190 <!-- <em>New Known Issues</em>
1197 <td width="60" nowrap>
1198 <div align="center">
1199 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1200 <em>25/10/2016</em></strong>
1203 <td><em>Application</em>
1205 <li>3D Structure chooser opens with 'Cached structures'
1206 view if structures already loaded</li>
1207 <li>Progress bar reports models as they are loaded to
1208 structure views</li>
1214 <li>Colour by conservation always enabled and no tick
1215 shown in menu when BLOSUM or PID shading applied</li>
1216 <li>FER1_ARATH and FER2_ARATH labels were switched in
1217 example sequences/projects/trees</li>
1219 <em>Application</em>
1221 <li>Jalview projects with views of local PDB structure
1222 files saved on Windows cannot be opened on OSX</li>
1223 <li>Multiple structure views can be opened and superposed
1224 without timeout for structures with multiple models or
1225 multiple sequences in alignment</li>
1226 <li>Cannot import or associated local PDB files without a
1227 PDB ID HEADER line</li>
1228 <li>RMSD is not output in Jmol console when superposition
1230 <li>Drag and drop of URL from Browser fails for Linux and
1231 OSX versions earlier than El Capitan</li>
1232 <li>ENA client ignores invalid content from ENA server</li>
1233 <li>Exceptions are not raised in console when ENA client
1234 attempts to fetch non-existent IDs via Fetch DB Refs UI
1236 <li>Exceptions are not raised in console when a new view
1237 is created on the alignment</li>
1238 <li>OSX right-click fixed for group selections: CMD-click
1239 to insert/remove gaps in groups and CTRL-click to open group
1242 <em>Build and deployment</em>
1244 <li>URL link checker now copes with multi-line anchor
1247 <em>New Known Issues</em>
1249 <li>Drag and drop from URL links in browsers do not work
1256 <td width="60" nowrap>
1257 <div align="center">
1258 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1261 <td><em>General</em>
1264 <!-- JAL-2124 -->Updated Spanish translations.
1267 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1268 for importing structure data to Jalview. Enables mmCIF and
1272 <!-- JAL-192 --->Alignment ruler shows positions relative to
1276 <!-- JAL-2202 -->Position/residue shown in status bar when
1277 mousing over sequence associated annotation
1280 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1284 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1285 '()', canonical '[]' and invalid '{}' base pair populations
1289 <!-- JAL-2092 -->Feature settings popup menu options for
1290 showing or hiding columns containing a feature
1293 <!-- JAL-1557 -->Edit selected group by double clicking on
1294 group and sequence associated annotation labels
1297 <!-- JAL-2236 -->Sequence name added to annotation label in
1298 select/hide columns by annotation and colour by annotation
1302 </ul> <em>Application</em>
1305 <!-- JAL-2050-->Automatically hide introns when opening a
1306 gene/transcript view
1309 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1313 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1314 structure mappings with the EMBL-EBI PDBe SIFTS database
1317 <!-- JAL-2079 -->Updated download sites used for Rfam and
1318 Pfam sources to xfam.org
1321 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1324 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1325 over sequences in Jalview
1328 <!-- JAL-2027-->Support for reverse-complement coding
1329 regions in ENA and EMBL
1332 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1333 for record retrieval via ENA rest API
1336 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1340 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1341 groovy script execution
1344 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1345 alignment window's Calculate menu
1348 <!-- JAL-1812 -->Allow groovy scripts that call
1349 Jalview.getAlignFrames() to run in headless mode
1352 <!-- JAL-2068 -->Support for creating new alignment
1353 calculation workers from groovy scripts
1356 <!-- JAL-1369 --->Store/restore reference sequence in
1360 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1361 associations are now saved/restored from project
1364 <!-- JAL-1993 -->Database selection dialog always shown
1365 before sequence fetcher is opened
1368 <!-- JAL-2183 -->Double click on an entry in Jalview's
1369 database chooser opens a sequence fetcher
1372 <!-- JAL-1563 -->Free-text search client for UniProt using
1373 the UniProt REST API
1376 <!-- JAL-2168 -->-nonews command line parameter to prevent
1377 the news reader opening
1380 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1381 querying stored in preferences
1384 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1388 <!-- JAL-1977-->Tooltips shown on database chooser
1391 <!-- JAL-391 -->Reverse complement function in calculate
1392 menu for nucleotide sequences
1395 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1396 and feature counts preserves alignment ordering (and
1397 debugged for complex feature sets).
1400 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1401 viewing structures with Jalview 2.10
1404 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1405 genome, transcript CCDS and gene ids via the Ensembl and
1406 Ensembl Genomes REST API
1409 <!-- JAL-2049 -->Protein sequence variant annotation
1410 computed for 'sequence_variant' annotation on CDS regions
1414 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1418 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1419 Ref Fetcher fails to match, or otherwise updates sequence
1420 data from external database records.
1423 <!-- JAL-2154 -->Revised Jalview Project format for
1424 efficient recovery of sequence coding and alignment
1425 annotation relationships.
1427 </ul> <!-- <em>Applet</em>
1438 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1442 <!-- JAL-2018-->Export features in Jalview format (again)
1443 includes graduated colourschemes
1446 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1447 working with big alignments and lots of hidden columns
1450 <!-- JAL-2053-->Hidden column markers not always rendered
1451 at right of alignment window
1454 <!-- JAL-2067 -->Tidied up links in help file table of
1458 <!-- JAL-2072 -->Feature based tree calculation not shown
1462 <!-- JAL-2075 -->Hidden columns ignored during feature
1463 based tree calculation
1466 <!-- JAL-2065 -->Alignment view stops updating when show
1467 unconserved enabled for group on alignment
1470 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1474 <!-- JAL-2146 -->Alignment column in status incorrectly
1475 shown as "Sequence position" when mousing over
1479 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1480 hidden columns present
1483 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1484 user created annotation added to alignment
1487 <!-- JAL-1841 -->RNA Structure consensus only computed for
1488 '()' base pair annotation
1491 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1492 in zero scores for all base pairs in RNA Structure
1496 <!-- JAL-2174-->Extend selection with columns containing
1500 <!-- JAL-2275 -->Pfam format writer puts extra space at
1501 beginning of sequence
1504 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1508 <!-- JAL-2238 -->Cannot create groups on an alignment from
1509 from a tree when t-coffee scores are shown
1512 <!-- JAL-1836,1967 -->Cannot import and view PDB
1513 structures with chains containing negative resnums (4q4h)
1516 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1520 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1521 to Clustal, PIR and PileUp output
1524 <!-- JAL-2008 -->Reordering sequence features that are
1525 not visible causes alignment window to repaint
1528 <!-- JAL-2006 -->Threshold sliders don't work in
1529 graduated colour and colour by annotation row for e-value
1530 scores associated with features and annotation rows
1533 <!-- JAL-1797 -->amino acid physicochemical conservation
1534 calculation should be case independent
1537 <!-- JAL-2173 -->Remove annotation also updates hidden
1541 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1542 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1543 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1546 <!-- JAL-2065 -->Null pointer exceptions and redraw
1547 problems when reference sequence defined and 'show
1548 non-conserved' enabled
1551 <!-- JAL-1306 -->Quality and Conservation are now shown on
1552 load even when Consensus calculation is disabled
1555 <!-- JAL-1932 -->Remove right on penultimate column of
1556 alignment does nothing
1559 <em>Application</em>
1562 <!-- JAL-1552-->URLs and links can't be imported by
1563 drag'n'drop on OSX when launched via webstart (note - not
1564 yet fixed for El Capitan)
1567 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1568 output when running on non-gb/us i18n platforms
1571 <!-- JAL-1944 -->Error thrown when exporting a view with
1572 hidden sequences as flat-file alignment
1575 <!-- JAL-2030-->InstallAnywhere distribution fails when
1579 <!-- JAL-2080-->Jalview very slow to launch via webstart
1580 (also hotfix for 2.9.0b2)
1583 <!-- JAL-2085 -->Cannot save project when view has a
1584 reference sequence defined
1587 <!-- JAL-1011 -->Columns are suddenly selected in other
1588 alignments and views when revealing hidden columns
1591 <!-- JAL-1989 -->Hide columns not mirrored in complement
1592 view in a cDNA/Protein splitframe
1595 <!-- JAL-1369 -->Cannot save/restore representative
1596 sequence from project when only one sequence is
1600 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1601 in Structure Chooser
1604 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1605 structure consensus didn't refresh annotation panel
1608 <!-- JAL-1962 -->View mapping in structure view shows
1609 mappings between sequence and all chains in a PDB file
1612 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1613 dialogs format columns correctly, don't display array
1614 data, sort columns according to type
1617 <!-- JAL-1975 -->Export complete shown after destination
1618 file chooser is cancelled during an image export
1621 <!-- JAL-2025 -->Error when querying PDB Service with
1622 sequence name containing special characters
1625 <!-- JAL-2024 -->Manual PDB structure querying should be
1629 <!-- JAL-2104 -->Large tooltips with broken HTML
1630 formatting don't wrap
1633 <!-- JAL-1128 -->Figures exported from wrapped view are
1634 truncated so L looks like I in consensus annotation
1637 <!-- JAL-2003 -->Export features should only export the
1638 currently displayed features for the current selection or
1642 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1643 after fetching cross-references, and restoring from
1647 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1648 followed in the structure viewer
1651 <!-- JAL-2163 -->Titles for individual alignments in
1652 splitframe not restored from project
1655 <!-- JAL-2145 -->missing autocalculated annotation at
1656 trailing end of protein alignment in transcript/product
1657 splitview when pad-gaps not enabled by default
1660 <!-- JAL-1797 -->amino acid physicochemical conservation
1664 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1665 article has been read (reopened issue due to
1666 internationalisation problems)
1669 <!-- JAL-1960 -->Only offer PDB structures in structure
1670 viewer based on sequence name, PDB and UniProt
1675 <!-- JAL-1976 -->No progress bar shown during export of
1679 <!-- JAL-2213 -->Structures not always superimposed after
1680 multiple structures are shown for one or more sequences.
1683 <!-- JAL-1370 -->Reference sequence characters should not
1684 be replaced with '.' when 'Show unconserved' format option
1688 <!-- JAL-1823 -->Cannot specify chain code when entering
1689 specific PDB id for sequence
1692 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1693 'Export hidden sequences' is enabled, but 'export hidden
1694 columns' is disabled.
1697 <!--JAL-2026-->Best Quality option in structure chooser
1698 selects lowest rather than highest resolution structures
1702 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1703 to sequence mapping in 'View Mappings' report
1706 <!-- JAL-2284 -->Unable to read old Jalview projects that
1707 contain non-XML data added after Jalvew wrote project.
1710 <!-- JAL-2118 -->Newly created annotation row reorders
1711 after clicking on it to create new annotation for a
1715 <!-- JAL-1980 -->Null Pointer Exception raised when
1716 pressing Add on an orphaned cut'n'paste window.
1718 <!-- may exclude, this is an external service stability issue JAL-1941
1719 -- > RNA 3D structure not added via DSSR service</li> -->
1724 <!-- JAL-2151 -->Incorrect columns are selected when
1725 hidden columns present before start of sequence
1728 <!-- JAL-1986 -->Missing dependencies on applet pages
1732 <!-- JAL-1947 -->Overview pixel size changes when
1733 sequences are hidden in applet
1736 <!-- JAL-1996 -->Updated instructions for applet
1737 deployment on examples pages.
1744 <td width="60" nowrap>
1745 <div align="center">
1746 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1747 <em>16/10/2015</em></strong>
1750 <td><em>General</em>
1752 <li>Time stamps for signed Jalview application and applet
1757 <em>Application</em>
1759 <li>Duplicate group consensus and conservation rows
1760 shown when tree is partitioned</li>
1761 <li>Erratic behaviour when tree partitions made with
1762 multiple cDNA/Protein split views</li>
1768 <td width="60" nowrap>
1769 <div align="center">
1770 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1771 <em>8/10/2015</em></strong>
1774 <td><em>General</em>
1776 <li>Updated Spanish translations of localized text for
1778 </ul> <em>Application</em>
1780 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1781 <li>Signed OSX InstallAnywhere installer<br></li>
1782 <li>Support for per-sequence based annotations in BioJSON</li>
1783 </ul> <em>Applet</em>
1785 <li>Split frame example added to applet examples page</li>
1786 </ul> <em>Build and Deployment</em>
1789 <!-- JAL-1888 -->New ant target for running Jalview's test
1797 <li>Mapping of cDNA to protein in split frames
1798 incorrect when sequence start > 1</li>
1799 <li>Broken images in filter column by annotation dialog
1801 <li>Feature colours not parsed from features file</li>
1802 <li>Exceptions and incomplete link URLs recovered when
1803 loading a features file containing HTML tags in feature
1807 <em>Application</em>
1809 <li>Annotations corrupted after BioJS export and
1811 <li>Incorrect sequence limits after Fetch DB References
1812 with 'trim retrieved sequences'</li>
1813 <li>Incorrect warning about deleting all data when
1814 deleting selected columns</li>
1815 <li>Patch to build system for shipping properly signed
1816 JNLP templates for webstart launch</li>
1817 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1818 unreleased structures for download or viewing</li>
1819 <li>Tab/space/return keystroke operation of EMBL-PDBe
1820 fetcher/viewer dialogs works correctly</li>
1821 <li>Disabled 'minimise' button on Jalview windows
1822 running on OSX to workaround redraw hang bug</li>
1823 <li>Split cDNA/Protein view position and geometry not
1824 recovered from jalview project</li>
1825 <li>Initial enabled/disabled state of annotation menu
1826 sorter 'show autocalculated first/last' corresponds to
1828 <li>Restoring of Clustal, RNA Helices and T-Coffee
1829 color schemes from BioJSON</li>
1833 <li>Reorder sequences mirrored in cDNA/Protein split
1835 <li>Applet with Jmol examples not loading correctly</li>
1841 <td><div align="center">
1842 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1844 <td><em>General</em>
1846 <li>Linked visualisation and analysis of DNA and Protein
1849 <li>Translated cDNA alignments shown as split protein
1850 and DNA alignment views</li>
1851 <li>Codon consensus annotation for linked protein and
1852 cDNA alignment views</li>
1853 <li>Link cDNA or Protein product sequences by loading
1854 them onto Protein or cDNA alignments</li>
1855 <li>Reconstruct linked cDNA alignment from aligned
1856 protein sequences</li>
1859 <li>Jmol integration updated to Jmol v14.2.14</li>
1860 <li>Import and export of Jalview alignment views as <a
1861 href="features/bioJsonFormat.html">BioJSON</a></li>
1862 <li>New alignment annotation file statements for
1863 reference sequences and marking hidden columns</li>
1864 <li>Reference sequence based alignment shading to
1865 highlight variation</li>
1866 <li>Select or hide columns according to alignment
1868 <li>Find option for locating sequences by description</li>
1869 <li>Conserved physicochemical properties shown in amino
1870 acid conservation row</li>
1871 <li>Alignments can be sorted by number of RNA helices</li>
1872 </ul> <em>Application</em>
1874 <li>New cDNA/Protein analysis capabilities
1876 <li>Get Cross-References should open a Split Frame
1877 view with cDNA/Protein</li>
1878 <li>Detect when nucleotide sequences and protein
1879 sequences are placed in the same alignment</li>
1880 <li>Split cDNA/Protein views are saved in Jalview
1885 <li>Use REST API to talk to Chimera</li>
1886 <li>Selected regions in Chimera are highlighted in linked
1887 Jalview windows</li>
1889 <li>VARNA RNA viewer updated to v3.93</li>
1890 <li>VARNA views are saved in Jalview Projects</li>
1891 <li>Pseudoknots displayed as Jalview RNA annotation can
1892 be shown in VARNA</li>
1894 <li>Make groups for selection uses marked columns as well
1895 as the active selected region</li>
1897 <li>Calculate UPGMA and NJ trees using sequence feature
1899 <li>New Export options
1901 <li>New Export Settings dialog to control hidden
1902 region export in flat file generation</li>
1904 <li>Export alignment views for display with the <a
1905 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1907 <li>Export scrollable SVG in HTML page</li>
1908 <li>Optional embedding of BioJSON data when exporting
1909 alignment figures to HTML</li>
1911 <li>3D structure retrieval and display
1913 <li>Free text and structured queries with the PDBe
1915 <li>PDBe Search API based discovery and selection of
1916 PDB structures for a sequence set</li>
1920 <li>JPred4 employed for protein secondary structure
1922 <li>Hide Insertions menu option to hide unaligned columns
1923 for one or a group of sequences</li>
1924 <li>Automatically hide insertions in alignments imported
1925 from the JPred4 web server</li>
1926 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1927 system on OSX<br />LGPL libraries courtesy of <a
1928 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1930 <li>changed 'View nucleotide structure' submenu to 'View
1931 VARNA 2D Structure'</li>
1932 <li>change "View protein structure" menu option to "3D
1935 </ul> <em>Applet</em>
1937 <li>New layout for applet example pages</li>
1938 <li>New parameters to enable SplitFrame view
1939 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1940 <li>New example demonstrating linked viewing of cDNA and
1941 Protein alignments</li>
1942 </ul> <em>Development and deployment</em>
1944 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1945 <li>Include installation type and git revision in build
1946 properties and console log output</li>
1947 <li>Jalview Github organisation, and new github site for
1948 storing BioJsMSA Templates</li>
1949 <li>Jalview's unit tests now managed with TestNG</li>
1952 <!-- <em>General</em>
1954 </ul> --> <!-- issues resolved --> <em>Application</em>
1956 <li>Escape should close any open find dialogs</li>
1957 <li>Typo in select-by-features status report</li>
1958 <li>Consensus RNA secondary secondary structure
1959 predictions are not highlighted in amber</li>
1960 <li>Missing gap character in v2.7 example file means
1961 alignment appears unaligned when pad-gaps is not enabled</li>
1962 <li>First switch to RNA Helices colouring doesn't colour
1963 associated structure views</li>
1964 <li>ID width preference option is greyed out when auto
1965 width checkbox not enabled</li>
1966 <li>Stopped a warning dialog from being shown when
1967 creating user defined colours</li>
1968 <li>'View Mapping' in structure viewer shows sequence
1969 mappings for just that viewer's sequences</li>
1970 <li>Workaround for superposing PDB files containing
1971 multiple models in Chimera</li>
1972 <li>Report sequence position in status bar when hovering
1973 over Jmol structure</li>
1974 <li>Cannot output gaps as '.' symbols with Selection ->
1975 output to text box</li>
1976 <li>Flat file exports of alignments with hidden columns
1977 have incorrect sequence start/end</li>
1978 <li>'Aligning' a second chain to a Chimera structure from
1980 <li>Colour schemes applied to structure viewers don't
1981 work for nucleotide</li>
1982 <li>Loading/cut'n'pasting an empty or invalid file leads
1983 to a grey/invisible alignment window</li>
1984 <li>Exported Jpred annotation from a sequence region
1985 imports to different position</li>
1986 <li>Space at beginning of sequence feature tooltips shown
1987 on some platforms</li>
1988 <li>Chimera viewer 'View | Show Chain' menu is not
1990 <li>'New View' fails with a Null Pointer Exception in
1991 console if Chimera has been opened</li>
1992 <li>Mouseover to Chimera not working</li>
1993 <li>Miscellaneous ENA XML feature qualifiers not
1995 <li>NPE in annotation renderer after 'Extract Scores'</li>
1996 <li>If two structures in one Chimera window, mouseover of
1997 either sequence shows on first structure</li>
1998 <li>'Show annotations' options should not make
1999 non-positional annotations visible</li>
2000 <li>Subsequence secondary structure annotation not shown
2001 in right place after 'view flanking regions'</li>
2002 <li>File Save As type unset when current file format is
2004 <li>Save as '.jar' option removed for saving Jalview
2006 <li>Colour by Sequence colouring in Chimera more
2008 <li>Cannot 'add reference annotation' for a sequence in
2009 several views on same alignment</li>
2010 <li>Cannot show linked products for EMBL / ENA records</li>
2011 <li>Jalview's tooltip wraps long texts containing no
2013 </ul> <em>Applet</em>
2015 <li>Jmol to JalviewLite mouseover/link not working</li>
2016 <li>JalviewLite can't import sequences with ID
2017 descriptions containing angle brackets</li>
2018 </ul> <em>General</em>
2020 <li>Cannot export and reimport RNA secondary structure
2021 via jalview annotation file</li>
2022 <li>Random helix colour palette for colour by annotation
2023 with RNA secondary structure</li>
2024 <li>Mouseover to cDNA from STOP residue in protein
2025 translation doesn't work.</li>
2026 <li>hints when using the select by annotation dialog box</li>
2027 <li>Jmol alignment incorrect if PDB file has alternate CA
2029 <li>FontChooser message dialog appears to hang after
2030 choosing 1pt font</li>
2031 <li>Peptide secondary structure incorrectly imported from
2032 annotation file when annotation display text includes 'e' or
2034 <li>Cannot set colour of new feature type whilst creating
2036 <li>cDNA translation alignment should not be sequence
2037 order dependent</li>
2038 <li>'Show unconserved' doesn't work for lower case
2040 <li>Nucleotide ambiguity codes involving R not recognised</li>
2041 </ul> <em>Deployment and Documentation</em>
2043 <li>Applet example pages appear different to the rest of
2044 www.jalview.org</li>
2045 </ul> <em>Application Known issues</em>
2047 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2048 <li>Misleading message appears after trying to delete
2050 <li>Jalview icon not shown in dock after InstallAnywhere
2051 version launches</li>
2052 <li>Fetching EMBL reference for an RNA sequence results
2053 fails with a sequence mismatch</li>
2054 <li>Corrupted or unreadable alignment display when
2055 scrolling alignment to right</li>
2056 <li>ArrayIndexOutOfBoundsException thrown when remove
2057 empty columns called on alignment with ragged gapped ends</li>
2058 <li>auto calculated alignment annotation rows do not get
2059 placed above or below non-autocalculated rows</li>
2060 <li>Jalview dekstop becomes sluggish at full screen in
2061 ultra-high resolution</li>
2062 <li>Cannot disable consensus calculation independently of
2063 quality and conservation</li>
2064 <li>Mouseover highlighting between cDNA and protein can
2065 become sluggish with more than one splitframe shown</li>
2066 </ul> <em>Applet Known Issues</em>
2068 <li>Core PDB parsing code requires Jmol</li>
2069 <li>Sequence canvas panel goes white when alignment
2070 window is being resized</li>
2076 <td><div align="center">
2077 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2079 <td><em>General</em>
2081 <li>Updated Java code signing certificate donated by
2083 <li>Features and annotation preserved when performing
2084 pairwise alignment</li>
2085 <li>RNA pseudoknot annotation can be
2086 imported/exported/displayed</li>
2087 <li>'colour by annotation' can colour by RNA and
2088 protein secondary structure</li>
2089 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2090 post-hoc with 2.9 release</em>)
2093 </ul> <em>Application</em>
2095 <li>Extract and display secondary structure for sequences
2096 with 3D structures</li>
2097 <li>Support for parsing RNAML</li>
2098 <li>Annotations menu for layout
2100 <li>sort sequence annotation rows by alignment</li>
2101 <li>place sequence annotation above/below alignment
2104 <li>Output in Stockholm format</li>
2105 <li>Internationalisation: improved Spanish (es)
2107 <li>Structure viewer preferences tab</li>
2108 <li>Disorder and Secondary Structure annotation tracks
2109 shared between alignments</li>
2110 <li>UCSF Chimera launch and linked highlighting from
2112 <li>Show/hide all sequence associated annotation rows for
2113 all or current selection</li>
2114 <li>disorder and secondary structure predictions
2115 available as dataset annotation</li>
2116 <li>Per-sequence rna helices colouring</li>
2119 <li>Sequence database accessions imported when fetching
2120 alignments from Rfam</li>
2121 <li>update VARNA version to 3.91</li>
2123 <li>New groovy scripts for exporting aligned positions,
2124 conservation values, and calculating sum of pairs scores.</li>
2125 <li>Command line argument to set default JABAWS server</li>
2126 <li>include installation type in build properties and
2127 console log output</li>
2128 <li>Updated Jalview project format to preserve dataset
2132 <!-- issues resolved --> <em>Application</em>
2134 <li>Distinguish alignment and sequence associated RNA
2135 structure in structure->view->VARNA</li>
2136 <li>Raise dialog box if user deletes all sequences in an
2138 <li>Pressing F1 results in documentation opening twice</li>
2139 <li>Sequence feature tooltip is wrapped</li>
2140 <li>Double click on sequence associated annotation
2141 selects only first column</li>
2142 <li>Redundancy removal doesn't result in unlinked
2143 leaves shown in tree</li>
2144 <li>Undos after several redundancy removals don't undo
2146 <li>Hide sequence doesn't hide associated annotation</li>
2147 <li>User defined colours dialog box too big to fit on
2148 screen and buttons not visible</li>
2149 <li>author list isn't updated if already written to
2150 Jalview properties</li>
2151 <li>Popup menu won't open after retrieving sequence
2153 <li>File open window for associate PDB doesn't open</li>
2154 <li>Left-then-right click on a sequence id opens a
2155 browser search window</li>
2156 <li>Cannot open sequence feature shading/sort popup menu
2157 in feature settings dialog</li>
2158 <li>better tooltip placement for some areas of Jalview
2160 <li>Allow addition of JABAWS Server which doesn't
2161 pass validation</li>
2162 <li>Web services parameters dialog box is too large to
2164 <li>Muscle nucleotide alignment preset obscured by
2166 <li>JABAWS preset submenus don't contain newly
2167 defined user preset</li>
2168 <li>MSA web services warns user if they were launched
2169 with invalid input</li>
2170 <li>Jalview cannot contact DAS Registy when running on
2173 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2174 'Superpose with' submenu not shown when new view
2178 </ul> <!-- <em>Applet</em>
2180 </ul> <em>General</em>
2182 </ul>--> <em>Deployment and Documentation</em>
2184 <li>2G and 1G options in launchApp have no effect on
2185 memory allocation</li>
2186 <li>launchApp service doesn't automatically open
2187 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2189 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2190 InstallAnywhere reports cannot find valid JVM when Java
2191 1.7_055 is available
2193 </ul> <em>Application Known issues</em>
2196 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2197 corrupted or unreadable alignment display when scrolling
2201 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2202 retrieval fails but progress bar continues for DAS retrieval
2203 with large number of ID
2206 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2207 flatfile output of visible region has incorrect sequence
2211 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2212 rna structure consensus doesn't update when secondary
2213 structure tracks are rearranged
2216 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2217 invalid rna structure positional highlighting does not
2218 highlight position of invalid base pairs
2221 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2222 out of memory errors are not raised when saving Jalview
2223 project from alignment window file menu
2226 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2227 Switching to RNA Helices colouring doesn't propagate to
2231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2232 colour by RNA Helices not enabled when user created
2233 annotation added to alignment
2236 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2237 Jalview icon not shown on dock in Mountain Lion/Webstart
2239 </ul> <em>Applet Known Issues</em>
2242 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2243 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2246 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2247 Jalview and Jmol example not compatible with IE9
2250 <li>Sort by annotation score doesn't reverse order
2256 <td><div align="center">
2257 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2260 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2263 <li>Internationalisation of user interface (usually
2264 called i18n support) and translation for Spanish locale</li>
2265 <li>Define/Undefine group on current selection with
2266 Ctrl-G/Shift Ctrl-G</li>
2267 <li>Improved group creation/removal options in
2268 alignment/sequence Popup menu</li>
2269 <li>Sensible precision for symbol distribution
2270 percentages shown in logo tooltip.</li>
2271 <li>Annotation panel height set according to amount of
2272 annotation when alignment first opened</li>
2273 </ul> <em>Application</em>
2275 <li>Interactive consensus RNA secondary structure
2276 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2277 <li>Select columns containing particular features from
2278 Feature Settings dialog</li>
2279 <li>View all 'representative' PDB structures for selected
2281 <li>Update Jalview project format:
2283 <li>New file extension for Jalview projects '.jvp'</li>
2284 <li>Preserve sequence and annotation dataset (to
2285 store secondary structure annotation,etc)</li>
2286 <li>Per group and alignment annotation and RNA helix
2290 <li>New similarity measures for PCA and Tree calculation
2292 <li>Experimental support for retrieval and viewing of
2293 flanking regions for an alignment</li>
2297 <!-- issues resolved --> <em>Application</em>
2299 <li>logo keeps spinning and status remains at queued or
2300 running after job is cancelled</li>
2301 <li>cannot export features from alignments imported from
2302 Jalview/VAMSAS projects</li>
2303 <li>Buggy slider for web service parameters that take
2305 <li>Newly created RNA secondary structure line doesn't
2306 have 'display all symbols' flag set</li>
2307 <li>T-COFFEE alignment score shading scheme and other
2308 annotation shading not saved in Jalview project</li>
2309 <li>Local file cannot be loaded in freshly downloaded
2311 <li>Jalview icon not shown on dock in Mountain
2313 <li>Load file from desktop file browser fails</li>
2314 <li>Occasional NPE thrown when calculating large trees</li>
2315 <li>Cannot reorder or slide sequences after dragging an
2316 alignment onto desktop</li>
2317 <li>Colour by annotation dialog throws NPE after using
2318 'extract scores' function</li>
2319 <li>Loading/cut'n'pasting an empty file leads to a grey
2320 alignment window</li>
2321 <li>Disorder thresholds rendered incorrectly after
2322 performing IUPred disorder prediction</li>
2323 <li>Multiple group annotated consensus rows shown when
2324 changing 'normalise logo' display setting</li>
2325 <li>Find shows blank dialog after 'finished searching' if
2326 nothing matches query</li>
2327 <li>Null Pointer Exceptions raised when sorting by
2328 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2330 <li>Errors in Jmol console when structures in alignment
2331 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2333 <li>Not all working JABAWS services are shown in
2335 <li>JAVAWS version of Jalview fails to launch with
2336 'invalid literal/length code'</li>
2337 <li>Annotation/RNA Helix colourschemes cannot be applied
2338 to alignment with groups (actually fixed in 2.8.0b1)</li>
2339 <li>RNA Helices and T-Coffee Scores available as default
2342 </ul> <em>Applet</em>
2344 <li>Remove group option is shown even when selection is
2346 <li>Apply to all groups ticked but colourscheme changes
2347 don't affect groups</li>
2348 <li>Documented RNA Helices and T-Coffee Scores as valid
2349 colourscheme name</li>
2350 <li>Annotation labels drawn on sequence IDs when
2351 Annotation panel is not displayed</li>
2352 <li>Increased font size for dropdown menus on OSX and
2353 embedded windows</li>
2354 </ul> <em>Other</em>
2356 <li>Consensus sequence for alignments/groups with a
2357 single sequence were not calculated</li>
2358 <li>annotation files that contain only groups imported as
2359 annotation and junk sequences</li>
2360 <li>Fasta files with sequences containing '*' incorrectly
2361 recognised as PFAM or BLC</li>
2362 <li>conservation/PID slider apply all groups option
2363 doesn't affect background (2.8.0b1)
2365 <li>redundancy highlighting is erratic at 0% and 100%</li>
2366 <li>Remove gapped columns fails for sequences with ragged
2368 <li>AMSA annotation row with leading spaces is not
2369 registered correctly on import</li>
2370 <li>Jalview crashes when selecting PCA analysis for
2371 certain alignments</li>
2372 <li>Opening the colour by annotation dialog for an
2373 existing annotation based 'use original colours'
2374 colourscheme loses original colours setting</li>
2379 <td><div align="center">
2380 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2381 <em>30/1/2014</em></strong>
2385 <li>Trusted certificates for JalviewLite applet and
2386 Jalview Desktop application<br />Certificate was donated by
2387 <a href="https://www.certum.eu">Certum</a> to the Jalview
2388 open source project).
2390 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2391 <li>Output in Stockholm format</li>
2392 <li>Allow import of data from gzipped files</li>
2393 <li>Export/import group and sequence associated line
2394 graph thresholds</li>
2395 <li>Nucleotide substitution matrix that supports RNA and
2396 ambiguity codes</li>
2397 <li>Allow disorder predictions to be made on the current
2398 selection (or visible selection) in the same way that JPred
2400 <li>Groovy scripting for headless Jalview operation</li>
2401 </ul> <em>Other improvements</em>
2403 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2404 <li>COMBINE statement uses current SEQUENCE_REF and
2405 GROUP_REF scope to group annotation rows</li>
2406 <li>Support '' style escaping of quotes in Newick
2408 <li>Group options for JABAWS service by command line name</li>
2409 <li>Empty tooltip shown for JABA service options with a
2410 link but no description</li>
2411 <li>Select primary source when selecting authority in
2412 database fetcher GUI</li>
2413 <li>Add .mfa to FASTA file extensions recognised by
2415 <li>Annotation label tooltip text wrap</li>
2420 <li>Slow scrolling when lots of annotation rows are
2422 <li>Lots of NPE (and slowness) after creating RNA
2423 secondary structure annotation line</li>
2424 <li>Sequence database accessions not imported when
2425 fetching alignments from Rfam</li>
2426 <li>Incorrect SHMR submission for sequences with
2428 <li>View all structures does not always superpose
2430 <li>Option widgets in service parameters not updated to
2431 reflect user or preset settings</li>
2432 <li>Null pointer exceptions for some services without
2433 presets or adjustable parameters</li>
2434 <li>Discover PDB IDs entry in structure menu doesn't
2435 discover PDB xRefs</li>
2436 <li>Exception encountered while trying to retrieve
2437 features with DAS</li>
2438 <li>Lowest value in annotation row isn't coloured
2439 when colour by annotation (per sequence) is coloured</li>
2440 <li>Keyboard mode P jumps to start of gapped region when
2441 residue follows a gap</li>
2442 <li>Jalview appears to hang importing an alignment with
2443 Wrap as default or after enabling Wrap</li>
2444 <li>'Right click to add annotations' message
2445 shown in wrap mode when no annotations present</li>
2446 <li>Disorder predictions fail with NPE if no automatic
2447 annotation already exists on alignment</li>
2448 <li>oninit javascript function should be called after
2449 initialisation completes</li>
2450 <li>Remove redundancy after disorder prediction corrupts
2451 alignment window display</li>
2452 <li>Example annotation file in documentation is invalid</li>
2453 <li>Grouped line graph annotation rows are not exported
2454 to annotation file</li>
2455 <li>Multi-harmony analysis cannot be run when only two
2457 <li>Cannot create multiple groups of line graphs with
2458 several 'combine' statements in annotation file</li>
2459 <li>Pressing return several times causes Number Format
2460 exceptions in keyboard mode</li>
2461 <li>Multi-harmony (SHMMR) method doesn't submit
2462 correct partitions for input data</li>
2463 <li>Translation from DNA to Amino Acids fails</li>
2464 <li>Jalview fail to load newick tree with quoted label</li>
2465 <li>--headless flag isn't understood</li>
2466 <li>ClassCastException when generating EPS in headless
2468 <li>Adjusting sequence-associated shading threshold only
2469 changes one row's threshold</li>
2470 <li>Preferences and Feature settings panel panel
2471 doesn't open</li>
2472 <li>hide consensus histogram also hides conservation and
2473 quality histograms</li>
2478 <td><div align="center">
2479 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2481 <td><em>Application</em>
2483 <li>Support for JABAWS 2.0 Services (AACon alignment
2484 conservation, protein disorder and Clustal Omega)</li>
2485 <li>JABAWS server status indicator in Web Services
2487 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2488 in Jalview alignment window</li>
2489 <li>Updated Jalview build and deploy framework for OSX
2490 mountain lion, windows 7, and 8</li>
2491 <li>Nucleotide substitution matrix for PCA that supports
2492 RNA and ambiguity codes</li>
2494 <li>Improved sequence database retrieval GUI</li>
2495 <li>Support fetching and database reference look up
2496 against multiple DAS sources (Fetch all from in 'fetch db
2498 <li>Jalview project improvements
2500 <li>Store and retrieve the 'belowAlignment'
2501 flag for annotation</li>
2502 <li>calcId attribute to group annotation rows on the
2504 <li>Store AACon calculation settings for a view in
2505 Jalview project</li>
2509 <li>horizontal scrolling gesture support</li>
2510 <li>Visual progress indicator when PCA calculation is
2512 <li>Simpler JABA web services menus</li>
2513 <li>visual indication that web service results are still
2514 being retrieved from server</li>
2515 <li>Serialise the dialogs that are shown when Jalview
2516 starts up for first time</li>
2517 <li>Jalview user agent string for interacting with HTTP
2519 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2521 <li>Examples directory and Groovy library included in
2522 InstallAnywhere distribution</li>
2523 </ul> <em>Applet</em>
2525 <li>RNA alignment and secondary structure annotation
2526 visualization applet example</li>
2527 </ul> <em>General</em>
2529 <li>Normalise option for consensus sequence logo</li>
2530 <li>Reset button in PCA window to return dimensions to
2532 <li>Allow seqspace or Jalview variant of alignment PCA
2534 <li>PCA with either nucleic acid and protein substitution
2536 <li>Allow windows containing HTML reports to be exported
2538 <li>Interactive display and editing of RNA secondary
2539 structure contacts</li>
2540 <li>RNA Helix Alignment Colouring</li>
2541 <li>RNA base pair logo consensus</li>
2542 <li>Parse sequence associated secondary structure
2543 information in Stockholm files</li>
2544 <li>HTML Export database accessions and annotation
2545 information presented in tooltip for sequences</li>
2546 <li>Import secondary structure from LOCARNA clustalw
2547 style RNA alignment files</li>
2548 <li>import and visualise T-COFFEE quality scores for an
2550 <li>'colour by annotation' per sequence option to
2551 shade each sequence according to its associated alignment
2553 <li>New Jalview Logo</li>
2554 </ul> <em>Documentation and Development</em>
2556 <li>documentation for score matrices used in Jalview</li>
2557 <li>New Website!</li>
2559 <td><em>Application</em>
2561 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2562 wsdbfetch REST service</li>
2563 <li>Stop windows being moved outside desktop on OSX</li>
2564 <li>Filetype associations not installed for webstart
2566 <li>Jalview does not always retrieve progress of a JABAWS
2567 job execution in full once it is complete</li>
2568 <li>revise SHMR RSBS definition to ensure alignment is
2569 uploaded via ali_file parameter</li>
2570 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2571 <li>View all structures superposed fails with exception</li>
2572 <li>Jnet job queues forever if a very short sequence is
2573 submitted for prediction</li>
2574 <li>Cut and paste menu not opened when mouse clicked on
2576 <li>Putting fractional value into integer text box in
2577 alignment parameter dialog causes Jalview to hang</li>
2578 <li>Structure view highlighting doesn't work on
2580 <li>View all structures fails with exception shown in
2582 <li>Characters in filename associated with PDBEntry not
2583 escaped in a platform independent way</li>
2584 <li>Jalview desktop fails to launch with exception when
2586 <li>Tree calculation reports 'you must have 2 or more
2587 sequences selected' when selection is empty</li>
2588 <li>Jalview desktop fails to launch with jar signature
2589 failure when java web start temporary file caching is
2591 <li>DAS Sequence retrieval with range qualification
2592 results in sequence xref which includes range qualification</li>
2593 <li>Errors during processing of command line arguments
2594 cause progress bar (JAL-898) to be removed</li>
2595 <li>Replace comma for semi-colon option not disabled for
2596 DAS sources in sequence fetcher</li>
2597 <li>Cannot close news reader when JABAWS server warning
2598 dialog is shown</li>
2599 <li>Option widgets not updated to reflect user settings</li>
2600 <li>Edited sequence not submitted to web service</li>
2601 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2602 <li>InstallAnywhere installer doesn't unpack and run
2603 on OSX Mountain Lion</li>
2604 <li>Annotation panel not given a scroll bar when
2605 sequences with alignment annotation are pasted into the
2607 <li>Sequence associated annotation rows not associated
2608 when loaded from Jalview project</li>
2609 <li>Browser launch fails with NPE on java 1.7</li>
2610 <li>JABAWS alignment marked as finished when job was
2611 cancelled or job failed due to invalid input</li>
2612 <li>NPE with v2.7 example when clicking on Tree
2613 associated with all views</li>
2614 <li>Exceptions when copy/paste sequences with grouped
2615 annotation rows to new window</li>
2616 </ul> <em>Applet</em>
2618 <li>Sequence features are momentarily displayed before
2619 they are hidden using hidefeaturegroups applet parameter</li>
2620 <li>loading features via javascript API automatically
2621 enables feature display</li>
2622 <li>scrollToColumnIn javascript API method doesn't
2624 </ul> <em>General</em>
2626 <li>Redundancy removal fails for rna alignment</li>
2627 <li>PCA calculation fails when sequence has been selected
2628 and then deselected</li>
2629 <li>PCA window shows grey box when first opened on OSX</li>
2630 <li>Letters coloured pink in sequence logo when alignment
2631 coloured with clustalx</li>
2632 <li>Choosing fonts without letter symbols defined causes
2633 exceptions and redraw errors</li>
2634 <li>Initial PCA plot view is not same as manually
2635 reconfigured view</li>
2636 <li>Grouped annotation graph label has incorrect line
2638 <li>Grouped annotation graph label display is corrupted
2639 for lots of labels</li>
2644 <div align="center">
2645 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2648 <td><em>Application</em>
2650 <li>Jalview Desktop News Reader</li>
2651 <li>Tweaked default layout of web services menu</li>
2652 <li>View/alignment association menu to enable user to
2653 easily specify which alignment a multi-structure view takes
2654 its colours/correspondences from</li>
2655 <li>Allow properties file location to be specified as URL</li>
2656 <li>Extend Jalview project to preserve associations
2657 between many alignment views and a single Jmol display</li>
2658 <li>Store annotation row height in Jalview project file</li>
2659 <li>Annotation row column label formatting attributes
2660 stored in project file</li>
2661 <li>Annotation row order for auto-calculated annotation
2662 rows preserved in Jalview project file</li>
2663 <li>Visual progress indication when Jalview state is
2664 saved using Desktop window menu</li>
2665 <li>Visual indication that command line arguments are
2666 still being processed</li>
2667 <li>Groovy script execution from URL</li>
2668 <li>Colour by annotation default min and max colours in
2670 <li>Automatically associate PDB files dragged onto an
2671 alignment with sequences that have high similarity and
2673 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2674 <li>'view structures' option to open many
2675 structures in same window</li>
2676 <li>Sort associated views menu option for tree panel</li>
2677 <li>Group all JABA and non-JABA services for a particular
2678 analysis function in its own submenu</li>
2679 </ul> <em>Applet</em>
2681 <li>Userdefined and autogenerated annotation rows for
2683 <li>Adjustment of alignment annotation pane height</li>
2684 <li>Annotation scrollbar for annotation panel</li>
2685 <li>Drag to reorder annotation rows in annotation panel</li>
2686 <li>'automaticScrolling' parameter</li>
2687 <li>Allow sequences with partial ID string matches to be
2688 annotated from GFF/Jalview features files</li>
2689 <li>Sequence logo annotation row in applet</li>
2690 <li>Absolute paths relative to host server in applet
2691 parameters are treated as such</li>
2692 <li>New in the JalviewLite javascript API:
2694 <li>JalviewLite.js javascript library</li>
2695 <li>Javascript callbacks for
2697 <li>Applet initialisation</li>
2698 <li>Sequence/alignment mouse-overs and selections</li>
2701 <li>scrollTo row and column alignment scrolling
2703 <li>Select sequence/alignment regions from javascript</li>
2704 <li>javascript structure viewer harness to pass
2705 messages between Jmol and Jalview when running as
2706 distinct applets</li>
2707 <li>sortBy method</li>
2708 <li>Set of applet and application examples shipped
2709 with documentation</li>
2710 <li>New example to demonstrate JalviewLite and Jmol
2711 javascript message exchange</li>
2713 </ul> <em>General</em>
2715 <li>Enable Jmol displays to be associated with multiple
2716 multiple alignments</li>
2717 <li>Option to automatically sort alignment with new tree</li>
2718 <li>User configurable link to enable redirects to a
2719 www.Jalview.org mirror</li>
2720 <li>Jmol colours option for Jmol displays</li>
2721 <li>Configurable newline string when writing alignment
2722 and other flat files</li>
2723 <li>Allow alignment annotation description lines to
2724 contain html tags</li>
2725 </ul> <em>Documentation and Development</em>
2727 <li>Add groovy test harness for bulk load testing to
2729 <li>Groovy script to load and align a set of sequences
2730 using a web service before displaying the result in the
2731 Jalview desktop</li>
2732 <li>Restructured javascript and applet api documentation</li>
2733 <li>Ant target to publish example html files with applet
2735 <li>Netbeans project for building Jalview from source</li>
2736 <li>ant task to create online javadoc for Jalview source</li>
2738 <td><em>Application</em>
2740 <li>User defined colourscheme throws exception when
2741 current built in colourscheme is saved as new scheme</li>
2742 <li>AlignFrame->Save in application pops up save
2743 dialog for valid filename/format</li>
2744 <li>Cannot view associated structure for UniProt sequence</li>
2745 <li>PDB file association breaks for UniProt sequence
2747 <li>Associate PDB from file dialog does not tell you
2748 which sequence is to be associated with the file</li>
2749 <li>Find All raises null pointer exception when query
2750 only matches sequence IDs</li>
2751 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2752 <li>Jalview project with Jmol views created with Jalview
2753 2.4 cannot be loaded</li>
2754 <li>Filetype associations not installed for webstart
2756 <li>Two or more chains in a single PDB file associated
2757 with sequences in different alignments do not get coloured
2758 by their associated sequence</li>
2759 <li>Visibility status of autocalculated annotation row
2760 not preserved when project is loaded</li>
2761 <li>Annotation row height and visibility attributes not
2762 stored in Jalview project</li>
2763 <li>Tree bootstraps are not preserved when saved as a
2764 Jalview project</li>
2765 <li>Envision2 workflow tooltips are corrupted</li>
2766 <li>Enabling show group conservation also enables colour
2767 by conservation</li>
2768 <li>Duplicate group associated conservation or consensus
2769 created on new view</li>
2770 <li>Annotation scrollbar not displayed after 'show
2771 all hidden annotation rows' option selected</li>
2772 <li>Alignment quality not updated after alignment
2773 annotation row is hidden then shown</li>
2774 <li>Preserve colouring of structures coloured by
2775 sequences in pre Jalview 2.7 projects</li>
2776 <li>Web service job parameter dialog is not laid out
2778 <li>Web services menu not refreshed after 'reset
2779 services' button is pressed in preferences</li>
2780 <li>Annotation off by one in Jalview v2_3 example project</li>
2781 <li>Structures imported from file and saved in project
2782 get name like jalview_pdb1234.txt when reloaded</li>
2783 <li>Jalview does not always retrieve progress of a JABAWS
2784 job execution in full once it is complete</li>
2785 </ul> <em>Applet</em>
2787 <li>Alignment height set incorrectly when lots of
2788 annotation rows are displayed</li>
2789 <li>Relative URLs in feature HTML text not resolved to
2791 <li>View follows highlighting does not work for positions
2793 <li><= shown as = in tooltip</li>
2794 <li>Export features raises exception when no features
2796 <li>Separator string used for serialising lists of IDs
2797 for javascript api is modified when separator string
2798 provided as parameter</li>
2799 <li>Null pointer exception when selecting tree leaves for
2800 alignment with no existing selection</li>
2801 <li>Relative URLs for datasources assumed to be relative
2802 to applet's codebase</li>
2803 <li>Status bar not updated after finished searching and
2804 search wraps around to first result</li>
2805 <li>StructureSelectionManager instance shared between
2806 several Jalview applets causes race conditions and memory
2808 <li>Hover tooltip and mouseover of position on structure
2809 not sent from Jmol in applet</li>
2810 <li>Certain sequences of javascript method calls to
2811 applet API fatally hang browser</li>
2812 </ul> <em>General</em>
2814 <li>View follows structure mouseover scrolls beyond
2815 position with wrapped view and hidden regions</li>
2816 <li>Find sequence position moves to wrong residue
2817 with/without hidden columns</li>
2818 <li>Sequence length given in alignment properties window
2820 <li>InvalidNumberFormat exceptions thrown when trying to
2821 import PDB like structure files</li>
2822 <li>Positional search results are only highlighted
2823 between user-supplied sequence start/end bounds</li>
2824 <li>End attribute of sequence is not validated</li>
2825 <li>Find dialog only finds first sequence containing a
2826 given sequence position</li>
2827 <li>Sequence numbering not preserved in MSF alignment
2829 <li>Jalview PDB file reader does not extract sequence
2830 from nucleotide chains correctly</li>
2831 <li>Structure colours not updated when tree partition
2832 changed in alignment</li>
2833 <li>Sequence associated secondary structure not correctly
2834 parsed in interleaved stockholm</li>
2835 <li>Colour by annotation dialog does not restore current
2837 <li>Hiding (nearly) all sequences doesn't work
2839 <li>Sequences containing lowercase letters are not
2840 properly associated with their pdb files</li>
2841 </ul> <em>Documentation and Development</em>
2843 <li>schemas/JalviewWsParamSet.xsd corrupted by
2844 ApplyCopyright tool</li>
2849 <div align="center">
2850 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2853 <td><em>Application</em>
2855 <li>New warning dialog when the Jalview Desktop cannot
2856 contact web services</li>
2857 <li>JABA service parameters for a preset are shown in
2858 service job window</li>
2859 <li>JABA Service menu entries reworded</li>
2863 <li>Modeller PIR IO broken - cannot correctly import a
2864 pir file emitted by Jalview</li>
2865 <li>Existing feature settings transferred to new
2866 alignment view created from cut'n'paste</li>
2867 <li>Improved test for mixed amino/nucleotide chains when
2868 parsing PDB files</li>
2869 <li>Consensus and conservation annotation rows
2870 occasionally become blank for all new windows</li>
2871 <li>Exception raised when right clicking above sequences
2872 in wrapped view mode</li>
2873 </ul> <em>Application</em>
2875 <li>multiple multiply aligned structure views cause cpu
2876 usage to hit 100% and computer to hang</li>
2877 <li>Web Service parameter layout breaks for long user
2878 parameter names</li>
2879 <li>Jaba service discovery hangs desktop if Jaba server
2886 <div align="center">
2887 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2890 <td><em>Application</em>
2892 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2893 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2896 <li>Web Services preference tab</li>
2897 <li>Analysis parameters dialog box and user defined
2899 <li>Improved speed and layout of Envision2 service menu</li>
2900 <li>Superpose structures using associated sequence
2902 <li>Export coordinates and projection as CSV from PCA
2904 </ul> <em>Applet</em>
2906 <li>enable javascript: execution by the applet via the
2907 link out mechanism</li>
2908 </ul> <em>Other</em>
2910 <li>Updated the Jmol Jalview interface to work with Jmol
2912 <li>The Jalview Desktop and JalviewLite applet now
2913 require Java 1.5</li>
2914 <li>Allow Jalview feature colour specification for GFF
2915 sequence annotation files</li>
2916 <li>New 'colour by label' keword in Jalview feature file
2917 type colour specification</li>
2918 <li>New Jalview Desktop Groovy API method that allows a
2919 script to check if it being run in an interactive session or
2920 in a batch operation from the Jalview command line</li>
2924 <li>clustalx colourscheme colours Ds preferentially when
2925 both D+E are present in over 50% of the column</li>
2926 </ul> <em>Application</em>
2928 <li>typo in AlignmentFrame->View->Hide->all but
2929 selected Regions menu item</li>
2930 <li>sequence fetcher replaces ',' for ';' when the ',' is
2931 part of a valid accession ID</li>
2932 <li>fatal OOM if object retrieved by sequence fetcher
2933 runs out of memory</li>
2934 <li>unhandled Out of Memory Error when viewing pca
2935 analysis results</li>
2936 <li>InstallAnywhere builds fail to launch on OS X java
2937 10.5 update 4 (due to apple Java 1.6 update)</li>
2938 <li>Installanywhere Jalview silently fails to launch</li>
2939 </ul> <em>Applet</em>
2941 <li>Jalview.getFeatureGroups() raises an
2942 ArrayIndexOutOfBoundsException if no feature groups are
2949 <div align="center">
2950 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2956 <li>Alignment prettyprinter doesn't cope with long
2958 <li>clustalx colourscheme colours Ds preferentially when
2959 both D+E are present in over 50% of the column</li>
2960 <li>nucleic acid structures retrieved from PDB do not
2961 import correctly</li>
2962 <li>More columns get selected than were clicked on when a
2963 number of columns are hidden</li>
2964 <li>annotation label popup menu not providing correct
2965 add/hide/show options when rows are hidden or none are
2967 <li>Stockholm format shown in list of readable formats,
2968 and parser copes better with alignments from RFAM.</li>
2969 <li>CSV output of consensus only includes the percentage
2970 of all symbols if sequence logo display is enabled</li>
2972 </ul> <em>Applet</em>
2974 <li>annotation panel disappears when annotation is
2976 </ul> <em>Application</em>
2978 <li>Alignment view not redrawn properly when new
2979 alignment opened where annotation panel is visible but no
2980 annotations are present on alignment</li>
2981 <li>pasted region containing hidden columns is
2982 incorrectly displayed in new alignment window</li>
2983 <li>Jalview slow to complete operations when stdout is
2984 flooded (fix is to close the Jalview console)</li>
2985 <li>typo in AlignmentFrame->View->Hide->all but
2986 selected Rregions menu item.</li>
2987 <li>inconsistent group submenu and Format submenu entry
2988 'Un' or 'Non'conserved</li>
2989 <li>Sequence feature settings are being shared by
2990 multiple distinct alignments</li>
2991 <li>group annotation not recreated when tree partition is
2993 <li>double click on group annotation to select sequences
2994 does not propagate to associated trees</li>
2995 <li>Mac OSX specific issues:
2997 <li>exception raised when mouse clicked on desktop
2998 window background</li>
2999 <li>Desktop menu placed on menu bar and application
3000 name set correctly</li>
3001 <li>sequence feature settings not wide enough for the
3002 save feature colourscheme button</li>
3011 <div align="center">
3012 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3015 <td><em>New Capabilities</em>
3017 <li>URL links generated from description line for
3018 regular-expression based URL links (applet and application)
3020 <li>Non-positional feature URL links are shown in link
3022 <li>Linked viewing of nucleic acid sequences and
3024 <li>Automatic Scrolling option in View menu to display
3025 the currently highlighted region of an alignment.</li>
3026 <li>Order an alignment by sequence length, or using the
3027 average score or total feature count for each sequence.</li>
3028 <li>Shading features by score or associated description</li>
3029 <li>Subdivide alignment and groups based on identity of
3030 selected subsequence (Make Groups from Selection).</li>
3031 <li>New hide/show options including Shift+Control+H to
3032 hide everything but the currently selected region.</li>
3033 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3034 </ul> <em>Application</em>
3036 <li>Fetch DB References capabilities and UI expanded to
3037 support retrieval from DAS sequence sources</li>
3038 <li>Local DAS Sequence sources can be added via the
3039 command line or via the Add local source dialog box.</li>
3040 <li>DAS Dbref and DbxRef feature types are parsed as
3041 database references and protein_name is parsed as
3042 description line (BioSapiens terms).</li>
3043 <li>Enable or disable non-positional feature and database
3044 references in sequence ID tooltip from View menu in
3046 <!-- <li>New hidden columns and rows and representatives capabilities
3047 in annotations file (in progress - not yet fully implemented)</li> -->
3048 <li>Group-associated consensus, sequence logos and
3049 conservation plots</li>
3050 <li>Symbol distributions for each column can be exported
3051 and visualized as sequence logos</li>
3052 <li>Optionally scale multi-character column labels to fit
3053 within each column of annotation row<!-- todo for applet -->
3055 <li>Optional automatic sort of associated alignment view
3056 when a new tree is opened.</li>
3057 <li>Jalview Java Console</li>
3058 <li>Better placement of desktop window when moving
3059 between different screens.</li>
3060 <li>New preference items for sequence ID tooltip and
3061 consensus annotation</li>
3062 <li>Client to submit sequences and IDs to Envision2
3064 <li><em>Vamsas Capabilities</em>
3066 <li>Improved VAMSAS synchronization (Jalview archive
3067 used to preserve views, structures, and tree display
3069 <li>Import of vamsas documents from disk or URL via
3071 <li>Sharing of selected regions between views and
3072 with other VAMSAS applications (Experimental feature!)</li>
3073 <li>Updated API to VAMSAS version 0.2</li>
3075 </ul> <em>Applet</em>
3077 <li>Middle button resizes annotation row height</li>
3080 <li>sortByTree (true/false) - automatically sort the
3081 associated alignment view by the tree when a new tree is
3083 <li>showTreeBootstraps (true/false) - show or hide
3084 branch bootstraps (default is to show them if available)</li>
3085 <li>showTreeDistances (true/false) - show or hide
3086 branch lengths (default is to show them if available)</li>
3087 <li>showUnlinkedTreeNodes (true/false) - indicate if
3088 unassociated nodes should be highlighted in the tree
3090 <li>heightScale and widthScale (1.0 or more) -
3091 increase the height or width of a cell in the alignment
3092 grid relative to the current font size.</li>
3095 <li>Non-positional features displayed in sequence ID
3097 </ul> <em>Other</em>
3099 <li>Features format: graduated colour definitions and
3100 specification of feature scores</li>
3101 <li>Alignment Annotations format: new keywords for group
3102 associated annotation (GROUP_REF) and annotation row display
3103 properties (ROW_PROPERTIES)</li>
3104 <li>XML formats extended to support graduated feature
3105 colourschemes, group associated annotation, and profile
3106 visualization settings.</li></td>
3109 <li>Source field in GFF files parsed as feature source
3110 rather than description</li>
3111 <li>Non-positional features are now included in sequence
3112 feature and gff files (controlled via non-positional feature
3113 visibility in tooltip).</li>
3114 <li>URL links generated for all feature links (bugfix)</li>
3115 <li>Added URL embedding instructions to features file
3117 <li>Codons containing ambiguous nucleotides translated as
3118 'X' in peptide product</li>
3119 <li>Match case switch in find dialog box works for both
3120 sequence ID and sequence string and query strings do not
3121 have to be in upper case to match case-insensitively.</li>
3122 <li>AMSA files only contain first column of
3123 multi-character column annotation labels</li>
3124 <li>Jalview Annotation File generation/parsing consistent
3125 with documentation (e.g. Stockholm annotation can be
3126 exported and re-imported)</li>
3127 <li>PDB files without embedded PDB IDs given a friendly
3129 <li>Find incrementally searches ID string matches as well
3130 as subsequence matches, and correctly reports total number
3134 <li>Better handling of exceptions during sequence
3136 <li>Dasobert generated non-positional feature URL
3137 link text excludes the start_end suffix</li>
3138 <li>DAS feature and source retrieval buttons disabled
3139 when fetch or registry operations in progress.</li>
3140 <li>PDB files retrieved from URLs are cached properly</li>
3141 <li>Sequence description lines properly shared via
3143 <li>Sequence fetcher fetches multiple records for all
3145 <li>Ensured that command line das feature retrieval
3146 completes before alignment figures are generated.</li>
3147 <li>Reduced time taken when opening file browser for
3149 <li>isAligned check prior to calculating tree, PCA or
3150 submitting an MSA to JNet now excludes hidden sequences.</li>
3151 <li>User defined group colours properly recovered
3152 from Jalview projects.</li>
3161 <div align="center">
3162 <strong>2.4.0.b2</strong><br> 28/10/2009
3167 <li>Experimental support for google analytics usage
3169 <li>Jalview privacy settings (user preferences and docs).</li>
3174 <li>Race condition in applet preventing startup in
3176 <li>Exception when feature created from selection beyond
3177 length of sequence.</li>
3178 <li>Allow synthetic PDB files to be imported gracefully</li>
3179 <li>Sequence associated annotation rows associate with
3180 all sequences with a given id</li>
3181 <li>Find function matches case-insensitively for sequence
3182 ID string searches</li>
3183 <li>Non-standard characters do not cause pairwise
3184 alignment to fail with exception</li>
3185 </ul> <em>Application Issues</em>
3187 <li>Sequences are now validated against EMBL database</li>
3188 <li>Sequence fetcher fetches multiple records for all
3190 </ul> <em>InstallAnywhere Issues</em>
3192 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3193 issue with installAnywhere mechanism)</li>
3194 <li>Command line launching of JARs from InstallAnywhere
3195 version (java class versioning error fixed)</li>
3202 <div align="center">
3203 <strong>2.4</strong><br> 27/8/2008
3206 <td><em>User Interface</em>
3208 <li>Linked highlighting of codon and amino acid from
3209 translation and protein products</li>
3210 <li>Linked highlighting of structure associated with
3211 residue mapping to codon position</li>
3212 <li>Sequence Fetcher provides example accession numbers
3213 and 'clear' button</li>
3214 <li>MemoryMonitor added as an option under Desktop's
3216 <li>Extract score function to parse whitespace separated
3217 numeric data in description line</li>
3218 <li>Column labels in alignment annotation can be centred.</li>
3219 <li>Tooltip for sequence associated annotation give name
3221 </ul> <em>Web Services and URL fetching</em>
3223 <li>JPred3 web service</li>
3224 <li>Prototype sequence search client (no public services
3226 <li>Fetch either seed alignment or full alignment from
3228 <li>URL Links created for matching database cross
3229 references as well as sequence ID</li>
3230 <li>URL Links can be created using regular-expressions</li>
3231 </ul> <em>Sequence Database Connectivity</em>
3233 <li>Retrieval of cross-referenced sequences from other
3235 <li>Generalised database reference retrieval and
3236 validation to all fetchable databases</li>
3237 <li>Fetch sequences from DAS sources supporting the
3238 sequence command</li>
3239 </ul> <em>Import and Export</em>
3240 <li>export annotation rows as CSV for spreadsheet import</li>
3241 <li>Jalview projects record alignment dataset associations,
3242 EMBL products, and cDNA sequence mappings</li>
3243 <li>Sequence Group colour can be specified in Annotation
3245 <li>Ad-hoc colouring of group in Annotation File using RGB
3246 triplet as name of colourscheme</li>
3247 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3249 <li>treenode binding for VAMSAS tree exchange</li>
3250 <li>local editing and update of sequences in VAMSAS
3251 alignments (experimental)</li>
3252 <li>Create new or select existing session to join</li>
3253 <li>load and save of vamsas documents</li>
3254 </ul> <em>Application command line</em>
3256 <li>-tree parameter to open trees (introduced for passing
3258 <li>-fetchfrom command line argument to specify nicknames
3259 of DAS servers to query for alignment features</li>
3260 <li>-dasserver command line argument to add new servers
3261 that are also automatically queried for features</li>
3262 <li>-groovy command line argument executes a given groovy
3263 script after all input data has been loaded and parsed</li>
3264 </ul> <em>Applet-Application data exchange</em>
3266 <li>Trees passed as applet parameters can be passed to
3267 application (when using "View in full
3268 application")</li>
3269 </ul> <em>Applet Parameters</em>
3271 <li>feature group display control parameter</li>
3272 <li>debug parameter</li>
3273 <li>showbutton parameter</li>
3274 </ul> <em>Applet API methods</em>
3276 <li>newView public method</li>
3277 <li>Window (current view) specific get/set public methods</li>
3278 <li>Feature display control methods</li>
3279 <li>get list of currently selected sequences</li>
3280 </ul> <em>New Jalview distribution features</em>
3282 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3283 <li>RELEASE file gives build properties for the latest
3284 Jalview release.</li>
3285 <li>Java 1.1 Applet build made easier and donotobfuscate
3286 property controls execution of obfuscator</li>
3287 <li>Build target for generating source distribution</li>
3288 <li>Debug flag for javacc</li>
3289 <li>.jalview_properties file is documented (slightly) in
3290 jalview.bin.Cache</li>
3291 <li>Continuous Build Integration for stable and
3292 development version of Application, Applet and source
3297 <li>selected region output includes visible annotations
3298 (for certain formats)</li>
3299 <li>edit label/displaychar contains existing label/char
3301 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3302 <li>shorter peptide product names from EMBL records</li>
3303 <li>Newick string generator makes compact representations</li>
3304 <li>bootstrap values parsed correctly for tree files with
3306 <li>pathological filechooser bug avoided by not allowing
3307 filenames containing a ':'</li>
3308 <li>Fixed exception when parsing GFF files containing
3309 global sequence features</li>
3310 <li>Alignment datasets are finalized only when number of
3311 references from alignment sequences goes to zero</li>
3312 <li>Close of tree branch colour box without colour
3313 selection causes cascading exceptions</li>
3314 <li>occasional negative imgwidth exceptions</li>
3315 <li>better reporting of non-fatal warnings to user when
3316 file parsing fails.</li>
3317 <li>Save works when Jalview project is default format</li>
3318 <li>Save as dialog opened if current alignment format is
3319 not a valid output format</li>
3320 <li>UniProt canonical names introduced for both das and
3322 <li>Histidine should be midblue (not pink!) in Zappo</li>
3323 <li>error messages passed up and output when data read
3325 <li>edit undo recovers previous dataset sequence when
3326 sequence is edited</li>
3327 <li>allow PDB files without pdb ID HEADER lines (like
3328 those generated by MODELLER) to be read in properly</li>
3329 <li>allow reading of JPred concise files as a normal
3331 <li>Stockholm annotation parsing and alignment properties
3332 import fixed for PFAM records</li>
3333 <li>Structure view windows have correct name in Desktop
3335 <li>annotation consisting of sequence associated scores
3336 can be read and written correctly to annotation file</li>
3337 <li>Aligned cDNA translation to aligned peptide works
3339 <li>Fixed display of hidden sequence markers and
3340 non-italic font for representatives in Applet</li>
3341 <li>Applet Menus are always embedded in applet window on
3343 <li>Newly shown features appear at top of stack (in
3345 <li>Annotations added via parameter not drawn properly
3346 due to null pointer exceptions</li>
3347 <li>Secondary structure lines are drawn starting from
3348 first column of alignment</li>
3349 <li>UniProt XML import updated for new schema release in
3351 <li>Sequence feature to sequence ID match for Features
3352 file is case-insensitive</li>
3353 <li>Sequence features read from Features file appended to
3354 all sequences with matching IDs</li>
3355 <li>PDB structure coloured correctly for associated views
3356 containing a sub-sequence</li>
3357 <li>PDB files can be retrieved by applet from Jar files</li>
3358 <li>feature and annotation file applet parameters
3359 referring to different directories are retrieved correctly</li>
3360 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3361 <li>Fixed application hang whilst waiting for
3362 splash-screen version check to complete</li>
3363 <li>Applet properly URLencodes input parameter values
3364 when passing them to the launchApp service</li>
3365 <li>display name and local features preserved in results
3366 retrieved from web service</li>
3367 <li>Visual delay indication for sequence retrieval and
3368 sequence fetcher initialisation</li>
3369 <li>updated Application to use DAS 1.53e version of
3370 dasobert DAS client</li>
3371 <li>Re-instated Full AMSA support and .amsa file
3373 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3381 <div align="center">
3382 <strong>2.3</strong><br> 9/5/07
3387 <li>Jmol 11.0.2 integration</li>
3388 <li>PDB views stored in Jalview XML files</li>
3389 <li>Slide sequences</li>
3390 <li>Edit sequence in place</li>
3391 <li>EMBL CDS features</li>
3392 <li>DAS Feature mapping</li>
3393 <li>Feature ordering</li>
3394 <li>Alignment Properties</li>
3395 <li>Annotation Scores</li>
3396 <li>Sort by scores</li>
3397 <li>Feature/annotation editing in applet</li>
3402 <li>Headless state operation in 2.2.1</li>
3403 <li>Incorrect and unstable DNA pairwise alignment</li>
3404 <li>Cut and paste of sequences with annotation</li>
3405 <li>Feature group display state in XML</li>
3406 <li>Feature ordering in XML</li>
3407 <li>blc file iteration selection using filename # suffix</li>
3408 <li>Stockholm alignment properties</li>
3409 <li>Stockhom alignment secondary structure annotation</li>
3410 <li>2.2.1 applet had no feature transparency</li>
3411 <li>Number pad keys can be used in cursor mode</li>
3412 <li>Structure Viewer mirror image resolved</li>
3419 <div align="center">
3420 <strong>2.2.1</strong><br> 12/2/07
3425 <li>Non standard characters can be read and displayed
3426 <li>Annotations/Features can be imported/exported to the
3428 <li>Applet allows editing of sequence/annotation/group
3429 name & description
3430 <li>Preference setting to display sequence name in
3432 <li>Annotation file format extended to allow
3433 Sequence_groups to be defined
3434 <li>Default opening of alignment overview panel can be
3435 specified in preferences
3436 <li>PDB residue numbering annotation added to associated
3442 <li>Applet crash under certain Linux OS with Java 1.6
3444 <li>Annotation file export / import bugs fixed
3445 <li>PNG / EPS image output bugs fixed
3451 <div align="center">
3452 <strong>2.2</strong><br> 27/11/06
3457 <li>Multiple views on alignment
3458 <li>Sequence feature editing
3459 <li>"Reload" alignment
3460 <li>"Save" to current filename
3461 <li>Background dependent text colour
3462 <li>Right align sequence ids
3463 <li>User-defined lower case residue colours
3466 <li>Menu item accelerator keys
3467 <li>Control-V pastes to current alignment
3468 <li>Cancel button for DAS Feature Fetching
3469 <li>PCA and PDB Viewers zoom via mouse roller
3470 <li>User-defined sub-tree colours and sub-tree selection
3472 <li>'New Window' button on the 'Output to Text box'
3477 <li>New memory efficient Undo/Redo System
3478 <li>Optimised symbol lookups and conservation/consensus
3480 <li>Region Conservation/Consensus recalculated after
3482 <li>Fixed Remove Empty Columns Bug (empty columns at end
3484 <li>Slowed DAS Feature Fetching for increased robustness.
3486 <li>Made angle brackets in ASCII feature descriptions
3488 <li>Re-instated Zoom function for PCA
3489 <li>Sequence descriptions conserved in web service
3491 <li>UniProt ID discoverer uses any word separated by
3493 <li>WsDbFetch query/result association resolved
3494 <li>Tree leaf to sequence mapping improved
3495 <li>Smooth fonts switch moved to FontChooser dialog box.
3502 <div align="center">
3503 <strong>2.1.1</strong><br> 12/9/06
3508 <li>Copy consensus sequence to clipboard</li>
3513 <li>Image output - rightmost residues are rendered if
3514 sequence id panel has been resized</li>
3515 <li>Image output - all offscreen group boundaries are
3517 <li>Annotation files with sequence references - all
3518 elements in file are relative to sequence position</li>
3519 <li>Mac Applet users can use Alt key for group editing</li>
3525 <div align="center">
3526 <strong>2.1</strong><br> 22/8/06
3531 <li>MAFFT Multiple Alignment in default Web Service list</li>
3532 <li>DAS Feature fetching</li>
3533 <li>Hide sequences and columns</li>
3534 <li>Export Annotations and Features</li>
3535 <li>GFF file reading / writing</li>
3536 <li>Associate structures with sequences from local PDB
3538 <li>Add sequences to exisiting alignment</li>
3539 <li>Recently opened files / URL lists</li>
3540 <li>Applet can launch the full application</li>
3541 <li>Applet has transparency for features (Java 1.2
3543 <li>Applet has user defined colours parameter</li>
3544 <li>Applet can load sequences from parameter
3545 "sequence<em>x</em>"
3551 <li>Redundancy Panel reinstalled in the Applet</li>
3552 <li>Monospaced font - EPS / rescaling bug fixed</li>
3553 <li>Annotation files with sequence references bug fixed</li>
3559 <div align="center">
3560 <strong>2.08.1</strong><br> 2/5/06
3565 <li>Change case of selected region from Popup menu</li>
3566 <li>Choose to match case when searching</li>
3567 <li>Middle mouse button and mouse movement can compress /
3568 expand the visible width and height of the alignment</li>
3573 <li>Annotation Panel displays complete JNet results</li>
3579 <div align="center">
3580 <strong>2.08b</strong><br> 18/4/06
3586 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3587 <li>Righthand label on wrapped alignments shows correct
3594 <div align="center">
3595 <strong>2.08</strong><br> 10/4/06
3600 <li>Editing can be locked to the selection area</li>
3601 <li>Keyboard editing</li>
3602 <li>Create sequence features from searches</li>
3603 <li>Precalculated annotations can be loaded onto
3605 <li>Features file allows grouping of features</li>
3606 <li>Annotation Colouring scheme added</li>
3607 <li>Smooth fonts off by default - Faster rendering</li>
3608 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3613 <li>Drag & Drop fixed on Linux</li>
3614 <li>Jalview Archive file faster to load/save, sequence
3615 descriptions saved.</li>
3621 <div align="center">
3622 <strong>2.07</strong><br> 12/12/05
3627 <li>PDB Structure Viewer enhanced</li>
3628 <li>Sequence Feature retrieval and display enhanced</li>
3629 <li>Choose to output sequence start-end after sequence
3630 name for file output</li>
3631 <li>Sequence Fetcher WSDBFetch@EBI</li>
3632 <li>Applet can read feature files, PDB files and can be
3633 used for HTML form input</li>
3638 <li>HTML output writes groups and features</li>
3639 <li>Group editing is Control and mouse click</li>
3640 <li>File IO bugs</li>
3646 <div align="center">
3647 <strong>2.06</strong><br> 28/9/05
3652 <li>View annotations in wrapped mode</li>
3653 <li>More options for PCA viewer</li>
3658 <li>GUI bugs resolved</li>
3659 <li>Runs with -nodisplay from command line</li>
3665 <div align="center">
3666 <strong>2.05b</strong><br> 15/9/05
3671 <li>Choose EPS export as lineart or text</li>
3672 <li>Jar files are executable</li>
3673 <li>Can read in Uracil - maps to unknown residue</li>
3678 <li>Known OutOfMemory errors give warning message</li>
3679 <li>Overview window calculated more efficiently</li>
3680 <li>Several GUI bugs resolved</li>
3686 <div align="center">
3687 <strong>2.05</strong><br> 30/8/05
3692 <li>Edit and annotate in "Wrapped" view</li>
3697 <li>Several GUI bugs resolved</li>
3703 <div align="center">
3704 <strong>2.04</strong><br> 24/8/05
3709 <li>Hold down mouse wheel & scroll to change font
3715 <li>Improved JPred client reliability</li>
3716 <li>Improved loading of Jalview files</li>
3722 <div align="center">
3723 <strong>2.03</strong><br> 18/8/05
3728 <li>Set Proxy server name and port in preferences</li>
3729 <li>Multiple URL links from sequence ids</li>
3730 <li>User Defined Colours can have a scheme name and added
3732 <li>Choose to ignore gaps in consensus calculation</li>
3733 <li>Unix users can set default web browser</li>
3734 <li>Runs without GUI for batch processing</li>
3735 <li>Dynamically generated Web Service Menus</li>
3740 <li>InstallAnywhere download for Sparc Solaris</li>
3746 <div align="center">
3747 <strong>2.02</strong><br> 18/7/05
3753 <li>Copy & Paste order of sequences maintains
3754 alignment order.</li>
3760 <div align="center">
3761 <strong>2.01</strong><br> 12/7/05
3766 <li>Use delete key for deleting selection.</li>
3767 <li>Use Mouse wheel to scroll sequences.</li>
3768 <li>Help file updated to describe how to add alignment
3770 <li>Version and build date written to build properties
3772 <li>InstallAnywhere installation will check for updates
3773 at launch of Jalview.</li>
3778 <li>Delete gaps bug fixed.</li>
3779 <li>FileChooser sorts columns.</li>
3780 <li>Can remove groups one by one.</li>
3781 <li>Filechooser icons installed.</li>
3782 <li>Finder ignores return character when searching.
3783 Return key will initiate a search.<br>
3790 <div align="center">
3791 <strong>2.0</strong><br> 20/6/05
3796 <li>New codebase</li>