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.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
76 <td><div align="left">
77 <ul><li>Updated Certum Codesigning Certificate
78 (Valid till 30th November 2018)</li></ul></div></td>
79 <td><div align="left">
82 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
83 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
84 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
85 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
86 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
87 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
88 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
94 <td width="60" nowrap>
96 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
99 <td><div align="left">
107 <td><div align="left">
112 <td width="60" nowrap>
114 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
117 <td><div align="left">
121 <!-- JAL-2446 -->Faster and more efficient management and
122 rendering of sequence features
125 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
126 429 rate limit request hander
129 <!-- JAL-2773 -->Structure views don't get updated unless
130 their colours have changed
133 <!-- JAL-2495 -->All linked sequences are highlighted for
134 a structure mousover (Jmol) or selection (Chimera)
137 <!-- JAL-2790 -->'Cancel' button in progress bar for
138 JABAWS AACon, RNAAliFold and Disorder prediction jobs
141 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
142 view from Ensembl locus cross-references
145 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
149 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
150 feature can be disabled
153 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
154 PDB easier retrieval of sequences for lists of IDs
157 <!-- JAL-2758 -->Short names for sequences retrieved from
163 <li>Groovy interpreter updated to 2.4.12</li>
164 <li>Example groovy script for generating a matrix of
165 percent identity scores for current alignment.</li>
167 <em>Testing and Deployment</em>
170 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
174 <td><div align="left">
178 <!-- JAL-2643 -->Pressing tab after updating the colour
179 threshold text field doesn't trigger an update to the
183 <!-- JAL-2682 -->Race condition when parsing sequence ID
187 <!-- JAL-2608 -->Overview windows are also closed when
188 alignment window is closed
191 <!-- JAL-2548 -->Export of features doesn't always respect
195 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
196 takes a long time in Cursor mode
202 <!-- JAL-2777 -->Structures with whitespace chainCode
203 cannot be viewed in Chimera
206 <!-- JAL-2728 -->Protein annotation panel too high in
210 <!-- JAL-2757 -->Can't edit the query after the server
211 error warning icon is shown in Uniprot and PDB Free Text
215 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
218 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
221 <!-- JAL-2739 -->Hidden column marker in last column not
222 rendered when switching back from Wrapped to normal view
225 <!-- JAL-2768 -->Annotation display corrupted when
226 scrolling right in unwapped alignment view
229 <!-- JAL-2542 -->Existing features on subsequence
230 incorrectly relocated when full sequence retrieved from
234 <!-- JAL-2733 -->Last reported memory still shown when
235 Desktop->Show Memory is unticked (OSX only)
238 <!-- JAL-2658 -->Amend Features dialog doesn't allow
239 features of same type and group to be selected for
243 <!-- JAL-2524 -->Jalview becomes sluggish in wide
244 alignments when hidden columns are present
247 <!-- JAL-2392 -->Jalview freezes when loading and
248 displaying several structures
251 <!-- JAL-2732 -->Black outlines left after resizing or
255 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
256 within the Jalview desktop on OSX
259 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
260 when in wrapped alignment mode
263 <!-- JAL-2636 -->Scale mark not shown when close to right
264 hand end of alignment
267 <!-- JAL-2684 -->Pairwise alignment of selected regions of
268 each selected sequence do not have correct start/end
272 <!-- JAL-2793 -->Alignment ruler height set incorrectly
273 after canceling the Alignment Window's Font dialog
276 <!-- JAL-2036 -->Show cross-references not enabled after
277 restoring project until a new view is created
280 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
281 URL links appears when only default EMBL-EBI link is
282 configured (since 2.10.2b2)
285 <!-- JAL-2775 -->Overview redraws whole window when box
289 <!-- JAL-2225 -->Structure viewer doesn't map all chains
290 in a multi-chain structure when viewing alignment
291 involving more than one chain (since 2.10)
294 <!-- JAL-2811 -->Double residue highlights in cursor mode
295 if new selection moves alignment window
298 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
299 arrow key in cursor mode to pass hidden column marker
302 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
303 that produces correctly annotated transcripts and products
306 <!-- JAL-2776 -->Toggling a feature group after first time
307 doesn't update associated structure view
310 <em>Applet</em><br />
313 <!-- JAL-2687 -->Concurrent modification exception when
314 closing alignment panel
317 <em>BioJSON</em><br />
320 <!-- JAL-2546 -->BioJSON export does not preserve
321 non-positional features
324 <em>New Known Issues</em>
327 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
328 sequence features correctly (for many previous versions of
332 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
333 using cursor in wrapped panel other than top
336 <!-- JAL-2791 -->Select columns containing feature ignores
337 graduated colour threshold
340 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
341 always preserve numbering and sequence features
344 <em>Known Java 9 Issues</em>
347 <!-- JAL-2902 -->Groovy Console very slow to open and is
348 not responsive when entering characters (Webstart, Java
355 <td width="60" nowrap>
357 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
358 <em>2/10/2017</em></strong>
361 <td><div align="left">
362 <em>New features in Jalview Desktop</em>
365 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
367 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
371 <td><div align="left">
375 <td width="60" nowrap>
377 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
378 <em>7/9/2017</em></strong>
381 <td><div align="left">
385 <!-- JAL-2588 -->Show gaps in overview window by colouring
386 in grey (sequences used to be coloured grey, and gaps were
390 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
394 <!-- JAL-2587 -->Overview updates immediately on increase
395 in size and progress bar shown as higher resolution
396 overview is recalculated
401 <td><div align="left">
405 <!-- JAL-2664 -->Overview window redraws every hidden
406 column region row by row
409 <!-- JAL-2681 -->duplicate protein sequences shown after
410 retrieving Ensembl crossrefs for sequences from Uniprot
413 <!-- JAL-2603 -->Overview window throws NPE if show boxes
414 format setting is unticked
417 <!-- JAL-2610 -->Groups are coloured wrongly in overview
418 if group has show boxes format setting unticked
421 <!-- JAL-2672,JAL-2665 -->Redraw problems when
422 autoscrolling whilst dragging current selection group to
423 include sequences and columns not currently displayed
426 <!-- JAL-2691 -->Not all chains are mapped when multimeric
427 assemblies are imported via CIF file
430 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
431 displayed when threshold or conservation colouring is also
435 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
439 <!-- JAL-2673 -->Jalview continues to scroll after
440 dragging a selected region off the visible region of the
444 <!-- JAL-2724 -->Cannot apply annotation based
445 colourscheme to all groups in a view
448 <!-- JAL-2511 -->IDs don't line up with sequences
449 initially after font size change using the Font chooser or
456 <td width="60" nowrap>
458 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
461 <td><div align="left">
462 <em>Calculations</em>
466 <!-- JAL-1933 -->Occupancy annotation row shows number of
467 ungapped positions in each column of the alignment.
470 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
471 a calculation dialog box
474 <!-- JAL-2379 -->Revised implementation of PCA for speed
475 and memory efficiency (~30x faster)
478 <!-- JAL-2403 -->Revised implementation of sequence
479 similarity scores as used by Tree, PCA, Shading Consensus
480 and other calculations
483 <!-- JAL-2416 -->Score matrices are stored as resource
484 files within the Jalview codebase
487 <!-- JAL-2500 -->Trees computed on Sequence Feature
488 Similarity may have different topology due to increased
495 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
496 model for alignments and groups
499 <!-- JAL-384 -->Custom shading schemes created via groovy
506 <!-- JAL-2526 -->Efficiency improvements for interacting
507 with alignment and overview windows
510 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
514 <!-- JAL-2388 -->Hidden columns and sequences can be
518 <!-- JAL-2611 -->Click-drag in visible area allows fine
519 adjustment of visible position
523 <em>Data import/export</em>
526 <!-- JAL-2535 -->Posterior probability annotation from
527 Stockholm files imported as sequence associated annotation
530 <!-- JAL-2507 -->More robust per-sequence positional
531 annotation input/output via stockholm flatfile
534 <!-- JAL-2533 -->Sequence names don't include file
535 extension when importing structure files without embedded
536 names or PDB accessions
539 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
540 format sequence substitution matrices
543 <em>User Interface</em>
546 <!-- JAL-2447 --> Experimental Features Checkbox in
547 Desktop's Tools menu to hide or show untested features in
551 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
552 via Overview or sequence motif search operations
555 <!-- JAL-2547 -->Amend sequence features dialog box can be
556 opened by double clicking gaps within sequence feature
560 <!-- JAL-1476 -->Status bar message shown when not enough
561 aligned positions were available to create a 3D structure
565 <em>3D Structure</em>
568 <!-- JAL-2430 -->Hidden regions in alignment views are not
569 coloured in linked structure views
572 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
573 file-based command exchange
576 <!-- JAL-2375 -->Structure chooser automatically shows
577 Cached Structures rather than querying the PDBe if
578 structures are already available for sequences
581 <!-- JAL-2520 -->Structures imported via URL are cached in
582 the Jalview project rather than downloaded again when the
586 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
587 to transfer Chimera's structure attributes as Jalview
588 features, and vice-versa (<strong>Experimental
592 <em>Web Services</em>
595 <!-- JAL-2549 -->Updated JABAWS client to v2.2
598 <!-- JAL-2335 -->Filter non-standard amino acids and
599 nucleotides when submitting to AACon and other MSA
603 <!-- JAL-2316, -->URLs for viewing database
604 cross-references provided by identifiers.org and the
612 <!-- JAL-2344 -->FileFormatI interface for describing and
613 identifying file formats (instead of String constants)
616 <!-- JAL-2228 -->FeatureCounter script refactored for
617 efficiency when counting all displayed features (not
618 backwards compatible with 2.10.1)
621 <em>Example files</em>
624 <!-- JAL-2631 -->Graduated feature colour style example
625 included in the example feature file
628 <em>Documentation</em>
631 <!-- JAL-2339 -->Release notes reformatted for readability
632 with the built-in Java help viewer
635 <!-- JAL-1644 -->Find documentation updated with 'search
636 sequence description' option
642 <!-- JAL-2485, -->External service integration tests for
643 Uniprot REST Free Text Search Client
646 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
649 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
654 <td><div align="left">
655 <em>Calculations</em>
658 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
659 matrix - C->R should be '-3'<br />Old matrix restored
660 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
662 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
663 Jalview's treatment of gaps in PCA and substitution matrix
664 based Tree calculations.<br /> <br />In earlier versions
665 of Jalview, gaps matching gaps were penalised, and gaps
666 matching non-gaps penalised even more. In the PCA
667 calculation, gaps were actually treated as non-gaps - so
668 different costs were applied, which meant Jalview's PCAs
669 were different to those produced by SeqSpace.<br />Jalview
670 now treats gaps in the same way as SeqSpace (ie it scores
671 them as 0). <br /> <br />Enter the following in the
672 Groovy console to restore pre-2.10.2 behaviour:<br />
673 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
674 // for 2.10.1 mode <br />
675 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
676 // to restore 2.10.2 mode <br /> <br /> <em>Note:
677 these settings will affect all subsequent tree and PCA
678 calculations (not recommended)</em></li>
680 <!-- JAL-2424 -->Fixed off-by-one bug that affected
681 scaling of branch lengths for trees computed using
682 Sequence Feature Similarity.
685 <!-- JAL-2377 -->PCA calculation could hang when
686 generating output report when working with highly
690 <!-- JAL-2544 --> Sort by features includes features to
691 right of selected region when gaps present on right-hand
695 <em>User Interface</em>
698 <!-- JAL-2346 -->Reopening Colour by annotation dialog
699 doesn't reselect a specific sequence's associated
700 annotation after it was used for colouring a view
703 <!-- JAL-2419 -->Current selection lost if popup menu
704 opened on a region of alignment without groups
707 <!-- JAL-2374 -->Popup menu not always shown for regions
708 of an alignment with overlapping groups
711 <!-- JAL-2310 -->Finder double counts if both a sequence's
712 name and description match
715 <!-- JAL-2370 -->Hiding column selection containing two
716 hidden regions results in incorrect hidden regions
719 <!-- JAL-2386 -->'Apply to all groups' setting when
720 changing colour does not apply Conservation slider value
724 <!-- JAL-2373 -->Percentage identity and conservation menu
725 items do not show a tick or allow shading to be disabled
728 <!-- JAL-2385 -->Conservation shading or PID threshold
729 lost when base colourscheme changed if slider not visible
732 <!-- JAL-2547 -->Sequence features shown in tooltip for
733 gaps before start of features
736 <!-- JAL-2623 -->Graduated feature colour threshold not
737 restored to UI when feature colour is edited
740 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
741 a time when scrolling vertically in wrapped mode.
744 <!-- JAL-2630 -->Structure and alignment overview update
745 as graduate feature colour settings are modified via the
749 <!-- JAL-2034 -->Overview window doesn't always update
750 when a group defined on the alignment is resized
753 <!-- JAL-2605 -->Mouseovers on left/right scale region in
754 wrapped view result in positional status updates
758 <!-- JAL-2563 -->Status bar doesn't show position for
759 ambiguous amino acid and nucleotide symbols
762 <!-- JAL-2602 -->Copy consensus sequence failed if
763 alignment included gapped columns
766 <!-- JAL-2473 -->Minimum size set for Jalview windows so
767 widgets don't permanently disappear
770 <!-- JAL-2503 -->Cannot select or filter quantitative
771 annotation that are shown only as column labels (e.g.
772 T-Coffee column reliability scores)
775 <!-- JAL-2594 -->Exception thrown if trying to create a
776 sequence feature on gaps only
779 <!-- JAL-2504 -->Features created with 'New feature'
780 button from a Find inherit previously defined feature type
781 rather than the Find query string
784 <!-- JAL-2423 -->incorrect title in output window when
785 exporting tree calculated in Jalview
788 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
789 and then revealing them reorders sequences on the
793 <!-- JAL-964 -->Group panel in sequence feature settings
794 doesn't update to reflect available set of groups after
795 interactively adding or modifying features
798 <!-- JAL-2225 -->Sequence Database chooser unusable on
802 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
803 only excluded gaps in current sequence and ignored
810 <!-- JAL-2421 -->Overview window visible region moves
811 erratically when hidden rows or columns are present
814 <!-- JAL-2362 -->Per-residue colourschemes applied via the
815 Structure Viewer's colour menu don't correspond to
819 <!-- JAL-2405 -->Protein specific colours only offered in
820 colour and group colour menu for protein alignments
823 <!-- JAL-2385 -->Colour threshold slider doesn't update to
824 reflect currently selected view or group's shading
828 <!-- JAL-2624 -->Feature colour thresholds not respected
829 when rendered on overview and structures when opacity at
833 <!-- JAL-2589 -->User defined gap colour not shown in
834 overview when features overlaid on alignment
837 <em>Data import/export</em>
840 <!-- JAL-2576 -->Very large alignments take a long time to
844 <!-- JAL-2507 -->Per-sequence RNA secondary structures
845 added after a sequence was imported are not written to
849 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
850 when importing RNA secondary structure via Stockholm
853 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
854 not shown in correct direction for simple pseudoknots
857 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
858 with lightGray or darkGray via features file (but can
862 <!-- JAL-2383 -->Above PID colour threshold not recovered
863 when alignment view imported from project
866 <!-- JAL-2520,JAL-2465 -->No mappings generated between
867 structure and sequences extracted from structure files
868 imported via URL and viewed in Jmol
871 <!-- JAL-2520 -->Structures loaded via URL are saved in
872 Jalview Projects rather than fetched via URL again when
873 the project is loaded and the structure viewed
876 <em>Web Services</em>
879 <!-- JAL-2519 -->EnsemblGenomes example failing after
880 release of Ensembl v.88
883 <!-- JAL-2366 -->Proxy server address and port always
884 appear enabled in Preferences->Connections
887 <!-- JAL-2461 -->DAS registry not found exceptions
888 removed from console output
891 <!-- JAL-2582 -->Cannot retrieve protein products from
892 Ensembl by Peptide ID
895 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
896 created from SIFTs, and spurious 'Couldn't open structure
897 in Chimera' errors raised after April 2017 update (problem
898 due to 'null' string rather than empty string used for
899 residues with no corresponding PDB mapping).
902 <em>Application UI</em>
905 <!-- JAL-2361 -->User Defined Colours not added to Colour
909 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
910 case' residues (button in colourscheme editor debugged and
911 new documentation and tooltips added)
914 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
915 doesn't restore group-specific text colour thresholds
918 <!-- JAL-2243 -->Feature settings panel does not update as
919 new features are added to alignment
922 <!-- JAL-2532 -->Cancel in feature settings reverts
923 changes to feature colours via the Amend features dialog
926 <!-- JAL-2506 -->Null pointer exception when attempting to
927 edit graduated feature colour via amend features dialog
931 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
932 selection menu changes colours of alignment views
935 <!-- JAL-2426 -->Spurious exceptions in console raised
936 from alignment calculation workers after alignment has
940 <!-- JAL-1608 -->Typo in selection popup menu - Create
941 groups now 'Create Group'
944 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
945 Create/Undefine group doesn't always work
948 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
949 shown again after pressing 'Cancel'
952 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
953 adjusts start position in wrap mode
956 <!-- JAL-2563 -->Status bar doesn't show positions for
957 ambiguous amino acids
960 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
961 CDS/Protein view after CDS sequences added for aligned
965 <!-- JAL-2592 -->User defined colourschemes called 'User
966 Defined' don't appear in Colours menu
972 <!-- JAL-2468 -->Switching between Nucleotide and Protein
973 score models doesn't always result in an updated PCA plot
976 <!-- JAL-2442 -->Features not rendered as transparent on
977 overview or linked structure view
980 <!-- JAL-2372 -->Colour group by conservation doesn't
984 <!-- JAL-2517 -->Hitting Cancel after applying
985 user-defined colourscheme doesn't restore original
992 <!-- JAL-2314 -->Unit test failure:
993 jalview.ws.jabaws.RNAStructExportImport setup fails
996 <!-- JAL-2307 -->Unit test failure:
997 jalview.ws.sifts.SiftsClientTest due to compatibility
998 problems with deep array comparison equality asserts in
999 successive versions of TestNG
1002 <!-- JAL-2479 -->Relocated StructureChooserTest and
1003 ParameterUtilsTest Unit tests to Network suite
1006 <em>New Known Issues</em>
1009 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
1010 phase after a sequence motif find operation
1013 <!-- JAL-2550 -->Importing annotation file with rows
1014 containing just upper and lower case letters are
1015 interpreted as WUSS RNA secondary structure symbols
1018 <!-- JAL-2590 -->Cannot load and display Newick trees
1019 reliably from eggnog Ortholog database
1022 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1023 containing features of type Highlight' when 'B' is pressed
1024 to mark columns containing highlighted regions.
1027 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1028 doesn't always add secondary structure annotation.
1033 <td width="60" nowrap>
1034 <div align="center">
1035 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1038 <td><div align="left">
1042 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1043 for all consensus calculations
1046 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1049 <li>Updated Jalview's Certum code signing certificate
1052 <em>Application</em>
1055 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1056 set of database cross-references, sorted alphabetically
1059 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1060 from database cross references. Users with custom links
1061 will receive a <a href="webServices/urllinks.html#warning">warning
1062 dialog</a> asking them to update their preferences.
1065 <!-- JAL-2287-->Cancel button and escape listener on
1066 dialog warning user about disconnecting Jalview from a
1070 <!-- JAL-2320-->Jalview's Chimera control window closes if
1071 the Chimera it is connected to is shut down
1074 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1075 columns menu item to mark columns containing highlighted
1076 regions (e.g. from structure selections or results of a
1080 <!-- JAL-2284-->Command line option for batch-generation
1081 of HTML pages rendering alignment data with the BioJS
1091 <!-- JAL-2286 -->Columns with more than one modal residue
1092 are not coloured or thresholded according to percent
1093 identity (first observed in Jalview 2.8.2)
1096 <!-- JAL-2301 -->Threonine incorrectly reported as not
1100 <!-- JAL-2318 -->Updates to documentation pages (above PID
1101 threshold, amino acid properties)
1104 <!-- JAL-2292 -->Lower case residues in sequences are not
1105 reported as mapped to residues in a structure file in the
1109 <!--JAL-2324 -->Identical features with non-numeric scores
1110 could be added multiple times to a sequence
1113 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1114 bond features shown as two highlighted residues rather
1115 than a range in linked structure views, and treated
1116 correctly when selecting and computing trees from features
1119 <!-- JAL-2281-->Custom URL links for database
1120 cross-references are matched to database name regardless
1125 <em>Application</em>
1128 <!-- JAL-2282-->Custom URL links for specific database
1129 names without regular expressions also offer links from
1133 <!-- JAL-2315-->Removing a single configured link in the
1134 URL links pane in Connections preferences doesn't actually
1135 update Jalview configuration
1138 <!-- JAL-2272-->CTRL-Click on a selected region to open
1139 the alignment area popup menu doesn't work on El-Capitan
1142 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1143 files with similarly named sequences if dropped onto the
1147 <!-- JAL-2312 -->Additional mappings are shown for PDB
1148 entries where more chains exist in the PDB accession than
1149 are reported in the SIFTS file
1152 <!-- JAL-2317-->Certain structures do not get mapped to
1153 the structure view when displayed with Chimera
1156 <!-- JAL-2317-->No chains shown in the Chimera view
1157 panel's View->Show Chains submenu
1160 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1161 work for wrapped alignment views
1164 <!--JAL-2197 -->Rename UI components for running JPred
1165 predictions from 'JNet' to 'JPred'
1168 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1169 corrupted when annotation panel vertical scroll is not at
1170 first annotation row
1173 <!--JAL-2332 -->Attempting to view structure for Hen
1174 lysozyme results in a PDB Client error dialog box
1177 <!-- JAL-2319 -->Structure View's mapping report switched
1178 ranges for PDB and sequence for SIFTS
1181 SIFTS 'Not_Observed' residues mapped to non-existant
1185 <!-- <em>New Known Issues</em>
1192 <td width="60" nowrap>
1193 <div align="center">
1194 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1195 <em>25/10/2016</em></strong>
1198 <td><em>Application</em>
1200 <li>3D Structure chooser opens with 'Cached structures'
1201 view if structures already loaded</li>
1202 <li>Progress bar reports models as they are loaded to
1203 structure views</li>
1209 <li>Colour by conservation always enabled and no tick
1210 shown in menu when BLOSUM or PID shading applied</li>
1211 <li>FER1_ARATH and FER2_ARATH labels were switched in
1212 example sequences/projects/trees</li>
1214 <em>Application</em>
1216 <li>Jalview projects with views of local PDB structure
1217 files saved on Windows cannot be opened on OSX</li>
1218 <li>Multiple structure views can be opened and superposed
1219 without timeout for structures with multiple models or
1220 multiple sequences in alignment</li>
1221 <li>Cannot import or associated local PDB files without a
1222 PDB ID HEADER line</li>
1223 <li>RMSD is not output in Jmol console when superposition
1225 <li>Drag and drop of URL from Browser fails for Linux and
1226 OSX versions earlier than El Capitan</li>
1227 <li>ENA client ignores invalid content from ENA server</li>
1228 <li>Exceptions are not raised in console when ENA client
1229 attempts to fetch non-existent IDs via Fetch DB Refs UI
1231 <li>Exceptions are not raised in console when a new view
1232 is created on the alignment</li>
1233 <li>OSX right-click fixed for group selections: CMD-click
1234 to insert/remove gaps in groups and CTRL-click to open group
1237 <em>Build and deployment</em>
1239 <li>URL link checker now copes with multi-line anchor
1242 <em>New Known Issues</em>
1244 <li>Drag and drop from URL links in browsers do not work
1251 <td width="60" nowrap>
1252 <div align="center">
1253 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1256 <td><em>General</em>
1259 <!-- JAL-2124 -->Updated Spanish translations.
1262 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1263 for importing structure data to Jalview. Enables mmCIF and
1267 <!-- JAL-192 --->Alignment ruler shows positions relative to
1271 <!-- JAL-2202 -->Position/residue shown in status bar when
1272 mousing over sequence associated annotation
1275 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1279 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1280 '()', canonical '[]' and invalid '{}' base pair populations
1284 <!-- JAL-2092 -->Feature settings popup menu options for
1285 showing or hiding columns containing a feature
1288 <!-- JAL-1557 -->Edit selected group by double clicking on
1289 group and sequence associated annotation labels
1292 <!-- JAL-2236 -->Sequence name added to annotation label in
1293 select/hide columns by annotation and colour by annotation
1297 </ul> <em>Application</em>
1300 <!-- JAL-2050-->Automatically hide introns when opening a
1301 gene/transcript view
1304 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1308 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1309 structure mappings with the EMBL-EBI PDBe SIFTS database
1312 <!-- JAL-2079 -->Updated download sites used for Rfam and
1313 Pfam sources to xfam.org
1316 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1319 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1320 over sequences in Jalview
1323 <!-- JAL-2027-->Support for reverse-complement coding
1324 regions in ENA and EMBL
1327 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1328 for record retrieval via ENA rest API
1331 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1335 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1336 groovy script execution
1339 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1340 alignment window's Calculate menu
1343 <!-- JAL-1812 -->Allow groovy scripts that call
1344 Jalview.getAlignFrames() to run in headless mode
1347 <!-- JAL-2068 -->Support for creating new alignment
1348 calculation workers from groovy scripts
1351 <!-- JAL-1369 --->Store/restore reference sequence in
1355 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1356 associations are now saved/restored from project
1359 <!-- JAL-1993 -->Database selection dialog always shown
1360 before sequence fetcher is opened
1363 <!-- JAL-2183 -->Double click on an entry in Jalview's
1364 database chooser opens a sequence fetcher
1367 <!-- JAL-1563 -->Free-text search client for UniProt using
1368 the UniProt REST API
1371 <!-- JAL-2168 -->-nonews command line parameter to prevent
1372 the news reader opening
1375 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1376 querying stored in preferences
1379 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1383 <!-- JAL-1977-->Tooltips shown on database chooser
1386 <!-- JAL-391 -->Reverse complement function in calculate
1387 menu for nucleotide sequences
1390 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1391 and feature counts preserves alignment ordering (and
1392 debugged for complex feature sets).
1395 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1396 viewing structures with Jalview 2.10
1399 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1400 genome, transcript CCDS and gene ids via the Ensembl and
1401 Ensembl Genomes REST API
1404 <!-- JAL-2049 -->Protein sequence variant annotation
1405 computed for 'sequence_variant' annotation on CDS regions
1409 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1413 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1414 Ref Fetcher fails to match, or otherwise updates sequence
1415 data from external database records.
1418 <!-- JAL-2154 -->Revised Jalview Project format for
1419 efficient recovery of sequence coding and alignment
1420 annotation relationships.
1422 </ul> <!-- <em>Applet</em>
1433 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1437 <!-- JAL-2018-->Export features in Jalview format (again)
1438 includes graduated colourschemes
1441 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1442 working with big alignments and lots of hidden columns
1445 <!-- JAL-2053-->Hidden column markers not always rendered
1446 at right of alignment window
1449 <!-- JAL-2067 -->Tidied up links in help file table of
1453 <!-- JAL-2072 -->Feature based tree calculation not shown
1457 <!-- JAL-2075 -->Hidden columns ignored during feature
1458 based tree calculation
1461 <!-- JAL-2065 -->Alignment view stops updating when show
1462 unconserved enabled for group on alignment
1465 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1469 <!-- JAL-2146 -->Alignment column in status incorrectly
1470 shown as "Sequence position" when mousing over
1474 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1475 hidden columns present
1478 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1479 user created annotation added to alignment
1482 <!-- JAL-1841 -->RNA Structure consensus only computed for
1483 '()' base pair annotation
1486 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1487 in zero scores for all base pairs in RNA Structure
1491 <!-- JAL-2174-->Extend selection with columns containing
1495 <!-- JAL-2275 -->Pfam format writer puts extra space at
1496 beginning of sequence
1499 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1503 <!-- JAL-2238 -->Cannot create groups on an alignment from
1504 from a tree when t-coffee scores are shown
1507 <!-- JAL-1836,1967 -->Cannot import and view PDB
1508 structures with chains containing negative resnums (4q4h)
1511 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1515 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1516 to Clustal, PIR and PileUp output
1519 <!-- JAL-2008 -->Reordering sequence features that are
1520 not visible causes alignment window to repaint
1523 <!-- JAL-2006 -->Threshold sliders don't work in
1524 graduated colour and colour by annotation row for e-value
1525 scores associated with features and annotation rows
1528 <!-- JAL-1797 -->amino acid physicochemical conservation
1529 calculation should be case independent
1532 <!-- JAL-2173 -->Remove annotation also updates hidden
1536 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1537 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1538 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1541 <!-- JAL-2065 -->Null pointer exceptions and redraw
1542 problems when reference sequence defined and 'show
1543 non-conserved' enabled
1546 <!-- JAL-1306 -->Quality and Conservation are now shown on
1547 load even when Consensus calculation is disabled
1550 <!-- JAL-1932 -->Remove right on penultimate column of
1551 alignment does nothing
1554 <em>Application</em>
1557 <!-- JAL-1552-->URLs and links can't be imported by
1558 drag'n'drop on OSX when launched via webstart (note - not
1559 yet fixed for El Capitan)
1562 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1563 output when running on non-gb/us i18n platforms
1566 <!-- JAL-1944 -->Error thrown when exporting a view with
1567 hidden sequences as flat-file alignment
1570 <!-- JAL-2030-->InstallAnywhere distribution fails when
1574 <!-- JAL-2080-->Jalview very slow to launch via webstart
1575 (also hotfix for 2.9.0b2)
1578 <!-- JAL-2085 -->Cannot save project when view has a
1579 reference sequence defined
1582 <!-- JAL-1011 -->Columns are suddenly selected in other
1583 alignments and views when revealing hidden columns
1586 <!-- JAL-1989 -->Hide columns not mirrored in complement
1587 view in a cDNA/Protein splitframe
1590 <!-- JAL-1369 -->Cannot save/restore representative
1591 sequence from project when only one sequence is
1595 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1596 in Structure Chooser
1599 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1600 structure consensus didn't refresh annotation panel
1603 <!-- JAL-1962 -->View mapping in structure view shows
1604 mappings between sequence and all chains in a PDB file
1607 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1608 dialogs format columns correctly, don't display array
1609 data, sort columns according to type
1612 <!-- JAL-1975 -->Export complete shown after destination
1613 file chooser is cancelled during an image export
1616 <!-- JAL-2025 -->Error when querying PDB Service with
1617 sequence name containing special characters
1620 <!-- JAL-2024 -->Manual PDB structure querying should be
1624 <!-- JAL-2104 -->Large tooltips with broken HTML
1625 formatting don't wrap
1628 <!-- JAL-1128 -->Figures exported from wrapped view are
1629 truncated so L looks like I in consensus annotation
1632 <!-- JAL-2003 -->Export features should only export the
1633 currently displayed features for the current selection or
1637 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1638 after fetching cross-references, and restoring from
1642 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1643 followed in the structure viewer
1646 <!-- JAL-2163 -->Titles for individual alignments in
1647 splitframe not restored from project
1650 <!-- JAL-2145 -->missing autocalculated annotation at
1651 trailing end of protein alignment in transcript/product
1652 splitview when pad-gaps not enabled by default
1655 <!-- JAL-1797 -->amino acid physicochemical conservation
1659 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1660 article has been read (reopened issue due to
1661 internationalisation problems)
1664 <!-- JAL-1960 -->Only offer PDB structures in structure
1665 viewer based on sequence name, PDB and UniProt
1670 <!-- JAL-1976 -->No progress bar shown during export of
1674 <!-- JAL-2213 -->Structures not always superimposed after
1675 multiple structures are shown for one or more sequences.
1678 <!-- JAL-1370 -->Reference sequence characters should not
1679 be replaced with '.' when 'Show unconserved' format option
1683 <!-- JAL-1823 -->Cannot specify chain code when entering
1684 specific PDB id for sequence
1687 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1688 'Export hidden sequences' is enabled, but 'export hidden
1689 columns' is disabled.
1692 <!--JAL-2026-->Best Quality option in structure chooser
1693 selects lowest rather than highest resolution structures
1697 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1698 to sequence mapping in 'View Mappings' report
1701 <!-- JAL-2284 -->Unable to read old Jalview projects that
1702 contain non-XML data added after Jalvew wrote project.
1705 <!-- JAL-2118 -->Newly created annotation row reorders
1706 after clicking on it to create new annotation for a
1710 <!-- JAL-1980 -->Null Pointer Exception raised when
1711 pressing Add on an orphaned cut'n'paste window.
1713 <!-- may exclude, this is an external service stability issue JAL-1941
1714 -- > RNA 3D structure not added via DSSR service</li> -->
1719 <!-- JAL-2151 -->Incorrect columns are selected when
1720 hidden columns present before start of sequence
1723 <!-- JAL-1986 -->Missing dependencies on applet pages
1727 <!-- JAL-1947 -->Overview pixel size changes when
1728 sequences are hidden in applet
1731 <!-- JAL-1996 -->Updated instructions for applet
1732 deployment on examples pages.
1739 <td width="60" nowrap>
1740 <div align="center">
1741 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1742 <em>16/10/2015</em></strong>
1745 <td><em>General</em>
1747 <li>Time stamps for signed Jalview application and applet
1752 <em>Application</em>
1754 <li>Duplicate group consensus and conservation rows
1755 shown when tree is partitioned</li>
1756 <li>Erratic behaviour when tree partitions made with
1757 multiple cDNA/Protein split views</li>
1763 <td width="60" nowrap>
1764 <div align="center">
1765 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1766 <em>8/10/2015</em></strong>
1769 <td><em>General</em>
1771 <li>Updated Spanish translations of localized text for
1773 </ul> <em>Application</em>
1775 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1776 <li>Signed OSX InstallAnywhere installer<br></li>
1777 <li>Support for per-sequence based annotations in BioJSON</li>
1778 </ul> <em>Applet</em>
1780 <li>Split frame example added to applet examples page</li>
1781 </ul> <em>Build and Deployment</em>
1784 <!-- JAL-1888 -->New ant target for running Jalview's test
1792 <li>Mapping of cDNA to protein in split frames
1793 incorrect when sequence start > 1</li>
1794 <li>Broken images in filter column by annotation dialog
1796 <li>Feature colours not parsed from features file</li>
1797 <li>Exceptions and incomplete link URLs recovered when
1798 loading a features file containing HTML tags in feature
1802 <em>Application</em>
1804 <li>Annotations corrupted after BioJS export and
1806 <li>Incorrect sequence limits after Fetch DB References
1807 with 'trim retrieved sequences'</li>
1808 <li>Incorrect warning about deleting all data when
1809 deleting selected columns</li>
1810 <li>Patch to build system for shipping properly signed
1811 JNLP templates for webstart launch</li>
1812 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1813 unreleased structures for download or viewing</li>
1814 <li>Tab/space/return keystroke operation of EMBL-PDBe
1815 fetcher/viewer dialogs works correctly</li>
1816 <li>Disabled 'minimise' button on Jalview windows
1817 running on OSX to workaround redraw hang bug</li>
1818 <li>Split cDNA/Protein view position and geometry not
1819 recovered from jalview project</li>
1820 <li>Initial enabled/disabled state of annotation menu
1821 sorter 'show autocalculated first/last' corresponds to
1823 <li>Restoring of Clustal, RNA Helices and T-Coffee
1824 color schemes from BioJSON</li>
1828 <li>Reorder sequences mirrored in cDNA/Protein split
1830 <li>Applet with Jmol examples not loading correctly</li>
1836 <td><div align="center">
1837 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1839 <td><em>General</em>
1841 <li>Linked visualisation and analysis of DNA and Protein
1844 <li>Translated cDNA alignments shown as split protein
1845 and DNA alignment views</li>
1846 <li>Codon consensus annotation for linked protein and
1847 cDNA alignment views</li>
1848 <li>Link cDNA or Protein product sequences by loading
1849 them onto Protein or cDNA alignments</li>
1850 <li>Reconstruct linked cDNA alignment from aligned
1851 protein sequences</li>
1854 <li>Jmol integration updated to Jmol v14.2.14</li>
1855 <li>Import and export of Jalview alignment views as <a
1856 href="features/bioJsonFormat.html">BioJSON</a></li>
1857 <li>New alignment annotation file statements for
1858 reference sequences and marking hidden columns</li>
1859 <li>Reference sequence based alignment shading to
1860 highlight variation</li>
1861 <li>Select or hide columns according to alignment
1863 <li>Find option for locating sequences by description</li>
1864 <li>Conserved physicochemical properties shown in amino
1865 acid conservation row</li>
1866 <li>Alignments can be sorted by number of RNA helices</li>
1867 </ul> <em>Application</em>
1869 <li>New cDNA/Protein analysis capabilities
1871 <li>Get Cross-References should open a Split Frame
1872 view with cDNA/Protein</li>
1873 <li>Detect when nucleotide sequences and protein
1874 sequences are placed in the same alignment</li>
1875 <li>Split cDNA/Protein views are saved in Jalview
1880 <li>Use REST API to talk to Chimera</li>
1881 <li>Selected regions in Chimera are highlighted in linked
1882 Jalview windows</li>
1884 <li>VARNA RNA viewer updated to v3.93</li>
1885 <li>VARNA views are saved in Jalview Projects</li>
1886 <li>Pseudoknots displayed as Jalview RNA annotation can
1887 be shown in VARNA</li>
1889 <li>Make groups for selection uses marked columns as well
1890 as the active selected region</li>
1892 <li>Calculate UPGMA and NJ trees using sequence feature
1894 <li>New Export options
1896 <li>New Export Settings dialog to control hidden
1897 region export in flat file generation</li>
1899 <li>Export alignment views for display with the <a
1900 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1902 <li>Export scrollable SVG in HTML page</li>
1903 <li>Optional embedding of BioJSON data when exporting
1904 alignment figures to HTML</li>
1906 <li>3D structure retrieval and display
1908 <li>Free text and structured queries with the PDBe
1910 <li>PDBe Search API based discovery and selection of
1911 PDB structures for a sequence set</li>
1915 <li>JPred4 employed for protein secondary structure
1917 <li>Hide Insertions menu option to hide unaligned columns
1918 for one or a group of sequences</li>
1919 <li>Automatically hide insertions in alignments imported
1920 from the JPred4 web server</li>
1921 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1922 system on OSX<br />LGPL libraries courtesy of <a
1923 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1925 <li>changed 'View nucleotide structure' submenu to 'View
1926 VARNA 2D Structure'</li>
1927 <li>change "View protein structure" menu option to "3D
1930 </ul> <em>Applet</em>
1932 <li>New layout for applet example pages</li>
1933 <li>New parameters to enable SplitFrame view
1934 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1935 <li>New example demonstrating linked viewing of cDNA and
1936 Protein alignments</li>
1937 </ul> <em>Development and deployment</em>
1939 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1940 <li>Include installation type and git revision in build
1941 properties and console log output</li>
1942 <li>Jalview Github organisation, and new github site for
1943 storing BioJsMSA Templates</li>
1944 <li>Jalview's unit tests now managed with TestNG</li>
1947 <!-- <em>General</em>
1949 </ul> --> <!-- issues resolved --> <em>Application</em>
1951 <li>Escape should close any open find dialogs</li>
1952 <li>Typo in select-by-features status report</li>
1953 <li>Consensus RNA secondary secondary structure
1954 predictions are not highlighted in amber</li>
1955 <li>Missing gap character in v2.7 example file means
1956 alignment appears unaligned when pad-gaps is not enabled</li>
1957 <li>First switch to RNA Helices colouring doesn't colour
1958 associated structure views</li>
1959 <li>ID width preference option is greyed out when auto
1960 width checkbox not enabled</li>
1961 <li>Stopped a warning dialog from being shown when
1962 creating user defined colours</li>
1963 <li>'View Mapping' in structure viewer shows sequence
1964 mappings for just that viewer's sequences</li>
1965 <li>Workaround for superposing PDB files containing
1966 multiple models in Chimera</li>
1967 <li>Report sequence position in status bar when hovering
1968 over Jmol structure</li>
1969 <li>Cannot output gaps as '.' symbols with Selection ->
1970 output to text box</li>
1971 <li>Flat file exports of alignments with hidden columns
1972 have incorrect sequence start/end</li>
1973 <li>'Aligning' a second chain to a Chimera structure from
1975 <li>Colour schemes applied to structure viewers don't
1976 work for nucleotide</li>
1977 <li>Loading/cut'n'pasting an empty or invalid file leads
1978 to a grey/invisible alignment window</li>
1979 <li>Exported Jpred annotation from a sequence region
1980 imports to different position</li>
1981 <li>Space at beginning of sequence feature tooltips shown
1982 on some platforms</li>
1983 <li>Chimera viewer 'View | Show Chain' menu is not
1985 <li>'New View' fails with a Null Pointer Exception in
1986 console if Chimera has been opened</li>
1987 <li>Mouseover to Chimera not working</li>
1988 <li>Miscellaneous ENA XML feature qualifiers not
1990 <li>NPE in annotation renderer after 'Extract Scores'</li>
1991 <li>If two structures in one Chimera window, mouseover of
1992 either sequence shows on first structure</li>
1993 <li>'Show annotations' options should not make
1994 non-positional annotations visible</li>
1995 <li>Subsequence secondary structure annotation not shown
1996 in right place after 'view flanking regions'</li>
1997 <li>File Save As type unset when current file format is
1999 <li>Save as '.jar' option removed for saving Jalview
2001 <li>Colour by Sequence colouring in Chimera more
2003 <li>Cannot 'add reference annotation' for a sequence in
2004 several views on same alignment</li>
2005 <li>Cannot show linked products for EMBL / ENA records</li>
2006 <li>Jalview's tooltip wraps long texts containing no
2008 </ul> <em>Applet</em>
2010 <li>Jmol to JalviewLite mouseover/link not working</li>
2011 <li>JalviewLite can't import sequences with ID
2012 descriptions containing angle brackets</li>
2013 </ul> <em>General</em>
2015 <li>Cannot export and reimport RNA secondary structure
2016 via jalview annotation file</li>
2017 <li>Random helix colour palette for colour by annotation
2018 with RNA secondary structure</li>
2019 <li>Mouseover to cDNA from STOP residue in protein
2020 translation doesn't work.</li>
2021 <li>hints when using the select by annotation dialog box</li>
2022 <li>Jmol alignment incorrect if PDB file has alternate CA
2024 <li>FontChooser message dialog appears to hang after
2025 choosing 1pt font</li>
2026 <li>Peptide secondary structure incorrectly imported from
2027 annotation file when annotation display text includes 'e' or
2029 <li>Cannot set colour of new feature type whilst creating
2031 <li>cDNA translation alignment should not be sequence
2032 order dependent</li>
2033 <li>'Show unconserved' doesn't work for lower case
2035 <li>Nucleotide ambiguity codes involving R not recognised</li>
2036 </ul> <em>Deployment and Documentation</em>
2038 <li>Applet example pages appear different to the rest of
2039 www.jalview.org</li>
2040 </ul> <em>Application Known issues</em>
2042 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2043 <li>Misleading message appears after trying to delete
2045 <li>Jalview icon not shown in dock after InstallAnywhere
2046 version launches</li>
2047 <li>Fetching EMBL reference for an RNA sequence results
2048 fails with a sequence mismatch</li>
2049 <li>Corrupted or unreadable alignment display when
2050 scrolling alignment to right</li>
2051 <li>ArrayIndexOutOfBoundsException thrown when remove
2052 empty columns called on alignment with ragged gapped ends</li>
2053 <li>auto calculated alignment annotation rows do not get
2054 placed above or below non-autocalculated rows</li>
2055 <li>Jalview dekstop becomes sluggish at full screen in
2056 ultra-high resolution</li>
2057 <li>Cannot disable consensus calculation independently of
2058 quality and conservation</li>
2059 <li>Mouseover highlighting between cDNA and protein can
2060 become sluggish with more than one splitframe shown</li>
2061 </ul> <em>Applet Known Issues</em>
2063 <li>Core PDB parsing code requires Jmol</li>
2064 <li>Sequence canvas panel goes white when alignment
2065 window is being resized</li>
2071 <td><div align="center">
2072 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2074 <td><em>General</em>
2076 <li>Updated Java code signing certificate donated by
2078 <li>Features and annotation preserved when performing
2079 pairwise alignment</li>
2080 <li>RNA pseudoknot annotation can be
2081 imported/exported/displayed</li>
2082 <li>'colour by annotation' can colour by RNA and
2083 protein secondary structure</li>
2084 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2085 post-hoc with 2.9 release</em>)
2088 </ul> <em>Application</em>
2090 <li>Extract and display secondary structure for sequences
2091 with 3D structures</li>
2092 <li>Support for parsing RNAML</li>
2093 <li>Annotations menu for layout
2095 <li>sort sequence annotation rows by alignment</li>
2096 <li>place sequence annotation above/below alignment
2099 <li>Output in Stockholm format</li>
2100 <li>Internationalisation: improved Spanish (es)
2102 <li>Structure viewer preferences tab</li>
2103 <li>Disorder and Secondary Structure annotation tracks
2104 shared between alignments</li>
2105 <li>UCSF Chimera launch and linked highlighting from
2107 <li>Show/hide all sequence associated annotation rows for
2108 all or current selection</li>
2109 <li>disorder and secondary structure predictions
2110 available as dataset annotation</li>
2111 <li>Per-sequence rna helices colouring</li>
2114 <li>Sequence database accessions imported when fetching
2115 alignments from Rfam</li>
2116 <li>update VARNA version to 3.91</li>
2118 <li>New groovy scripts for exporting aligned positions,
2119 conservation values, and calculating sum of pairs scores.</li>
2120 <li>Command line argument to set default JABAWS server</li>
2121 <li>include installation type in build properties and
2122 console log output</li>
2123 <li>Updated Jalview project format to preserve dataset
2127 <!-- issues resolved --> <em>Application</em>
2129 <li>Distinguish alignment and sequence associated RNA
2130 structure in structure->view->VARNA</li>
2131 <li>Raise dialog box if user deletes all sequences in an
2133 <li>Pressing F1 results in documentation opening twice</li>
2134 <li>Sequence feature tooltip is wrapped</li>
2135 <li>Double click on sequence associated annotation
2136 selects only first column</li>
2137 <li>Redundancy removal doesn't result in unlinked
2138 leaves shown in tree</li>
2139 <li>Undos after several redundancy removals don't undo
2141 <li>Hide sequence doesn't hide associated annotation</li>
2142 <li>User defined colours dialog box too big to fit on
2143 screen and buttons not visible</li>
2144 <li>author list isn't updated if already written to
2145 Jalview properties</li>
2146 <li>Popup menu won't open after retrieving sequence
2148 <li>File open window for associate PDB doesn't open</li>
2149 <li>Left-then-right click on a sequence id opens a
2150 browser search window</li>
2151 <li>Cannot open sequence feature shading/sort popup menu
2152 in feature settings dialog</li>
2153 <li>better tooltip placement for some areas of Jalview
2155 <li>Allow addition of JABAWS Server which doesn't
2156 pass validation</li>
2157 <li>Web services parameters dialog box is too large to
2159 <li>Muscle nucleotide alignment preset obscured by
2161 <li>JABAWS preset submenus don't contain newly
2162 defined user preset</li>
2163 <li>MSA web services warns user if they were launched
2164 with invalid input</li>
2165 <li>Jalview cannot contact DAS Registy when running on
2168 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2169 'Superpose with' submenu not shown when new view
2173 </ul> <!-- <em>Applet</em>
2175 </ul> <em>General</em>
2177 </ul>--> <em>Deployment and Documentation</em>
2179 <li>2G and 1G options in launchApp have no effect on
2180 memory allocation</li>
2181 <li>launchApp service doesn't automatically open
2182 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2184 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2185 InstallAnywhere reports cannot find valid JVM when Java
2186 1.7_055 is available
2188 </ul> <em>Application Known issues</em>
2191 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2192 corrupted or unreadable alignment display when scrolling
2196 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2197 retrieval fails but progress bar continues for DAS retrieval
2198 with large number of ID
2201 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2202 flatfile output of visible region has incorrect sequence
2206 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2207 rna structure consensus doesn't update when secondary
2208 structure tracks are rearranged
2211 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2212 invalid rna structure positional highlighting does not
2213 highlight position of invalid base pairs
2216 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2217 out of memory errors are not raised when saving Jalview
2218 project from alignment window file menu
2221 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2222 Switching to RNA Helices colouring doesn't propagate to
2226 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2227 colour by RNA Helices not enabled when user created
2228 annotation added to alignment
2231 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2232 Jalview icon not shown on dock in Mountain Lion/Webstart
2234 </ul> <em>Applet Known Issues</em>
2237 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2238 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2241 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2242 Jalview and Jmol example not compatible with IE9
2245 <li>Sort by annotation score doesn't reverse order
2251 <td><div align="center">
2252 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2255 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2258 <li>Internationalisation of user interface (usually
2259 called i18n support) and translation for Spanish locale</li>
2260 <li>Define/Undefine group on current selection with
2261 Ctrl-G/Shift Ctrl-G</li>
2262 <li>Improved group creation/removal options in
2263 alignment/sequence Popup menu</li>
2264 <li>Sensible precision for symbol distribution
2265 percentages shown in logo tooltip.</li>
2266 <li>Annotation panel height set according to amount of
2267 annotation when alignment first opened</li>
2268 </ul> <em>Application</em>
2270 <li>Interactive consensus RNA secondary structure
2271 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2272 <li>Select columns containing particular features from
2273 Feature Settings dialog</li>
2274 <li>View all 'representative' PDB structures for selected
2276 <li>Update Jalview project format:
2278 <li>New file extension for Jalview projects '.jvp'</li>
2279 <li>Preserve sequence and annotation dataset (to
2280 store secondary structure annotation,etc)</li>
2281 <li>Per group and alignment annotation and RNA helix
2285 <li>New similarity measures for PCA and Tree calculation
2287 <li>Experimental support for retrieval and viewing of
2288 flanking regions for an alignment</li>
2292 <!-- issues resolved --> <em>Application</em>
2294 <li>logo keeps spinning and status remains at queued or
2295 running after job is cancelled</li>
2296 <li>cannot export features from alignments imported from
2297 Jalview/VAMSAS projects</li>
2298 <li>Buggy slider for web service parameters that take
2300 <li>Newly created RNA secondary structure line doesn't
2301 have 'display all symbols' flag set</li>
2302 <li>T-COFFEE alignment score shading scheme and other
2303 annotation shading not saved in Jalview project</li>
2304 <li>Local file cannot be loaded in freshly downloaded
2306 <li>Jalview icon not shown on dock in Mountain
2308 <li>Load file from desktop file browser fails</li>
2309 <li>Occasional NPE thrown when calculating large trees</li>
2310 <li>Cannot reorder or slide sequences after dragging an
2311 alignment onto desktop</li>
2312 <li>Colour by annotation dialog throws NPE after using
2313 'extract scores' function</li>
2314 <li>Loading/cut'n'pasting an empty file leads to a grey
2315 alignment window</li>
2316 <li>Disorder thresholds rendered incorrectly after
2317 performing IUPred disorder prediction</li>
2318 <li>Multiple group annotated consensus rows shown when
2319 changing 'normalise logo' display setting</li>
2320 <li>Find shows blank dialog after 'finished searching' if
2321 nothing matches query</li>
2322 <li>Null Pointer Exceptions raised when sorting by
2323 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2325 <li>Errors in Jmol console when structures in alignment
2326 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2328 <li>Not all working JABAWS services are shown in
2330 <li>JAVAWS version of Jalview fails to launch with
2331 'invalid literal/length code'</li>
2332 <li>Annotation/RNA Helix colourschemes cannot be applied
2333 to alignment with groups (actually fixed in 2.8.0b1)</li>
2334 <li>RNA Helices and T-Coffee Scores available as default
2337 </ul> <em>Applet</em>
2339 <li>Remove group option is shown even when selection is
2341 <li>Apply to all groups ticked but colourscheme changes
2342 don't affect groups</li>
2343 <li>Documented RNA Helices and T-Coffee Scores as valid
2344 colourscheme name</li>
2345 <li>Annotation labels drawn on sequence IDs when
2346 Annotation panel is not displayed</li>
2347 <li>Increased font size for dropdown menus on OSX and
2348 embedded windows</li>
2349 </ul> <em>Other</em>
2351 <li>Consensus sequence for alignments/groups with a
2352 single sequence were not calculated</li>
2353 <li>annotation files that contain only groups imported as
2354 annotation and junk sequences</li>
2355 <li>Fasta files with sequences containing '*' incorrectly
2356 recognised as PFAM or BLC</li>
2357 <li>conservation/PID slider apply all groups option
2358 doesn't affect background (2.8.0b1)
2360 <li>redundancy highlighting is erratic at 0% and 100%</li>
2361 <li>Remove gapped columns fails for sequences with ragged
2363 <li>AMSA annotation row with leading spaces is not
2364 registered correctly on import</li>
2365 <li>Jalview crashes when selecting PCA analysis for
2366 certain alignments</li>
2367 <li>Opening the colour by annotation dialog for an
2368 existing annotation based 'use original colours'
2369 colourscheme loses original colours setting</li>
2374 <td><div align="center">
2375 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2376 <em>30/1/2014</em></strong>
2380 <li>Trusted certificates for JalviewLite applet and
2381 Jalview Desktop application<br />Certificate was donated by
2382 <a href="https://www.certum.eu">Certum</a> to the Jalview
2383 open source project).
2385 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2386 <li>Output in Stockholm format</li>
2387 <li>Allow import of data from gzipped files</li>
2388 <li>Export/import group and sequence associated line
2389 graph thresholds</li>
2390 <li>Nucleotide substitution matrix that supports RNA and
2391 ambiguity codes</li>
2392 <li>Allow disorder predictions to be made on the current
2393 selection (or visible selection) in the same way that JPred
2395 <li>Groovy scripting for headless Jalview operation</li>
2396 </ul> <em>Other improvements</em>
2398 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2399 <li>COMBINE statement uses current SEQUENCE_REF and
2400 GROUP_REF scope to group annotation rows</li>
2401 <li>Support '' style escaping of quotes in Newick
2403 <li>Group options for JABAWS service by command line name</li>
2404 <li>Empty tooltip shown for JABA service options with a
2405 link but no description</li>
2406 <li>Select primary source when selecting authority in
2407 database fetcher GUI</li>
2408 <li>Add .mfa to FASTA file extensions recognised by
2410 <li>Annotation label tooltip text wrap</li>
2415 <li>Slow scrolling when lots of annotation rows are
2417 <li>Lots of NPE (and slowness) after creating RNA
2418 secondary structure annotation line</li>
2419 <li>Sequence database accessions not imported when
2420 fetching alignments from Rfam</li>
2421 <li>Incorrect SHMR submission for sequences with
2423 <li>View all structures does not always superpose
2425 <li>Option widgets in service parameters not updated to
2426 reflect user or preset settings</li>
2427 <li>Null pointer exceptions for some services without
2428 presets or adjustable parameters</li>
2429 <li>Discover PDB IDs entry in structure menu doesn't
2430 discover PDB xRefs</li>
2431 <li>Exception encountered while trying to retrieve
2432 features with DAS</li>
2433 <li>Lowest value in annotation row isn't coloured
2434 when colour by annotation (per sequence) is coloured</li>
2435 <li>Keyboard mode P jumps to start of gapped region when
2436 residue follows a gap</li>
2437 <li>Jalview appears to hang importing an alignment with
2438 Wrap as default or after enabling Wrap</li>
2439 <li>'Right click to add annotations' message
2440 shown in wrap mode when no annotations present</li>
2441 <li>Disorder predictions fail with NPE if no automatic
2442 annotation already exists on alignment</li>
2443 <li>oninit javascript function should be called after
2444 initialisation completes</li>
2445 <li>Remove redundancy after disorder prediction corrupts
2446 alignment window display</li>
2447 <li>Example annotation file in documentation is invalid</li>
2448 <li>Grouped line graph annotation rows are not exported
2449 to annotation file</li>
2450 <li>Multi-harmony analysis cannot be run when only two
2452 <li>Cannot create multiple groups of line graphs with
2453 several 'combine' statements in annotation file</li>
2454 <li>Pressing return several times causes Number Format
2455 exceptions in keyboard mode</li>
2456 <li>Multi-harmony (SHMMR) method doesn't submit
2457 correct partitions for input data</li>
2458 <li>Translation from DNA to Amino Acids fails</li>
2459 <li>Jalview fail to load newick tree with quoted label</li>
2460 <li>--headless flag isn't understood</li>
2461 <li>ClassCastException when generating EPS in headless
2463 <li>Adjusting sequence-associated shading threshold only
2464 changes one row's threshold</li>
2465 <li>Preferences and Feature settings panel panel
2466 doesn't open</li>
2467 <li>hide consensus histogram also hides conservation and
2468 quality histograms</li>
2473 <td><div align="center">
2474 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2476 <td><em>Application</em>
2478 <li>Support for JABAWS 2.0 Services (AACon alignment
2479 conservation, protein disorder and Clustal Omega)</li>
2480 <li>JABAWS server status indicator in Web Services
2482 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2483 in Jalview alignment window</li>
2484 <li>Updated Jalview build and deploy framework for OSX
2485 mountain lion, windows 7, and 8</li>
2486 <li>Nucleotide substitution matrix for PCA that supports
2487 RNA and ambiguity codes</li>
2489 <li>Improved sequence database retrieval GUI</li>
2490 <li>Support fetching and database reference look up
2491 against multiple DAS sources (Fetch all from in 'fetch db
2493 <li>Jalview project improvements
2495 <li>Store and retrieve the 'belowAlignment'
2496 flag for annotation</li>
2497 <li>calcId attribute to group annotation rows on the
2499 <li>Store AACon calculation settings for a view in
2500 Jalview project</li>
2504 <li>horizontal scrolling gesture support</li>
2505 <li>Visual progress indicator when PCA calculation is
2507 <li>Simpler JABA web services menus</li>
2508 <li>visual indication that web service results are still
2509 being retrieved from server</li>
2510 <li>Serialise the dialogs that are shown when Jalview
2511 starts up for first time</li>
2512 <li>Jalview user agent string for interacting with HTTP
2514 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2516 <li>Examples directory and Groovy library included in
2517 InstallAnywhere distribution</li>
2518 </ul> <em>Applet</em>
2520 <li>RNA alignment and secondary structure annotation
2521 visualization applet example</li>
2522 </ul> <em>General</em>
2524 <li>Normalise option for consensus sequence logo</li>
2525 <li>Reset button in PCA window to return dimensions to
2527 <li>Allow seqspace or Jalview variant of alignment PCA
2529 <li>PCA with either nucleic acid and protein substitution
2531 <li>Allow windows containing HTML reports to be exported
2533 <li>Interactive display and editing of RNA secondary
2534 structure contacts</li>
2535 <li>RNA Helix Alignment Colouring</li>
2536 <li>RNA base pair logo consensus</li>
2537 <li>Parse sequence associated secondary structure
2538 information in Stockholm files</li>
2539 <li>HTML Export database accessions and annotation
2540 information presented in tooltip for sequences</li>
2541 <li>Import secondary structure from LOCARNA clustalw
2542 style RNA alignment files</li>
2543 <li>import and visualise T-COFFEE quality scores for an
2545 <li>'colour by annotation' per sequence option to
2546 shade each sequence according to its associated alignment
2548 <li>New Jalview Logo</li>
2549 </ul> <em>Documentation and Development</em>
2551 <li>documentation for score matrices used in Jalview</li>
2552 <li>New Website!</li>
2554 <td><em>Application</em>
2556 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2557 wsdbfetch REST service</li>
2558 <li>Stop windows being moved outside desktop on OSX</li>
2559 <li>Filetype associations not installed for webstart
2561 <li>Jalview does not always retrieve progress of a JABAWS
2562 job execution in full once it is complete</li>
2563 <li>revise SHMR RSBS definition to ensure alignment is
2564 uploaded via ali_file parameter</li>
2565 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2566 <li>View all structures superposed fails with exception</li>
2567 <li>Jnet job queues forever if a very short sequence is
2568 submitted for prediction</li>
2569 <li>Cut and paste menu not opened when mouse clicked on
2571 <li>Putting fractional value into integer text box in
2572 alignment parameter dialog causes Jalview to hang</li>
2573 <li>Structure view highlighting doesn't work on
2575 <li>View all structures fails with exception shown in
2577 <li>Characters in filename associated with PDBEntry not
2578 escaped in a platform independent way</li>
2579 <li>Jalview desktop fails to launch with exception when
2581 <li>Tree calculation reports 'you must have 2 or more
2582 sequences selected' when selection is empty</li>
2583 <li>Jalview desktop fails to launch with jar signature
2584 failure when java web start temporary file caching is
2586 <li>DAS Sequence retrieval with range qualification
2587 results in sequence xref which includes range qualification</li>
2588 <li>Errors during processing of command line arguments
2589 cause progress bar (JAL-898) to be removed</li>
2590 <li>Replace comma for semi-colon option not disabled for
2591 DAS sources in sequence fetcher</li>
2592 <li>Cannot close news reader when JABAWS server warning
2593 dialog is shown</li>
2594 <li>Option widgets not updated to reflect user settings</li>
2595 <li>Edited sequence not submitted to web service</li>
2596 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2597 <li>InstallAnywhere installer doesn't unpack and run
2598 on OSX Mountain Lion</li>
2599 <li>Annotation panel not given a scroll bar when
2600 sequences with alignment annotation are pasted into the
2602 <li>Sequence associated annotation rows not associated
2603 when loaded from Jalview project</li>
2604 <li>Browser launch fails with NPE on java 1.7</li>
2605 <li>JABAWS alignment marked as finished when job was
2606 cancelled or job failed due to invalid input</li>
2607 <li>NPE with v2.7 example when clicking on Tree
2608 associated with all views</li>
2609 <li>Exceptions when copy/paste sequences with grouped
2610 annotation rows to new window</li>
2611 </ul> <em>Applet</em>
2613 <li>Sequence features are momentarily displayed before
2614 they are hidden using hidefeaturegroups applet parameter</li>
2615 <li>loading features via javascript API automatically
2616 enables feature display</li>
2617 <li>scrollToColumnIn javascript API method doesn't
2619 </ul> <em>General</em>
2621 <li>Redundancy removal fails for rna alignment</li>
2622 <li>PCA calculation fails when sequence has been selected
2623 and then deselected</li>
2624 <li>PCA window shows grey box when first opened on OSX</li>
2625 <li>Letters coloured pink in sequence logo when alignment
2626 coloured with clustalx</li>
2627 <li>Choosing fonts without letter symbols defined causes
2628 exceptions and redraw errors</li>
2629 <li>Initial PCA plot view is not same as manually
2630 reconfigured view</li>
2631 <li>Grouped annotation graph label has incorrect line
2633 <li>Grouped annotation graph label display is corrupted
2634 for lots of labels</li>
2639 <div align="center">
2640 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2643 <td><em>Application</em>
2645 <li>Jalview Desktop News Reader</li>
2646 <li>Tweaked default layout of web services menu</li>
2647 <li>View/alignment association menu to enable user to
2648 easily specify which alignment a multi-structure view takes
2649 its colours/correspondences from</li>
2650 <li>Allow properties file location to be specified as URL</li>
2651 <li>Extend Jalview project to preserve associations
2652 between many alignment views and a single Jmol display</li>
2653 <li>Store annotation row height in Jalview project file</li>
2654 <li>Annotation row column label formatting attributes
2655 stored in project file</li>
2656 <li>Annotation row order for auto-calculated annotation
2657 rows preserved in Jalview project file</li>
2658 <li>Visual progress indication when Jalview state is
2659 saved using Desktop window menu</li>
2660 <li>Visual indication that command line arguments are
2661 still being processed</li>
2662 <li>Groovy script execution from URL</li>
2663 <li>Colour by annotation default min and max colours in
2665 <li>Automatically associate PDB files dragged onto an
2666 alignment with sequences that have high similarity and
2668 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2669 <li>'view structures' option to open many
2670 structures in same window</li>
2671 <li>Sort associated views menu option for tree panel</li>
2672 <li>Group all JABA and non-JABA services for a particular
2673 analysis function in its own submenu</li>
2674 </ul> <em>Applet</em>
2676 <li>Userdefined and autogenerated annotation rows for
2678 <li>Adjustment of alignment annotation pane height</li>
2679 <li>Annotation scrollbar for annotation panel</li>
2680 <li>Drag to reorder annotation rows in annotation panel</li>
2681 <li>'automaticScrolling' parameter</li>
2682 <li>Allow sequences with partial ID string matches to be
2683 annotated from GFF/Jalview features files</li>
2684 <li>Sequence logo annotation row in applet</li>
2685 <li>Absolute paths relative to host server in applet
2686 parameters are treated as such</li>
2687 <li>New in the JalviewLite javascript API:
2689 <li>JalviewLite.js javascript library</li>
2690 <li>Javascript callbacks for
2692 <li>Applet initialisation</li>
2693 <li>Sequence/alignment mouse-overs and selections</li>
2696 <li>scrollTo row and column alignment scrolling
2698 <li>Select sequence/alignment regions from javascript</li>
2699 <li>javascript structure viewer harness to pass
2700 messages between Jmol and Jalview when running as
2701 distinct applets</li>
2702 <li>sortBy method</li>
2703 <li>Set of applet and application examples shipped
2704 with documentation</li>
2705 <li>New example to demonstrate JalviewLite and Jmol
2706 javascript message exchange</li>
2708 </ul> <em>General</em>
2710 <li>Enable Jmol displays to be associated with multiple
2711 multiple alignments</li>
2712 <li>Option to automatically sort alignment with new tree</li>
2713 <li>User configurable link to enable redirects to a
2714 www.Jalview.org mirror</li>
2715 <li>Jmol colours option for Jmol displays</li>
2716 <li>Configurable newline string when writing alignment
2717 and other flat files</li>
2718 <li>Allow alignment annotation description lines to
2719 contain html tags</li>
2720 </ul> <em>Documentation and Development</em>
2722 <li>Add groovy test harness for bulk load testing to
2724 <li>Groovy script to load and align a set of sequences
2725 using a web service before displaying the result in the
2726 Jalview desktop</li>
2727 <li>Restructured javascript and applet api documentation</li>
2728 <li>Ant target to publish example html files with applet
2730 <li>Netbeans project for building Jalview from source</li>
2731 <li>ant task to create online javadoc for Jalview source</li>
2733 <td><em>Application</em>
2735 <li>User defined colourscheme throws exception when
2736 current built in colourscheme is saved as new scheme</li>
2737 <li>AlignFrame->Save in application pops up save
2738 dialog for valid filename/format</li>
2739 <li>Cannot view associated structure for UniProt sequence</li>
2740 <li>PDB file association breaks for UniProt sequence
2742 <li>Associate PDB from file dialog does not tell you
2743 which sequence is to be associated with the file</li>
2744 <li>Find All raises null pointer exception when query
2745 only matches sequence IDs</li>
2746 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2747 <li>Jalview project with Jmol views created with Jalview
2748 2.4 cannot be loaded</li>
2749 <li>Filetype associations not installed for webstart
2751 <li>Two or more chains in a single PDB file associated
2752 with sequences in different alignments do not get coloured
2753 by their associated sequence</li>
2754 <li>Visibility status of autocalculated annotation row
2755 not preserved when project is loaded</li>
2756 <li>Annotation row height and visibility attributes not
2757 stored in Jalview project</li>
2758 <li>Tree bootstraps are not preserved when saved as a
2759 Jalview project</li>
2760 <li>Envision2 workflow tooltips are corrupted</li>
2761 <li>Enabling show group conservation also enables colour
2762 by conservation</li>
2763 <li>Duplicate group associated conservation or consensus
2764 created on new view</li>
2765 <li>Annotation scrollbar not displayed after 'show
2766 all hidden annotation rows' option selected</li>
2767 <li>Alignment quality not updated after alignment
2768 annotation row is hidden then shown</li>
2769 <li>Preserve colouring of structures coloured by
2770 sequences in pre Jalview 2.7 projects</li>
2771 <li>Web service job parameter dialog is not laid out
2773 <li>Web services menu not refreshed after 'reset
2774 services' button is pressed in preferences</li>
2775 <li>Annotation off by one in Jalview v2_3 example project</li>
2776 <li>Structures imported from file and saved in project
2777 get name like jalview_pdb1234.txt when reloaded</li>
2778 <li>Jalview does not always retrieve progress of a JABAWS
2779 job execution in full once it is complete</li>
2780 </ul> <em>Applet</em>
2782 <li>Alignment height set incorrectly when lots of
2783 annotation rows are displayed</li>
2784 <li>Relative URLs in feature HTML text not resolved to
2786 <li>View follows highlighting does not work for positions
2788 <li><= shown as = in tooltip</li>
2789 <li>Export features raises exception when no features
2791 <li>Separator string used for serialising lists of IDs
2792 for javascript api is modified when separator string
2793 provided as parameter</li>
2794 <li>Null pointer exception when selecting tree leaves for
2795 alignment with no existing selection</li>
2796 <li>Relative URLs for datasources assumed to be relative
2797 to applet's codebase</li>
2798 <li>Status bar not updated after finished searching and
2799 search wraps around to first result</li>
2800 <li>StructureSelectionManager instance shared between
2801 several Jalview applets causes race conditions and memory
2803 <li>Hover tooltip and mouseover of position on structure
2804 not sent from Jmol in applet</li>
2805 <li>Certain sequences of javascript method calls to
2806 applet API fatally hang browser</li>
2807 </ul> <em>General</em>
2809 <li>View follows structure mouseover scrolls beyond
2810 position with wrapped view and hidden regions</li>
2811 <li>Find sequence position moves to wrong residue
2812 with/without hidden columns</li>
2813 <li>Sequence length given in alignment properties window
2815 <li>InvalidNumberFormat exceptions thrown when trying to
2816 import PDB like structure files</li>
2817 <li>Positional search results are only highlighted
2818 between user-supplied sequence start/end bounds</li>
2819 <li>End attribute of sequence is not validated</li>
2820 <li>Find dialog only finds first sequence containing a
2821 given sequence position</li>
2822 <li>Sequence numbering not preserved in MSF alignment
2824 <li>Jalview PDB file reader does not extract sequence
2825 from nucleotide chains correctly</li>
2826 <li>Structure colours not updated when tree partition
2827 changed in alignment</li>
2828 <li>Sequence associated secondary structure not correctly
2829 parsed in interleaved stockholm</li>
2830 <li>Colour by annotation dialog does not restore current
2832 <li>Hiding (nearly) all sequences doesn't work
2834 <li>Sequences containing lowercase letters are not
2835 properly associated with their pdb files</li>
2836 </ul> <em>Documentation and Development</em>
2838 <li>schemas/JalviewWsParamSet.xsd corrupted by
2839 ApplyCopyright tool</li>
2844 <div align="center">
2845 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2848 <td><em>Application</em>
2850 <li>New warning dialog when the Jalview Desktop cannot
2851 contact web services</li>
2852 <li>JABA service parameters for a preset are shown in
2853 service job window</li>
2854 <li>JABA Service menu entries reworded</li>
2858 <li>Modeller PIR IO broken - cannot correctly import a
2859 pir file emitted by Jalview</li>
2860 <li>Existing feature settings transferred to new
2861 alignment view created from cut'n'paste</li>
2862 <li>Improved test for mixed amino/nucleotide chains when
2863 parsing PDB files</li>
2864 <li>Consensus and conservation annotation rows
2865 occasionally become blank for all new windows</li>
2866 <li>Exception raised when right clicking above sequences
2867 in wrapped view mode</li>
2868 </ul> <em>Application</em>
2870 <li>multiple multiply aligned structure views cause cpu
2871 usage to hit 100% and computer to hang</li>
2872 <li>Web Service parameter layout breaks for long user
2873 parameter names</li>
2874 <li>Jaba service discovery hangs desktop if Jaba server
2881 <div align="center">
2882 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2885 <td><em>Application</em>
2887 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2888 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2891 <li>Web Services preference tab</li>
2892 <li>Analysis parameters dialog box and user defined
2894 <li>Improved speed and layout of Envision2 service menu</li>
2895 <li>Superpose structures using associated sequence
2897 <li>Export coordinates and projection as CSV from PCA
2899 </ul> <em>Applet</em>
2901 <li>enable javascript: execution by the applet via the
2902 link out mechanism</li>
2903 </ul> <em>Other</em>
2905 <li>Updated the Jmol Jalview interface to work with Jmol
2907 <li>The Jalview Desktop and JalviewLite applet now
2908 require Java 1.5</li>
2909 <li>Allow Jalview feature colour specification for GFF
2910 sequence annotation files</li>
2911 <li>New 'colour by label' keword in Jalview feature file
2912 type colour specification</li>
2913 <li>New Jalview Desktop Groovy API method that allows a
2914 script to check if it being run in an interactive session or
2915 in a batch operation from the Jalview command line</li>
2919 <li>clustalx colourscheme colours Ds preferentially when
2920 both D+E are present in over 50% of the column</li>
2921 </ul> <em>Application</em>
2923 <li>typo in AlignmentFrame->View->Hide->all but
2924 selected Regions menu item</li>
2925 <li>sequence fetcher replaces ',' for ';' when the ',' is
2926 part of a valid accession ID</li>
2927 <li>fatal OOM if object retrieved by sequence fetcher
2928 runs out of memory</li>
2929 <li>unhandled Out of Memory Error when viewing pca
2930 analysis results</li>
2931 <li>InstallAnywhere builds fail to launch on OS X java
2932 10.5 update 4 (due to apple Java 1.6 update)</li>
2933 <li>Installanywhere Jalview silently fails to launch</li>
2934 </ul> <em>Applet</em>
2936 <li>Jalview.getFeatureGroups() raises an
2937 ArrayIndexOutOfBoundsException if no feature groups are
2944 <div align="center">
2945 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2951 <li>Alignment prettyprinter doesn't cope with long
2953 <li>clustalx colourscheme colours Ds preferentially when
2954 both D+E are present in over 50% of the column</li>
2955 <li>nucleic acid structures retrieved from PDB do not
2956 import correctly</li>
2957 <li>More columns get selected than were clicked on when a
2958 number of columns are hidden</li>
2959 <li>annotation label popup menu not providing correct
2960 add/hide/show options when rows are hidden or none are
2962 <li>Stockholm format shown in list of readable formats,
2963 and parser copes better with alignments from RFAM.</li>
2964 <li>CSV output of consensus only includes the percentage
2965 of all symbols if sequence logo display is enabled</li>
2967 </ul> <em>Applet</em>
2969 <li>annotation panel disappears when annotation is
2971 </ul> <em>Application</em>
2973 <li>Alignment view not redrawn properly when new
2974 alignment opened where annotation panel is visible but no
2975 annotations are present on alignment</li>
2976 <li>pasted region containing hidden columns is
2977 incorrectly displayed in new alignment window</li>
2978 <li>Jalview slow to complete operations when stdout is
2979 flooded (fix is to close the Jalview console)</li>
2980 <li>typo in AlignmentFrame->View->Hide->all but
2981 selected Rregions menu item.</li>
2982 <li>inconsistent group submenu and Format submenu entry
2983 'Un' or 'Non'conserved</li>
2984 <li>Sequence feature settings are being shared by
2985 multiple distinct alignments</li>
2986 <li>group annotation not recreated when tree partition is
2988 <li>double click on group annotation to select sequences
2989 does not propagate to associated trees</li>
2990 <li>Mac OSX specific issues:
2992 <li>exception raised when mouse clicked on desktop
2993 window background</li>
2994 <li>Desktop menu placed on menu bar and application
2995 name set correctly</li>
2996 <li>sequence feature settings not wide enough for the
2997 save feature colourscheme button</li>
3006 <div align="center">
3007 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
3010 <td><em>New Capabilities</em>
3012 <li>URL links generated from description line for
3013 regular-expression based URL links (applet and application)
3015 <li>Non-positional feature URL links are shown in link
3017 <li>Linked viewing of nucleic acid sequences and
3019 <li>Automatic Scrolling option in View menu to display
3020 the currently highlighted region of an alignment.</li>
3021 <li>Order an alignment by sequence length, or using the
3022 average score or total feature count for each sequence.</li>
3023 <li>Shading features by score or associated description</li>
3024 <li>Subdivide alignment and groups based on identity of
3025 selected subsequence (Make Groups from Selection).</li>
3026 <li>New hide/show options including Shift+Control+H to
3027 hide everything but the currently selected region.</li>
3028 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3029 </ul> <em>Application</em>
3031 <li>Fetch DB References capabilities and UI expanded to
3032 support retrieval from DAS sequence sources</li>
3033 <li>Local DAS Sequence sources can be added via the
3034 command line or via the Add local source dialog box.</li>
3035 <li>DAS Dbref and DbxRef feature types are parsed as
3036 database references and protein_name is parsed as
3037 description line (BioSapiens terms).</li>
3038 <li>Enable or disable non-positional feature and database
3039 references in sequence ID tooltip from View menu in
3041 <!-- <li>New hidden columns and rows and representatives capabilities
3042 in annotations file (in progress - not yet fully implemented)</li> -->
3043 <li>Group-associated consensus, sequence logos and
3044 conservation plots</li>
3045 <li>Symbol distributions for each column can be exported
3046 and visualized as sequence logos</li>
3047 <li>Optionally scale multi-character column labels to fit
3048 within each column of annotation row<!-- todo for applet -->
3050 <li>Optional automatic sort of associated alignment view
3051 when a new tree is opened.</li>
3052 <li>Jalview Java Console</li>
3053 <li>Better placement of desktop window when moving
3054 between different screens.</li>
3055 <li>New preference items for sequence ID tooltip and
3056 consensus annotation</li>
3057 <li>Client to submit sequences and IDs to Envision2
3059 <li><em>Vamsas Capabilities</em>
3061 <li>Improved VAMSAS synchronization (Jalview archive
3062 used to preserve views, structures, and tree display
3064 <li>Import of vamsas documents from disk or URL via
3066 <li>Sharing of selected regions between views and
3067 with other VAMSAS applications (Experimental feature!)</li>
3068 <li>Updated API to VAMSAS version 0.2</li>
3070 </ul> <em>Applet</em>
3072 <li>Middle button resizes annotation row height</li>
3075 <li>sortByTree (true/false) - automatically sort the
3076 associated alignment view by the tree when a new tree is
3078 <li>showTreeBootstraps (true/false) - show or hide
3079 branch bootstraps (default is to show them if available)</li>
3080 <li>showTreeDistances (true/false) - show or hide
3081 branch lengths (default is to show them if available)</li>
3082 <li>showUnlinkedTreeNodes (true/false) - indicate if
3083 unassociated nodes should be highlighted in the tree
3085 <li>heightScale and widthScale (1.0 or more) -
3086 increase the height or width of a cell in the alignment
3087 grid relative to the current font size.</li>
3090 <li>Non-positional features displayed in sequence ID
3092 </ul> <em>Other</em>
3094 <li>Features format: graduated colour definitions and
3095 specification of feature scores</li>
3096 <li>Alignment Annotations format: new keywords for group
3097 associated annotation (GROUP_REF) and annotation row display
3098 properties (ROW_PROPERTIES)</li>
3099 <li>XML formats extended to support graduated feature
3100 colourschemes, group associated annotation, and profile
3101 visualization settings.</li></td>
3104 <li>Source field in GFF files parsed as feature source
3105 rather than description</li>
3106 <li>Non-positional features are now included in sequence
3107 feature and gff files (controlled via non-positional feature
3108 visibility in tooltip).</li>
3109 <li>URL links generated for all feature links (bugfix)</li>
3110 <li>Added URL embedding instructions to features file
3112 <li>Codons containing ambiguous nucleotides translated as
3113 'X' in peptide product</li>
3114 <li>Match case switch in find dialog box works for both
3115 sequence ID and sequence string and query strings do not
3116 have to be in upper case to match case-insensitively.</li>
3117 <li>AMSA files only contain first column of
3118 multi-character column annotation labels</li>
3119 <li>Jalview Annotation File generation/parsing consistent
3120 with documentation (e.g. Stockholm annotation can be
3121 exported and re-imported)</li>
3122 <li>PDB files without embedded PDB IDs given a friendly
3124 <li>Find incrementally searches ID string matches as well
3125 as subsequence matches, and correctly reports total number
3129 <li>Better handling of exceptions during sequence
3131 <li>Dasobert generated non-positional feature URL
3132 link text excludes the start_end suffix</li>
3133 <li>DAS feature and source retrieval buttons disabled
3134 when fetch or registry operations in progress.</li>
3135 <li>PDB files retrieved from URLs are cached properly</li>
3136 <li>Sequence description lines properly shared via
3138 <li>Sequence fetcher fetches multiple records for all
3140 <li>Ensured that command line das feature retrieval
3141 completes before alignment figures are generated.</li>
3142 <li>Reduced time taken when opening file browser for
3144 <li>isAligned check prior to calculating tree, PCA or
3145 submitting an MSA to JNet now excludes hidden sequences.</li>
3146 <li>User defined group colours properly recovered
3147 from Jalview projects.</li>
3156 <div align="center">
3157 <strong>2.4.0.b2</strong><br> 28/10/2009
3162 <li>Experimental support for google analytics usage
3164 <li>Jalview privacy settings (user preferences and docs).</li>
3169 <li>Race condition in applet preventing startup in
3171 <li>Exception when feature created from selection beyond
3172 length of sequence.</li>
3173 <li>Allow synthetic PDB files to be imported gracefully</li>
3174 <li>Sequence associated annotation rows associate with
3175 all sequences with a given id</li>
3176 <li>Find function matches case-insensitively for sequence
3177 ID string searches</li>
3178 <li>Non-standard characters do not cause pairwise
3179 alignment to fail with exception</li>
3180 </ul> <em>Application Issues</em>
3182 <li>Sequences are now validated against EMBL database</li>
3183 <li>Sequence fetcher fetches multiple records for all
3185 </ul> <em>InstallAnywhere Issues</em>
3187 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3188 issue with installAnywhere mechanism)</li>
3189 <li>Command line launching of JARs from InstallAnywhere
3190 version (java class versioning error fixed)</li>
3197 <div align="center">
3198 <strong>2.4</strong><br> 27/8/2008
3201 <td><em>User Interface</em>
3203 <li>Linked highlighting of codon and amino acid from
3204 translation and protein products</li>
3205 <li>Linked highlighting of structure associated with
3206 residue mapping to codon position</li>
3207 <li>Sequence Fetcher provides example accession numbers
3208 and 'clear' button</li>
3209 <li>MemoryMonitor added as an option under Desktop's
3211 <li>Extract score function to parse whitespace separated
3212 numeric data in description line</li>
3213 <li>Column labels in alignment annotation can be centred.</li>
3214 <li>Tooltip for sequence associated annotation give name
3216 </ul> <em>Web Services and URL fetching</em>
3218 <li>JPred3 web service</li>
3219 <li>Prototype sequence search client (no public services
3221 <li>Fetch either seed alignment or full alignment from
3223 <li>URL Links created for matching database cross
3224 references as well as sequence ID</li>
3225 <li>URL Links can be created using regular-expressions</li>
3226 </ul> <em>Sequence Database Connectivity</em>
3228 <li>Retrieval of cross-referenced sequences from other
3230 <li>Generalised database reference retrieval and
3231 validation to all fetchable databases</li>
3232 <li>Fetch sequences from DAS sources supporting the
3233 sequence command</li>
3234 </ul> <em>Import and Export</em>
3235 <li>export annotation rows as CSV for spreadsheet import</li>
3236 <li>Jalview projects record alignment dataset associations,
3237 EMBL products, and cDNA sequence mappings</li>
3238 <li>Sequence Group colour can be specified in Annotation
3240 <li>Ad-hoc colouring of group in Annotation File using RGB
3241 triplet as name of colourscheme</li>
3242 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3244 <li>treenode binding for VAMSAS tree exchange</li>
3245 <li>local editing and update of sequences in VAMSAS
3246 alignments (experimental)</li>
3247 <li>Create new or select existing session to join</li>
3248 <li>load and save of vamsas documents</li>
3249 </ul> <em>Application command line</em>
3251 <li>-tree parameter to open trees (introduced for passing
3253 <li>-fetchfrom command line argument to specify nicknames
3254 of DAS servers to query for alignment features</li>
3255 <li>-dasserver command line argument to add new servers
3256 that are also automatically queried for features</li>
3257 <li>-groovy command line argument executes a given groovy
3258 script after all input data has been loaded and parsed</li>
3259 </ul> <em>Applet-Application data exchange</em>
3261 <li>Trees passed as applet parameters can be passed to
3262 application (when using "View in full
3263 application")</li>
3264 </ul> <em>Applet Parameters</em>
3266 <li>feature group display control parameter</li>
3267 <li>debug parameter</li>
3268 <li>showbutton parameter</li>
3269 </ul> <em>Applet API methods</em>
3271 <li>newView public method</li>
3272 <li>Window (current view) specific get/set public methods</li>
3273 <li>Feature display control methods</li>
3274 <li>get list of currently selected sequences</li>
3275 </ul> <em>New Jalview distribution features</em>
3277 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3278 <li>RELEASE file gives build properties for the latest
3279 Jalview release.</li>
3280 <li>Java 1.1 Applet build made easier and donotobfuscate
3281 property controls execution of obfuscator</li>
3282 <li>Build target for generating source distribution</li>
3283 <li>Debug flag for javacc</li>
3284 <li>.jalview_properties file is documented (slightly) in
3285 jalview.bin.Cache</li>
3286 <li>Continuous Build Integration for stable and
3287 development version of Application, Applet and source
3292 <li>selected region output includes visible annotations
3293 (for certain formats)</li>
3294 <li>edit label/displaychar contains existing label/char
3296 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3297 <li>shorter peptide product names from EMBL records</li>
3298 <li>Newick string generator makes compact representations</li>
3299 <li>bootstrap values parsed correctly for tree files with
3301 <li>pathological filechooser bug avoided by not allowing
3302 filenames containing a ':'</li>
3303 <li>Fixed exception when parsing GFF files containing
3304 global sequence features</li>
3305 <li>Alignment datasets are finalized only when number of
3306 references from alignment sequences goes to zero</li>
3307 <li>Close of tree branch colour box without colour
3308 selection causes cascading exceptions</li>
3309 <li>occasional negative imgwidth exceptions</li>
3310 <li>better reporting of non-fatal warnings to user when
3311 file parsing fails.</li>
3312 <li>Save works when Jalview project is default format</li>
3313 <li>Save as dialog opened if current alignment format is
3314 not a valid output format</li>
3315 <li>UniProt canonical names introduced for both das and
3317 <li>Histidine should be midblue (not pink!) in Zappo</li>
3318 <li>error messages passed up and output when data read
3320 <li>edit undo recovers previous dataset sequence when
3321 sequence is edited</li>
3322 <li>allow PDB files without pdb ID HEADER lines (like
3323 those generated by MODELLER) to be read in properly</li>
3324 <li>allow reading of JPred concise files as a normal
3326 <li>Stockholm annotation parsing and alignment properties
3327 import fixed for PFAM records</li>
3328 <li>Structure view windows have correct name in Desktop
3330 <li>annotation consisting of sequence associated scores
3331 can be read and written correctly to annotation file</li>
3332 <li>Aligned cDNA translation to aligned peptide works
3334 <li>Fixed display of hidden sequence markers and
3335 non-italic font for representatives in Applet</li>
3336 <li>Applet Menus are always embedded in applet window on
3338 <li>Newly shown features appear at top of stack (in
3340 <li>Annotations added via parameter not drawn properly
3341 due to null pointer exceptions</li>
3342 <li>Secondary structure lines are drawn starting from
3343 first column of alignment</li>
3344 <li>UniProt XML import updated for new schema release in
3346 <li>Sequence feature to sequence ID match for Features
3347 file is case-insensitive</li>
3348 <li>Sequence features read from Features file appended to
3349 all sequences with matching IDs</li>
3350 <li>PDB structure coloured correctly for associated views
3351 containing a sub-sequence</li>
3352 <li>PDB files can be retrieved by applet from Jar files</li>
3353 <li>feature and annotation file applet parameters
3354 referring to different directories are retrieved correctly</li>
3355 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3356 <li>Fixed application hang whilst waiting for
3357 splash-screen version check to complete</li>
3358 <li>Applet properly URLencodes input parameter values
3359 when passing them to the launchApp service</li>
3360 <li>display name and local features preserved in results
3361 retrieved from web service</li>
3362 <li>Visual delay indication for sequence retrieval and
3363 sequence fetcher initialisation</li>
3364 <li>updated Application to use DAS 1.53e version of
3365 dasobert DAS client</li>
3366 <li>Re-instated Full AMSA support and .amsa file
3368 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3376 <div align="center">
3377 <strong>2.3</strong><br> 9/5/07
3382 <li>Jmol 11.0.2 integration</li>
3383 <li>PDB views stored in Jalview XML files</li>
3384 <li>Slide sequences</li>
3385 <li>Edit sequence in place</li>
3386 <li>EMBL CDS features</li>
3387 <li>DAS Feature mapping</li>
3388 <li>Feature ordering</li>
3389 <li>Alignment Properties</li>
3390 <li>Annotation Scores</li>
3391 <li>Sort by scores</li>
3392 <li>Feature/annotation editing in applet</li>
3397 <li>Headless state operation in 2.2.1</li>
3398 <li>Incorrect and unstable DNA pairwise alignment</li>
3399 <li>Cut and paste of sequences with annotation</li>
3400 <li>Feature group display state in XML</li>
3401 <li>Feature ordering in XML</li>
3402 <li>blc file iteration selection using filename # suffix</li>
3403 <li>Stockholm alignment properties</li>
3404 <li>Stockhom alignment secondary structure annotation</li>
3405 <li>2.2.1 applet had no feature transparency</li>
3406 <li>Number pad keys can be used in cursor mode</li>
3407 <li>Structure Viewer mirror image resolved</li>
3414 <div align="center">
3415 <strong>2.2.1</strong><br> 12/2/07
3420 <li>Non standard characters can be read and displayed
3421 <li>Annotations/Features can be imported/exported to the
3423 <li>Applet allows editing of sequence/annotation/group
3424 name & description
3425 <li>Preference setting to display sequence name in
3427 <li>Annotation file format extended to allow
3428 Sequence_groups to be defined
3429 <li>Default opening of alignment overview panel can be
3430 specified in preferences
3431 <li>PDB residue numbering annotation added to associated
3437 <li>Applet crash under certain Linux OS with Java 1.6
3439 <li>Annotation file export / import bugs fixed
3440 <li>PNG / EPS image output bugs fixed
3446 <div align="center">
3447 <strong>2.2</strong><br> 27/11/06
3452 <li>Multiple views on alignment
3453 <li>Sequence feature editing
3454 <li>"Reload" alignment
3455 <li>"Save" to current filename
3456 <li>Background dependent text colour
3457 <li>Right align sequence ids
3458 <li>User-defined lower case residue colours
3461 <li>Menu item accelerator keys
3462 <li>Control-V pastes to current alignment
3463 <li>Cancel button for DAS Feature Fetching
3464 <li>PCA and PDB Viewers zoom via mouse roller
3465 <li>User-defined sub-tree colours and sub-tree selection
3467 <li>'New Window' button on the 'Output to Text box'
3472 <li>New memory efficient Undo/Redo System
3473 <li>Optimised symbol lookups and conservation/consensus
3475 <li>Region Conservation/Consensus recalculated after
3477 <li>Fixed Remove Empty Columns Bug (empty columns at end
3479 <li>Slowed DAS Feature Fetching for increased robustness.
3481 <li>Made angle brackets in ASCII feature descriptions
3483 <li>Re-instated Zoom function for PCA
3484 <li>Sequence descriptions conserved in web service
3486 <li>UniProt ID discoverer uses any word separated by
3488 <li>WsDbFetch query/result association resolved
3489 <li>Tree leaf to sequence mapping improved
3490 <li>Smooth fonts switch moved to FontChooser dialog box.
3497 <div align="center">
3498 <strong>2.1.1</strong><br> 12/9/06
3503 <li>Copy consensus sequence to clipboard</li>
3508 <li>Image output - rightmost residues are rendered if
3509 sequence id panel has been resized</li>
3510 <li>Image output - all offscreen group boundaries are
3512 <li>Annotation files with sequence references - all
3513 elements in file are relative to sequence position</li>
3514 <li>Mac Applet users can use Alt key for group editing</li>
3520 <div align="center">
3521 <strong>2.1</strong><br> 22/8/06
3526 <li>MAFFT Multiple Alignment in default Web Service list</li>
3527 <li>DAS Feature fetching</li>
3528 <li>Hide sequences and columns</li>
3529 <li>Export Annotations and Features</li>
3530 <li>GFF file reading / writing</li>
3531 <li>Associate structures with sequences from local PDB
3533 <li>Add sequences to exisiting alignment</li>
3534 <li>Recently opened files / URL lists</li>
3535 <li>Applet can launch the full application</li>
3536 <li>Applet has transparency for features (Java 1.2
3538 <li>Applet has user defined colours parameter</li>
3539 <li>Applet can load sequences from parameter
3540 "sequence<em>x</em>"
3546 <li>Redundancy Panel reinstalled in the Applet</li>
3547 <li>Monospaced font - EPS / rescaling bug fixed</li>
3548 <li>Annotation files with sequence references bug fixed</li>
3554 <div align="center">
3555 <strong>2.08.1</strong><br> 2/5/06
3560 <li>Change case of selected region from Popup menu</li>
3561 <li>Choose to match case when searching</li>
3562 <li>Middle mouse button and mouse movement can compress /
3563 expand the visible width and height of the alignment</li>
3568 <li>Annotation Panel displays complete JNet results</li>
3574 <div align="center">
3575 <strong>2.08b</strong><br> 18/4/06
3581 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3582 <li>Righthand label on wrapped alignments shows correct
3589 <div align="center">
3590 <strong>2.08</strong><br> 10/4/06
3595 <li>Editing can be locked to the selection area</li>
3596 <li>Keyboard editing</li>
3597 <li>Create sequence features from searches</li>
3598 <li>Precalculated annotations can be loaded onto
3600 <li>Features file allows grouping of features</li>
3601 <li>Annotation Colouring scheme added</li>
3602 <li>Smooth fonts off by default - Faster rendering</li>
3603 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3608 <li>Drag & Drop fixed on Linux</li>
3609 <li>Jalview Archive file faster to load/save, sequence
3610 descriptions saved.</li>
3616 <div align="center">
3617 <strong>2.07</strong><br> 12/12/05
3622 <li>PDB Structure Viewer enhanced</li>
3623 <li>Sequence Feature retrieval and display enhanced</li>
3624 <li>Choose to output sequence start-end after sequence
3625 name for file output</li>
3626 <li>Sequence Fetcher WSDBFetch@EBI</li>
3627 <li>Applet can read feature files, PDB files and can be
3628 used for HTML form input</li>
3633 <li>HTML output writes groups and features</li>
3634 <li>Group editing is Control and mouse click</li>
3635 <li>File IO bugs</li>
3641 <div align="center">
3642 <strong>2.06</strong><br> 28/9/05
3647 <li>View annotations in wrapped mode</li>
3648 <li>More options for PCA viewer</li>
3653 <li>GUI bugs resolved</li>
3654 <li>Runs with -nodisplay from command line</li>
3660 <div align="center">
3661 <strong>2.05b</strong><br> 15/9/05
3666 <li>Choose EPS export as lineart or text</li>
3667 <li>Jar files are executable</li>
3668 <li>Can read in Uracil - maps to unknown residue</li>
3673 <li>Known OutOfMemory errors give warning message</li>
3674 <li>Overview window calculated more efficiently</li>
3675 <li>Several GUI bugs resolved</li>
3681 <div align="center">
3682 <strong>2.05</strong><br> 30/8/05
3687 <li>Edit and annotate in "Wrapped" view</li>
3692 <li>Several GUI bugs resolved</li>
3698 <div align="center">
3699 <strong>2.04</strong><br> 24/8/05
3704 <li>Hold down mouse wheel & scroll to change font
3710 <li>Improved JPred client reliability</li>
3711 <li>Improved loading of Jalview files</li>
3717 <div align="center">
3718 <strong>2.03</strong><br> 18/8/05
3723 <li>Set Proxy server name and port in preferences</li>
3724 <li>Multiple URL links from sequence ids</li>
3725 <li>User Defined Colours can have a scheme name and added
3727 <li>Choose to ignore gaps in consensus calculation</li>
3728 <li>Unix users can set default web browser</li>
3729 <li>Runs without GUI for batch processing</li>
3730 <li>Dynamically generated Web Service Menus</li>
3735 <li>InstallAnywhere download for Sparc Solaris</li>
3741 <div align="center">
3742 <strong>2.02</strong><br> 18/7/05
3748 <li>Copy & Paste order of sequences maintains
3749 alignment order.</li>
3755 <div align="center">
3756 <strong>2.01</strong><br> 12/7/05
3761 <li>Use delete key for deleting selection.</li>
3762 <li>Use Mouse wheel to scroll sequences.</li>
3763 <li>Help file updated to describe how to add alignment
3765 <li>Version and build date written to build properties
3767 <li>InstallAnywhere installation will check for updates
3768 at launch of Jalview.</li>
3773 <li>Delete gaps bug fixed.</li>
3774 <li>FileChooser sorts columns.</li>
3775 <li>Can remove groups one by one.</li>
3776 <li>Filechooser icons installed.</li>
3777 <li>Finder ignores return character when searching.
3778 Return key will initiate a search.<br>
3785 <div align="center">
3786 <strong>2.0</strong><br> 20/6/05
3791 <li>New codebase</li>