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;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
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>5/12/2017</em></strong>
76 <td><div align="left">
79 <td><div align="left">
81 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
82 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
83 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
84 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
85 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
90 <td width="60" nowrap>
92 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
95 <td><div align="left">
99 <!-- JAL-2446 -->Faster and more efficient management and
100 rendering of sequence features
103 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
104 429 rate limit request hander
107 <!-- JAL-2773 -->Structure views don't get updated unless
108 their colours have changed
111 <!-- JAL-2495 -->All linked sequences are highlighted for
112 a structure mousover (Jmol) or selection (Chimera)
115 <!-- JAL-2790 -->'Cancel' button in progress bar for
116 JABAWS AACon, RNAAliFold and Disorder prediction jobs
119 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
120 view from Ensembl locus cross-references
123 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
127 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
128 feature can be disabled
131 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
132 PDB easier retrieval of sequences for lists of IDs
135 <!-- JAL-2758 -->Short names for sequences retrieved from
141 <li>Groovy interpreter updated to 2.4.12</li>
142 <li>Example groovy script for generating a matrix of
143 percent identity scores for current alignment.</li>
145 <em>Testing and Deployment</em>
148 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
152 <td><div align="left">
156 <!-- JAL-2643 -->Pressing tab after updating the colour
157 threshold text field doesn't trigger an update to the
161 <!-- JAL-2682 -->Race condition when parsing sequence ID
165 <!-- JAL-2608 -->Overview windows are also closed when
166 alignment window is closed
169 <!-- JAL-2548 -->Export of features doesn't always respect
173 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
174 takes a long time in Cursor mode
180 <!-- JAL-2777 -->Structures with whitespace chainCode
181 cannot be viewed in Chimera
184 <!-- JAL-2728 -->Protein annotation panel too high in
188 <!-- JAL-2757 -->Can't edit the query after the server
189 error warning icon is shown in Uniprot and PDB Free Text
193 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
196 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
199 <!-- JAL-2739 -->Hidden column marker in last column not
200 rendered when switching back from Wrapped to normal view
203 <!-- JAL-2768 -->Annotation display corrupted when
204 scrolling right in unwapped alignment view
207 <!-- JAL-2542 -->Existing features on subsequence
208 incorrectly relocated when full sequence retrieved from
212 <!-- JAL-2733 -->Last reported memory still shown when
213 Desktop->Show Memory is unticked (OSX only)
216 <!-- JAL-2658 -->Amend Features dialog doesn't allow
217 features of same type and group to be selected for
221 <!-- JAL-2524 -->Jalview becomes sluggish in wide
222 alignments when hidden columns are present
225 <!-- JAL-2392 -->Jalview freezes when loading and
226 displaying several structures
229 <!-- JAL-2732 -->Black outlines left after resizing or
233 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
234 within the Jalview desktop on OSX
237 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
238 when in wrapped alignment mode
241 <!-- JAL-2636 -->Scale mark not shown when close to right
242 hand end of alignment
245 <!-- JAL-2684 -->Pairwise alignment of selected regions of
246 each selected sequence do not have correct start/end
250 <!-- JAL-2793 -->Alignment ruler height set incorrectly
251 after canceling the Alignment Window's Font dialog
254 <!-- JAL-2036 -->Show cross-references not enabled after
255 restoring project until a new view is created
258 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
259 URL links appears when only default EMBL-EBI link is
260 configured (since 2.10.2b2)
263 <!-- JAL-2775 -->Overview redraws whole window when box
267 <!-- JAL-2225 -->Structure viewer doesn't map all chains
268 in a multi-chain structure when viewing alignment
269 involving more than one chain (since 2.10)
272 <!-- JAL-2811 -->Double residue highlights in cursor mode
273 if new selection moves alignment window
276 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
277 arrow key in cursor mode to pass hidden column marker
280 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
281 that produces correctly annotated transcripts and products
284 <!-- JAL-2776 -->Toggling a feature group after first time
285 doesn't update associated structure view
288 <em>Applet</em><br />
291 <!-- JAL-2687 -->Concurrent modification exception when
292 closing alignment panel
295 <em>BioJSON</em><br />
298 <!-- JAL-2546 -->BioJSON export does not preserve
299 non-positional features
302 <em>New Known Issues</em>
305 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
306 sequence features correctly (for many previous versions of
310 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
311 using cursor in wrapped panel other than top
314 <!-- JAL-2791 -->Select columns containing feature ignores
315 graduated colour threshold
318 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
319 always preserve numbering and sequence features
322 <em>Known Java 9 Issues</em>
325 <!-- JAL-2902 -->Groovy Console very slow to open and is
326 not responsive when entering characters (Webstart, Java
333 <td width="60" nowrap>
335 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
336 <em>2/10/2017</em></strong>
339 <td><div align="left">
340 <em>New features in Jalview Desktop</em>
343 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
345 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
349 <td><div align="left">
353 <td width="60" nowrap>
355 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
356 <em>7/9/2017</em></strong>
359 <td><div align="left">
363 <!-- JAL-2588 -->Show gaps in overview window by colouring
364 in grey (sequences used to be coloured grey, and gaps were
368 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
372 <!-- JAL-2587 -->Overview updates immediately on increase
373 in size and progress bar shown as higher resolution
374 overview is recalculated
379 <td><div align="left">
383 <!-- JAL-2664 -->Overview window redraws every hidden
384 column region row by row
387 <!-- JAL-2681 -->duplicate protein sequences shown after
388 retrieving Ensembl crossrefs for sequences from Uniprot
391 <!-- JAL-2603 -->Overview window throws NPE if show boxes
392 format setting is unticked
395 <!-- JAL-2610 -->Groups are coloured wrongly in overview
396 if group has show boxes format setting unticked
399 <!-- JAL-2672,JAL-2665 -->Redraw problems when
400 autoscrolling whilst dragging current selection group to
401 include sequences and columns not currently displayed
404 <!-- JAL-2691 -->Not all chains are mapped when multimeric
405 assemblies are imported via CIF file
408 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
409 displayed when threshold or conservation colouring is also
413 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
417 <!-- JAL-2673 -->Jalview continues to scroll after
418 dragging a selected region off the visible region of the
422 <!-- JAL-2724 -->Cannot apply annotation based
423 colourscheme to all groups in a view
426 <!-- JAL-2511 -->IDs don't line up with sequences
427 initially after font size change using the Font chooser or
434 <td width="60" nowrap>
436 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
439 <td><div align="left">
440 <em>Calculations</em>
444 <!-- JAL-1933 -->Occupancy annotation row shows number of
445 ungapped positions in each column of the alignment.
448 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
449 a calculation dialog box
452 <!-- JAL-2379 -->Revised implementation of PCA for speed
453 and memory efficiency (~30x faster)
456 <!-- JAL-2403 -->Revised implementation of sequence
457 similarity scores as used by Tree, PCA, Shading Consensus
458 and other calculations
461 <!-- JAL-2416 -->Score matrices are stored as resource
462 files within the Jalview codebase
465 <!-- JAL-2500 -->Trees computed on Sequence Feature
466 Similarity may have different topology due to increased
473 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
474 model for alignments and groups
477 <!-- JAL-384 -->Custom shading schemes created via groovy
484 <!-- JAL-2526 -->Efficiency improvements for interacting
485 with alignment and overview windows
488 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
492 <!-- JAL-2388 -->Hidden columns and sequences can be
496 <!-- JAL-2611 -->Click-drag in visible area allows fine
497 adjustment of visible position
501 <em>Data import/export</em>
504 <!-- JAL-2535 -->Posterior probability annotation from
505 Stockholm files imported as sequence associated annotation
508 <!-- JAL-2507 -->More robust per-sequence positional
509 annotation input/output via stockholm flatfile
512 <!-- JAL-2533 -->Sequence names don't include file
513 extension when importing structure files without embedded
514 names or PDB accessions
517 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
518 format sequence substitution matrices
521 <em>User Interface</em>
524 <!-- JAL-2447 --> Experimental Features Checkbox in
525 Desktop's Tools menu to hide or show untested features in
529 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
530 via Overview or sequence motif search operations
533 <!-- JAL-2547 -->Amend sequence features dialog box can be
534 opened by double clicking gaps within sequence feature
538 <!-- JAL-1476 -->Status bar message shown when not enough
539 aligned positions were available to create a 3D structure
543 <em>3D Structure</em>
546 <!-- JAL-2430 -->Hidden regions in alignment views are not
547 coloured in linked structure views
550 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
551 file-based command exchange
554 <!-- JAL-2375 -->Structure chooser automatically shows
555 Cached Structures rather than querying the PDBe if
556 structures are already available for sequences
559 <!-- JAL-2520 -->Structures imported via URL are cached in
560 the Jalview project rather than downloaded again when the
564 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
565 to transfer Chimera's structure attributes as Jalview
566 features, and vice-versa (<strong>Experimental
570 <em>Web Services</em>
573 <!-- JAL-2549 -->Updated JABAWS client to v2.2
576 <!-- JAL-2335 -->Filter non-standard amino acids and
577 nucleotides when submitting to AACon and other MSA
581 <!-- JAL-2316, -->URLs for viewing database
582 cross-references provided by identifiers.org and the
590 <!-- JAL-2344 -->FileFormatI interface for describing and
591 identifying file formats (instead of String constants)
594 <!-- JAL-2228 -->FeatureCounter script refactored for
595 efficiency when counting all displayed features (not
596 backwards compatible with 2.10.1)
599 <em>Example files</em>
602 <!-- JAL-2631 -->Graduated feature colour style example
603 included in the example feature file
606 <em>Documentation</em>
609 <!-- JAL-2339 -->Release notes reformatted for readability
610 with the built-in Java help viewer
613 <!-- JAL-1644 -->Find documentation updated with 'search
614 sequence description' option
620 <!-- JAL-2485, -->External service integration tests for
621 Uniprot REST Free Text Search Client
624 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
627 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
632 <td><div align="left">
633 <em>Calculations</em>
636 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
637 matrix - C->R should be '-3'<br />Old matrix restored
638 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
640 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
641 Jalview's treatment of gaps in PCA and substitution matrix
642 based Tree calculations.<br /> <br />In earlier versions
643 of Jalview, gaps matching gaps were penalised, and gaps
644 matching non-gaps penalised even more. In the PCA
645 calculation, gaps were actually treated as non-gaps - so
646 different costs were applied, which meant Jalview's PCAs
647 were different to those produced by SeqSpace.<br />Jalview
648 now treats gaps in the same way as SeqSpace (ie it scores
649 them as 0). <br /> <br />Enter the following in the
650 Groovy console to restore pre-2.10.2 behaviour:<br />
651 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
652 // for 2.10.1 mode <br />
653 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
654 // to restore 2.10.2 mode <br /> <br /> <em>Note:
655 these settings will affect all subsequent tree and PCA
656 calculations (not recommended)</em></li>
658 <!-- JAL-2424 -->Fixed off-by-one bug that affected
659 scaling of branch lengths for trees computed using
660 Sequence Feature Similarity.
663 <!-- JAL-2377 -->PCA calculation could hang when
664 generating output report when working with highly
668 <!-- JAL-2544 --> Sort by features includes features to
669 right of selected region when gaps present on right-hand
673 <em>User Interface</em>
676 <!-- JAL-2346 -->Reopening Colour by annotation dialog
677 doesn't reselect a specific sequence's associated
678 annotation after it was used for colouring a view
681 <!-- JAL-2419 -->Current selection lost if popup menu
682 opened on a region of alignment without groups
685 <!-- JAL-2374 -->Popup menu not always shown for regions
686 of an alignment with overlapping groups
689 <!-- JAL-2310 -->Finder double counts if both a sequence's
690 name and description match
693 <!-- JAL-2370 -->Hiding column selection containing two
694 hidden regions results in incorrect hidden regions
697 <!-- JAL-2386 -->'Apply to all groups' setting when
698 changing colour does not apply Conservation slider value
702 <!-- JAL-2373 -->Percentage identity and conservation menu
703 items do not show a tick or allow shading to be disabled
706 <!-- JAL-2385 -->Conservation shading or PID threshold
707 lost when base colourscheme changed if slider not visible
710 <!-- JAL-2547 -->Sequence features shown in tooltip for
711 gaps before start of features
714 <!-- JAL-2623 -->Graduated feature colour threshold not
715 restored to UI when feature colour is edited
718 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
719 a time when scrolling vertically in wrapped mode.
722 <!-- JAL-2630 -->Structure and alignment overview update
723 as graduate feature colour settings are modified via the
727 <!-- JAL-2034 -->Overview window doesn't always update
728 when a group defined on the alignment is resized
731 <!-- JAL-2605 -->Mouseovers on left/right scale region in
732 wrapped view result in positional status updates
736 <!-- JAL-2563 -->Status bar doesn't show position for
737 ambiguous amino acid and nucleotide symbols
740 <!-- JAL-2602 -->Copy consensus sequence failed if
741 alignment included gapped columns
744 <!-- JAL-2473 -->Minimum size set for Jalview windows so
745 widgets don't permanently disappear
748 <!-- JAL-2503 -->Cannot select or filter quantitative
749 annotation that are shown only as column labels (e.g.
750 T-Coffee column reliability scores)
753 <!-- JAL-2594 -->Exception thrown if trying to create a
754 sequence feature on gaps only
757 <!-- JAL-2504 -->Features created with 'New feature'
758 button from a Find inherit previously defined feature type
759 rather than the Find query string
762 <!-- JAL-2423 -->incorrect title in output window when
763 exporting tree calculated in Jalview
766 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
767 and then revealing them reorders sequences on the
771 <!-- JAL-964 -->Group panel in sequence feature settings
772 doesn't update to reflect available set of groups after
773 interactively adding or modifying features
776 <!-- JAL-2225 -->Sequence Database chooser unusable on
780 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
781 only excluded gaps in current sequence and ignored
788 <!-- JAL-2421 -->Overview window visible region moves
789 erratically when hidden rows or columns are present
792 <!-- JAL-2362 -->Per-residue colourschemes applied via the
793 Structure Viewer's colour menu don't correspond to
797 <!-- JAL-2405 -->Protein specific colours only offered in
798 colour and group colour menu for protein alignments
801 <!-- JAL-2385 -->Colour threshold slider doesn't update to
802 reflect currently selected view or group's shading
806 <!-- JAL-2624 -->Feature colour thresholds not respected
807 when rendered on overview and structures when opacity at
811 <!-- JAL-2589 -->User defined gap colour not shown in
812 overview when features overlaid on alignment
815 <em>Data import/export</em>
818 <!-- JAL-2576 -->Very large alignments take a long time to
822 <!-- JAL-2507 -->Per-sequence RNA secondary structures
823 added after a sequence was imported are not written to
827 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
828 when importing RNA secondary structure via Stockholm
831 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
832 not shown in correct direction for simple pseudoknots
835 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
836 with lightGray or darkGray via features file (but can
840 <!-- JAL-2383 -->Above PID colour threshold not recovered
841 when alignment view imported from project
844 <!-- JAL-2520,JAL-2465 -->No mappings generated between
845 structure and sequences extracted from structure files
846 imported via URL and viewed in Jmol
849 <!-- JAL-2520 -->Structures loaded via URL are saved in
850 Jalview Projects rather than fetched via URL again when
851 the project is loaded and the structure viewed
854 <em>Web Services</em>
857 <!-- JAL-2519 -->EnsemblGenomes example failing after
858 release of Ensembl v.88
861 <!-- JAL-2366 -->Proxy server address and port always
862 appear enabled in Preferences->Connections
865 <!-- JAL-2461 -->DAS registry not found exceptions
866 removed from console output
869 <!-- JAL-2582 -->Cannot retrieve protein products from
870 Ensembl by Peptide ID
873 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
874 created from SIFTs, and spurious 'Couldn't open structure
875 in Chimera' errors raised after April 2017 update (problem
876 due to 'null' string rather than empty string used for
877 residues with no corresponding PDB mapping).
880 <em>Application UI</em>
883 <!-- JAL-2361 -->User Defined Colours not added to Colour
887 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
888 case' residues (button in colourscheme editor debugged and
889 new documentation and tooltips added)
892 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
893 doesn't restore group-specific text colour thresholds
896 <!-- JAL-2243 -->Feature settings panel does not update as
897 new features are added to alignment
900 <!-- JAL-2532 -->Cancel in feature settings reverts
901 changes to feature colours via the Amend features dialog
904 <!-- JAL-2506 -->Null pointer exception when attempting to
905 edit graduated feature colour via amend features dialog
909 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
910 selection menu changes colours of alignment views
913 <!-- JAL-2426 -->Spurious exceptions in console raised
914 from alignment calculation workers after alignment has
918 <!-- JAL-1608 -->Typo in selection popup menu - Create
919 groups now 'Create Group'
922 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
923 Create/Undefine group doesn't always work
926 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
927 shown again after pressing 'Cancel'
930 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
931 adjusts start position in wrap mode
934 <!-- JAL-2563 -->Status bar doesn't show positions for
935 ambiguous amino acids
938 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
939 CDS/Protein view after CDS sequences added for aligned
943 <!-- JAL-2592 -->User defined colourschemes called 'User
944 Defined' don't appear in Colours menu
950 <!-- JAL-2468 -->Switching between Nucleotide and Protein
951 score models doesn't always result in an updated PCA plot
954 <!-- JAL-2442 -->Features not rendered as transparent on
955 overview or linked structure view
958 <!-- JAL-2372 -->Colour group by conservation doesn't
962 <!-- JAL-2517 -->Hitting Cancel after applying
963 user-defined colourscheme doesn't restore original
970 <!-- JAL-2314 -->Unit test failure:
971 jalview.ws.jabaws.RNAStructExportImport setup fails
974 <!-- JAL-2307 -->Unit test failure:
975 jalview.ws.sifts.SiftsClientTest due to compatibility
976 problems with deep array comparison equality asserts in
977 successive versions of TestNG
980 <!-- JAL-2479 -->Relocated StructureChooserTest and
981 ParameterUtilsTest Unit tests to Network suite
984 <em>New Known Issues</em>
987 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
988 phase after a sequence motif find operation
991 <!-- JAL-2550 -->Importing annotation file with rows
992 containing just upper and lower case letters are
993 interpreted as WUSS RNA secondary structure symbols
996 <!-- JAL-2590 -->Cannot load and display Newick trees
997 reliably from eggnog Ortholog database
1000 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1001 containing features of type Highlight' when 'B' is pressed
1002 to mark columns containing highlighted regions.
1005 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1006 doesn't always add secondary structure annotation.
1011 <td width="60" nowrap>
1012 <div align="center">
1013 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1016 <td><div align="left">
1020 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1021 for all consensus calculations
1024 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1027 <li>Updated Jalview's Certum code signing certificate
1030 <em>Application</em>
1033 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1034 set of database cross-references, sorted alphabetically
1037 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1038 from database cross references. Users with custom links
1039 will receive a <a href="webServices/urllinks.html#warning">warning
1040 dialog</a> asking them to update their preferences.
1043 <!-- JAL-2287-->Cancel button and escape listener on
1044 dialog warning user about disconnecting Jalview from a
1048 <!-- JAL-2320-->Jalview's Chimera control window closes if
1049 the Chimera it is connected to is shut down
1052 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1053 columns menu item to mark columns containing highlighted
1054 regions (e.g. from structure selections or results of a
1058 <!-- JAL-2284-->Command line option for batch-generation
1059 of HTML pages rendering alignment data with the BioJS
1069 <!-- JAL-2286 -->Columns with more than one modal residue
1070 are not coloured or thresholded according to percent
1071 identity (first observed in Jalview 2.8.2)
1074 <!-- JAL-2301 -->Threonine incorrectly reported as not
1078 <!-- JAL-2318 -->Updates to documentation pages (above PID
1079 threshold, amino acid properties)
1082 <!-- JAL-2292 -->Lower case residues in sequences are not
1083 reported as mapped to residues in a structure file in the
1087 <!--JAL-2324 -->Identical features with non-numeric scores
1088 could be added multiple times to a sequence
1091 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1092 bond features shown as two highlighted residues rather
1093 than a range in linked structure views, and treated
1094 correctly when selecting and computing trees from features
1097 <!-- JAL-2281-->Custom URL links for database
1098 cross-references are matched to database name regardless
1103 <em>Application</em>
1106 <!-- JAL-2282-->Custom URL links for specific database
1107 names without regular expressions also offer links from
1111 <!-- JAL-2315-->Removing a single configured link in the
1112 URL links pane in Connections preferences doesn't actually
1113 update Jalview configuration
1116 <!-- JAL-2272-->CTRL-Click on a selected region to open
1117 the alignment area popup menu doesn't work on El-Capitan
1120 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1121 files with similarly named sequences if dropped onto the
1125 <!-- JAL-2312 -->Additional mappings are shown for PDB
1126 entries where more chains exist in the PDB accession than
1127 are reported in the SIFTS file
1130 <!-- JAL-2317-->Certain structures do not get mapped to
1131 the structure view when displayed with Chimera
1134 <!-- JAL-2317-->No chains shown in the Chimera view
1135 panel's View->Show Chains submenu
1138 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1139 work for wrapped alignment views
1142 <!--JAL-2197 -->Rename UI components for running JPred
1143 predictions from 'JNet' to 'JPred'
1146 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1147 corrupted when annotation panel vertical scroll is not at
1148 first annotation row
1151 <!--JAL-2332 -->Attempting to view structure for Hen
1152 lysozyme results in a PDB Client error dialog box
1155 <!-- JAL-2319 -->Structure View's mapping report switched
1156 ranges for PDB and sequence for SIFTS
1159 SIFTS 'Not_Observed' residues mapped to non-existant
1163 <!-- <em>New Known Issues</em>
1170 <td width="60" nowrap>
1171 <div align="center">
1172 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1173 <em>25/10/2016</em></strong>
1176 <td><em>Application</em>
1178 <li>3D Structure chooser opens with 'Cached structures'
1179 view if structures already loaded</li>
1180 <li>Progress bar reports models as they are loaded to
1181 structure views</li>
1187 <li>Colour by conservation always enabled and no tick
1188 shown in menu when BLOSUM or PID shading applied</li>
1189 <li>FER1_ARATH and FER2_ARATH labels were switched in
1190 example sequences/projects/trees</li>
1192 <em>Application</em>
1194 <li>Jalview projects with views of local PDB structure
1195 files saved on Windows cannot be opened on OSX</li>
1196 <li>Multiple structure views can be opened and superposed
1197 without timeout for structures with multiple models or
1198 multiple sequences in alignment</li>
1199 <li>Cannot import or associated local PDB files without a
1200 PDB ID HEADER line</li>
1201 <li>RMSD is not output in Jmol console when superposition
1203 <li>Drag and drop of URL from Browser fails for Linux and
1204 OSX versions earlier than El Capitan</li>
1205 <li>ENA client ignores invalid content from ENA server</li>
1206 <li>Exceptions are not raised in console when ENA client
1207 attempts to fetch non-existent IDs via Fetch DB Refs UI
1209 <li>Exceptions are not raised in console when a new view
1210 is created on the alignment</li>
1211 <li>OSX right-click fixed for group selections: CMD-click
1212 to insert/remove gaps in groups and CTRL-click to open group
1215 <em>Build and deployment</em>
1217 <li>URL link checker now copes with multi-line anchor
1220 <em>New Known Issues</em>
1222 <li>Drag and drop from URL links in browsers do not work
1229 <td width="60" nowrap>
1230 <div align="center">
1231 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1234 <td><em>General</em>
1237 <!-- JAL-2124 -->Updated Spanish translations.
1240 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1241 for importing structure data to Jalview. Enables mmCIF and
1245 <!-- JAL-192 --->Alignment ruler shows positions relative to
1249 <!-- JAL-2202 -->Position/residue shown in status bar when
1250 mousing over sequence associated annotation
1253 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1257 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1258 '()', canonical '[]' and invalid '{}' base pair populations
1262 <!-- JAL-2092 -->Feature settings popup menu options for
1263 showing or hiding columns containing a feature
1266 <!-- JAL-1557 -->Edit selected group by double clicking on
1267 group and sequence associated annotation labels
1270 <!-- JAL-2236 -->Sequence name added to annotation label in
1271 select/hide columns by annotation and colour by annotation
1275 </ul> <em>Application</em>
1278 <!-- JAL-2050-->Automatically hide introns when opening a
1279 gene/transcript view
1282 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1286 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1287 structure mappings with the EMBL-EBI PDBe SIFTS database
1290 <!-- JAL-2079 -->Updated download sites used for Rfam and
1291 Pfam sources to xfam.org
1294 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1297 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1298 over sequences in Jalview
1301 <!-- JAL-2027-->Support for reverse-complement coding
1302 regions in ENA and EMBL
1305 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1306 for record retrieval via ENA rest API
1309 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1313 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1314 groovy script execution
1317 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1318 alignment window's Calculate menu
1321 <!-- JAL-1812 -->Allow groovy scripts that call
1322 Jalview.getAlignFrames() to run in headless mode
1325 <!-- JAL-2068 -->Support for creating new alignment
1326 calculation workers from groovy scripts
1329 <!-- JAL-1369 --->Store/restore reference sequence in
1333 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1334 associations are now saved/restored from project
1337 <!-- JAL-1993 -->Database selection dialog always shown
1338 before sequence fetcher is opened
1341 <!-- JAL-2183 -->Double click on an entry in Jalview's
1342 database chooser opens a sequence fetcher
1345 <!-- JAL-1563 -->Free-text search client for UniProt using
1346 the UniProt REST API
1349 <!-- JAL-2168 -->-nonews command line parameter to prevent
1350 the news reader opening
1353 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1354 querying stored in preferences
1357 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1361 <!-- JAL-1977-->Tooltips shown on database chooser
1364 <!-- JAL-391 -->Reverse complement function in calculate
1365 menu for nucleotide sequences
1368 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1369 and feature counts preserves alignment ordering (and
1370 debugged for complex feature sets).
1373 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1374 viewing structures with Jalview 2.10
1377 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1378 genome, transcript CCDS and gene ids via the Ensembl and
1379 Ensembl Genomes REST API
1382 <!-- JAL-2049 -->Protein sequence variant annotation
1383 computed for 'sequence_variant' annotation on CDS regions
1387 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1391 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1392 Ref Fetcher fails to match, or otherwise updates sequence
1393 data from external database records.
1396 <!-- JAL-2154 -->Revised Jalview Project format for
1397 efficient recovery of sequence coding and alignment
1398 annotation relationships.
1400 </ul> <!-- <em>Applet</em>
1411 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1415 <!-- JAL-2018-->Export features in Jalview format (again)
1416 includes graduated colourschemes
1419 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1420 working with big alignments and lots of hidden columns
1423 <!-- JAL-2053-->Hidden column markers not always rendered
1424 at right of alignment window
1427 <!-- JAL-2067 -->Tidied up links in help file table of
1431 <!-- JAL-2072 -->Feature based tree calculation not shown
1435 <!-- JAL-2075 -->Hidden columns ignored during feature
1436 based tree calculation
1439 <!-- JAL-2065 -->Alignment view stops updating when show
1440 unconserved enabled for group on alignment
1443 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1447 <!-- JAL-2146 -->Alignment column in status incorrectly
1448 shown as "Sequence position" when mousing over
1452 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1453 hidden columns present
1456 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1457 user created annotation added to alignment
1460 <!-- JAL-1841 -->RNA Structure consensus only computed for
1461 '()' base pair annotation
1464 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1465 in zero scores for all base pairs in RNA Structure
1469 <!-- JAL-2174-->Extend selection with columns containing
1473 <!-- JAL-2275 -->Pfam format writer puts extra space at
1474 beginning of sequence
1477 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1481 <!-- JAL-2238 -->Cannot create groups on an alignment from
1482 from a tree when t-coffee scores are shown
1485 <!-- JAL-1836,1967 -->Cannot import and view PDB
1486 structures with chains containing negative resnums (4q4h)
1489 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1493 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1494 to Clustal, PIR and PileUp output
1497 <!-- JAL-2008 -->Reordering sequence features that are
1498 not visible causes alignment window to repaint
1501 <!-- JAL-2006 -->Threshold sliders don't work in
1502 graduated colour and colour by annotation row for e-value
1503 scores associated with features and annotation rows
1506 <!-- JAL-1797 -->amino acid physicochemical conservation
1507 calculation should be case independent
1510 <!-- JAL-2173 -->Remove annotation also updates hidden
1514 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1515 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1516 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1519 <!-- JAL-2065 -->Null pointer exceptions and redraw
1520 problems when reference sequence defined and 'show
1521 non-conserved' enabled
1524 <!-- JAL-1306 -->Quality and Conservation are now shown on
1525 load even when Consensus calculation is disabled
1528 <!-- JAL-1932 -->Remove right on penultimate column of
1529 alignment does nothing
1532 <em>Application</em>
1535 <!-- JAL-1552-->URLs and links can't be imported by
1536 drag'n'drop on OSX when launched via webstart (note - not
1537 yet fixed for El Capitan)
1540 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1541 output when running on non-gb/us i18n platforms
1544 <!-- JAL-1944 -->Error thrown when exporting a view with
1545 hidden sequences as flat-file alignment
1548 <!-- JAL-2030-->InstallAnywhere distribution fails when
1552 <!-- JAL-2080-->Jalview very slow to launch via webstart
1553 (also hotfix for 2.9.0b2)
1556 <!-- JAL-2085 -->Cannot save project when view has a
1557 reference sequence defined
1560 <!-- JAL-1011 -->Columns are suddenly selected in other
1561 alignments and views when revealing hidden columns
1564 <!-- JAL-1989 -->Hide columns not mirrored in complement
1565 view in a cDNA/Protein splitframe
1568 <!-- JAL-1369 -->Cannot save/restore representative
1569 sequence from project when only one sequence is
1573 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1574 in Structure Chooser
1577 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1578 structure consensus didn't refresh annotation panel
1581 <!-- JAL-1962 -->View mapping in structure view shows
1582 mappings between sequence and all chains in a PDB file
1585 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1586 dialogs format columns correctly, don't display array
1587 data, sort columns according to type
1590 <!-- JAL-1975 -->Export complete shown after destination
1591 file chooser is cancelled during an image export
1594 <!-- JAL-2025 -->Error when querying PDB Service with
1595 sequence name containing special characters
1598 <!-- JAL-2024 -->Manual PDB structure querying should be
1602 <!-- JAL-2104 -->Large tooltips with broken HTML
1603 formatting don't wrap
1606 <!-- JAL-1128 -->Figures exported from wrapped view are
1607 truncated so L looks like I in consensus annotation
1610 <!-- JAL-2003 -->Export features should only export the
1611 currently displayed features for the current selection or
1615 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1616 after fetching cross-references, and restoring from
1620 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1621 followed in the structure viewer
1624 <!-- JAL-2163 -->Titles for individual alignments in
1625 splitframe not restored from project
1628 <!-- JAL-2145 -->missing autocalculated annotation at
1629 trailing end of protein alignment in transcript/product
1630 splitview when pad-gaps not enabled by default
1633 <!-- JAL-1797 -->amino acid physicochemical conservation
1637 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1638 article has been read (reopened issue due to
1639 internationalisation problems)
1642 <!-- JAL-1960 -->Only offer PDB structures in structure
1643 viewer based on sequence name, PDB and UniProt
1648 <!-- JAL-1976 -->No progress bar shown during export of
1652 <!-- JAL-2213 -->Structures not always superimposed after
1653 multiple structures are shown for one or more sequences.
1656 <!-- JAL-1370 -->Reference sequence characters should not
1657 be replaced with '.' when 'Show unconserved' format option
1661 <!-- JAL-1823 -->Cannot specify chain code when entering
1662 specific PDB id for sequence
1665 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1666 'Export hidden sequences' is enabled, but 'export hidden
1667 columns' is disabled.
1670 <!--JAL-2026-->Best Quality option in structure chooser
1671 selects lowest rather than highest resolution structures
1675 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1676 to sequence mapping in 'View Mappings' report
1679 <!-- JAL-2284 -->Unable to read old Jalview projects that
1680 contain non-XML data added after Jalvew wrote project.
1683 <!-- JAL-2118 -->Newly created annotation row reorders
1684 after clicking on it to create new annotation for a
1688 <!-- JAL-1980 -->Null Pointer Exception raised when
1689 pressing Add on an orphaned cut'n'paste window.
1691 <!-- may exclude, this is an external service stability issue JAL-1941
1692 -- > RNA 3D structure not added via DSSR service</li> -->
1697 <!-- JAL-2151 -->Incorrect columns are selected when
1698 hidden columns present before start of sequence
1701 <!-- JAL-1986 -->Missing dependencies on applet pages
1705 <!-- JAL-1947 -->Overview pixel size changes when
1706 sequences are hidden in applet
1709 <!-- JAL-1996 -->Updated instructions for applet
1710 deployment on examples pages.
1717 <td width="60" nowrap>
1718 <div align="center">
1719 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1720 <em>16/10/2015</em></strong>
1723 <td><em>General</em>
1725 <li>Time stamps for signed Jalview application and applet
1730 <em>Application</em>
1732 <li>Duplicate group consensus and conservation rows
1733 shown when tree is partitioned</li>
1734 <li>Erratic behaviour when tree partitions made with
1735 multiple cDNA/Protein split views</li>
1741 <td width="60" nowrap>
1742 <div align="center">
1743 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1744 <em>8/10/2015</em></strong>
1747 <td><em>General</em>
1749 <li>Updated Spanish translations of localized text for
1751 </ul> <em>Application</em>
1753 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1754 <li>Signed OSX InstallAnywhere installer<br></li>
1755 <li>Support for per-sequence based annotations in BioJSON</li>
1756 </ul> <em>Applet</em>
1758 <li>Split frame example added to applet examples page</li>
1759 </ul> <em>Build and Deployment</em>
1762 <!-- JAL-1888 -->New ant target for running Jalview's test
1770 <li>Mapping of cDNA to protein in split frames
1771 incorrect when sequence start > 1</li>
1772 <li>Broken images in filter column by annotation dialog
1774 <li>Feature colours not parsed from features file</li>
1775 <li>Exceptions and incomplete link URLs recovered when
1776 loading a features file containing HTML tags in feature
1780 <em>Application</em>
1782 <li>Annotations corrupted after BioJS export and
1784 <li>Incorrect sequence limits after Fetch DB References
1785 with 'trim retrieved sequences'</li>
1786 <li>Incorrect warning about deleting all data when
1787 deleting selected columns</li>
1788 <li>Patch to build system for shipping properly signed
1789 JNLP templates for webstart launch</li>
1790 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1791 unreleased structures for download or viewing</li>
1792 <li>Tab/space/return keystroke operation of EMBL-PDBe
1793 fetcher/viewer dialogs works correctly</li>
1794 <li>Disabled 'minimise' button on Jalview windows
1795 running on OSX to workaround redraw hang bug</li>
1796 <li>Split cDNA/Protein view position and geometry not
1797 recovered from jalview project</li>
1798 <li>Initial enabled/disabled state of annotation menu
1799 sorter 'show autocalculated first/last' corresponds to
1801 <li>Restoring of Clustal, RNA Helices and T-Coffee
1802 color schemes from BioJSON</li>
1806 <li>Reorder sequences mirrored in cDNA/Protein split
1808 <li>Applet with Jmol examples not loading correctly</li>
1814 <td><div align="center">
1815 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1817 <td><em>General</em>
1819 <li>Linked visualisation and analysis of DNA and Protein
1822 <li>Translated cDNA alignments shown as split protein
1823 and DNA alignment views</li>
1824 <li>Codon consensus annotation for linked protein and
1825 cDNA alignment views</li>
1826 <li>Link cDNA or Protein product sequences by loading
1827 them onto Protein or cDNA alignments</li>
1828 <li>Reconstruct linked cDNA alignment from aligned
1829 protein sequences</li>
1832 <li>Jmol integration updated to Jmol v14.2.14</li>
1833 <li>Import and export of Jalview alignment views as <a
1834 href="features/bioJsonFormat.html">BioJSON</a></li>
1835 <li>New alignment annotation file statements for
1836 reference sequences and marking hidden columns</li>
1837 <li>Reference sequence based alignment shading to
1838 highlight variation</li>
1839 <li>Select or hide columns according to alignment
1841 <li>Find option for locating sequences by description</li>
1842 <li>Conserved physicochemical properties shown in amino
1843 acid conservation row</li>
1844 <li>Alignments can be sorted by number of RNA helices</li>
1845 </ul> <em>Application</em>
1847 <li>New cDNA/Protein analysis capabilities
1849 <li>Get Cross-References should open a Split Frame
1850 view with cDNA/Protein</li>
1851 <li>Detect when nucleotide sequences and protein
1852 sequences are placed in the same alignment</li>
1853 <li>Split cDNA/Protein views are saved in Jalview
1858 <li>Use REST API to talk to Chimera</li>
1859 <li>Selected regions in Chimera are highlighted in linked
1860 Jalview windows</li>
1862 <li>VARNA RNA viewer updated to v3.93</li>
1863 <li>VARNA views are saved in Jalview Projects</li>
1864 <li>Pseudoknots displayed as Jalview RNA annotation can
1865 be shown in VARNA</li>
1867 <li>Make groups for selection uses marked columns as well
1868 as the active selected region</li>
1870 <li>Calculate UPGMA and NJ trees using sequence feature
1872 <li>New Export options
1874 <li>New Export Settings dialog to control hidden
1875 region export in flat file generation</li>
1877 <li>Export alignment views for display with the <a
1878 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1880 <li>Export scrollable SVG in HTML page</li>
1881 <li>Optional embedding of BioJSON data when exporting
1882 alignment figures to HTML</li>
1884 <li>3D structure retrieval and display
1886 <li>Free text and structured queries with the PDBe
1888 <li>PDBe Search API based discovery and selection of
1889 PDB structures for a sequence set</li>
1893 <li>JPred4 employed for protein secondary structure
1895 <li>Hide Insertions menu option to hide unaligned columns
1896 for one or a group of sequences</li>
1897 <li>Automatically hide insertions in alignments imported
1898 from the JPred4 web server</li>
1899 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1900 system on OSX<br />LGPL libraries courtesy of <a
1901 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1903 <li>changed 'View nucleotide structure' submenu to 'View
1904 VARNA 2D Structure'</li>
1905 <li>change "View protein structure" menu option to "3D
1908 </ul> <em>Applet</em>
1910 <li>New layout for applet example pages</li>
1911 <li>New parameters to enable SplitFrame view
1912 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1913 <li>New example demonstrating linked viewing of cDNA and
1914 Protein alignments</li>
1915 </ul> <em>Development and deployment</em>
1917 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1918 <li>Include installation type and git revision in build
1919 properties and console log output</li>
1920 <li>Jalview Github organisation, and new github site for
1921 storing BioJsMSA Templates</li>
1922 <li>Jalview's unit tests now managed with TestNG</li>
1925 <!-- <em>General</em>
1927 </ul> --> <!-- issues resolved --> <em>Application</em>
1929 <li>Escape should close any open find dialogs</li>
1930 <li>Typo in select-by-features status report</li>
1931 <li>Consensus RNA secondary secondary structure
1932 predictions are not highlighted in amber</li>
1933 <li>Missing gap character in v2.7 example file means
1934 alignment appears unaligned when pad-gaps is not enabled</li>
1935 <li>First switch to RNA Helices colouring doesn't colour
1936 associated structure views</li>
1937 <li>ID width preference option is greyed out when auto
1938 width checkbox not enabled</li>
1939 <li>Stopped a warning dialog from being shown when
1940 creating user defined colours</li>
1941 <li>'View Mapping' in structure viewer shows sequence
1942 mappings for just that viewer's sequences</li>
1943 <li>Workaround for superposing PDB files containing
1944 multiple models in Chimera</li>
1945 <li>Report sequence position in status bar when hovering
1946 over Jmol structure</li>
1947 <li>Cannot output gaps as '.' symbols with Selection ->
1948 output to text box</li>
1949 <li>Flat file exports of alignments with hidden columns
1950 have incorrect sequence start/end</li>
1951 <li>'Aligning' a second chain to a Chimera structure from
1953 <li>Colour schemes applied to structure viewers don't
1954 work for nucleotide</li>
1955 <li>Loading/cut'n'pasting an empty or invalid file leads
1956 to a grey/invisible alignment window</li>
1957 <li>Exported Jpred annotation from a sequence region
1958 imports to different position</li>
1959 <li>Space at beginning of sequence feature tooltips shown
1960 on some platforms</li>
1961 <li>Chimera viewer 'View | Show Chain' menu is not
1963 <li>'New View' fails with a Null Pointer Exception in
1964 console if Chimera has been opened</li>
1965 <li>Mouseover to Chimera not working</li>
1966 <li>Miscellaneous ENA XML feature qualifiers not
1968 <li>NPE in annotation renderer after 'Extract Scores'</li>
1969 <li>If two structures in one Chimera window, mouseover of
1970 either sequence shows on first structure</li>
1971 <li>'Show annotations' options should not make
1972 non-positional annotations visible</li>
1973 <li>Subsequence secondary structure annotation not shown
1974 in right place after 'view flanking regions'</li>
1975 <li>File Save As type unset when current file format is
1977 <li>Save as '.jar' option removed for saving Jalview
1979 <li>Colour by Sequence colouring in Chimera more
1981 <li>Cannot 'add reference annotation' for a sequence in
1982 several views on same alignment</li>
1983 <li>Cannot show linked products for EMBL / ENA records</li>
1984 <li>Jalview's tooltip wraps long texts containing no
1986 </ul> <em>Applet</em>
1988 <li>Jmol to JalviewLite mouseover/link not working</li>
1989 <li>JalviewLite can't import sequences with ID
1990 descriptions containing angle brackets</li>
1991 </ul> <em>General</em>
1993 <li>Cannot export and reimport RNA secondary structure
1994 via jalview annotation file</li>
1995 <li>Random helix colour palette for colour by annotation
1996 with RNA secondary structure</li>
1997 <li>Mouseover to cDNA from STOP residue in protein
1998 translation doesn't work.</li>
1999 <li>hints when using the select by annotation dialog box</li>
2000 <li>Jmol alignment incorrect if PDB file has alternate CA
2002 <li>FontChooser message dialog appears to hang after
2003 choosing 1pt font</li>
2004 <li>Peptide secondary structure incorrectly imported from
2005 annotation file when annotation display text includes 'e' or
2007 <li>Cannot set colour of new feature type whilst creating
2009 <li>cDNA translation alignment should not be sequence
2010 order dependent</li>
2011 <li>'Show unconserved' doesn't work for lower case
2013 <li>Nucleotide ambiguity codes involving R not recognised</li>
2014 </ul> <em>Deployment and Documentation</em>
2016 <li>Applet example pages appear different to the rest of
2017 www.jalview.org</li>
2018 </ul> <em>Application Known issues</em>
2020 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2021 <li>Misleading message appears after trying to delete
2023 <li>Jalview icon not shown in dock after InstallAnywhere
2024 version launches</li>
2025 <li>Fetching EMBL reference for an RNA sequence results
2026 fails with a sequence mismatch</li>
2027 <li>Corrupted or unreadable alignment display when
2028 scrolling alignment to right</li>
2029 <li>ArrayIndexOutOfBoundsException thrown when remove
2030 empty columns called on alignment with ragged gapped ends</li>
2031 <li>auto calculated alignment annotation rows do not get
2032 placed above or below non-autocalculated rows</li>
2033 <li>Jalview dekstop becomes sluggish at full screen in
2034 ultra-high resolution</li>
2035 <li>Cannot disable consensus calculation independently of
2036 quality and conservation</li>
2037 <li>Mouseover highlighting between cDNA and protein can
2038 become sluggish with more than one splitframe shown</li>
2039 </ul> <em>Applet Known Issues</em>
2041 <li>Core PDB parsing code requires Jmol</li>
2042 <li>Sequence canvas panel goes white when alignment
2043 window is being resized</li>
2049 <td><div align="center">
2050 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2052 <td><em>General</em>
2054 <li>Updated Java code signing certificate donated by
2056 <li>Features and annotation preserved when performing
2057 pairwise alignment</li>
2058 <li>RNA pseudoknot annotation can be
2059 imported/exported/displayed</li>
2060 <li>'colour by annotation' can colour by RNA and
2061 protein secondary structure</li>
2062 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2063 post-hoc with 2.9 release</em>)
2066 </ul> <em>Application</em>
2068 <li>Extract and display secondary structure for sequences
2069 with 3D structures</li>
2070 <li>Support for parsing RNAML</li>
2071 <li>Annotations menu for layout
2073 <li>sort sequence annotation rows by alignment</li>
2074 <li>place sequence annotation above/below alignment
2077 <li>Output in Stockholm format</li>
2078 <li>Internationalisation: improved Spanish (es)
2080 <li>Structure viewer preferences tab</li>
2081 <li>Disorder and Secondary Structure annotation tracks
2082 shared between alignments</li>
2083 <li>UCSF Chimera launch and linked highlighting from
2085 <li>Show/hide all sequence associated annotation rows for
2086 all or current selection</li>
2087 <li>disorder and secondary structure predictions
2088 available as dataset annotation</li>
2089 <li>Per-sequence rna helices colouring</li>
2092 <li>Sequence database accessions imported when fetching
2093 alignments from Rfam</li>
2094 <li>update VARNA version to 3.91</li>
2096 <li>New groovy scripts for exporting aligned positions,
2097 conservation values, and calculating sum of pairs scores.</li>
2098 <li>Command line argument to set default JABAWS server</li>
2099 <li>include installation type in build properties and
2100 console log output</li>
2101 <li>Updated Jalview project format to preserve dataset
2105 <!-- issues resolved --> <em>Application</em>
2107 <li>Distinguish alignment and sequence associated RNA
2108 structure in structure->view->VARNA</li>
2109 <li>Raise dialog box if user deletes all sequences in an
2111 <li>Pressing F1 results in documentation opening twice</li>
2112 <li>Sequence feature tooltip is wrapped</li>
2113 <li>Double click on sequence associated annotation
2114 selects only first column</li>
2115 <li>Redundancy removal doesn't result in unlinked
2116 leaves shown in tree</li>
2117 <li>Undos after several redundancy removals don't undo
2119 <li>Hide sequence doesn't hide associated annotation</li>
2120 <li>User defined colours dialog box too big to fit on
2121 screen and buttons not visible</li>
2122 <li>author list isn't updated if already written to
2123 Jalview properties</li>
2124 <li>Popup menu won't open after retrieving sequence
2126 <li>File open window for associate PDB doesn't open</li>
2127 <li>Left-then-right click on a sequence id opens a
2128 browser search window</li>
2129 <li>Cannot open sequence feature shading/sort popup menu
2130 in feature settings dialog</li>
2131 <li>better tooltip placement for some areas of Jalview
2133 <li>Allow addition of JABAWS Server which doesn't
2134 pass validation</li>
2135 <li>Web services parameters dialog box is too large to
2137 <li>Muscle nucleotide alignment preset obscured by
2139 <li>JABAWS preset submenus don't contain newly
2140 defined user preset</li>
2141 <li>MSA web services warns user if they were launched
2142 with invalid input</li>
2143 <li>Jalview cannot contact DAS Registy when running on
2146 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2147 'Superpose with' submenu not shown when new view
2151 </ul> <!-- <em>Applet</em>
2153 </ul> <em>General</em>
2155 </ul>--> <em>Deployment and Documentation</em>
2157 <li>2G and 1G options in launchApp have no effect on
2158 memory allocation</li>
2159 <li>launchApp service doesn't automatically open
2160 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2162 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2163 InstallAnywhere reports cannot find valid JVM when Java
2164 1.7_055 is available
2166 </ul> <em>Application Known issues</em>
2169 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2170 corrupted or unreadable alignment display when scrolling
2174 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2175 retrieval fails but progress bar continues for DAS retrieval
2176 with large number of ID
2179 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2180 flatfile output of visible region has incorrect sequence
2184 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2185 rna structure consensus doesn't update when secondary
2186 structure tracks are rearranged
2189 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2190 invalid rna structure positional highlighting does not
2191 highlight position of invalid base pairs
2194 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2195 out of memory errors are not raised when saving Jalview
2196 project from alignment window file menu
2199 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2200 Switching to RNA Helices colouring doesn't propagate to
2204 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2205 colour by RNA Helices not enabled when user created
2206 annotation added to alignment
2209 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2210 Jalview icon not shown on dock in Mountain Lion/Webstart
2212 </ul> <em>Applet Known Issues</em>
2215 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2216 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2219 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2220 Jalview and Jmol example not compatible with IE9
2223 <li>Sort by annotation score doesn't reverse order
2229 <td><div align="center">
2230 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2233 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2236 <li>Internationalisation of user interface (usually
2237 called i18n support) and translation for Spanish locale</li>
2238 <li>Define/Undefine group on current selection with
2239 Ctrl-G/Shift Ctrl-G</li>
2240 <li>Improved group creation/removal options in
2241 alignment/sequence Popup menu</li>
2242 <li>Sensible precision for symbol distribution
2243 percentages shown in logo tooltip.</li>
2244 <li>Annotation panel height set according to amount of
2245 annotation when alignment first opened</li>
2246 </ul> <em>Application</em>
2248 <li>Interactive consensus RNA secondary structure
2249 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2250 <li>Select columns containing particular features from
2251 Feature Settings dialog</li>
2252 <li>View all 'representative' PDB structures for selected
2254 <li>Update Jalview project format:
2256 <li>New file extension for Jalview projects '.jvp'</li>
2257 <li>Preserve sequence and annotation dataset (to
2258 store secondary structure annotation,etc)</li>
2259 <li>Per group and alignment annotation and RNA helix
2263 <li>New similarity measures for PCA and Tree calculation
2265 <li>Experimental support for retrieval and viewing of
2266 flanking regions for an alignment</li>
2270 <!-- issues resolved --> <em>Application</em>
2272 <li>logo keeps spinning and status remains at queued or
2273 running after job is cancelled</li>
2274 <li>cannot export features from alignments imported from
2275 Jalview/VAMSAS projects</li>
2276 <li>Buggy slider for web service parameters that take
2278 <li>Newly created RNA secondary structure line doesn't
2279 have 'display all symbols' flag set</li>
2280 <li>T-COFFEE alignment score shading scheme and other
2281 annotation shading not saved in Jalview project</li>
2282 <li>Local file cannot be loaded in freshly downloaded
2284 <li>Jalview icon not shown on dock in Mountain
2286 <li>Load file from desktop file browser fails</li>
2287 <li>Occasional NPE thrown when calculating large trees</li>
2288 <li>Cannot reorder or slide sequences after dragging an
2289 alignment onto desktop</li>
2290 <li>Colour by annotation dialog throws NPE after using
2291 'extract scores' function</li>
2292 <li>Loading/cut'n'pasting an empty file leads to a grey
2293 alignment window</li>
2294 <li>Disorder thresholds rendered incorrectly after
2295 performing IUPred disorder prediction</li>
2296 <li>Multiple group annotated consensus rows shown when
2297 changing 'normalise logo' display setting</li>
2298 <li>Find shows blank dialog after 'finished searching' if
2299 nothing matches query</li>
2300 <li>Null Pointer Exceptions raised when sorting by
2301 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2303 <li>Errors in Jmol console when structures in alignment
2304 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2306 <li>Not all working JABAWS services are shown in
2308 <li>JAVAWS version of Jalview fails to launch with
2309 'invalid literal/length code'</li>
2310 <li>Annotation/RNA Helix colourschemes cannot be applied
2311 to alignment with groups (actually fixed in 2.8.0b1)</li>
2312 <li>RNA Helices and T-Coffee Scores available as default
2315 </ul> <em>Applet</em>
2317 <li>Remove group option is shown even when selection is
2319 <li>Apply to all groups ticked but colourscheme changes
2320 don't affect groups</li>
2321 <li>Documented RNA Helices and T-Coffee Scores as valid
2322 colourscheme name</li>
2323 <li>Annotation labels drawn on sequence IDs when
2324 Annotation panel is not displayed</li>
2325 <li>Increased font size for dropdown menus on OSX and
2326 embedded windows</li>
2327 </ul> <em>Other</em>
2329 <li>Consensus sequence for alignments/groups with a
2330 single sequence were not calculated</li>
2331 <li>annotation files that contain only groups imported as
2332 annotation and junk sequences</li>
2333 <li>Fasta files with sequences containing '*' incorrectly
2334 recognised as PFAM or BLC</li>
2335 <li>conservation/PID slider apply all groups option
2336 doesn't affect background (2.8.0b1)
2338 <li>redundancy highlighting is erratic at 0% and 100%</li>
2339 <li>Remove gapped columns fails for sequences with ragged
2341 <li>AMSA annotation row with leading spaces is not
2342 registered correctly on import</li>
2343 <li>Jalview crashes when selecting PCA analysis for
2344 certain alignments</li>
2345 <li>Opening the colour by annotation dialog for an
2346 existing annotation based 'use original colours'
2347 colourscheme loses original colours setting</li>
2352 <td><div align="center">
2353 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2354 <em>30/1/2014</em></strong>
2358 <li>Trusted certificates for JalviewLite applet and
2359 Jalview Desktop application<br />Certificate was donated by
2360 <a href="https://www.certum.eu">Certum</a> to the Jalview
2361 open source project).
2363 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2364 <li>Output in Stockholm format</li>
2365 <li>Allow import of data from gzipped files</li>
2366 <li>Export/import group and sequence associated line
2367 graph thresholds</li>
2368 <li>Nucleotide substitution matrix that supports RNA and
2369 ambiguity codes</li>
2370 <li>Allow disorder predictions to be made on the current
2371 selection (or visible selection) in the same way that JPred
2373 <li>Groovy scripting for headless Jalview operation</li>
2374 </ul> <em>Other improvements</em>
2376 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2377 <li>COMBINE statement uses current SEQUENCE_REF and
2378 GROUP_REF scope to group annotation rows</li>
2379 <li>Support '' style escaping of quotes in Newick
2381 <li>Group options for JABAWS service by command line name</li>
2382 <li>Empty tooltip shown for JABA service options with a
2383 link but no description</li>
2384 <li>Select primary source when selecting authority in
2385 database fetcher GUI</li>
2386 <li>Add .mfa to FASTA file extensions recognised by
2388 <li>Annotation label tooltip text wrap</li>
2393 <li>Slow scrolling when lots of annotation rows are
2395 <li>Lots of NPE (and slowness) after creating RNA
2396 secondary structure annotation line</li>
2397 <li>Sequence database accessions not imported when
2398 fetching alignments from Rfam</li>
2399 <li>Incorrect SHMR submission for sequences with
2401 <li>View all structures does not always superpose
2403 <li>Option widgets in service parameters not updated to
2404 reflect user or preset settings</li>
2405 <li>Null pointer exceptions for some services without
2406 presets or adjustable parameters</li>
2407 <li>Discover PDB IDs entry in structure menu doesn't
2408 discover PDB xRefs</li>
2409 <li>Exception encountered while trying to retrieve
2410 features with DAS</li>
2411 <li>Lowest value in annotation row isn't coloured
2412 when colour by annotation (per sequence) is coloured</li>
2413 <li>Keyboard mode P jumps to start of gapped region when
2414 residue follows a gap</li>
2415 <li>Jalview appears to hang importing an alignment with
2416 Wrap as default or after enabling Wrap</li>
2417 <li>'Right click to add annotations' message
2418 shown in wrap mode when no annotations present</li>
2419 <li>Disorder predictions fail with NPE if no automatic
2420 annotation already exists on alignment</li>
2421 <li>oninit javascript function should be called after
2422 initialisation completes</li>
2423 <li>Remove redundancy after disorder prediction corrupts
2424 alignment window display</li>
2425 <li>Example annotation file in documentation is invalid</li>
2426 <li>Grouped line graph annotation rows are not exported
2427 to annotation file</li>
2428 <li>Multi-harmony analysis cannot be run when only two
2430 <li>Cannot create multiple groups of line graphs with
2431 several 'combine' statements in annotation file</li>
2432 <li>Pressing return several times causes Number Format
2433 exceptions in keyboard mode</li>
2434 <li>Multi-harmony (SHMMR) method doesn't submit
2435 correct partitions for input data</li>
2436 <li>Translation from DNA to Amino Acids fails</li>
2437 <li>Jalview fail to load newick tree with quoted label</li>
2438 <li>--headless flag isn't understood</li>
2439 <li>ClassCastException when generating EPS in headless
2441 <li>Adjusting sequence-associated shading threshold only
2442 changes one row's threshold</li>
2443 <li>Preferences and Feature settings panel panel
2444 doesn't open</li>
2445 <li>hide consensus histogram also hides conservation and
2446 quality histograms</li>
2451 <td><div align="center">
2452 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2454 <td><em>Application</em>
2456 <li>Support for JABAWS 2.0 Services (AACon alignment
2457 conservation, protein disorder and Clustal Omega)</li>
2458 <li>JABAWS server status indicator in Web Services
2460 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2461 in Jalview alignment window</li>
2462 <li>Updated Jalview build and deploy framework for OSX
2463 mountain lion, windows 7, and 8</li>
2464 <li>Nucleotide substitution matrix for PCA that supports
2465 RNA and ambiguity codes</li>
2467 <li>Improved sequence database retrieval GUI</li>
2468 <li>Support fetching and database reference look up
2469 against multiple DAS sources (Fetch all from in 'fetch db
2471 <li>Jalview project improvements
2473 <li>Store and retrieve the 'belowAlignment'
2474 flag for annotation</li>
2475 <li>calcId attribute to group annotation rows on the
2477 <li>Store AACon calculation settings for a view in
2478 Jalview project</li>
2482 <li>horizontal scrolling gesture support</li>
2483 <li>Visual progress indicator when PCA calculation is
2485 <li>Simpler JABA web services menus</li>
2486 <li>visual indication that web service results are still
2487 being retrieved from server</li>
2488 <li>Serialise the dialogs that are shown when Jalview
2489 starts up for first time</li>
2490 <li>Jalview user agent string for interacting with HTTP
2492 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2494 <li>Examples directory and Groovy library included in
2495 InstallAnywhere distribution</li>
2496 </ul> <em>Applet</em>
2498 <li>RNA alignment and secondary structure annotation
2499 visualization applet example</li>
2500 </ul> <em>General</em>
2502 <li>Normalise option for consensus sequence logo</li>
2503 <li>Reset button in PCA window to return dimensions to
2505 <li>Allow seqspace or Jalview variant of alignment PCA
2507 <li>PCA with either nucleic acid and protein substitution
2509 <li>Allow windows containing HTML reports to be exported
2511 <li>Interactive display and editing of RNA secondary
2512 structure contacts</li>
2513 <li>RNA Helix Alignment Colouring</li>
2514 <li>RNA base pair logo consensus</li>
2515 <li>Parse sequence associated secondary structure
2516 information in Stockholm files</li>
2517 <li>HTML Export database accessions and annotation
2518 information presented in tooltip for sequences</li>
2519 <li>Import secondary structure from LOCARNA clustalw
2520 style RNA alignment files</li>
2521 <li>import and visualise T-COFFEE quality scores for an
2523 <li>'colour by annotation' per sequence option to
2524 shade each sequence according to its associated alignment
2526 <li>New Jalview Logo</li>
2527 </ul> <em>Documentation and Development</em>
2529 <li>documentation for score matrices used in Jalview</li>
2530 <li>New Website!</li>
2532 <td><em>Application</em>
2534 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2535 wsdbfetch REST service</li>
2536 <li>Stop windows being moved outside desktop on OSX</li>
2537 <li>Filetype associations not installed for webstart
2539 <li>Jalview does not always retrieve progress of a JABAWS
2540 job execution in full once it is complete</li>
2541 <li>revise SHMR RSBS definition to ensure alignment is
2542 uploaded via ali_file parameter</li>
2543 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2544 <li>View all structures superposed fails with exception</li>
2545 <li>Jnet job queues forever if a very short sequence is
2546 submitted for prediction</li>
2547 <li>Cut and paste menu not opened when mouse clicked on
2549 <li>Putting fractional value into integer text box in
2550 alignment parameter dialog causes Jalview to hang</li>
2551 <li>Structure view highlighting doesn't work on
2553 <li>View all structures fails with exception shown in
2555 <li>Characters in filename associated with PDBEntry not
2556 escaped in a platform independent way</li>
2557 <li>Jalview desktop fails to launch with exception when
2559 <li>Tree calculation reports 'you must have 2 or more
2560 sequences selected' when selection is empty</li>
2561 <li>Jalview desktop fails to launch with jar signature
2562 failure when java web start temporary file caching is
2564 <li>DAS Sequence retrieval with range qualification
2565 results in sequence xref which includes range qualification</li>
2566 <li>Errors during processing of command line arguments
2567 cause progress bar (JAL-898) to be removed</li>
2568 <li>Replace comma for semi-colon option not disabled for
2569 DAS sources in sequence fetcher</li>
2570 <li>Cannot close news reader when JABAWS server warning
2571 dialog is shown</li>
2572 <li>Option widgets not updated to reflect user settings</li>
2573 <li>Edited sequence not submitted to web service</li>
2574 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2575 <li>InstallAnywhere installer doesn't unpack and run
2576 on OSX Mountain Lion</li>
2577 <li>Annotation panel not given a scroll bar when
2578 sequences with alignment annotation are pasted into the
2580 <li>Sequence associated annotation rows not associated
2581 when loaded from Jalview project</li>
2582 <li>Browser launch fails with NPE on java 1.7</li>
2583 <li>JABAWS alignment marked as finished when job was
2584 cancelled or job failed due to invalid input</li>
2585 <li>NPE with v2.7 example when clicking on Tree
2586 associated with all views</li>
2587 <li>Exceptions when copy/paste sequences with grouped
2588 annotation rows to new window</li>
2589 </ul> <em>Applet</em>
2591 <li>Sequence features are momentarily displayed before
2592 they are hidden using hidefeaturegroups applet parameter</li>
2593 <li>loading features via javascript API automatically
2594 enables feature display</li>
2595 <li>scrollToColumnIn javascript API method doesn't
2597 </ul> <em>General</em>
2599 <li>Redundancy removal fails for rna alignment</li>
2600 <li>PCA calculation fails when sequence has been selected
2601 and then deselected</li>
2602 <li>PCA window shows grey box when first opened on OSX</li>
2603 <li>Letters coloured pink in sequence logo when alignment
2604 coloured with clustalx</li>
2605 <li>Choosing fonts without letter symbols defined causes
2606 exceptions and redraw errors</li>
2607 <li>Initial PCA plot view is not same as manually
2608 reconfigured view</li>
2609 <li>Grouped annotation graph label has incorrect line
2611 <li>Grouped annotation graph label display is corrupted
2612 for lots of labels</li>
2617 <div align="center">
2618 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2621 <td><em>Application</em>
2623 <li>Jalview Desktop News Reader</li>
2624 <li>Tweaked default layout of web services menu</li>
2625 <li>View/alignment association menu to enable user to
2626 easily specify which alignment a multi-structure view takes
2627 its colours/correspondences from</li>
2628 <li>Allow properties file location to be specified as URL</li>
2629 <li>Extend Jalview project to preserve associations
2630 between many alignment views and a single Jmol display</li>
2631 <li>Store annotation row height in Jalview project file</li>
2632 <li>Annotation row column label formatting attributes
2633 stored in project file</li>
2634 <li>Annotation row order for auto-calculated annotation
2635 rows preserved in Jalview project file</li>
2636 <li>Visual progress indication when Jalview state is
2637 saved using Desktop window menu</li>
2638 <li>Visual indication that command line arguments are
2639 still being processed</li>
2640 <li>Groovy script execution from URL</li>
2641 <li>Colour by annotation default min and max colours in
2643 <li>Automatically associate PDB files dragged onto an
2644 alignment with sequences that have high similarity and
2646 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2647 <li>'view structures' option to open many
2648 structures in same window</li>
2649 <li>Sort associated views menu option for tree panel</li>
2650 <li>Group all JABA and non-JABA services for a particular
2651 analysis function in its own submenu</li>
2652 </ul> <em>Applet</em>
2654 <li>Userdefined and autogenerated annotation rows for
2656 <li>Adjustment of alignment annotation pane height</li>
2657 <li>Annotation scrollbar for annotation panel</li>
2658 <li>Drag to reorder annotation rows in annotation panel</li>
2659 <li>'automaticScrolling' parameter</li>
2660 <li>Allow sequences with partial ID string matches to be
2661 annotated from GFF/Jalview features files</li>
2662 <li>Sequence logo annotation row in applet</li>
2663 <li>Absolute paths relative to host server in applet
2664 parameters are treated as such</li>
2665 <li>New in the JalviewLite javascript API:
2667 <li>JalviewLite.js javascript library</li>
2668 <li>Javascript callbacks for
2670 <li>Applet initialisation</li>
2671 <li>Sequence/alignment mouse-overs and selections</li>
2674 <li>scrollTo row and column alignment scrolling
2676 <li>Select sequence/alignment regions from javascript</li>
2677 <li>javascript structure viewer harness to pass
2678 messages between Jmol and Jalview when running as
2679 distinct applets</li>
2680 <li>sortBy method</li>
2681 <li>Set of applet and application examples shipped
2682 with documentation</li>
2683 <li>New example to demonstrate JalviewLite and Jmol
2684 javascript message exchange</li>
2686 </ul> <em>General</em>
2688 <li>Enable Jmol displays to be associated with multiple
2689 multiple alignments</li>
2690 <li>Option to automatically sort alignment with new tree</li>
2691 <li>User configurable link to enable redirects to a
2692 www.Jalview.org mirror</li>
2693 <li>Jmol colours option for Jmol displays</li>
2694 <li>Configurable newline string when writing alignment
2695 and other flat files</li>
2696 <li>Allow alignment annotation description lines to
2697 contain html tags</li>
2698 </ul> <em>Documentation and Development</em>
2700 <li>Add groovy test harness for bulk load testing to
2702 <li>Groovy script to load and align a set of sequences
2703 using a web service before displaying the result in the
2704 Jalview desktop</li>
2705 <li>Restructured javascript and applet api documentation</li>
2706 <li>Ant target to publish example html files with applet
2708 <li>Netbeans project for building Jalview from source</li>
2709 <li>ant task to create online javadoc for Jalview source</li>
2711 <td><em>Application</em>
2713 <li>User defined colourscheme throws exception when
2714 current built in colourscheme is saved as new scheme</li>
2715 <li>AlignFrame->Save in application pops up save
2716 dialog for valid filename/format</li>
2717 <li>Cannot view associated structure for UniProt sequence</li>
2718 <li>PDB file association breaks for UniProt sequence
2720 <li>Associate PDB from file dialog does not tell you
2721 which sequence is to be associated with the file</li>
2722 <li>Find All raises null pointer exception when query
2723 only matches sequence IDs</li>
2724 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2725 <li>Jalview project with Jmol views created with Jalview
2726 2.4 cannot be loaded</li>
2727 <li>Filetype associations not installed for webstart
2729 <li>Two or more chains in a single PDB file associated
2730 with sequences in different alignments do not get coloured
2731 by their associated sequence</li>
2732 <li>Visibility status of autocalculated annotation row
2733 not preserved when project is loaded</li>
2734 <li>Annotation row height and visibility attributes not
2735 stored in Jalview project</li>
2736 <li>Tree bootstraps are not preserved when saved as a
2737 Jalview project</li>
2738 <li>Envision2 workflow tooltips are corrupted</li>
2739 <li>Enabling show group conservation also enables colour
2740 by conservation</li>
2741 <li>Duplicate group associated conservation or consensus
2742 created on new view</li>
2743 <li>Annotation scrollbar not displayed after 'show
2744 all hidden annotation rows' option selected</li>
2745 <li>Alignment quality not updated after alignment
2746 annotation row is hidden then shown</li>
2747 <li>Preserve colouring of structures coloured by
2748 sequences in pre Jalview 2.7 projects</li>
2749 <li>Web service job parameter dialog is not laid out
2751 <li>Web services menu not refreshed after 'reset
2752 services' button is pressed in preferences</li>
2753 <li>Annotation off by one in Jalview v2_3 example project</li>
2754 <li>Structures imported from file and saved in project
2755 get name like jalview_pdb1234.txt when reloaded</li>
2756 <li>Jalview does not always retrieve progress of a JABAWS
2757 job execution in full once it is complete</li>
2758 </ul> <em>Applet</em>
2760 <li>Alignment height set incorrectly when lots of
2761 annotation rows are displayed</li>
2762 <li>Relative URLs in feature HTML text not resolved to
2764 <li>View follows highlighting does not work for positions
2766 <li><= shown as = in tooltip</li>
2767 <li>Export features raises exception when no features
2769 <li>Separator string used for serialising lists of IDs
2770 for javascript api is modified when separator string
2771 provided as parameter</li>
2772 <li>Null pointer exception when selecting tree leaves for
2773 alignment with no existing selection</li>
2774 <li>Relative URLs for datasources assumed to be relative
2775 to applet's codebase</li>
2776 <li>Status bar not updated after finished searching and
2777 search wraps around to first result</li>
2778 <li>StructureSelectionManager instance shared between
2779 several Jalview applets causes race conditions and memory
2781 <li>Hover tooltip and mouseover of position on structure
2782 not sent from Jmol in applet</li>
2783 <li>Certain sequences of javascript method calls to
2784 applet API fatally hang browser</li>
2785 </ul> <em>General</em>
2787 <li>View follows structure mouseover scrolls beyond
2788 position with wrapped view and hidden regions</li>
2789 <li>Find sequence position moves to wrong residue
2790 with/without hidden columns</li>
2791 <li>Sequence length given in alignment properties window
2793 <li>InvalidNumberFormat exceptions thrown when trying to
2794 import PDB like structure files</li>
2795 <li>Positional search results are only highlighted
2796 between user-supplied sequence start/end bounds</li>
2797 <li>End attribute of sequence is not validated</li>
2798 <li>Find dialog only finds first sequence containing a
2799 given sequence position</li>
2800 <li>Sequence numbering not preserved in MSF alignment
2802 <li>Jalview PDB file reader does not extract sequence
2803 from nucleotide chains correctly</li>
2804 <li>Structure colours not updated when tree partition
2805 changed in alignment</li>
2806 <li>Sequence associated secondary structure not correctly
2807 parsed in interleaved stockholm</li>
2808 <li>Colour by annotation dialog does not restore current
2810 <li>Hiding (nearly) all sequences doesn't work
2812 <li>Sequences containing lowercase letters are not
2813 properly associated with their pdb files</li>
2814 </ul> <em>Documentation and Development</em>
2816 <li>schemas/JalviewWsParamSet.xsd corrupted by
2817 ApplyCopyright tool</li>
2822 <div align="center">
2823 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2826 <td><em>Application</em>
2828 <li>New warning dialog when the Jalview Desktop cannot
2829 contact web services</li>
2830 <li>JABA service parameters for a preset are shown in
2831 service job window</li>
2832 <li>JABA Service menu entries reworded</li>
2836 <li>Modeller PIR IO broken - cannot correctly import a
2837 pir file emitted by Jalview</li>
2838 <li>Existing feature settings transferred to new
2839 alignment view created from cut'n'paste</li>
2840 <li>Improved test for mixed amino/nucleotide chains when
2841 parsing PDB files</li>
2842 <li>Consensus and conservation annotation rows
2843 occasionally become blank for all new windows</li>
2844 <li>Exception raised when right clicking above sequences
2845 in wrapped view mode</li>
2846 </ul> <em>Application</em>
2848 <li>multiple multiply aligned structure views cause cpu
2849 usage to hit 100% and computer to hang</li>
2850 <li>Web Service parameter layout breaks for long user
2851 parameter names</li>
2852 <li>Jaba service discovery hangs desktop if Jaba server
2859 <div align="center">
2860 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2863 <td><em>Application</em>
2865 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2866 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2869 <li>Web Services preference tab</li>
2870 <li>Analysis parameters dialog box and user defined
2872 <li>Improved speed and layout of Envision2 service menu</li>
2873 <li>Superpose structures using associated sequence
2875 <li>Export coordinates and projection as CSV from PCA
2877 </ul> <em>Applet</em>
2879 <li>enable javascript: execution by the applet via the
2880 link out mechanism</li>
2881 </ul> <em>Other</em>
2883 <li>Updated the Jmol Jalview interface to work with Jmol
2885 <li>The Jalview Desktop and JalviewLite applet now
2886 require Java 1.5</li>
2887 <li>Allow Jalview feature colour specification for GFF
2888 sequence annotation files</li>
2889 <li>New 'colour by label' keword in Jalview feature file
2890 type colour specification</li>
2891 <li>New Jalview Desktop Groovy API method that allows a
2892 script to check if it being run in an interactive session or
2893 in a batch operation from the Jalview command line</li>
2897 <li>clustalx colourscheme colours Ds preferentially when
2898 both D+E are present in over 50% of the column</li>
2899 </ul> <em>Application</em>
2901 <li>typo in AlignmentFrame->View->Hide->all but
2902 selected Regions menu item</li>
2903 <li>sequence fetcher replaces ',' for ';' when the ',' is
2904 part of a valid accession ID</li>
2905 <li>fatal OOM if object retrieved by sequence fetcher
2906 runs out of memory</li>
2907 <li>unhandled Out of Memory Error when viewing pca
2908 analysis results</li>
2909 <li>InstallAnywhere builds fail to launch on OS X java
2910 10.5 update 4 (due to apple Java 1.6 update)</li>
2911 <li>Installanywhere Jalview silently fails to launch</li>
2912 </ul> <em>Applet</em>
2914 <li>Jalview.getFeatureGroups() raises an
2915 ArrayIndexOutOfBoundsException if no feature groups are
2922 <div align="center">
2923 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2929 <li>Alignment prettyprinter doesn't cope with long
2931 <li>clustalx colourscheme colours Ds preferentially when
2932 both D+E are present in over 50% of the column</li>
2933 <li>nucleic acid structures retrieved from PDB do not
2934 import correctly</li>
2935 <li>More columns get selected than were clicked on when a
2936 number of columns are hidden</li>
2937 <li>annotation label popup menu not providing correct
2938 add/hide/show options when rows are hidden or none are
2940 <li>Stockholm format shown in list of readable formats,
2941 and parser copes better with alignments from RFAM.</li>
2942 <li>CSV output of consensus only includes the percentage
2943 of all symbols if sequence logo display is enabled</li>
2945 </ul> <em>Applet</em>
2947 <li>annotation panel disappears when annotation is
2949 </ul> <em>Application</em>
2951 <li>Alignment view not redrawn properly when new
2952 alignment opened where annotation panel is visible but no
2953 annotations are present on alignment</li>
2954 <li>pasted region containing hidden columns is
2955 incorrectly displayed in new alignment window</li>
2956 <li>Jalview slow to complete operations when stdout is
2957 flooded (fix is to close the Jalview console)</li>
2958 <li>typo in AlignmentFrame->View->Hide->all but
2959 selected Rregions menu item.</li>
2960 <li>inconsistent group submenu and Format submenu entry
2961 'Un' or 'Non'conserved</li>
2962 <li>Sequence feature settings are being shared by
2963 multiple distinct alignments</li>
2964 <li>group annotation not recreated when tree partition is
2966 <li>double click on group annotation to select sequences
2967 does not propagate to associated trees</li>
2968 <li>Mac OSX specific issues:
2970 <li>exception raised when mouse clicked on desktop
2971 window background</li>
2972 <li>Desktop menu placed on menu bar and application
2973 name set correctly</li>
2974 <li>sequence feature settings not wide enough for the
2975 save feature colourscheme button</li>
2984 <div align="center">
2985 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2988 <td><em>New Capabilities</em>
2990 <li>URL links generated from description line for
2991 regular-expression based URL links (applet and application)
2993 <li>Non-positional feature URL links are shown in link
2995 <li>Linked viewing of nucleic acid sequences and
2997 <li>Automatic Scrolling option in View menu to display
2998 the currently highlighted region of an alignment.</li>
2999 <li>Order an alignment by sequence length, or using the
3000 average score or total feature count for each sequence.</li>
3001 <li>Shading features by score or associated description</li>
3002 <li>Subdivide alignment and groups based on identity of
3003 selected subsequence (Make Groups from Selection).</li>
3004 <li>New hide/show options including Shift+Control+H to
3005 hide everything but the currently selected region.</li>
3006 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3007 </ul> <em>Application</em>
3009 <li>Fetch DB References capabilities and UI expanded to
3010 support retrieval from DAS sequence sources</li>
3011 <li>Local DAS Sequence sources can be added via the
3012 command line or via the Add local source dialog box.</li>
3013 <li>DAS Dbref and DbxRef feature types are parsed as
3014 database references and protein_name is parsed as
3015 description line (BioSapiens terms).</li>
3016 <li>Enable or disable non-positional feature and database
3017 references in sequence ID tooltip from View menu in
3019 <!-- <li>New hidden columns and rows and representatives capabilities
3020 in annotations file (in progress - not yet fully implemented)</li> -->
3021 <li>Group-associated consensus, sequence logos and
3022 conservation plots</li>
3023 <li>Symbol distributions for each column can be exported
3024 and visualized as sequence logos</li>
3025 <li>Optionally scale multi-character column labels to fit
3026 within each column of annotation row<!-- todo for applet -->
3028 <li>Optional automatic sort of associated alignment view
3029 when a new tree is opened.</li>
3030 <li>Jalview Java Console</li>
3031 <li>Better placement of desktop window when moving
3032 between different screens.</li>
3033 <li>New preference items for sequence ID tooltip and
3034 consensus annotation</li>
3035 <li>Client to submit sequences and IDs to Envision2
3037 <li><em>Vamsas Capabilities</em>
3039 <li>Improved VAMSAS synchronization (Jalview archive
3040 used to preserve views, structures, and tree display
3042 <li>Import of vamsas documents from disk or URL via
3044 <li>Sharing of selected regions between views and
3045 with other VAMSAS applications (Experimental feature!)</li>
3046 <li>Updated API to VAMSAS version 0.2</li>
3048 </ul> <em>Applet</em>
3050 <li>Middle button resizes annotation row height</li>
3053 <li>sortByTree (true/false) - automatically sort the
3054 associated alignment view by the tree when a new tree is
3056 <li>showTreeBootstraps (true/false) - show or hide
3057 branch bootstraps (default is to show them if available)</li>
3058 <li>showTreeDistances (true/false) - show or hide
3059 branch lengths (default is to show them if available)</li>
3060 <li>showUnlinkedTreeNodes (true/false) - indicate if
3061 unassociated nodes should be highlighted in the tree
3063 <li>heightScale and widthScale (1.0 or more) -
3064 increase the height or width of a cell in the alignment
3065 grid relative to the current font size.</li>
3068 <li>Non-positional features displayed in sequence ID
3070 </ul> <em>Other</em>
3072 <li>Features format: graduated colour definitions and
3073 specification of feature scores</li>
3074 <li>Alignment Annotations format: new keywords for group
3075 associated annotation (GROUP_REF) and annotation row display
3076 properties (ROW_PROPERTIES)</li>
3077 <li>XML formats extended to support graduated feature
3078 colourschemes, group associated annotation, and profile
3079 visualization settings.</li></td>
3082 <li>Source field in GFF files parsed as feature source
3083 rather than description</li>
3084 <li>Non-positional features are now included in sequence
3085 feature and gff files (controlled via non-positional feature
3086 visibility in tooltip).</li>
3087 <li>URL links generated for all feature links (bugfix)</li>
3088 <li>Added URL embedding instructions to features file
3090 <li>Codons containing ambiguous nucleotides translated as
3091 'X' in peptide product</li>
3092 <li>Match case switch in find dialog box works for both
3093 sequence ID and sequence string and query strings do not
3094 have to be in upper case to match case-insensitively.</li>
3095 <li>AMSA files only contain first column of
3096 multi-character column annotation labels</li>
3097 <li>Jalview Annotation File generation/parsing consistent
3098 with documentation (e.g. Stockholm annotation can be
3099 exported and re-imported)</li>
3100 <li>PDB files without embedded PDB IDs given a friendly
3102 <li>Find incrementally searches ID string matches as well
3103 as subsequence matches, and correctly reports total number
3107 <li>Better handling of exceptions during sequence
3109 <li>Dasobert generated non-positional feature URL
3110 link text excludes the start_end suffix</li>
3111 <li>DAS feature and source retrieval buttons disabled
3112 when fetch or registry operations in progress.</li>
3113 <li>PDB files retrieved from URLs are cached properly</li>
3114 <li>Sequence description lines properly shared via
3116 <li>Sequence fetcher fetches multiple records for all
3118 <li>Ensured that command line das feature retrieval
3119 completes before alignment figures are generated.</li>
3120 <li>Reduced time taken when opening file browser for
3122 <li>isAligned check prior to calculating tree, PCA or
3123 submitting an MSA to JNet now excludes hidden sequences.</li>
3124 <li>User defined group colours properly recovered
3125 from Jalview projects.</li>
3134 <div align="center">
3135 <strong>2.4.0.b2</strong><br> 28/10/2009
3140 <li>Experimental support for google analytics usage
3142 <li>Jalview privacy settings (user preferences and docs).</li>
3147 <li>Race condition in applet preventing startup in
3149 <li>Exception when feature created from selection beyond
3150 length of sequence.</li>
3151 <li>Allow synthetic PDB files to be imported gracefully</li>
3152 <li>Sequence associated annotation rows associate with
3153 all sequences with a given id</li>
3154 <li>Find function matches case-insensitively for sequence
3155 ID string searches</li>
3156 <li>Non-standard characters do not cause pairwise
3157 alignment to fail with exception</li>
3158 </ul> <em>Application Issues</em>
3160 <li>Sequences are now validated against EMBL database</li>
3161 <li>Sequence fetcher fetches multiple records for all
3163 </ul> <em>InstallAnywhere Issues</em>
3165 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3166 issue with installAnywhere mechanism)</li>
3167 <li>Command line launching of JARs from InstallAnywhere
3168 version (java class versioning error fixed)</li>
3175 <div align="center">
3176 <strong>2.4</strong><br> 27/8/2008
3179 <td><em>User Interface</em>
3181 <li>Linked highlighting of codon and amino acid from
3182 translation and protein products</li>
3183 <li>Linked highlighting of structure associated with
3184 residue mapping to codon position</li>
3185 <li>Sequence Fetcher provides example accession numbers
3186 and 'clear' button</li>
3187 <li>MemoryMonitor added as an option under Desktop's
3189 <li>Extract score function to parse whitespace separated
3190 numeric data in description line</li>
3191 <li>Column labels in alignment annotation can be centred.</li>
3192 <li>Tooltip for sequence associated annotation give name
3194 </ul> <em>Web Services and URL fetching</em>
3196 <li>JPred3 web service</li>
3197 <li>Prototype sequence search client (no public services
3199 <li>Fetch either seed alignment or full alignment from
3201 <li>URL Links created for matching database cross
3202 references as well as sequence ID</li>
3203 <li>URL Links can be created using regular-expressions</li>
3204 </ul> <em>Sequence Database Connectivity</em>
3206 <li>Retrieval of cross-referenced sequences from other
3208 <li>Generalised database reference retrieval and
3209 validation to all fetchable databases</li>
3210 <li>Fetch sequences from DAS sources supporting the
3211 sequence command</li>
3212 </ul> <em>Import and Export</em>
3213 <li>export annotation rows as CSV for spreadsheet import</li>
3214 <li>Jalview projects record alignment dataset associations,
3215 EMBL products, and cDNA sequence mappings</li>
3216 <li>Sequence Group colour can be specified in Annotation
3218 <li>Ad-hoc colouring of group in Annotation File using RGB
3219 triplet as name of colourscheme</li>
3220 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3222 <li>treenode binding for VAMSAS tree exchange</li>
3223 <li>local editing and update of sequences in VAMSAS
3224 alignments (experimental)</li>
3225 <li>Create new or select existing session to join</li>
3226 <li>load and save of vamsas documents</li>
3227 </ul> <em>Application command line</em>
3229 <li>-tree parameter to open trees (introduced for passing
3231 <li>-fetchfrom command line argument to specify nicknames
3232 of DAS servers to query for alignment features</li>
3233 <li>-dasserver command line argument to add new servers
3234 that are also automatically queried for features</li>
3235 <li>-groovy command line argument executes a given groovy
3236 script after all input data has been loaded and parsed</li>
3237 </ul> <em>Applet-Application data exchange</em>
3239 <li>Trees passed as applet parameters can be passed to
3240 application (when using "View in full
3241 application")</li>
3242 </ul> <em>Applet Parameters</em>
3244 <li>feature group display control parameter</li>
3245 <li>debug parameter</li>
3246 <li>showbutton parameter</li>
3247 </ul> <em>Applet API methods</em>
3249 <li>newView public method</li>
3250 <li>Window (current view) specific get/set public methods</li>
3251 <li>Feature display control methods</li>
3252 <li>get list of currently selected sequences</li>
3253 </ul> <em>New Jalview distribution features</em>
3255 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3256 <li>RELEASE file gives build properties for the latest
3257 Jalview release.</li>
3258 <li>Java 1.1 Applet build made easier and donotobfuscate
3259 property controls execution of obfuscator</li>
3260 <li>Build target for generating source distribution</li>
3261 <li>Debug flag for javacc</li>
3262 <li>.jalview_properties file is documented (slightly) in
3263 jalview.bin.Cache</li>
3264 <li>Continuous Build Integration for stable and
3265 development version of Application, Applet and source
3270 <li>selected region output includes visible annotations
3271 (for certain formats)</li>
3272 <li>edit label/displaychar contains existing label/char
3274 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3275 <li>shorter peptide product names from EMBL records</li>
3276 <li>Newick string generator makes compact representations</li>
3277 <li>bootstrap values parsed correctly for tree files with
3279 <li>pathological filechooser bug avoided by not allowing
3280 filenames containing a ':'</li>
3281 <li>Fixed exception when parsing GFF files containing
3282 global sequence features</li>
3283 <li>Alignment datasets are finalized only when number of
3284 references from alignment sequences goes to zero</li>
3285 <li>Close of tree branch colour box without colour
3286 selection causes cascading exceptions</li>
3287 <li>occasional negative imgwidth exceptions</li>
3288 <li>better reporting of non-fatal warnings to user when
3289 file parsing fails.</li>
3290 <li>Save works when Jalview project is default format</li>
3291 <li>Save as dialog opened if current alignment format is
3292 not a valid output format</li>
3293 <li>UniProt canonical names introduced for both das and
3295 <li>Histidine should be midblue (not pink!) in Zappo</li>
3296 <li>error messages passed up and output when data read
3298 <li>edit undo recovers previous dataset sequence when
3299 sequence is edited</li>
3300 <li>allow PDB files without pdb ID HEADER lines (like
3301 those generated by MODELLER) to be read in properly</li>
3302 <li>allow reading of JPred concise files as a normal
3304 <li>Stockholm annotation parsing and alignment properties
3305 import fixed for PFAM records</li>
3306 <li>Structure view windows have correct name in Desktop
3308 <li>annotation consisting of sequence associated scores
3309 can be read and written correctly to annotation file</li>
3310 <li>Aligned cDNA translation to aligned peptide works
3312 <li>Fixed display of hidden sequence markers and
3313 non-italic font for representatives in Applet</li>
3314 <li>Applet Menus are always embedded in applet window on
3316 <li>Newly shown features appear at top of stack (in
3318 <li>Annotations added via parameter not drawn properly
3319 due to null pointer exceptions</li>
3320 <li>Secondary structure lines are drawn starting from
3321 first column of alignment</li>
3322 <li>UniProt XML import updated for new schema release in
3324 <li>Sequence feature to sequence ID match for Features
3325 file is case-insensitive</li>
3326 <li>Sequence features read from Features file appended to
3327 all sequences with matching IDs</li>
3328 <li>PDB structure coloured correctly for associated views
3329 containing a sub-sequence</li>
3330 <li>PDB files can be retrieved by applet from Jar files</li>
3331 <li>feature and annotation file applet parameters
3332 referring to different directories are retrieved correctly</li>
3333 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3334 <li>Fixed application hang whilst waiting for
3335 splash-screen version check to complete</li>
3336 <li>Applet properly URLencodes input parameter values
3337 when passing them to the launchApp service</li>
3338 <li>display name and local features preserved in results
3339 retrieved from web service</li>
3340 <li>Visual delay indication for sequence retrieval and
3341 sequence fetcher initialisation</li>
3342 <li>updated Application to use DAS 1.53e version of
3343 dasobert DAS client</li>
3344 <li>Re-instated Full AMSA support and .amsa file
3346 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3354 <div align="center">
3355 <strong>2.3</strong><br> 9/5/07
3360 <li>Jmol 11.0.2 integration</li>
3361 <li>PDB views stored in Jalview XML files</li>
3362 <li>Slide sequences</li>
3363 <li>Edit sequence in place</li>
3364 <li>EMBL CDS features</li>
3365 <li>DAS Feature mapping</li>
3366 <li>Feature ordering</li>
3367 <li>Alignment Properties</li>
3368 <li>Annotation Scores</li>
3369 <li>Sort by scores</li>
3370 <li>Feature/annotation editing in applet</li>
3375 <li>Headless state operation in 2.2.1</li>
3376 <li>Incorrect and unstable DNA pairwise alignment</li>
3377 <li>Cut and paste of sequences with annotation</li>
3378 <li>Feature group display state in XML</li>
3379 <li>Feature ordering in XML</li>
3380 <li>blc file iteration selection using filename # suffix</li>
3381 <li>Stockholm alignment properties</li>
3382 <li>Stockhom alignment secondary structure annotation</li>
3383 <li>2.2.1 applet had no feature transparency</li>
3384 <li>Number pad keys can be used in cursor mode</li>
3385 <li>Structure Viewer mirror image resolved</li>
3392 <div align="center">
3393 <strong>2.2.1</strong><br> 12/2/07
3398 <li>Non standard characters can be read and displayed
3399 <li>Annotations/Features can be imported/exported to the
3401 <li>Applet allows editing of sequence/annotation/group
3402 name & description
3403 <li>Preference setting to display sequence name in
3405 <li>Annotation file format extended to allow
3406 Sequence_groups to be defined
3407 <li>Default opening of alignment overview panel can be
3408 specified in preferences
3409 <li>PDB residue numbering annotation added to associated
3415 <li>Applet crash under certain Linux OS with Java 1.6
3417 <li>Annotation file export / import bugs fixed
3418 <li>PNG / EPS image output bugs fixed
3424 <div align="center">
3425 <strong>2.2</strong><br> 27/11/06
3430 <li>Multiple views on alignment
3431 <li>Sequence feature editing
3432 <li>"Reload" alignment
3433 <li>"Save" to current filename
3434 <li>Background dependent text colour
3435 <li>Right align sequence ids
3436 <li>User-defined lower case residue colours
3439 <li>Menu item accelerator keys
3440 <li>Control-V pastes to current alignment
3441 <li>Cancel button for DAS Feature Fetching
3442 <li>PCA and PDB Viewers zoom via mouse roller
3443 <li>User-defined sub-tree colours and sub-tree selection
3445 <li>'New Window' button on the 'Output to Text box'
3450 <li>New memory efficient Undo/Redo System
3451 <li>Optimised symbol lookups and conservation/consensus
3453 <li>Region Conservation/Consensus recalculated after
3455 <li>Fixed Remove Empty Columns Bug (empty columns at end
3457 <li>Slowed DAS Feature Fetching for increased robustness.
3459 <li>Made angle brackets in ASCII feature descriptions
3461 <li>Re-instated Zoom function for PCA
3462 <li>Sequence descriptions conserved in web service
3464 <li>UniProt ID discoverer uses any word separated by
3466 <li>WsDbFetch query/result association resolved
3467 <li>Tree leaf to sequence mapping improved
3468 <li>Smooth fonts switch moved to FontChooser dialog box.
3475 <div align="center">
3476 <strong>2.1.1</strong><br> 12/9/06
3481 <li>Copy consensus sequence to clipboard</li>
3486 <li>Image output - rightmost residues are rendered if
3487 sequence id panel has been resized</li>
3488 <li>Image output - all offscreen group boundaries are
3490 <li>Annotation files with sequence references - all
3491 elements in file are relative to sequence position</li>
3492 <li>Mac Applet users can use Alt key for group editing</li>
3498 <div align="center">
3499 <strong>2.1</strong><br> 22/8/06
3504 <li>MAFFT Multiple Alignment in default Web Service list</li>
3505 <li>DAS Feature fetching</li>
3506 <li>Hide sequences and columns</li>
3507 <li>Export Annotations and Features</li>
3508 <li>GFF file reading / writing</li>
3509 <li>Associate structures with sequences from local PDB
3511 <li>Add sequences to exisiting alignment</li>
3512 <li>Recently opened files / URL lists</li>
3513 <li>Applet can launch the full application</li>
3514 <li>Applet has transparency for features (Java 1.2
3516 <li>Applet has user defined colours parameter</li>
3517 <li>Applet can load sequences from parameter
3518 "sequence<em>x</em>"
3524 <li>Redundancy Panel reinstalled in the Applet</li>
3525 <li>Monospaced font - EPS / rescaling bug fixed</li>
3526 <li>Annotation files with sequence references bug fixed</li>
3532 <div align="center">
3533 <strong>2.08.1</strong><br> 2/5/06
3538 <li>Change case of selected region from Popup menu</li>
3539 <li>Choose to match case when searching</li>
3540 <li>Middle mouse button and mouse movement can compress /
3541 expand the visible width and height of the alignment</li>
3546 <li>Annotation Panel displays complete JNet results</li>
3552 <div align="center">
3553 <strong>2.08b</strong><br> 18/4/06
3559 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3560 <li>Righthand label on wrapped alignments shows correct
3567 <div align="center">
3568 <strong>2.08</strong><br> 10/4/06
3573 <li>Editing can be locked to the selection area</li>
3574 <li>Keyboard editing</li>
3575 <li>Create sequence features from searches</li>
3576 <li>Precalculated annotations can be loaded onto
3578 <li>Features file allows grouping of features</li>
3579 <li>Annotation Colouring scheme added</li>
3580 <li>Smooth fonts off by default - Faster rendering</li>
3581 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3586 <li>Drag & Drop fixed on Linux</li>
3587 <li>Jalview Archive file faster to load/save, sequence
3588 descriptions saved.</li>
3594 <div align="center">
3595 <strong>2.07</strong><br> 12/12/05
3600 <li>PDB Structure Viewer enhanced</li>
3601 <li>Sequence Feature retrieval and display enhanced</li>
3602 <li>Choose to output sequence start-end after sequence
3603 name for file output</li>
3604 <li>Sequence Fetcher WSDBFetch@EBI</li>
3605 <li>Applet can read feature files, PDB files and can be
3606 used for HTML form input</li>
3611 <li>HTML output writes groups and features</li>
3612 <li>Group editing is Control and mouse click</li>
3613 <li>File IO bugs</li>
3619 <div align="center">
3620 <strong>2.06</strong><br> 28/9/05
3625 <li>View annotations in wrapped mode</li>
3626 <li>More options for PCA viewer</li>
3631 <li>GUI bugs resolved</li>
3632 <li>Runs with -nodisplay from command line</li>
3638 <div align="center">
3639 <strong>2.05b</strong><br> 15/9/05
3644 <li>Choose EPS export as lineart or text</li>
3645 <li>Jar files are executable</li>
3646 <li>Can read in Uracil - maps to unknown residue</li>
3651 <li>Known OutOfMemory errors give warning message</li>
3652 <li>Overview window calculated more efficiently</li>
3653 <li>Several GUI bugs resolved</li>
3659 <div align="center">
3660 <strong>2.05</strong><br> 30/8/05
3665 <li>Edit and annotate in "Wrapped" view</li>
3670 <li>Several GUI bugs resolved</li>
3676 <div align="center">
3677 <strong>2.04</strong><br> 24/8/05
3682 <li>Hold down mouse wheel & scroll to change font
3688 <li>Improved JPred client reliability</li>
3689 <li>Improved loading of Jalview files</li>
3695 <div align="center">
3696 <strong>2.03</strong><br> 18/8/05
3701 <li>Set Proxy server name and port in preferences</li>
3702 <li>Multiple URL links from sequence ids</li>
3703 <li>User Defined Colours can have a scheme name and added
3705 <li>Choose to ignore gaps in consensus calculation</li>
3706 <li>Unix users can set default web browser</li>
3707 <li>Runs without GUI for batch processing</li>
3708 <li>Dynamically generated Web Service Menus</li>
3713 <li>InstallAnywhere download for Sparc Solaris</li>
3719 <div align="center">
3720 <strong>2.02</strong><br> 18/7/05
3726 <li>Copy & Paste order of sequences maintains
3727 alignment order.</li>
3733 <div align="center">
3734 <strong>2.01</strong><br> 12/7/05
3739 <li>Use delete key for deleting selection.</li>
3740 <li>Use Mouse wheel to scroll sequences.</li>
3741 <li>Help file updated to describe how to add alignment
3743 <li>Version and build date written to build properties
3745 <li>InstallAnywhere installation will check for updates
3746 at launch of Jalview.</li>
3751 <li>Delete gaps bug fixed.</li>
3752 <li>FileChooser sorts columns.</li>
3753 <li>Can remove groups one by one.</li>
3754 <li>Filechooser icons installed.</li>
3755 <li>Finder ignores return character when searching.
3756 Return key will initiate a search.<br>
3763 <div align="center">
3764 <strong>2.0</strong><br> 20/6/05
3769 <li>New codebase</li>