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>24/1/2018</em></strong>
76 <td><div align="left">
77 <ul><li>Updated Certum Codesigning Certificate
78 (Valid till 30th November 2018)</li></ul></div></td>
79 <td><div align="left">
82 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
83 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
84 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
85 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
86 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
87 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
88 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
94 <td width="60" nowrap>
96 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
99 <td><div align="left">
103 <!-- JAL-2446 -->Faster and more efficient management and
104 rendering of sequence features
107 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
108 429 rate limit request hander
111 <!-- JAL-2773 -->Structure views don't get updated unless
112 their colours have changed
115 <!-- JAL-2495 -->All linked sequences are highlighted for
116 a structure mousover (Jmol) or selection (Chimera)
119 <!-- JAL-2790 -->'Cancel' button in progress bar for
120 JABAWS AACon, RNAAliFold and Disorder prediction jobs
123 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
124 view from Ensembl locus cross-references
127 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
131 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
132 feature can be disabled
135 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
136 PDB easier retrieval of sequences for lists of IDs
139 <!-- JAL-2758 -->Short names for sequences retrieved from
145 <li>Groovy interpreter updated to 2.4.12</li>
146 <li>Example groovy script for generating a matrix of
147 percent identity scores for current alignment.</li>
149 <em>Testing and Deployment</em>
152 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
156 <td><div align="left">
160 <!-- JAL-2643 -->Pressing tab after updating the colour
161 threshold text field doesn't trigger an update to the
165 <!-- JAL-2682 -->Race condition when parsing sequence ID
169 <!-- JAL-2608 -->Overview windows are also closed when
170 alignment window is closed
173 <!-- JAL-2548 -->Export of features doesn't always respect
177 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
178 takes a long time in Cursor mode
184 <!-- JAL-2777 -->Structures with whitespace chainCode
185 cannot be viewed in Chimera
188 <!-- JAL-2728 -->Protein annotation panel too high in
192 <!-- JAL-2757 -->Can't edit the query after the server
193 error warning icon is shown in Uniprot and PDB Free Text
197 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
200 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
203 <!-- JAL-2739 -->Hidden column marker in last column not
204 rendered when switching back from Wrapped to normal view
207 <!-- JAL-2768 -->Annotation display corrupted when
208 scrolling right in unwapped alignment view
211 <!-- JAL-2542 -->Existing features on subsequence
212 incorrectly relocated when full sequence retrieved from
216 <!-- JAL-2733 -->Last reported memory still shown when
217 Desktop->Show Memory is unticked (OSX only)
220 <!-- JAL-2658 -->Amend Features dialog doesn't allow
221 features of same type and group to be selected for
225 <!-- JAL-2524 -->Jalview becomes sluggish in wide
226 alignments when hidden columns are present
229 <!-- JAL-2392 -->Jalview freezes when loading and
230 displaying several structures
233 <!-- JAL-2732 -->Black outlines left after resizing or
237 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
238 within the Jalview desktop on OSX
241 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
242 when in wrapped alignment mode
245 <!-- JAL-2636 -->Scale mark not shown when close to right
246 hand end of alignment
249 <!-- JAL-2684 -->Pairwise alignment of selected regions of
250 each selected sequence do not have correct start/end
254 <!-- JAL-2793 -->Alignment ruler height set incorrectly
255 after canceling the Alignment Window's Font dialog
258 <!-- JAL-2036 -->Show cross-references not enabled after
259 restoring project until a new view is created
262 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
263 URL links appears when only default EMBL-EBI link is
264 configured (since 2.10.2b2)
267 <!-- JAL-2775 -->Overview redraws whole window when box
271 <!-- JAL-2225 -->Structure viewer doesn't map all chains
272 in a multi-chain structure when viewing alignment
273 involving more than one chain (since 2.10)
276 <!-- JAL-2811 -->Double residue highlights in cursor mode
277 if new selection moves alignment window
280 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
281 arrow key in cursor mode to pass hidden column marker
284 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
285 that produces correctly annotated transcripts and products
288 <!-- JAL-2776 -->Toggling a feature group after first time
289 doesn't update associated structure view
292 <em>Applet</em><br />
295 <!-- JAL-2687 -->Concurrent modification exception when
296 closing alignment panel
299 <em>BioJSON</em><br />
302 <!-- JAL-2546 -->BioJSON export does not preserve
303 non-positional features
306 <em>New Known Issues</em>
309 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
310 sequence features correctly (for many previous versions of
314 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
315 using cursor in wrapped panel other than top
318 <!-- JAL-2791 -->Select columns containing feature ignores
319 graduated colour threshold
322 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
323 always preserve numbering and sequence features
326 <em>Known Java 9 Issues</em>
329 <!-- JAL-2902 -->Groovy Console very slow to open and is
330 not responsive when entering characters (Webstart, Java
337 <td width="60" nowrap>
339 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
340 <em>2/10/2017</em></strong>
343 <td><div align="left">
344 <em>New features in Jalview Desktop</em>
347 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
349 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
353 <td><div align="left">
357 <td width="60" nowrap>
359 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
360 <em>7/9/2017</em></strong>
363 <td><div align="left">
367 <!-- JAL-2588 -->Show gaps in overview window by colouring
368 in grey (sequences used to be coloured grey, and gaps were
372 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
376 <!-- JAL-2587 -->Overview updates immediately on increase
377 in size and progress bar shown as higher resolution
378 overview is recalculated
383 <td><div align="left">
387 <!-- JAL-2664 -->Overview window redraws every hidden
388 column region row by row
391 <!-- JAL-2681 -->duplicate protein sequences shown after
392 retrieving Ensembl crossrefs for sequences from Uniprot
395 <!-- JAL-2603 -->Overview window throws NPE if show boxes
396 format setting is unticked
399 <!-- JAL-2610 -->Groups are coloured wrongly in overview
400 if group has show boxes format setting unticked
403 <!-- JAL-2672,JAL-2665 -->Redraw problems when
404 autoscrolling whilst dragging current selection group to
405 include sequences and columns not currently displayed
408 <!-- JAL-2691 -->Not all chains are mapped when multimeric
409 assemblies are imported via CIF file
412 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
413 displayed when threshold or conservation colouring is also
417 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
421 <!-- JAL-2673 -->Jalview continues to scroll after
422 dragging a selected region off the visible region of the
426 <!-- JAL-2724 -->Cannot apply annotation based
427 colourscheme to all groups in a view
430 <!-- JAL-2511 -->IDs don't line up with sequences
431 initially after font size change using the Font chooser or
438 <td width="60" nowrap>
440 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
443 <td><div align="left">
444 <em>Calculations</em>
448 <!-- JAL-1933 -->Occupancy annotation row shows number of
449 ungapped positions in each column of the alignment.
452 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
453 a calculation dialog box
456 <!-- JAL-2379 -->Revised implementation of PCA for speed
457 and memory efficiency (~30x faster)
460 <!-- JAL-2403 -->Revised implementation of sequence
461 similarity scores as used by Tree, PCA, Shading Consensus
462 and other calculations
465 <!-- JAL-2416 -->Score matrices are stored as resource
466 files within the Jalview codebase
469 <!-- JAL-2500 -->Trees computed on Sequence Feature
470 Similarity may have different topology due to increased
477 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
478 model for alignments and groups
481 <!-- JAL-384 -->Custom shading schemes created via groovy
488 <!-- JAL-2526 -->Efficiency improvements for interacting
489 with alignment and overview windows
492 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
496 <!-- JAL-2388 -->Hidden columns and sequences can be
500 <!-- JAL-2611 -->Click-drag in visible area allows fine
501 adjustment of visible position
505 <em>Data import/export</em>
508 <!-- JAL-2535 -->Posterior probability annotation from
509 Stockholm files imported as sequence associated annotation
512 <!-- JAL-2507 -->More robust per-sequence positional
513 annotation input/output via stockholm flatfile
516 <!-- JAL-2533 -->Sequence names don't include file
517 extension when importing structure files without embedded
518 names or PDB accessions
521 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
522 format sequence substitution matrices
525 <em>User Interface</em>
528 <!-- JAL-2447 --> Experimental Features Checkbox in
529 Desktop's Tools menu to hide or show untested features in
533 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
534 via Overview or sequence motif search operations
537 <!-- JAL-2547 -->Amend sequence features dialog box can be
538 opened by double clicking gaps within sequence feature
542 <!-- JAL-1476 -->Status bar message shown when not enough
543 aligned positions were available to create a 3D structure
547 <em>3D Structure</em>
550 <!-- JAL-2430 -->Hidden regions in alignment views are not
551 coloured in linked structure views
554 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
555 file-based command exchange
558 <!-- JAL-2375 -->Structure chooser automatically shows
559 Cached Structures rather than querying the PDBe if
560 structures are already available for sequences
563 <!-- JAL-2520 -->Structures imported via URL are cached in
564 the Jalview project rather than downloaded again when the
568 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
569 to transfer Chimera's structure attributes as Jalview
570 features, and vice-versa (<strong>Experimental
574 <em>Web Services</em>
577 <!-- JAL-2549 -->Updated JABAWS client to v2.2
580 <!-- JAL-2335 -->Filter non-standard amino acids and
581 nucleotides when submitting to AACon and other MSA
585 <!-- JAL-2316, -->URLs for viewing database
586 cross-references provided by identifiers.org and the
594 <!-- JAL-2344 -->FileFormatI interface for describing and
595 identifying file formats (instead of String constants)
598 <!-- JAL-2228 -->FeatureCounter script refactored for
599 efficiency when counting all displayed features (not
600 backwards compatible with 2.10.1)
603 <em>Example files</em>
606 <!-- JAL-2631 -->Graduated feature colour style example
607 included in the example feature file
610 <em>Documentation</em>
613 <!-- JAL-2339 -->Release notes reformatted for readability
614 with the built-in Java help viewer
617 <!-- JAL-1644 -->Find documentation updated with 'search
618 sequence description' option
624 <!-- JAL-2485, -->External service integration tests for
625 Uniprot REST Free Text Search Client
628 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
631 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
636 <td><div align="left">
637 <em>Calculations</em>
640 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
641 matrix - C->R should be '-3'<br />Old matrix restored
642 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
644 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
645 Jalview's treatment of gaps in PCA and substitution matrix
646 based Tree calculations.<br /> <br />In earlier versions
647 of Jalview, gaps matching gaps were penalised, and gaps
648 matching non-gaps penalised even more. In the PCA
649 calculation, gaps were actually treated as non-gaps - so
650 different costs were applied, which meant Jalview's PCAs
651 were different to those produced by SeqSpace.<br />Jalview
652 now treats gaps in the same way as SeqSpace (ie it scores
653 them as 0). <br /> <br />Enter the following in the
654 Groovy console to restore pre-2.10.2 behaviour:<br />
655 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
656 // for 2.10.1 mode <br />
657 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
658 // to restore 2.10.2 mode <br /> <br /> <em>Note:
659 these settings will affect all subsequent tree and PCA
660 calculations (not recommended)</em></li>
662 <!-- JAL-2424 -->Fixed off-by-one bug that affected
663 scaling of branch lengths for trees computed using
664 Sequence Feature Similarity.
667 <!-- JAL-2377 -->PCA calculation could hang when
668 generating output report when working with highly
672 <!-- JAL-2544 --> Sort by features includes features to
673 right of selected region when gaps present on right-hand
677 <em>User Interface</em>
680 <!-- JAL-2346 -->Reopening Colour by annotation dialog
681 doesn't reselect a specific sequence's associated
682 annotation after it was used for colouring a view
685 <!-- JAL-2419 -->Current selection lost if popup menu
686 opened on a region of alignment without groups
689 <!-- JAL-2374 -->Popup menu not always shown for regions
690 of an alignment with overlapping groups
693 <!-- JAL-2310 -->Finder double counts if both a sequence's
694 name and description match
697 <!-- JAL-2370 -->Hiding column selection containing two
698 hidden regions results in incorrect hidden regions
701 <!-- JAL-2386 -->'Apply to all groups' setting when
702 changing colour does not apply Conservation slider value
706 <!-- JAL-2373 -->Percentage identity and conservation menu
707 items do not show a tick or allow shading to be disabled
710 <!-- JAL-2385 -->Conservation shading or PID threshold
711 lost when base colourscheme changed if slider not visible
714 <!-- JAL-2547 -->Sequence features shown in tooltip for
715 gaps before start of features
718 <!-- JAL-2623 -->Graduated feature colour threshold not
719 restored to UI when feature colour is edited
722 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
723 a time when scrolling vertically in wrapped mode.
726 <!-- JAL-2630 -->Structure and alignment overview update
727 as graduate feature colour settings are modified via the
731 <!-- JAL-2034 -->Overview window doesn't always update
732 when a group defined on the alignment is resized
735 <!-- JAL-2605 -->Mouseovers on left/right scale region in
736 wrapped view result in positional status updates
740 <!-- JAL-2563 -->Status bar doesn't show position for
741 ambiguous amino acid and nucleotide symbols
744 <!-- JAL-2602 -->Copy consensus sequence failed if
745 alignment included gapped columns
748 <!-- JAL-2473 -->Minimum size set for Jalview windows so
749 widgets don't permanently disappear
752 <!-- JAL-2503 -->Cannot select or filter quantitative
753 annotation that are shown only as column labels (e.g.
754 T-Coffee column reliability scores)
757 <!-- JAL-2594 -->Exception thrown if trying to create a
758 sequence feature on gaps only
761 <!-- JAL-2504 -->Features created with 'New feature'
762 button from a Find inherit previously defined feature type
763 rather than the Find query string
766 <!-- JAL-2423 -->incorrect title in output window when
767 exporting tree calculated in Jalview
770 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
771 and then revealing them reorders sequences on the
775 <!-- JAL-964 -->Group panel in sequence feature settings
776 doesn't update to reflect available set of groups after
777 interactively adding or modifying features
780 <!-- JAL-2225 -->Sequence Database chooser unusable on
784 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
785 only excluded gaps in current sequence and ignored
792 <!-- JAL-2421 -->Overview window visible region moves
793 erratically when hidden rows or columns are present
796 <!-- JAL-2362 -->Per-residue colourschemes applied via the
797 Structure Viewer's colour menu don't correspond to
801 <!-- JAL-2405 -->Protein specific colours only offered in
802 colour and group colour menu for protein alignments
805 <!-- JAL-2385 -->Colour threshold slider doesn't update to
806 reflect currently selected view or group's shading
810 <!-- JAL-2624 -->Feature colour thresholds not respected
811 when rendered on overview and structures when opacity at
815 <!-- JAL-2589 -->User defined gap colour not shown in
816 overview when features overlaid on alignment
819 <em>Data import/export</em>
822 <!-- JAL-2576 -->Very large alignments take a long time to
826 <!-- JAL-2507 -->Per-sequence RNA secondary structures
827 added after a sequence was imported are not written to
831 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
832 when importing RNA secondary structure via Stockholm
835 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
836 not shown in correct direction for simple pseudoknots
839 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
840 with lightGray or darkGray via features file (but can
844 <!-- JAL-2383 -->Above PID colour threshold not recovered
845 when alignment view imported from project
848 <!-- JAL-2520,JAL-2465 -->No mappings generated between
849 structure and sequences extracted from structure files
850 imported via URL and viewed in Jmol
853 <!-- JAL-2520 -->Structures loaded via URL are saved in
854 Jalview Projects rather than fetched via URL again when
855 the project is loaded and the structure viewed
858 <em>Web Services</em>
861 <!-- JAL-2519 -->EnsemblGenomes example failing after
862 release of Ensembl v.88
865 <!-- JAL-2366 -->Proxy server address and port always
866 appear enabled in Preferences->Connections
869 <!-- JAL-2461 -->DAS registry not found exceptions
870 removed from console output
873 <!-- JAL-2582 -->Cannot retrieve protein products from
874 Ensembl by Peptide ID
877 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
878 created from SIFTs, and spurious 'Couldn't open structure
879 in Chimera' errors raised after April 2017 update (problem
880 due to 'null' string rather than empty string used for
881 residues with no corresponding PDB mapping).
884 <em>Application UI</em>
887 <!-- JAL-2361 -->User Defined Colours not added to Colour
891 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
892 case' residues (button in colourscheme editor debugged and
893 new documentation and tooltips added)
896 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
897 doesn't restore group-specific text colour thresholds
900 <!-- JAL-2243 -->Feature settings panel does not update as
901 new features are added to alignment
904 <!-- JAL-2532 -->Cancel in feature settings reverts
905 changes to feature colours via the Amend features dialog
908 <!-- JAL-2506 -->Null pointer exception when attempting to
909 edit graduated feature colour via amend features dialog
913 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
914 selection menu changes colours of alignment views
917 <!-- JAL-2426 -->Spurious exceptions in console raised
918 from alignment calculation workers after alignment has
922 <!-- JAL-1608 -->Typo in selection popup menu - Create
923 groups now 'Create Group'
926 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
927 Create/Undefine group doesn't always work
930 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
931 shown again after pressing 'Cancel'
934 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
935 adjusts start position in wrap mode
938 <!-- JAL-2563 -->Status bar doesn't show positions for
939 ambiguous amino acids
942 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
943 CDS/Protein view after CDS sequences added for aligned
947 <!-- JAL-2592 -->User defined colourschemes called 'User
948 Defined' don't appear in Colours menu
954 <!-- JAL-2468 -->Switching between Nucleotide and Protein
955 score models doesn't always result in an updated PCA plot
958 <!-- JAL-2442 -->Features not rendered as transparent on
959 overview or linked structure view
962 <!-- JAL-2372 -->Colour group by conservation doesn't
966 <!-- JAL-2517 -->Hitting Cancel after applying
967 user-defined colourscheme doesn't restore original
974 <!-- JAL-2314 -->Unit test failure:
975 jalview.ws.jabaws.RNAStructExportImport setup fails
978 <!-- JAL-2307 -->Unit test failure:
979 jalview.ws.sifts.SiftsClientTest due to compatibility
980 problems with deep array comparison equality asserts in
981 successive versions of TestNG
984 <!-- JAL-2479 -->Relocated StructureChooserTest and
985 ParameterUtilsTest Unit tests to Network suite
988 <em>New Known Issues</em>
991 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
992 phase after a sequence motif find operation
995 <!-- JAL-2550 -->Importing annotation file with rows
996 containing just upper and lower case letters are
997 interpreted as WUSS RNA secondary structure symbols
1000 <!-- JAL-2590 -->Cannot load and display Newick trees
1001 reliably from eggnog Ortholog database
1004 <!-- JAL-2468 -->Status bar shows 'Marked x columns
1005 containing features of type Highlight' when 'B' is pressed
1006 to mark columns containing highlighted regions.
1009 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
1010 doesn't always add secondary structure annotation.
1015 <td width="60" nowrap>
1016 <div align="center">
1017 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
1020 <td><div align="left">
1024 <!-- JAL-98 -->Improved memory usage: sparse arrays used
1025 for all consensus calculations
1028 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
1031 <li>Updated Jalview's Certum code signing certificate
1034 <em>Application</em>
1037 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
1038 set of database cross-references, sorted alphabetically
1041 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
1042 from database cross references. Users with custom links
1043 will receive a <a href="webServices/urllinks.html#warning">warning
1044 dialog</a> asking them to update their preferences.
1047 <!-- JAL-2287-->Cancel button and escape listener on
1048 dialog warning user about disconnecting Jalview from a
1052 <!-- JAL-2320-->Jalview's Chimera control window closes if
1053 the Chimera it is connected to is shut down
1056 <!-- JAL-1738-->New keystroke (B) and Select highlighted
1057 columns menu item to mark columns containing highlighted
1058 regions (e.g. from structure selections or results of a
1062 <!-- JAL-2284-->Command line option for batch-generation
1063 of HTML pages rendering alignment data with the BioJS
1073 <!-- JAL-2286 -->Columns with more than one modal residue
1074 are not coloured or thresholded according to percent
1075 identity (first observed in Jalview 2.8.2)
1078 <!-- JAL-2301 -->Threonine incorrectly reported as not
1082 <!-- JAL-2318 -->Updates to documentation pages (above PID
1083 threshold, amino acid properties)
1086 <!-- JAL-2292 -->Lower case residues in sequences are not
1087 reported as mapped to residues in a structure file in the
1091 <!--JAL-2324 -->Identical features with non-numeric scores
1092 could be added multiple times to a sequence
1095 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
1096 bond features shown as two highlighted residues rather
1097 than a range in linked structure views, and treated
1098 correctly when selecting and computing trees from features
1101 <!-- JAL-2281-->Custom URL links for database
1102 cross-references are matched to database name regardless
1107 <em>Application</em>
1110 <!-- JAL-2282-->Custom URL links for specific database
1111 names without regular expressions also offer links from
1115 <!-- JAL-2315-->Removing a single configured link in the
1116 URL links pane in Connections preferences doesn't actually
1117 update Jalview configuration
1120 <!-- JAL-2272-->CTRL-Click on a selected region to open
1121 the alignment area popup menu doesn't work on El-Capitan
1124 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
1125 files with similarly named sequences if dropped onto the
1129 <!-- JAL-2312 -->Additional mappings are shown for PDB
1130 entries where more chains exist in the PDB accession than
1131 are reported in the SIFTS file
1134 <!-- JAL-2317-->Certain structures do not get mapped to
1135 the structure view when displayed with Chimera
1138 <!-- JAL-2317-->No chains shown in the Chimera view
1139 panel's View->Show Chains submenu
1142 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
1143 work for wrapped alignment views
1146 <!--JAL-2197 -->Rename UI components for running JPred
1147 predictions from 'JNet' to 'JPred'
1150 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
1151 corrupted when annotation panel vertical scroll is not at
1152 first annotation row
1155 <!--JAL-2332 -->Attempting to view structure for Hen
1156 lysozyme results in a PDB Client error dialog box
1159 <!-- JAL-2319 -->Structure View's mapping report switched
1160 ranges for PDB and sequence for SIFTS
1163 SIFTS 'Not_Observed' residues mapped to non-existant
1167 <!-- <em>New Known Issues</em>
1174 <td width="60" nowrap>
1175 <div align="center">
1176 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
1177 <em>25/10/2016</em></strong>
1180 <td><em>Application</em>
1182 <li>3D Structure chooser opens with 'Cached structures'
1183 view if structures already loaded</li>
1184 <li>Progress bar reports models as they are loaded to
1185 structure views</li>
1191 <li>Colour by conservation always enabled and no tick
1192 shown in menu when BLOSUM or PID shading applied</li>
1193 <li>FER1_ARATH and FER2_ARATH labels were switched in
1194 example sequences/projects/trees</li>
1196 <em>Application</em>
1198 <li>Jalview projects with views of local PDB structure
1199 files saved on Windows cannot be opened on OSX</li>
1200 <li>Multiple structure views can be opened and superposed
1201 without timeout for structures with multiple models or
1202 multiple sequences in alignment</li>
1203 <li>Cannot import or associated local PDB files without a
1204 PDB ID HEADER line</li>
1205 <li>RMSD is not output in Jmol console when superposition
1207 <li>Drag and drop of URL from Browser fails for Linux and
1208 OSX versions earlier than El Capitan</li>
1209 <li>ENA client ignores invalid content from ENA server</li>
1210 <li>Exceptions are not raised in console when ENA client
1211 attempts to fetch non-existent IDs via Fetch DB Refs UI
1213 <li>Exceptions are not raised in console when a new view
1214 is created on the alignment</li>
1215 <li>OSX right-click fixed for group selections: CMD-click
1216 to insert/remove gaps in groups and CTRL-click to open group
1219 <em>Build and deployment</em>
1221 <li>URL link checker now copes with multi-line anchor
1224 <em>New Known Issues</em>
1226 <li>Drag and drop from URL links in browsers do not work
1233 <td width="60" nowrap>
1234 <div align="center">
1235 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
1238 <td><em>General</em>
1241 <!-- JAL-2124 -->Updated Spanish translations.
1244 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
1245 for importing structure data to Jalview. Enables mmCIF and
1249 <!-- JAL-192 --->Alignment ruler shows positions relative to
1253 <!-- JAL-2202 -->Position/residue shown in status bar when
1254 mousing over sequence associated annotation
1257 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1261 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1262 '()', canonical '[]' and invalid '{}' base pair populations
1266 <!-- JAL-2092 -->Feature settings popup menu options for
1267 showing or hiding columns containing a feature
1270 <!-- JAL-1557 -->Edit selected group by double clicking on
1271 group and sequence associated annotation labels
1274 <!-- JAL-2236 -->Sequence name added to annotation label in
1275 select/hide columns by annotation and colour by annotation
1279 </ul> <em>Application</em>
1282 <!-- JAL-2050-->Automatically hide introns when opening a
1283 gene/transcript view
1286 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1290 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1291 structure mappings with the EMBL-EBI PDBe SIFTS database
1294 <!-- JAL-2079 -->Updated download sites used for Rfam and
1295 Pfam sources to xfam.org
1298 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1301 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1302 over sequences in Jalview
1305 <!-- JAL-2027-->Support for reverse-complement coding
1306 regions in ENA and EMBL
1309 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1310 for record retrieval via ENA rest API
1313 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1317 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1318 groovy script execution
1321 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1322 alignment window's Calculate menu
1325 <!-- JAL-1812 -->Allow groovy scripts that call
1326 Jalview.getAlignFrames() to run in headless mode
1329 <!-- JAL-2068 -->Support for creating new alignment
1330 calculation workers from groovy scripts
1333 <!-- JAL-1369 --->Store/restore reference sequence in
1337 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1338 associations are now saved/restored from project
1341 <!-- JAL-1993 -->Database selection dialog always shown
1342 before sequence fetcher is opened
1345 <!-- JAL-2183 -->Double click on an entry in Jalview's
1346 database chooser opens a sequence fetcher
1349 <!-- JAL-1563 -->Free-text search client for UniProt using
1350 the UniProt REST API
1353 <!-- JAL-2168 -->-nonews command line parameter to prevent
1354 the news reader opening
1357 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1358 querying stored in preferences
1361 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1365 <!-- JAL-1977-->Tooltips shown on database chooser
1368 <!-- JAL-391 -->Reverse complement function in calculate
1369 menu for nucleotide sequences
1372 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1373 and feature counts preserves alignment ordering (and
1374 debugged for complex feature sets).
1377 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1378 viewing structures with Jalview 2.10
1381 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1382 genome, transcript CCDS and gene ids via the Ensembl and
1383 Ensembl Genomes REST API
1386 <!-- JAL-2049 -->Protein sequence variant annotation
1387 computed for 'sequence_variant' annotation on CDS regions
1391 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1395 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1396 Ref Fetcher fails to match, or otherwise updates sequence
1397 data from external database records.
1400 <!-- JAL-2154 -->Revised Jalview Project format for
1401 efficient recovery of sequence coding and alignment
1402 annotation relationships.
1404 </ul> <!-- <em>Applet</em>
1415 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1419 <!-- JAL-2018-->Export features in Jalview format (again)
1420 includes graduated colourschemes
1423 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1424 working with big alignments and lots of hidden columns
1427 <!-- JAL-2053-->Hidden column markers not always rendered
1428 at right of alignment window
1431 <!-- JAL-2067 -->Tidied up links in help file table of
1435 <!-- JAL-2072 -->Feature based tree calculation not shown
1439 <!-- JAL-2075 -->Hidden columns ignored during feature
1440 based tree calculation
1443 <!-- JAL-2065 -->Alignment view stops updating when show
1444 unconserved enabled for group on alignment
1447 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1451 <!-- JAL-2146 -->Alignment column in status incorrectly
1452 shown as "Sequence position" when mousing over
1456 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1457 hidden columns present
1460 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1461 user created annotation added to alignment
1464 <!-- JAL-1841 -->RNA Structure consensus only computed for
1465 '()' base pair annotation
1468 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1469 in zero scores for all base pairs in RNA Structure
1473 <!-- JAL-2174-->Extend selection with columns containing
1477 <!-- JAL-2275 -->Pfam format writer puts extra space at
1478 beginning of sequence
1481 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1485 <!-- JAL-2238 -->Cannot create groups on an alignment from
1486 from a tree when t-coffee scores are shown
1489 <!-- JAL-1836,1967 -->Cannot import and view PDB
1490 structures with chains containing negative resnums (4q4h)
1493 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1497 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1498 to Clustal, PIR and PileUp output
1501 <!-- JAL-2008 -->Reordering sequence features that are
1502 not visible causes alignment window to repaint
1505 <!-- JAL-2006 -->Threshold sliders don't work in
1506 graduated colour and colour by annotation row for e-value
1507 scores associated with features and annotation rows
1510 <!-- JAL-1797 -->amino acid physicochemical conservation
1511 calculation should be case independent
1514 <!-- JAL-2173 -->Remove annotation also updates hidden
1518 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1519 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1520 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1523 <!-- JAL-2065 -->Null pointer exceptions and redraw
1524 problems when reference sequence defined and 'show
1525 non-conserved' enabled
1528 <!-- JAL-1306 -->Quality and Conservation are now shown on
1529 load even when Consensus calculation is disabled
1532 <!-- JAL-1932 -->Remove right on penultimate column of
1533 alignment does nothing
1536 <em>Application</em>
1539 <!-- JAL-1552-->URLs and links can't be imported by
1540 drag'n'drop on OSX when launched via webstart (note - not
1541 yet fixed for El Capitan)
1544 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1545 output when running on non-gb/us i18n platforms
1548 <!-- JAL-1944 -->Error thrown when exporting a view with
1549 hidden sequences as flat-file alignment
1552 <!-- JAL-2030-->InstallAnywhere distribution fails when
1556 <!-- JAL-2080-->Jalview very slow to launch via webstart
1557 (also hotfix for 2.9.0b2)
1560 <!-- JAL-2085 -->Cannot save project when view has a
1561 reference sequence defined
1564 <!-- JAL-1011 -->Columns are suddenly selected in other
1565 alignments and views when revealing hidden columns
1568 <!-- JAL-1989 -->Hide columns not mirrored in complement
1569 view in a cDNA/Protein splitframe
1572 <!-- JAL-1369 -->Cannot save/restore representative
1573 sequence from project when only one sequence is
1577 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1578 in Structure Chooser
1581 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1582 structure consensus didn't refresh annotation panel
1585 <!-- JAL-1962 -->View mapping in structure view shows
1586 mappings between sequence and all chains in a PDB file
1589 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1590 dialogs format columns correctly, don't display array
1591 data, sort columns according to type
1594 <!-- JAL-1975 -->Export complete shown after destination
1595 file chooser is cancelled during an image export
1598 <!-- JAL-2025 -->Error when querying PDB Service with
1599 sequence name containing special characters
1602 <!-- JAL-2024 -->Manual PDB structure querying should be
1606 <!-- JAL-2104 -->Large tooltips with broken HTML
1607 formatting don't wrap
1610 <!-- JAL-1128 -->Figures exported from wrapped view are
1611 truncated so L looks like I in consensus annotation
1614 <!-- JAL-2003 -->Export features should only export the
1615 currently displayed features for the current selection or
1619 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1620 after fetching cross-references, and restoring from
1624 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1625 followed in the structure viewer
1628 <!-- JAL-2163 -->Titles for individual alignments in
1629 splitframe not restored from project
1632 <!-- JAL-2145 -->missing autocalculated annotation at
1633 trailing end of protein alignment in transcript/product
1634 splitview when pad-gaps not enabled by default
1637 <!-- JAL-1797 -->amino acid physicochemical conservation
1641 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1642 article has been read (reopened issue due to
1643 internationalisation problems)
1646 <!-- JAL-1960 -->Only offer PDB structures in structure
1647 viewer based on sequence name, PDB and UniProt
1652 <!-- JAL-1976 -->No progress bar shown during export of
1656 <!-- JAL-2213 -->Structures not always superimposed after
1657 multiple structures are shown for one or more sequences.
1660 <!-- JAL-1370 -->Reference sequence characters should not
1661 be replaced with '.' when 'Show unconserved' format option
1665 <!-- JAL-1823 -->Cannot specify chain code when entering
1666 specific PDB id for sequence
1669 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1670 'Export hidden sequences' is enabled, but 'export hidden
1671 columns' is disabled.
1674 <!--JAL-2026-->Best Quality option in structure chooser
1675 selects lowest rather than highest resolution structures
1679 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1680 to sequence mapping in 'View Mappings' report
1683 <!-- JAL-2284 -->Unable to read old Jalview projects that
1684 contain non-XML data added after Jalvew wrote project.
1687 <!-- JAL-2118 -->Newly created annotation row reorders
1688 after clicking on it to create new annotation for a
1692 <!-- JAL-1980 -->Null Pointer Exception raised when
1693 pressing Add on an orphaned cut'n'paste window.
1695 <!-- may exclude, this is an external service stability issue JAL-1941
1696 -- > RNA 3D structure not added via DSSR service</li> -->
1701 <!-- JAL-2151 -->Incorrect columns are selected when
1702 hidden columns present before start of sequence
1705 <!-- JAL-1986 -->Missing dependencies on applet pages
1709 <!-- JAL-1947 -->Overview pixel size changes when
1710 sequences are hidden in applet
1713 <!-- JAL-1996 -->Updated instructions for applet
1714 deployment on examples pages.
1721 <td width="60" nowrap>
1722 <div align="center">
1723 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1724 <em>16/10/2015</em></strong>
1727 <td><em>General</em>
1729 <li>Time stamps for signed Jalview application and applet
1734 <em>Application</em>
1736 <li>Duplicate group consensus and conservation rows
1737 shown when tree is partitioned</li>
1738 <li>Erratic behaviour when tree partitions made with
1739 multiple cDNA/Protein split views</li>
1745 <td width="60" nowrap>
1746 <div align="center">
1747 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1748 <em>8/10/2015</em></strong>
1751 <td><em>General</em>
1753 <li>Updated Spanish translations of localized text for
1755 </ul> <em>Application</em>
1757 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1758 <li>Signed OSX InstallAnywhere installer<br></li>
1759 <li>Support for per-sequence based annotations in BioJSON</li>
1760 </ul> <em>Applet</em>
1762 <li>Split frame example added to applet examples page</li>
1763 </ul> <em>Build and Deployment</em>
1766 <!-- JAL-1888 -->New ant target for running Jalview's test
1774 <li>Mapping of cDNA to protein in split frames
1775 incorrect when sequence start > 1</li>
1776 <li>Broken images in filter column by annotation dialog
1778 <li>Feature colours not parsed from features file</li>
1779 <li>Exceptions and incomplete link URLs recovered when
1780 loading a features file containing HTML tags in feature
1784 <em>Application</em>
1786 <li>Annotations corrupted after BioJS export and
1788 <li>Incorrect sequence limits after Fetch DB References
1789 with 'trim retrieved sequences'</li>
1790 <li>Incorrect warning about deleting all data when
1791 deleting selected columns</li>
1792 <li>Patch to build system for shipping properly signed
1793 JNLP templates for webstart launch</li>
1794 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1795 unreleased structures for download or viewing</li>
1796 <li>Tab/space/return keystroke operation of EMBL-PDBe
1797 fetcher/viewer dialogs works correctly</li>
1798 <li>Disabled 'minimise' button on Jalview windows
1799 running on OSX to workaround redraw hang bug</li>
1800 <li>Split cDNA/Protein view position and geometry not
1801 recovered from jalview project</li>
1802 <li>Initial enabled/disabled state of annotation menu
1803 sorter 'show autocalculated first/last' corresponds to
1805 <li>Restoring of Clustal, RNA Helices and T-Coffee
1806 color schemes from BioJSON</li>
1810 <li>Reorder sequences mirrored in cDNA/Protein split
1812 <li>Applet with Jmol examples not loading correctly</li>
1818 <td><div align="center">
1819 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1821 <td><em>General</em>
1823 <li>Linked visualisation and analysis of DNA and Protein
1826 <li>Translated cDNA alignments shown as split protein
1827 and DNA alignment views</li>
1828 <li>Codon consensus annotation for linked protein and
1829 cDNA alignment views</li>
1830 <li>Link cDNA or Protein product sequences by loading
1831 them onto Protein or cDNA alignments</li>
1832 <li>Reconstruct linked cDNA alignment from aligned
1833 protein sequences</li>
1836 <li>Jmol integration updated to Jmol v14.2.14</li>
1837 <li>Import and export of Jalview alignment views as <a
1838 href="features/bioJsonFormat.html">BioJSON</a></li>
1839 <li>New alignment annotation file statements for
1840 reference sequences and marking hidden columns</li>
1841 <li>Reference sequence based alignment shading to
1842 highlight variation</li>
1843 <li>Select or hide columns according to alignment
1845 <li>Find option for locating sequences by description</li>
1846 <li>Conserved physicochemical properties shown in amino
1847 acid conservation row</li>
1848 <li>Alignments can be sorted by number of RNA helices</li>
1849 </ul> <em>Application</em>
1851 <li>New cDNA/Protein analysis capabilities
1853 <li>Get Cross-References should open a Split Frame
1854 view with cDNA/Protein</li>
1855 <li>Detect when nucleotide sequences and protein
1856 sequences are placed in the same alignment</li>
1857 <li>Split cDNA/Protein views are saved in Jalview
1862 <li>Use REST API to talk to Chimera</li>
1863 <li>Selected regions in Chimera are highlighted in linked
1864 Jalview windows</li>
1866 <li>VARNA RNA viewer updated to v3.93</li>
1867 <li>VARNA views are saved in Jalview Projects</li>
1868 <li>Pseudoknots displayed as Jalview RNA annotation can
1869 be shown in VARNA</li>
1871 <li>Make groups for selection uses marked columns as well
1872 as the active selected region</li>
1874 <li>Calculate UPGMA and NJ trees using sequence feature
1876 <li>New Export options
1878 <li>New Export Settings dialog to control hidden
1879 region export in flat file generation</li>
1881 <li>Export alignment views for display with the <a
1882 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1884 <li>Export scrollable SVG in HTML page</li>
1885 <li>Optional embedding of BioJSON data when exporting
1886 alignment figures to HTML</li>
1888 <li>3D structure retrieval and display
1890 <li>Free text and structured queries with the PDBe
1892 <li>PDBe Search API based discovery and selection of
1893 PDB structures for a sequence set</li>
1897 <li>JPred4 employed for protein secondary structure
1899 <li>Hide Insertions menu option to hide unaligned columns
1900 for one or a group of sequences</li>
1901 <li>Automatically hide insertions in alignments imported
1902 from the JPred4 web server</li>
1903 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1904 system on OSX<br />LGPL libraries courtesy of <a
1905 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1907 <li>changed 'View nucleotide structure' submenu to 'View
1908 VARNA 2D Structure'</li>
1909 <li>change "View protein structure" menu option to "3D
1912 </ul> <em>Applet</em>
1914 <li>New layout for applet example pages</li>
1915 <li>New parameters to enable SplitFrame view
1916 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1917 <li>New example demonstrating linked viewing of cDNA and
1918 Protein alignments</li>
1919 </ul> <em>Development and deployment</em>
1921 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1922 <li>Include installation type and git revision in build
1923 properties and console log output</li>
1924 <li>Jalview Github organisation, and new github site for
1925 storing BioJsMSA Templates</li>
1926 <li>Jalview's unit tests now managed with TestNG</li>
1929 <!-- <em>General</em>
1931 </ul> --> <!-- issues resolved --> <em>Application</em>
1933 <li>Escape should close any open find dialogs</li>
1934 <li>Typo in select-by-features status report</li>
1935 <li>Consensus RNA secondary secondary structure
1936 predictions are not highlighted in amber</li>
1937 <li>Missing gap character in v2.7 example file means
1938 alignment appears unaligned when pad-gaps is not enabled</li>
1939 <li>First switch to RNA Helices colouring doesn't colour
1940 associated structure views</li>
1941 <li>ID width preference option is greyed out when auto
1942 width checkbox not enabled</li>
1943 <li>Stopped a warning dialog from being shown when
1944 creating user defined colours</li>
1945 <li>'View Mapping' in structure viewer shows sequence
1946 mappings for just that viewer's sequences</li>
1947 <li>Workaround for superposing PDB files containing
1948 multiple models in Chimera</li>
1949 <li>Report sequence position in status bar when hovering
1950 over Jmol structure</li>
1951 <li>Cannot output gaps as '.' symbols with Selection ->
1952 output to text box</li>
1953 <li>Flat file exports of alignments with hidden columns
1954 have incorrect sequence start/end</li>
1955 <li>'Aligning' a second chain to a Chimera structure from
1957 <li>Colour schemes applied to structure viewers don't
1958 work for nucleotide</li>
1959 <li>Loading/cut'n'pasting an empty or invalid file leads
1960 to a grey/invisible alignment window</li>
1961 <li>Exported Jpred annotation from a sequence region
1962 imports to different position</li>
1963 <li>Space at beginning of sequence feature tooltips shown
1964 on some platforms</li>
1965 <li>Chimera viewer 'View | Show Chain' menu is not
1967 <li>'New View' fails with a Null Pointer Exception in
1968 console if Chimera has been opened</li>
1969 <li>Mouseover to Chimera not working</li>
1970 <li>Miscellaneous ENA XML feature qualifiers not
1972 <li>NPE in annotation renderer after 'Extract Scores'</li>
1973 <li>If two structures in one Chimera window, mouseover of
1974 either sequence shows on first structure</li>
1975 <li>'Show annotations' options should not make
1976 non-positional annotations visible</li>
1977 <li>Subsequence secondary structure annotation not shown
1978 in right place after 'view flanking regions'</li>
1979 <li>File Save As type unset when current file format is
1981 <li>Save as '.jar' option removed for saving Jalview
1983 <li>Colour by Sequence colouring in Chimera more
1985 <li>Cannot 'add reference annotation' for a sequence in
1986 several views on same alignment</li>
1987 <li>Cannot show linked products for EMBL / ENA records</li>
1988 <li>Jalview's tooltip wraps long texts containing no
1990 </ul> <em>Applet</em>
1992 <li>Jmol to JalviewLite mouseover/link not working</li>
1993 <li>JalviewLite can't import sequences with ID
1994 descriptions containing angle brackets</li>
1995 </ul> <em>General</em>
1997 <li>Cannot export and reimport RNA secondary structure
1998 via jalview annotation file</li>
1999 <li>Random helix colour palette for colour by annotation
2000 with RNA secondary structure</li>
2001 <li>Mouseover to cDNA from STOP residue in protein
2002 translation doesn't work.</li>
2003 <li>hints when using the select by annotation dialog box</li>
2004 <li>Jmol alignment incorrect if PDB file has alternate CA
2006 <li>FontChooser message dialog appears to hang after
2007 choosing 1pt font</li>
2008 <li>Peptide secondary structure incorrectly imported from
2009 annotation file when annotation display text includes 'e' or
2011 <li>Cannot set colour of new feature type whilst creating
2013 <li>cDNA translation alignment should not be sequence
2014 order dependent</li>
2015 <li>'Show unconserved' doesn't work for lower case
2017 <li>Nucleotide ambiguity codes involving R not recognised</li>
2018 </ul> <em>Deployment and Documentation</em>
2020 <li>Applet example pages appear different to the rest of
2021 www.jalview.org</li>
2022 </ul> <em>Application Known issues</em>
2024 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
2025 <li>Misleading message appears after trying to delete
2027 <li>Jalview icon not shown in dock after InstallAnywhere
2028 version launches</li>
2029 <li>Fetching EMBL reference for an RNA sequence results
2030 fails with a sequence mismatch</li>
2031 <li>Corrupted or unreadable alignment display when
2032 scrolling alignment to right</li>
2033 <li>ArrayIndexOutOfBoundsException thrown when remove
2034 empty columns called on alignment with ragged gapped ends</li>
2035 <li>auto calculated alignment annotation rows do not get
2036 placed above or below non-autocalculated rows</li>
2037 <li>Jalview dekstop becomes sluggish at full screen in
2038 ultra-high resolution</li>
2039 <li>Cannot disable consensus calculation independently of
2040 quality and conservation</li>
2041 <li>Mouseover highlighting between cDNA and protein can
2042 become sluggish with more than one splitframe shown</li>
2043 </ul> <em>Applet Known Issues</em>
2045 <li>Core PDB parsing code requires Jmol</li>
2046 <li>Sequence canvas panel goes white when alignment
2047 window is being resized</li>
2053 <td><div align="center">
2054 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
2056 <td><em>General</em>
2058 <li>Updated Java code signing certificate donated by
2060 <li>Features and annotation preserved when performing
2061 pairwise alignment</li>
2062 <li>RNA pseudoknot annotation can be
2063 imported/exported/displayed</li>
2064 <li>'colour by annotation' can colour by RNA and
2065 protein secondary structure</li>
2066 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
2067 post-hoc with 2.9 release</em>)
2070 </ul> <em>Application</em>
2072 <li>Extract and display secondary structure for sequences
2073 with 3D structures</li>
2074 <li>Support for parsing RNAML</li>
2075 <li>Annotations menu for layout
2077 <li>sort sequence annotation rows by alignment</li>
2078 <li>place sequence annotation above/below alignment
2081 <li>Output in Stockholm format</li>
2082 <li>Internationalisation: improved Spanish (es)
2084 <li>Structure viewer preferences tab</li>
2085 <li>Disorder and Secondary Structure annotation tracks
2086 shared between alignments</li>
2087 <li>UCSF Chimera launch and linked highlighting from
2089 <li>Show/hide all sequence associated annotation rows for
2090 all or current selection</li>
2091 <li>disorder and secondary structure predictions
2092 available as dataset annotation</li>
2093 <li>Per-sequence rna helices colouring</li>
2096 <li>Sequence database accessions imported when fetching
2097 alignments from Rfam</li>
2098 <li>update VARNA version to 3.91</li>
2100 <li>New groovy scripts for exporting aligned positions,
2101 conservation values, and calculating sum of pairs scores.</li>
2102 <li>Command line argument to set default JABAWS server</li>
2103 <li>include installation type in build properties and
2104 console log output</li>
2105 <li>Updated Jalview project format to preserve dataset
2109 <!-- issues resolved --> <em>Application</em>
2111 <li>Distinguish alignment and sequence associated RNA
2112 structure in structure->view->VARNA</li>
2113 <li>Raise dialog box if user deletes all sequences in an
2115 <li>Pressing F1 results in documentation opening twice</li>
2116 <li>Sequence feature tooltip is wrapped</li>
2117 <li>Double click on sequence associated annotation
2118 selects only first column</li>
2119 <li>Redundancy removal doesn't result in unlinked
2120 leaves shown in tree</li>
2121 <li>Undos after several redundancy removals don't undo
2123 <li>Hide sequence doesn't hide associated annotation</li>
2124 <li>User defined colours dialog box too big to fit on
2125 screen and buttons not visible</li>
2126 <li>author list isn't updated if already written to
2127 Jalview properties</li>
2128 <li>Popup menu won't open after retrieving sequence
2130 <li>File open window for associate PDB doesn't open</li>
2131 <li>Left-then-right click on a sequence id opens a
2132 browser search window</li>
2133 <li>Cannot open sequence feature shading/sort popup menu
2134 in feature settings dialog</li>
2135 <li>better tooltip placement for some areas of Jalview
2137 <li>Allow addition of JABAWS Server which doesn't
2138 pass validation</li>
2139 <li>Web services parameters dialog box is too large to
2141 <li>Muscle nucleotide alignment preset obscured by
2143 <li>JABAWS preset submenus don't contain newly
2144 defined user preset</li>
2145 <li>MSA web services warns user if they were launched
2146 with invalid input</li>
2147 <li>Jalview cannot contact DAS Registy when running on
2150 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
2151 'Superpose with' submenu not shown when new view
2155 </ul> <!-- <em>Applet</em>
2157 </ul> <em>General</em>
2159 </ul>--> <em>Deployment and Documentation</em>
2161 <li>2G and 1G options in launchApp have no effect on
2162 memory allocation</li>
2163 <li>launchApp service doesn't automatically open
2164 www.jalview.org/examples/exampleFile.jar if no file is given</li>
2166 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
2167 InstallAnywhere reports cannot find valid JVM when Java
2168 1.7_055 is available
2170 </ul> <em>Application Known issues</em>
2173 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
2174 corrupted or unreadable alignment display when scrolling
2178 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
2179 retrieval fails but progress bar continues for DAS retrieval
2180 with large number of ID
2183 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
2184 flatfile output of visible region has incorrect sequence
2188 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
2189 rna structure consensus doesn't update when secondary
2190 structure tracks are rearranged
2193 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
2194 invalid rna structure positional highlighting does not
2195 highlight position of invalid base pairs
2198 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
2199 out of memory errors are not raised when saving Jalview
2200 project from alignment window file menu
2203 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
2204 Switching to RNA Helices colouring doesn't propagate to
2208 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
2209 colour by RNA Helices not enabled when user created
2210 annotation added to alignment
2213 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
2214 Jalview icon not shown on dock in Mountain Lion/Webstart
2216 </ul> <em>Applet Known Issues</em>
2219 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
2220 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
2223 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
2224 Jalview and Jmol example not compatible with IE9
2227 <li>Sort by annotation score doesn't reverse order
2233 <td><div align="center">
2234 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
2237 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
2240 <li>Internationalisation of user interface (usually
2241 called i18n support) and translation for Spanish locale</li>
2242 <li>Define/Undefine group on current selection with
2243 Ctrl-G/Shift Ctrl-G</li>
2244 <li>Improved group creation/removal options in
2245 alignment/sequence Popup menu</li>
2246 <li>Sensible precision for symbol distribution
2247 percentages shown in logo tooltip.</li>
2248 <li>Annotation panel height set according to amount of
2249 annotation when alignment first opened</li>
2250 </ul> <em>Application</em>
2252 <li>Interactive consensus RNA secondary structure
2253 prediction VIENNA RNAAliFold JABA 2.1 service</li>
2254 <li>Select columns containing particular features from
2255 Feature Settings dialog</li>
2256 <li>View all 'representative' PDB structures for selected
2258 <li>Update Jalview project format:
2260 <li>New file extension for Jalview projects '.jvp'</li>
2261 <li>Preserve sequence and annotation dataset (to
2262 store secondary structure annotation,etc)</li>
2263 <li>Per group and alignment annotation and RNA helix
2267 <li>New similarity measures for PCA and Tree calculation
2269 <li>Experimental support for retrieval and viewing of
2270 flanking regions for an alignment</li>
2274 <!-- issues resolved --> <em>Application</em>
2276 <li>logo keeps spinning and status remains at queued or
2277 running after job is cancelled</li>
2278 <li>cannot export features from alignments imported from
2279 Jalview/VAMSAS projects</li>
2280 <li>Buggy slider for web service parameters that take
2282 <li>Newly created RNA secondary structure line doesn't
2283 have 'display all symbols' flag set</li>
2284 <li>T-COFFEE alignment score shading scheme and other
2285 annotation shading not saved in Jalview project</li>
2286 <li>Local file cannot be loaded in freshly downloaded
2288 <li>Jalview icon not shown on dock in Mountain
2290 <li>Load file from desktop file browser fails</li>
2291 <li>Occasional NPE thrown when calculating large trees</li>
2292 <li>Cannot reorder or slide sequences after dragging an
2293 alignment onto desktop</li>
2294 <li>Colour by annotation dialog throws NPE after using
2295 'extract scores' function</li>
2296 <li>Loading/cut'n'pasting an empty file leads to a grey
2297 alignment window</li>
2298 <li>Disorder thresholds rendered incorrectly after
2299 performing IUPred disorder prediction</li>
2300 <li>Multiple group annotated consensus rows shown when
2301 changing 'normalise logo' display setting</li>
2302 <li>Find shows blank dialog after 'finished searching' if
2303 nothing matches query</li>
2304 <li>Null Pointer Exceptions raised when sorting by
2305 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2307 <li>Errors in Jmol console when structures in alignment
2308 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2310 <li>Not all working JABAWS services are shown in
2312 <li>JAVAWS version of Jalview fails to launch with
2313 'invalid literal/length code'</li>
2314 <li>Annotation/RNA Helix colourschemes cannot be applied
2315 to alignment with groups (actually fixed in 2.8.0b1)</li>
2316 <li>RNA Helices and T-Coffee Scores available as default
2319 </ul> <em>Applet</em>
2321 <li>Remove group option is shown even when selection is
2323 <li>Apply to all groups ticked but colourscheme changes
2324 don't affect groups</li>
2325 <li>Documented RNA Helices and T-Coffee Scores as valid
2326 colourscheme name</li>
2327 <li>Annotation labels drawn on sequence IDs when
2328 Annotation panel is not displayed</li>
2329 <li>Increased font size for dropdown menus on OSX and
2330 embedded windows</li>
2331 </ul> <em>Other</em>
2333 <li>Consensus sequence for alignments/groups with a
2334 single sequence were not calculated</li>
2335 <li>annotation files that contain only groups imported as
2336 annotation and junk sequences</li>
2337 <li>Fasta files with sequences containing '*' incorrectly
2338 recognised as PFAM or BLC</li>
2339 <li>conservation/PID slider apply all groups option
2340 doesn't affect background (2.8.0b1)
2342 <li>redundancy highlighting is erratic at 0% and 100%</li>
2343 <li>Remove gapped columns fails for sequences with ragged
2345 <li>AMSA annotation row with leading spaces is not
2346 registered correctly on import</li>
2347 <li>Jalview crashes when selecting PCA analysis for
2348 certain alignments</li>
2349 <li>Opening the colour by annotation dialog for an
2350 existing annotation based 'use original colours'
2351 colourscheme loses original colours setting</li>
2356 <td><div align="center">
2357 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2358 <em>30/1/2014</em></strong>
2362 <li>Trusted certificates for JalviewLite applet and
2363 Jalview Desktop application<br />Certificate was donated by
2364 <a href="https://www.certum.eu">Certum</a> to the Jalview
2365 open source project).
2367 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2368 <li>Output in Stockholm format</li>
2369 <li>Allow import of data from gzipped files</li>
2370 <li>Export/import group and sequence associated line
2371 graph thresholds</li>
2372 <li>Nucleotide substitution matrix that supports RNA and
2373 ambiguity codes</li>
2374 <li>Allow disorder predictions to be made on the current
2375 selection (or visible selection) in the same way that JPred
2377 <li>Groovy scripting for headless Jalview operation</li>
2378 </ul> <em>Other improvements</em>
2380 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2381 <li>COMBINE statement uses current SEQUENCE_REF and
2382 GROUP_REF scope to group annotation rows</li>
2383 <li>Support '' style escaping of quotes in Newick
2385 <li>Group options for JABAWS service by command line name</li>
2386 <li>Empty tooltip shown for JABA service options with a
2387 link but no description</li>
2388 <li>Select primary source when selecting authority in
2389 database fetcher GUI</li>
2390 <li>Add .mfa to FASTA file extensions recognised by
2392 <li>Annotation label tooltip text wrap</li>
2397 <li>Slow scrolling when lots of annotation rows are
2399 <li>Lots of NPE (and slowness) after creating RNA
2400 secondary structure annotation line</li>
2401 <li>Sequence database accessions not imported when
2402 fetching alignments from Rfam</li>
2403 <li>Incorrect SHMR submission for sequences with
2405 <li>View all structures does not always superpose
2407 <li>Option widgets in service parameters not updated to
2408 reflect user or preset settings</li>
2409 <li>Null pointer exceptions for some services without
2410 presets or adjustable parameters</li>
2411 <li>Discover PDB IDs entry in structure menu doesn't
2412 discover PDB xRefs</li>
2413 <li>Exception encountered while trying to retrieve
2414 features with DAS</li>
2415 <li>Lowest value in annotation row isn't coloured
2416 when colour by annotation (per sequence) is coloured</li>
2417 <li>Keyboard mode P jumps to start of gapped region when
2418 residue follows a gap</li>
2419 <li>Jalview appears to hang importing an alignment with
2420 Wrap as default or after enabling Wrap</li>
2421 <li>'Right click to add annotations' message
2422 shown in wrap mode when no annotations present</li>
2423 <li>Disorder predictions fail with NPE if no automatic
2424 annotation already exists on alignment</li>
2425 <li>oninit javascript function should be called after
2426 initialisation completes</li>
2427 <li>Remove redundancy after disorder prediction corrupts
2428 alignment window display</li>
2429 <li>Example annotation file in documentation is invalid</li>
2430 <li>Grouped line graph annotation rows are not exported
2431 to annotation file</li>
2432 <li>Multi-harmony analysis cannot be run when only two
2434 <li>Cannot create multiple groups of line graphs with
2435 several 'combine' statements in annotation file</li>
2436 <li>Pressing return several times causes Number Format
2437 exceptions in keyboard mode</li>
2438 <li>Multi-harmony (SHMMR) method doesn't submit
2439 correct partitions for input data</li>
2440 <li>Translation from DNA to Amino Acids fails</li>
2441 <li>Jalview fail to load newick tree with quoted label</li>
2442 <li>--headless flag isn't understood</li>
2443 <li>ClassCastException when generating EPS in headless
2445 <li>Adjusting sequence-associated shading threshold only
2446 changes one row's threshold</li>
2447 <li>Preferences and Feature settings panel panel
2448 doesn't open</li>
2449 <li>hide consensus histogram also hides conservation and
2450 quality histograms</li>
2455 <td><div align="center">
2456 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2458 <td><em>Application</em>
2460 <li>Support for JABAWS 2.0 Services (AACon alignment
2461 conservation, protein disorder and Clustal Omega)</li>
2462 <li>JABAWS server status indicator in Web Services
2464 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2465 in Jalview alignment window</li>
2466 <li>Updated Jalview build and deploy framework for OSX
2467 mountain lion, windows 7, and 8</li>
2468 <li>Nucleotide substitution matrix for PCA that supports
2469 RNA and ambiguity codes</li>
2471 <li>Improved sequence database retrieval GUI</li>
2472 <li>Support fetching and database reference look up
2473 against multiple DAS sources (Fetch all from in 'fetch db
2475 <li>Jalview project improvements
2477 <li>Store and retrieve the 'belowAlignment'
2478 flag for annotation</li>
2479 <li>calcId attribute to group annotation rows on the
2481 <li>Store AACon calculation settings for a view in
2482 Jalview project</li>
2486 <li>horizontal scrolling gesture support</li>
2487 <li>Visual progress indicator when PCA calculation is
2489 <li>Simpler JABA web services menus</li>
2490 <li>visual indication that web service results are still
2491 being retrieved from server</li>
2492 <li>Serialise the dialogs that are shown when Jalview
2493 starts up for first time</li>
2494 <li>Jalview user agent string for interacting with HTTP
2496 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2498 <li>Examples directory and Groovy library included in
2499 InstallAnywhere distribution</li>
2500 </ul> <em>Applet</em>
2502 <li>RNA alignment and secondary structure annotation
2503 visualization applet example</li>
2504 </ul> <em>General</em>
2506 <li>Normalise option for consensus sequence logo</li>
2507 <li>Reset button in PCA window to return dimensions to
2509 <li>Allow seqspace or Jalview variant of alignment PCA
2511 <li>PCA with either nucleic acid and protein substitution
2513 <li>Allow windows containing HTML reports to be exported
2515 <li>Interactive display and editing of RNA secondary
2516 structure contacts</li>
2517 <li>RNA Helix Alignment Colouring</li>
2518 <li>RNA base pair logo consensus</li>
2519 <li>Parse sequence associated secondary structure
2520 information in Stockholm files</li>
2521 <li>HTML Export database accessions and annotation
2522 information presented in tooltip for sequences</li>
2523 <li>Import secondary structure from LOCARNA clustalw
2524 style RNA alignment files</li>
2525 <li>import and visualise T-COFFEE quality scores for an
2527 <li>'colour by annotation' per sequence option to
2528 shade each sequence according to its associated alignment
2530 <li>New Jalview Logo</li>
2531 </ul> <em>Documentation and Development</em>
2533 <li>documentation for score matrices used in Jalview</li>
2534 <li>New Website!</li>
2536 <td><em>Application</em>
2538 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2539 wsdbfetch REST service</li>
2540 <li>Stop windows being moved outside desktop on OSX</li>
2541 <li>Filetype associations not installed for webstart
2543 <li>Jalview does not always retrieve progress of a JABAWS
2544 job execution in full once it is complete</li>
2545 <li>revise SHMR RSBS definition to ensure alignment is
2546 uploaded via ali_file parameter</li>
2547 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2548 <li>View all structures superposed fails with exception</li>
2549 <li>Jnet job queues forever if a very short sequence is
2550 submitted for prediction</li>
2551 <li>Cut and paste menu not opened when mouse clicked on
2553 <li>Putting fractional value into integer text box in
2554 alignment parameter dialog causes Jalview to hang</li>
2555 <li>Structure view highlighting doesn't work on
2557 <li>View all structures fails with exception shown in
2559 <li>Characters in filename associated with PDBEntry not
2560 escaped in a platform independent way</li>
2561 <li>Jalview desktop fails to launch with exception when
2563 <li>Tree calculation reports 'you must have 2 or more
2564 sequences selected' when selection is empty</li>
2565 <li>Jalview desktop fails to launch with jar signature
2566 failure when java web start temporary file caching is
2568 <li>DAS Sequence retrieval with range qualification
2569 results in sequence xref which includes range qualification</li>
2570 <li>Errors during processing of command line arguments
2571 cause progress bar (JAL-898) to be removed</li>
2572 <li>Replace comma for semi-colon option not disabled for
2573 DAS sources in sequence fetcher</li>
2574 <li>Cannot close news reader when JABAWS server warning
2575 dialog is shown</li>
2576 <li>Option widgets not updated to reflect user settings</li>
2577 <li>Edited sequence not submitted to web service</li>
2578 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2579 <li>InstallAnywhere installer doesn't unpack and run
2580 on OSX Mountain Lion</li>
2581 <li>Annotation panel not given a scroll bar when
2582 sequences with alignment annotation are pasted into the
2584 <li>Sequence associated annotation rows not associated
2585 when loaded from Jalview project</li>
2586 <li>Browser launch fails with NPE on java 1.7</li>
2587 <li>JABAWS alignment marked as finished when job was
2588 cancelled or job failed due to invalid input</li>
2589 <li>NPE with v2.7 example when clicking on Tree
2590 associated with all views</li>
2591 <li>Exceptions when copy/paste sequences with grouped
2592 annotation rows to new window</li>
2593 </ul> <em>Applet</em>
2595 <li>Sequence features are momentarily displayed before
2596 they are hidden using hidefeaturegroups applet parameter</li>
2597 <li>loading features via javascript API automatically
2598 enables feature display</li>
2599 <li>scrollToColumnIn javascript API method doesn't
2601 </ul> <em>General</em>
2603 <li>Redundancy removal fails for rna alignment</li>
2604 <li>PCA calculation fails when sequence has been selected
2605 and then deselected</li>
2606 <li>PCA window shows grey box when first opened on OSX</li>
2607 <li>Letters coloured pink in sequence logo when alignment
2608 coloured with clustalx</li>
2609 <li>Choosing fonts without letter symbols defined causes
2610 exceptions and redraw errors</li>
2611 <li>Initial PCA plot view is not same as manually
2612 reconfigured view</li>
2613 <li>Grouped annotation graph label has incorrect line
2615 <li>Grouped annotation graph label display is corrupted
2616 for lots of labels</li>
2621 <div align="center">
2622 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2625 <td><em>Application</em>
2627 <li>Jalview Desktop News Reader</li>
2628 <li>Tweaked default layout of web services menu</li>
2629 <li>View/alignment association menu to enable user to
2630 easily specify which alignment a multi-structure view takes
2631 its colours/correspondences from</li>
2632 <li>Allow properties file location to be specified as URL</li>
2633 <li>Extend Jalview project to preserve associations
2634 between many alignment views and a single Jmol display</li>
2635 <li>Store annotation row height in Jalview project file</li>
2636 <li>Annotation row column label formatting attributes
2637 stored in project file</li>
2638 <li>Annotation row order for auto-calculated annotation
2639 rows preserved in Jalview project file</li>
2640 <li>Visual progress indication when Jalview state is
2641 saved using Desktop window menu</li>
2642 <li>Visual indication that command line arguments are
2643 still being processed</li>
2644 <li>Groovy script execution from URL</li>
2645 <li>Colour by annotation default min and max colours in
2647 <li>Automatically associate PDB files dragged onto an
2648 alignment with sequences that have high similarity and
2650 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2651 <li>'view structures' option to open many
2652 structures in same window</li>
2653 <li>Sort associated views menu option for tree panel</li>
2654 <li>Group all JABA and non-JABA services for a particular
2655 analysis function in its own submenu</li>
2656 </ul> <em>Applet</em>
2658 <li>Userdefined and autogenerated annotation rows for
2660 <li>Adjustment of alignment annotation pane height</li>
2661 <li>Annotation scrollbar for annotation panel</li>
2662 <li>Drag to reorder annotation rows in annotation panel</li>
2663 <li>'automaticScrolling' parameter</li>
2664 <li>Allow sequences with partial ID string matches to be
2665 annotated from GFF/Jalview features files</li>
2666 <li>Sequence logo annotation row in applet</li>
2667 <li>Absolute paths relative to host server in applet
2668 parameters are treated as such</li>
2669 <li>New in the JalviewLite javascript API:
2671 <li>JalviewLite.js javascript library</li>
2672 <li>Javascript callbacks for
2674 <li>Applet initialisation</li>
2675 <li>Sequence/alignment mouse-overs and selections</li>
2678 <li>scrollTo row and column alignment scrolling
2680 <li>Select sequence/alignment regions from javascript</li>
2681 <li>javascript structure viewer harness to pass
2682 messages between Jmol and Jalview when running as
2683 distinct applets</li>
2684 <li>sortBy method</li>
2685 <li>Set of applet and application examples shipped
2686 with documentation</li>
2687 <li>New example to demonstrate JalviewLite and Jmol
2688 javascript message exchange</li>
2690 </ul> <em>General</em>
2692 <li>Enable Jmol displays to be associated with multiple
2693 multiple alignments</li>
2694 <li>Option to automatically sort alignment with new tree</li>
2695 <li>User configurable link to enable redirects to a
2696 www.Jalview.org mirror</li>
2697 <li>Jmol colours option for Jmol displays</li>
2698 <li>Configurable newline string when writing alignment
2699 and other flat files</li>
2700 <li>Allow alignment annotation description lines to
2701 contain html tags</li>
2702 </ul> <em>Documentation and Development</em>
2704 <li>Add groovy test harness for bulk load testing to
2706 <li>Groovy script to load and align a set of sequences
2707 using a web service before displaying the result in the
2708 Jalview desktop</li>
2709 <li>Restructured javascript and applet api documentation</li>
2710 <li>Ant target to publish example html files with applet
2712 <li>Netbeans project for building Jalview from source</li>
2713 <li>ant task to create online javadoc for Jalview source</li>
2715 <td><em>Application</em>
2717 <li>User defined colourscheme throws exception when
2718 current built in colourscheme is saved as new scheme</li>
2719 <li>AlignFrame->Save in application pops up save
2720 dialog for valid filename/format</li>
2721 <li>Cannot view associated structure for UniProt sequence</li>
2722 <li>PDB file association breaks for UniProt sequence
2724 <li>Associate PDB from file dialog does not tell you
2725 which sequence is to be associated with the file</li>
2726 <li>Find All raises null pointer exception when query
2727 only matches sequence IDs</li>
2728 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2729 <li>Jalview project with Jmol views created with Jalview
2730 2.4 cannot be loaded</li>
2731 <li>Filetype associations not installed for webstart
2733 <li>Two or more chains in a single PDB file associated
2734 with sequences in different alignments do not get coloured
2735 by their associated sequence</li>
2736 <li>Visibility status of autocalculated annotation row
2737 not preserved when project is loaded</li>
2738 <li>Annotation row height and visibility attributes not
2739 stored in Jalview project</li>
2740 <li>Tree bootstraps are not preserved when saved as a
2741 Jalview project</li>
2742 <li>Envision2 workflow tooltips are corrupted</li>
2743 <li>Enabling show group conservation also enables colour
2744 by conservation</li>
2745 <li>Duplicate group associated conservation or consensus
2746 created on new view</li>
2747 <li>Annotation scrollbar not displayed after 'show
2748 all hidden annotation rows' option selected</li>
2749 <li>Alignment quality not updated after alignment
2750 annotation row is hidden then shown</li>
2751 <li>Preserve colouring of structures coloured by
2752 sequences in pre Jalview 2.7 projects</li>
2753 <li>Web service job parameter dialog is not laid out
2755 <li>Web services menu not refreshed after 'reset
2756 services' button is pressed in preferences</li>
2757 <li>Annotation off by one in Jalview v2_3 example project</li>
2758 <li>Structures imported from file and saved in project
2759 get name like jalview_pdb1234.txt when reloaded</li>
2760 <li>Jalview does not always retrieve progress of a JABAWS
2761 job execution in full once it is complete</li>
2762 </ul> <em>Applet</em>
2764 <li>Alignment height set incorrectly when lots of
2765 annotation rows are displayed</li>
2766 <li>Relative URLs in feature HTML text not resolved to
2768 <li>View follows highlighting does not work for positions
2770 <li><= shown as = in tooltip</li>
2771 <li>Export features raises exception when no features
2773 <li>Separator string used for serialising lists of IDs
2774 for javascript api is modified when separator string
2775 provided as parameter</li>
2776 <li>Null pointer exception when selecting tree leaves for
2777 alignment with no existing selection</li>
2778 <li>Relative URLs for datasources assumed to be relative
2779 to applet's codebase</li>
2780 <li>Status bar not updated after finished searching and
2781 search wraps around to first result</li>
2782 <li>StructureSelectionManager instance shared between
2783 several Jalview applets causes race conditions and memory
2785 <li>Hover tooltip and mouseover of position on structure
2786 not sent from Jmol in applet</li>
2787 <li>Certain sequences of javascript method calls to
2788 applet API fatally hang browser</li>
2789 </ul> <em>General</em>
2791 <li>View follows structure mouseover scrolls beyond
2792 position with wrapped view and hidden regions</li>
2793 <li>Find sequence position moves to wrong residue
2794 with/without hidden columns</li>
2795 <li>Sequence length given in alignment properties window
2797 <li>InvalidNumberFormat exceptions thrown when trying to
2798 import PDB like structure files</li>
2799 <li>Positional search results are only highlighted
2800 between user-supplied sequence start/end bounds</li>
2801 <li>End attribute of sequence is not validated</li>
2802 <li>Find dialog only finds first sequence containing a
2803 given sequence position</li>
2804 <li>Sequence numbering not preserved in MSF alignment
2806 <li>Jalview PDB file reader does not extract sequence
2807 from nucleotide chains correctly</li>
2808 <li>Structure colours not updated when tree partition
2809 changed in alignment</li>
2810 <li>Sequence associated secondary structure not correctly
2811 parsed in interleaved stockholm</li>
2812 <li>Colour by annotation dialog does not restore current
2814 <li>Hiding (nearly) all sequences doesn't work
2816 <li>Sequences containing lowercase letters are not
2817 properly associated with their pdb files</li>
2818 </ul> <em>Documentation and Development</em>
2820 <li>schemas/JalviewWsParamSet.xsd corrupted by
2821 ApplyCopyright tool</li>
2826 <div align="center">
2827 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2830 <td><em>Application</em>
2832 <li>New warning dialog when the Jalview Desktop cannot
2833 contact web services</li>
2834 <li>JABA service parameters for a preset are shown in
2835 service job window</li>
2836 <li>JABA Service menu entries reworded</li>
2840 <li>Modeller PIR IO broken - cannot correctly import a
2841 pir file emitted by Jalview</li>
2842 <li>Existing feature settings transferred to new
2843 alignment view created from cut'n'paste</li>
2844 <li>Improved test for mixed amino/nucleotide chains when
2845 parsing PDB files</li>
2846 <li>Consensus and conservation annotation rows
2847 occasionally become blank for all new windows</li>
2848 <li>Exception raised when right clicking above sequences
2849 in wrapped view mode</li>
2850 </ul> <em>Application</em>
2852 <li>multiple multiply aligned structure views cause cpu
2853 usage to hit 100% and computer to hang</li>
2854 <li>Web Service parameter layout breaks for long user
2855 parameter names</li>
2856 <li>Jaba service discovery hangs desktop if Jaba server
2863 <div align="center">
2864 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2867 <td><em>Application</em>
2869 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2870 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2873 <li>Web Services preference tab</li>
2874 <li>Analysis parameters dialog box and user defined
2876 <li>Improved speed and layout of Envision2 service menu</li>
2877 <li>Superpose structures using associated sequence
2879 <li>Export coordinates and projection as CSV from PCA
2881 </ul> <em>Applet</em>
2883 <li>enable javascript: execution by the applet via the
2884 link out mechanism</li>
2885 </ul> <em>Other</em>
2887 <li>Updated the Jmol Jalview interface to work with Jmol
2889 <li>The Jalview Desktop and JalviewLite applet now
2890 require Java 1.5</li>
2891 <li>Allow Jalview feature colour specification for GFF
2892 sequence annotation files</li>
2893 <li>New 'colour by label' keword in Jalview feature file
2894 type colour specification</li>
2895 <li>New Jalview Desktop Groovy API method that allows a
2896 script to check if it being run in an interactive session or
2897 in a batch operation from the Jalview command line</li>
2901 <li>clustalx colourscheme colours Ds preferentially when
2902 both D+E are present in over 50% of the column</li>
2903 </ul> <em>Application</em>
2905 <li>typo in AlignmentFrame->View->Hide->all but
2906 selected Regions menu item</li>
2907 <li>sequence fetcher replaces ',' for ';' when the ',' is
2908 part of a valid accession ID</li>
2909 <li>fatal OOM if object retrieved by sequence fetcher
2910 runs out of memory</li>
2911 <li>unhandled Out of Memory Error when viewing pca
2912 analysis results</li>
2913 <li>InstallAnywhere builds fail to launch on OS X java
2914 10.5 update 4 (due to apple Java 1.6 update)</li>
2915 <li>Installanywhere Jalview silently fails to launch</li>
2916 </ul> <em>Applet</em>
2918 <li>Jalview.getFeatureGroups() raises an
2919 ArrayIndexOutOfBoundsException if no feature groups are
2926 <div align="center">
2927 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2933 <li>Alignment prettyprinter doesn't cope with long
2935 <li>clustalx colourscheme colours Ds preferentially when
2936 both D+E are present in over 50% of the column</li>
2937 <li>nucleic acid structures retrieved from PDB do not
2938 import correctly</li>
2939 <li>More columns get selected than were clicked on when a
2940 number of columns are hidden</li>
2941 <li>annotation label popup menu not providing correct
2942 add/hide/show options when rows are hidden or none are
2944 <li>Stockholm format shown in list of readable formats,
2945 and parser copes better with alignments from RFAM.</li>
2946 <li>CSV output of consensus only includes the percentage
2947 of all symbols if sequence logo display is enabled</li>
2949 </ul> <em>Applet</em>
2951 <li>annotation panel disappears when annotation is
2953 </ul> <em>Application</em>
2955 <li>Alignment view not redrawn properly when new
2956 alignment opened where annotation panel is visible but no
2957 annotations are present on alignment</li>
2958 <li>pasted region containing hidden columns is
2959 incorrectly displayed in new alignment window</li>
2960 <li>Jalview slow to complete operations when stdout is
2961 flooded (fix is to close the Jalview console)</li>
2962 <li>typo in AlignmentFrame->View->Hide->all but
2963 selected Rregions menu item.</li>
2964 <li>inconsistent group submenu and Format submenu entry
2965 'Un' or 'Non'conserved</li>
2966 <li>Sequence feature settings are being shared by
2967 multiple distinct alignments</li>
2968 <li>group annotation not recreated when tree partition is
2970 <li>double click on group annotation to select sequences
2971 does not propagate to associated trees</li>
2972 <li>Mac OSX specific issues:
2974 <li>exception raised when mouse clicked on desktop
2975 window background</li>
2976 <li>Desktop menu placed on menu bar and application
2977 name set correctly</li>
2978 <li>sequence feature settings not wide enough for the
2979 save feature colourscheme button</li>
2988 <div align="center">
2989 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2992 <td><em>New Capabilities</em>
2994 <li>URL links generated from description line for
2995 regular-expression based URL links (applet and application)
2997 <li>Non-positional feature URL links are shown in link
2999 <li>Linked viewing of nucleic acid sequences and
3001 <li>Automatic Scrolling option in View menu to display
3002 the currently highlighted region of an alignment.</li>
3003 <li>Order an alignment by sequence length, or using the
3004 average score or total feature count for each sequence.</li>
3005 <li>Shading features by score or associated description</li>
3006 <li>Subdivide alignment and groups based on identity of
3007 selected subsequence (Make Groups from Selection).</li>
3008 <li>New hide/show options including Shift+Control+H to
3009 hide everything but the currently selected region.</li>
3010 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
3011 </ul> <em>Application</em>
3013 <li>Fetch DB References capabilities and UI expanded to
3014 support retrieval from DAS sequence sources</li>
3015 <li>Local DAS Sequence sources can be added via the
3016 command line or via the Add local source dialog box.</li>
3017 <li>DAS Dbref and DbxRef feature types are parsed as
3018 database references and protein_name is parsed as
3019 description line (BioSapiens terms).</li>
3020 <li>Enable or disable non-positional feature and database
3021 references in sequence ID tooltip from View menu in
3023 <!-- <li>New hidden columns and rows and representatives capabilities
3024 in annotations file (in progress - not yet fully implemented)</li> -->
3025 <li>Group-associated consensus, sequence logos and
3026 conservation plots</li>
3027 <li>Symbol distributions for each column can be exported
3028 and visualized as sequence logos</li>
3029 <li>Optionally scale multi-character column labels to fit
3030 within each column of annotation row<!-- todo for applet -->
3032 <li>Optional automatic sort of associated alignment view
3033 when a new tree is opened.</li>
3034 <li>Jalview Java Console</li>
3035 <li>Better placement of desktop window when moving
3036 between different screens.</li>
3037 <li>New preference items for sequence ID tooltip and
3038 consensus annotation</li>
3039 <li>Client to submit sequences and IDs to Envision2
3041 <li><em>Vamsas Capabilities</em>
3043 <li>Improved VAMSAS synchronization (Jalview archive
3044 used to preserve views, structures, and tree display
3046 <li>Import of vamsas documents from disk or URL via
3048 <li>Sharing of selected regions between views and
3049 with other VAMSAS applications (Experimental feature!)</li>
3050 <li>Updated API to VAMSAS version 0.2</li>
3052 </ul> <em>Applet</em>
3054 <li>Middle button resizes annotation row height</li>
3057 <li>sortByTree (true/false) - automatically sort the
3058 associated alignment view by the tree when a new tree is
3060 <li>showTreeBootstraps (true/false) - show or hide
3061 branch bootstraps (default is to show them if available)</li>
3062 <li>showTreeDistances (true/false) - show or hide
3063 branch lengths (default is to show them if available)</li>
3064 <li>showUnlinkedTreeNodes (true/false) - indicate if
3065 unassociated nodes should be highlighted in the tree
3067 <li>heightScale and widthScale (1.0 or more) -
3068 increase the height or width of a cell in the alignment
3069 grid relative to the current font size.</li>
3072 <li>Non-positional features displayed in sequence ID
3074 </ul> <em>Other</em>
3076 <li>Features format: graduated colour definitions and
3077 specification of feature scores</li>
3078 <li>Alignment Annotations format: new keywords for group
3079 associated annotation (GROUP_REF) and annotation row display
3080 properties (ROW_PROPERTIES)</li>
3081 <li>XML formats extended to support graduated feature
3082 colourschemes, group associated annotation, and profile
3083 visualization settings.</li></td>
3086 <li>Source field in GFF files parsed as feature source
3087 rather than description</li>
3088 <li>Non-positional features are now included in sequence
3089 feature and gff files (controlled via non-positional feature
3090 visibility in tooltip).</li>
3091 <li>URL links generated for all feature links (bugfix)</li>
3092 <li>Added URL embedding instructions to features file
3094 <li>Codons containing ambiguous nucleotides translated as
3095 'X' in peptide product</li>
3096 <li>Match case switch in find dialog box works for both
3097 sequence ID and sequence string and query strings do not
3098 have to be in upper case to match case-insensitively.</li>
3099 <li>AMSA files only contain first column of
3100 multi-character column annotation labels</li>
3101 <li>Jalview Annotation File generation/parsing consistent
3102 with documentation (e.g. Stockholm annotation can be
3103 exported and re-imported)</li>
3104 <li>PDB files without embedded PDB IDs given a friendly
3106 <li>Find incrementally searches ID string matches as well
3107 as subsequence matches, and correctly reports total number
3111 <li>Better handling of exceptions during sequence
3113 <li>Dasobert generated non-positional feature URL
3114 link text excludes the start_end suffix</li>
3115 <li>DAS feature and source retrieval buttons disabled
3116 when fetch or registry operations in progress.</li>
3117 <li>PDB files retrieved from URLs are cached properly</li>
3118 <li>Sequence description lines properly shared via
3120 <li>Sequence fetcher fetches multiple records for all
3122 <li>Ensured that command line das feature retrieval
3123 completes before alignment figures are generated.</li>
3124 <li>Reduced time taken when opening file browser for
3126 <li>isAligned check prior to calculating tree, PCA or
3127 submitting an MSA to JNet now excludes hidden sequences.</li>
3128 <li>User defined group colours properly recovered
3129 from Jalview projects.</li>
3138 <div align="center">
3139 <strong>2.4.0.b2</strong><br> 28/10/2009
3144 <li>Experimental support for google analytics usage
3146 <li>Jalview privacy settings (user preferences and docs).</li>
3151 <li>Race condition in applet preventing startup in
3153 <li>Exception when feature created from selection beyond
3154 length of sequence.</li>
3155 <li>Allow synthetic PDB files to be imported gracefully</li>
3156 <li>Sequence associated annotation rows associate with
3157 all sequences with a given id</li>
3158 <li>Find function matches case-insensitively for sequence
3159 ID string searches</li>
3160 <li>Non-standard characters do not cause pairwise
3161 alignment to fail with exception</li>
3162 </ul> <em>Application Issues</em>
3164 <li>Sequences are now validated against EMBL database</li>
3165 <li>Sequence fetcher fetches multiple records for all
3167 </ul> <em>InstallAnywhere Issues</em>
3169 <li>Dock icon works for Mac OS X java (Mac 1.6 update
3170 issue with installAnywhere mechanism)</li>
3171 <li>Command line launching of JARs from InstallAnywhere
3172 version (java class versioning error fixed)</li>
3179 <div align="center">
3180 <strong>2.4</strong><br> 27/8/2008
3183 <td><em>User Interface</em>
3185 <li>Linked highlighting of codon and amino acid from
3186 translation and protein products</li>
3187 <li>Linked highlighting of structure associated with
3188 residue mapping to codon position</li>
3189 <li>Sequence Fetcher provides example accession numbers
3190 and 'clear' button</li>
3191 <li>MemoryMonitor added as an option under Desktop's
3193 <li>Extract score function to parse whitespace separated
3194 numeric data in description line</li>
3195 <li>Column labels in alignment annotation can be centred.</li>
3196 <li>Tooltip for sequence associated annotation give name
3198 </ul> <em>Web Services and URL fetching</em>
3200 <li>JPred3 web service</li>
3201 <li>Prototype sequence search client (no public services
3203 <li>Fetch either seed alignment or full alignment from
3205 <li>URL Links created for matching database cross
3206 references as well as sequence ID</li>
3207 <li>URL Links can be created using regular-expressions</li>
3208 </ul> <em>Sequence Database Connectivity</em>
3210 <li>Retrieval of cross-referenced sequences from other
3212 <li>Generalised database reference retrieval and
3213 validation to all fetchable databases</li>
3214 <li>Fetch sequences from DAS sources supporting the
3215 sequence command</li>
3216 </ul> <em>Import and Export</em>
3217 <li>export annotation rows as CSV for spreadsheet import</li>
3218 <li>Jalview projects record alignment dataset associations,
3219 EMBL products, and cDNA sequence mappings</li>
3220 <li>Sequence Group colour can be specified in Annotation
3222 <li>Ad-hoc colouring of group in Annotation File using RGB
3223 triplet as name of colourscheme</li>
3224 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
3226 <li>treenode binding for VAMSAS tree exchange</li>
3227 <li>local editing and update of sequences in VAMSAS
3228 alignments (experimental)</li>
3229 <li>Create new or select existing session to join</li>
3230 <li>load and save of vamsas documents</li>
3231 </ul> <em>Application command line</em>
3233 <li>-tree parameter to open trees (introduced for passing
3235 <li>-fetchfrom command line argument to specify nicknames
3236 of DAS servers to query for alignment features</li>
3237 <li>-dasserver command line argument to add new servers
3238 that are also automatically queried for features</li>
3239 <li>-groovy command line argument executes a given groovy
3240 script after all input data has been loaded and parsed</li>
3241 </ul> <em>Applet-Application data exchange</em>
3243 <li>Trees passed as applet parameters can be passed to
3244 application (when using "View in full
3245 application")</li>
3246 </ul> <em>Applet Parameters</em>
3248 <li>feature group display control parameter</li>
3249 <li>debug parameter</li>
3250 <li>showbutton parameter</li>
3251 </ul> <em>Applet API methods</em>
3253 <li>newView public method</li>
3254 <li>Window (current view) specific get/set public methods</li>
3255 <li>Feature display control methods</li>
3256 <li>get list of currently selected sequences</li>
3257 </ul> <em>New Jalview distribution features</em>
3259 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
3260 <li>RELEASE file gives build properties for the latest
3261 Jalview release.</li>
3262 <li>Java 1.1 Applet build made easier and donotobfuscate
3263 property controls execution of obfuscator</li>
3264 <li>Build target for generating source distribution</li>
3265 <li>Debug flag for javacc</li>
3266 <li>.jalview_properties file is documented (slightly) in
3267 jalview.bin.Cache</li>
3268 <li>Continuous Build Integration for stable and
3269 development version of Application, Applet and source
3274 <li>selected region output includes visible annotations
3275 (for certain formats)</li>
3276 <li>edit label/displaychar contains existing label/char
3278 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3279 <li>shorter peptide product names from EMBL records</li>
3280 <li>Newick string generator makes compact representations</li>
3281 <li>bootstrap values parsed correctly for tree files with
3283 <li>pathological filechooser bug avoided by not allowing
3284 filenames containing a ':'</li>
3285 <li>Fixed exception when parsing GFF files containing
3286 global sequence features</li>
3287 <li>Alignment datasets are finalized only when number of
3288 references from alignment sequences goes to zero</li>
3289 <li>Close of tree branch colour box without colour
3290 selection causes cascading exceptions</li>
3291 <li>occasional negative imgwidth exceptions</li>
3292 <li>better reporting of non-fatal warnings to user when
3293 file parsing fails.</li>
3294 <li>Save works when Jalview project is default format</li>
3295 <li>Save as dialog opened if current alignment format is
3296 not a valid output format</li>
3297 <li>UniProt canonical names introduced for both das and
3299 <li>Histidine should be midblue (not pink!) in Zappo</li>
3300 <li>error messages passed up and output when data read
3302 <li>edit undo recovers previous dataset sequence when
3303 sequence is edited</li>
3304 <li>allow PDB files without pdb ID HEADER lines (like
3305 those generated by MODELLER) to be read in properly</li>
3306 <li>allow reading of JPred concise files as a normal
3308 <li>Stockholm annotation parsing and alignment properties
3309 import fixed for PFAM records</li>
3310 <li>Structure view windows have correct name in Desktop
3312 <li>annotation consisting of sequence associated scores
3313 can be read and written correctly to annotation file</li>
3314 <li>Aligned cDNA translation to aligned peptide works
3316 <li>Fixed display of hidden sequence markers and
3317 non-italic font for representatives in Applet</li>
3318 <li>Applet Menus are always embedded in applet window on
3320 <li>Newly shown features appear at top of stack (in
3322 <li>Annotations added via parameter not drawn properly
3323 due to null pointer exceptions</li>
3324 <li>Secondary structure lines are drawn starting from
3325 first column of alignment</li>
3326 <li>UniProt XML import updated for new schema release in
3328 <li>Sequence feature to sequence ID match for Features
3329 file is case-insensitive</li>
3330 <li>Sequence features read from Features file appended to
3331 all sequences with matching IDs</li>
3332 <li>PDB structure coloured correctly for associated views
3333 containing a sub-sequence</li>
3334 <li>PDB files can be retrieved by applet from Jar files</li>
3335 <li>feature and annotation file applet parameters
3336 referring to different directories are retrieved correctly</li>
3337 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3338 <li>Fixed application hang whilst waiting for
3339 splash-screen version check to complete</li>
3340 <li>Applet properly URLencodes input parameter values
3341 when passing them to the launchApp service</li>
3342 <li>display name and local features preserved in results
3343 retrieved from web service</li>
3344 <li>Visual delay indication for sequence retrieval and
3345 sequence fetcher initialisation</li>
3346 <li>updated Application to use DAS 1.53e version of
3347 dasobert DAS client</li>
3348 <li>Re-instated Full AMSA support and .amsa file
3350 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3358 <div align="center">
3359 <strong>2.3</strong><br> 9/5/07
3364 <li>Jmol 11.0.2 integration</li>
3365 <li>PDB views stored in Jalview XML files</li>
3366 <li>Slide sequences</li>
3367 <li>Edit sequence in place</li>
3368 <li>EMBL CDS features</li>
3369 <li>DAS Feature mapping</li>
3370 <li>Feature ordering</li>
3371 <li>Alignment Properties</li>
3372 <li>Annotation Scores</li>
3373 <li>Sort by scores</li>
3374 <li>Feature/annotation editing in applet</li>
3379 <li>Headless state operation in 2.2.1</li>
3380 <li>Incorrect and unstable DNA pairwise alignment</li>
3381 <li>Cut and paste of sequences with annotation</li>
3382 <li>Feature group display state in XML</li>
3383 <li>Feature ordering in XML</li>
3384 <li>blc file iteration selection using filename # suffix</li>
3385 <li>Stockholm alignment properties</li>
3386 <li>Stockhom alignment secondary structure annotation</li>
3387 <li>2.2.1 applet had no feature transparency</li>
3388 <li>Number pad keys can be used in cursor mode</li>
3389 <li>Structure Viewer mirror image resolved</li>
3396 <div align="center">
3397 <strong>2.2.1</strong><br> 12/2/07
3402 <li>Non standard characters can be read and displayed
3403 <li>Annotations/Features can be imported/exported to the
3405 <li>Applet allows editing of sequence/annotation/group
3406 name & description
3407 <li>Preference setting to display sequence name in
3409 <li>Annotation file format extended to allow
3410 Sequence_groups to be defined
3411 <li>Default opening of alignment overview panel can be
3412 specified in preferences
3413 <li>PDB residue numbering annotation added to associated
3419 <li>Applet crash under certain Linux OS with Java 1.6
3421 <li>Annotation file export / import bugs fixed
3422 <li>PNG / EPS image output bugs fixed
3428 <div align="center">
3429 <strong>2.2</strong><br> 27/11/06
3434 <li>Multiple views on alignment
3435 <li>Sequence feature editing
3436 <li>"Reload" alignment
3437 <li>"Save" to current filename
3438 <li>Background dependent text colour
3439 <li>Right align sequence ids
3440 <li>User-defined lower case residue colours
3443 <li>Menu item accelerator keys
3444 <li>Control-V pastes to current alignment
3445 <li>Cancel button for DAS Feature Fetching
3446 <li>PCA and PDB Viewers zoom via mouse roller
3447 <li>User-defined sub-tree colours and sub-tree selection
3449 <li>'New Window' button on the 'Output to Text box'
3454 <li>New memory efficient Undo/Redo System
3455 <li>Optimised symbol lookups and conservation/consensus
3457 <li>Region Conservation/Consensus recalculated after
3459 <li>Fixed Remove Empty Columns Bug (empty columns at end
3461 <li>Slowed DAS Feature Fetching for increased robustness.
3463 <li>Made angle brackets in ASCII feature descriptions
3465 <li>Re-instated Zoom function for PCA
3466 <li>Sequence descriptions conserved in web service
3468 <li>UniProt ID discoverer uses any word separated by
3470 <li>WsDbFetch query/result association resolved
3471 <li>Tree leaf to sequence mapping improved
3472 <li>Smooth fonts switch moved to FontChooser dialog box.
3479 <div align="center">
3480 <strong>2.1.1</strong><br> 12/9/06
3485 <li>Copy consensus sequence to clipboard</li>
3490 <li>Image output - rightmost residues are rendered if
3491 sequence id panel has been resized</li>
3492 <li>Image output - all offscreen group boundaries are
3494 <li>Annotation files with sequence references - all
3495 elements in file are relative to sequence position</li>
3496 <li>Mac Applet users can use Alt key for group editing</li>
3502 <div align="center">
3503 <strong>2.1</strong><br> 22/8/06
3508 <li>MAFFT Multiple Alignment in default Web Service list</li>
3509 <li>DAS Feature fetching</li>
3510 <li>Hide sequences and columns</li>
3511 <li>Export Annotations and Features</li>
3512 <li>GFF file reading / writing</li>
3513 <li>Associate structures with sequences from local PDB
3515 <li>Add sequences to exisiting alignment</li>
3516 <li>Recently opened files / URL lists</li>
3517 <li>Applet can launch the full application</li>
3518 <li>Applet has transparency for features (Java 1.2
3520 <li>Applet has user defined colours parameter</li>
3521 <li>Applet can load sequences from parameter
3522 "sequence<em>x</em>"
3528 <li>Redundancy Panel reinstalled in the Applet</li>
3529 <li>Monospaced font - EPS / rescaling bug fixed</li>
3530 <li>Annotation files with sequence references bug fixed</li>
3536 <div align="center">
3537 <strong>2.08.1</strong><br> 2/5/06
3542 <li>Change case of selected region from Popup menu</li>
3543 <li>Choose to match case when searching</li>
3544 <li>Middle mouse button and mouse movement can compress /
3545 expand the visible width and height of the alignment</li>
3550 <li>Annotation Panel displays complete JNet results</li>
3556 <div align="center">
3557 <strong>2.08b</strong><br> 18/4/06
3563 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3564 <li>Righthand label on wrapped alignments shows correct
3571 <div align="center">
3572 <strong>2.08</strong><br> 10/4/06
3577 <li>Editing can be locked to the selection area</li>
3578 <li>Keyboard editing</li>
3579 <li>Create sequence features from searches</li>
3580 <li>Precalculated annotations can be loaded onto
3582 <li>Features file allows grouping of features</li>
3583 <li>Annotation Colouring scheme added</li>
3584 <li>Smooth fonts off by default - Faster rendering</li>
3585 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3590 <li>Drag & Drop fixed on Linux</li>
3591 <li>Jalview Archive file faster to load/save, sequence
3592 descriptions saved.</li>
3598 <div align="center">
3599 <strong>2.07</strong><br> 12/12/05
3604 <li>PDB Structure Viewer enhanced</li>
3605 <li>Sequence Feature retrieval and display enhanced</li>
3606 <li>Choose to output sequence start-end after sequence
3607 name for file output</li>
3608 <li>Sequence Fetcher WSDBFetch@EBI</li>
3609 <li>Applet can read feature files, PDB files and can be
3610 used for HTML form input</li>
3615 <li>HTML output writes groups and features</li>
3616 <li>Group editing is Control and mouse click</li>
3617 <li>File IO bugs</li>
3623 <div align="center">
3624 <strong>2.06</strong><br> 28/9/05
3629 <li>View annotations in wrapped mode</li>
3630 <li>More options for PCA viewer</li>
3635 <li>GUI bugs resolved</li>
3636 <li>Runs with -nodisplay from command line</li>
3642 <div align="center">
3643 <strong>2.05b</strong><br> 15/9/05
3648 <li>Choose EPS export as lineart or text</li>
3649 <li>Jar files are executable</li>
3650 <li>Can read in Uracil - maps to unknown residue</li>
3655 <li>Known OutOfMemory errors give warning message</li>
3656 <li>Overview window calculated more efficiently</li>
3657 <li>Several GUI bugs resolved</li>
3663 <div align="center">
3664 <strong>2.05</strong><br> 30/8/05
3669 <li>Edit and annotate in "Wrapped" view</li>
3674 <li>Several GUI bugs resolved</li>
3680 <div align="center">
3681 <strong>2.04</strong><br> 24/8/05
3686 <li>Hold down mouse wheel & scroll to change font
3692 <li>Improved JPred client reliability</li>
3693 <li>Improved loading of Jalview files</li>
3699 <div align="center">
3700 <strong>2.03</strong><br> 18/8/05
3705 <li>Set Proxy server name and port in preferences</li>
3706 <li>Multiple URL links from sequence ids</li>
3707 <li>User Defined Colours can have a scheme name and added
3709 <li>Choose to ignore gaps in consensus calculation</li>
3710 <li>Unix users can set default web browser</li>
3711 <li>Runs without GUI for batch processing</li>
3712 <li>Dynamically generated Web Service Menus</li>
3717 <li>InstallAnywhere download for Sparc Solaris</li>
3723 <div align="center">
3724 <strong>2.02</strong><br> 18/7/05
3730 <li>Copy & Paste order of sequences maintains
3731 alignment order.</li>
3737 <div align="center">
3738 <strong>2.01</strong><br> 12/7/05
3743 <li>Use delete key for deleting selection.</li>
3744 <li>Use Mouse wheel to scroll sequences.</li>
3745 <li>Help file updated to describe how to add alignment
3747 <li>Version and build date written to build properties
3749 <li>InstallAnywhere installation will check for updates
3750 at launch of Jalview.</li>
3755 <li>Delete gaps bug fixed.</li>
3756 <li>FileChooser sorts columns.</li>
3757 <li>Can remove groups one by one.</li>
3758 <li>Filechooser icons installed.</li>
3759 <li>Finder ignores return character when searching.
3760 Return key will initiate a search.<br>
3767 <div align="center">
3768 <strong>2.0</strong><br> 20/6/05
3773 <li>New codebase</li>